Zotero.bib

@article{mittelbach_evolution_2007,
	title = {Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography},
	volume = {10},
	issn = {1461-023X, 1461-0248},
	shorttitle = {Evolution and the latitudinal diversity gradient},
	url = {http://doi.wiley.com/10.1111/j.1461-0248.2007.01020.x},
	doi = {10.1111/j.1461-0248.2007.01020.x},
	language = {en},
	number = {4},
	urldate = {2016-11-01},
	journal = {Ecology Letters},
	author = {Mittelbach, Gary G. and {others}},
	month = apr,
	year = {2007},
	pages = {315--331}
}

@article{mittelbach_evolution_2007-1,
	title = {Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography},
	volume = {10},
	issn = {1461-023X, 1461-0248},
	shorttitle = {Evolution and the latitudinal diversity gradient},
	url = {http://doi.wiley.com/10.1111/j.1461-0248.2007.01020.x},
	doi = {10.1111/j.1461-0248.2007.01020.x},
	language = {en},
	number = {4},
	urldate = {2016-11-01TZ},
	journal = {Ecology Letters},
	author = {Mittelbach, Gary G. and Schemske, Douglas W. and Cornell, Howard V. and Allen, Andrew P. and Brown, Jonathan M. and Bush, Mark B. and Harrison, Susan P. and Hurlbert, Allen H. and Knowlton, Nancy and Lessios, Harilaos A. and McCain, Christy M. and McCune, Amy R. and McDade, Lucinda A. and McPeek, Mark A. and Near, Thomas J. and Price, Trevor D. and Ricklefs, Robert E. and Roy, Kaustuv and Sax, Dov F. and Schluter, Dolph and Sobel, James M. and Turelli, Michael},
	month = apr,
	year = {2007},
	pages = {315--331}
}

@article{doebeli_speciation_2003,
	title = {Speciation along environmental gradients},
	volume = {421},
	copyright = {© 2003 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v421/n6920/abs/nature01274.html},
	doi = {10.1038/nature01274},
	abstract = {Traditional discussions of speciation are based on geographical patterns of species ranges. In allopatric speciation, long-term geographical isolation generates reproductively isolated and spatially segregated descendant species. In the absence of geographical barriers, diversification is hindered by gene flow. Yet a growing body of phylogenetic and experimental data suggests that closely related species often occur in sympatry or have adjacent ranges in regions over which environmental changes are gradual and do not prevent gene flow. Theory has identified a variety of evolutionary processes that can result in speciation under sympatric conditions, with some recent advances concentrating on the phenomenon of evolutionary branching. Here we establish a link between geographical patterns and ecological processes of speciation by studying evolutionary branching in spatially structured populations. We show that along an environmental gradient, evolutionary branching can occur much more easily than in non-spatial models. This facilitation is most pronounced for gradients of intermediate slope. Moreover, spatial evolutionary branching readily generates patterns of spatial segregation and abutment between the emerging species. Our results highlight the importance of local processes of adaptive divergence for geographical patterns of speciation, and caution against pitfalls of inferring past speciation processes from present biogeographical patterns.},
	language = {en},
	number = {6920},
	urldate = {2017-06-12TZ},
	journal = {Nature},
	author = {Doebeli, Michael and Dieckmann, Ulf},
	month = jan,
	year = {2003},
	pages = {259--264}
}

@book{r_core_development_team_r:_2013,
	address = {Vienna, Austria},
	title = {R: {A} {Language} and {Environment} for {Statistical} {Computing}},
	url = {http://www.R-project.org},
	author = {{R Core Development Team}},
	year = {2013}
}

@book{r_core_team_r:_2014,
	address = {Vienna, Austria},
	title = {R: {A} {Language} and {Environment} for {Statistical} {Computing}},
	url = {http://www.R-project.org},
	publisher = {R Foundation for Statistical Computing},
	author = {{\{R Core Team\}}},
	year = {2014}
}

@article{baym_spatiotemporal_2016,
	title = {Spatiotemporal microbial evolution on antibiotic landscapes},
	volume = {353},
	copyright = {Copyright © 2016, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/353/6304/1147},
	doi = {10.1126/science.aag0822},
	abstract = {A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)–plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front. While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front, we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behind more sensitive lineages. The MEGA-plate provides a versatile platform for studying microbial adaption and directly visualizing evolutionary dynamics.},
	language = {en},
	number = {6304},
	urldate = {2017-06-12TZ},
	journal = {Science},
	author = {Baym, Michael and Lieberman, Tami D. and Kelsic, Eric D. and Chait, Remy and Gross, Rotem and Yelin, Idan and Kishony, Roy},
	month = sep,
	year = {2016},
	pmid = {27609891},
	pages = {1147--1151}
}

@article{knight_knowing_2008,
	title = {Knowing {But} {Not} {Doing}: {Selecting} {Priority} {Conservation} {Areas} and the {Research}?{Implementation} {Gap}},
	volume = {22},
	issn = {0888-8892, 1523-1739},
	shorttitle = {Knowing {But} {Not} {Doing}},
	url = {http://doi.wiley.com/10.1111/j.1523-1739.2008.00914.x},
	doi = {10.1111/j.1523-1739.2008.00914.x},
	language = {en},
	number = {3},
	urldate = {2017-06-12TZ},
	journal = {Conservation Biology},
	author = {Knight, Andrew T. and Cowling, Richard M. and Rouget, Mathieu and Balmford, Andrew and Lombard, Amanda T. and Campbell, Bruce M.},
	month = jun,
	year = {2008},
	pages = {610--617}
}

@article{paudyal_dirhodium-catalyzed_2016,
	title = {Dirhodium-catalyzed {C}-{H} arene amination using hydroxylamines},
	volume = {353},
	issn = {0036-8075, 1095-9203},
	url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aaf8713},
	doi = {10.1126/science.aaf8713},
	language = {en},
	number = {6304},
	urldate = {2017-06-12TZ},
	journal = {Science},
	author = {Paudyal, M. P. and Adebesin, A. M. and Burt, S. R. and Ess, D. H. and Ma, Z. and Kurti, L. and Falck, J. R.},
	month = sep,
	year = {2016},
	pages = {1144--1147}
}

@article{dolson_spatial_2017,
	title = {Spatial resource heterogeneity increases diversity and evolutionary potential},
	journal = {bioRxiv},
	author = {Dolson, Emily and Perez, Samuel and Olson, Randal,  and Ofria, Charles},
	year = {2017}
}

@article{frenoy_second-order_nodate,
	title = {Second-order cooperation: {Cooperative} offspring as a living public good arising from second-order selection on non-cooperative individuals},
	issn = {1558-5646},
	shorttitle = {Second-order cooperation},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/evo.13279/abstract},
	doi = {10.1111/evo.13279},
	abstract = {Switching rate between cooperating and non-cooperating genotypes is a crucial social evolution factor, often neglected by game theory-inspired theoretical and experimental frameworks. We show that the evolution of alleles increasing the mutation or phenotypic switching rates toward cooperation is in itself a social dilemma. Although cooperative offspring are often unlikely to reproduce, due to high cost of cooperation, they can be seen both as a living public good and a part of the extended parental phenotype. The competition between individuals that generate cooperators and ones that do not is often more relevant than the competition between cooperators and non-cooperators. The dilemma of second-order cooperation we describe relates directly to eusociality, but can be also interpreted as a division of labor or a soma-germline distinction. The results of our simulations shine a new light on what Darwin had already termed a “special difficulty” of evolutionary theory and describe a novel type of cooperation dynamics. This article is protected by copyright. All rights reserved},
	language = {en},
	journal = {Evolution},
	author = {Frénoy, Antoine and Taddei, François and Misevic, Dusan},
	keywords = {Cooperation, division of labour, mutation rate, mutational landscape, phenotypic switching, second-order evolution, soma-germline distinction},
	pages = {n/a--n/a}
}

@article{mckinney_urbanization_2006,
	series = {Urbanization},
	title = {Urbanization as a major cause of biotic homogenization},
	volume = {127},
	issn = {0006-3207},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320705003563},
	doi = {10.1016/j.biocon.2005.09.005},
	abstract = {When measured by extent and intensity, urbanization is one of the most homogenizing of all major human activities. Cities homogenize the physical environment because they are built to meet the relatively narrow needs of just one species, our own. Also, cities are maintained for centuries in a disequilibrium state from the local natural environment by the importation of vast resources of energy and materials. Consequently, as cities expand across the planet, biological homogenization increases because the same “urban-adaptable” species become increasingly widespread and locally abundant in cities across the planet. As urbanization often produces a local gradient of disturbance, one can also observe a gradient of homogenization. Synanthropic species adapted to intensely modified built habitats at the urban core are “global homogenizers”, found in cities worldwide. However, many suburban and urban fringe habitats are occupied by native species that become regionally widespread. These suburban adapters typically consist of early successional plants and “edge” animal species such as mesopredator mammals, and ground-foraging, omnivorous and frugivorous birds that can utilize gardens, forest fragments and many other habitats available in the suburbs. A basic conservation challenge is that urban biota is often quite diverse and very abundant. The intentional and unintentional importation of species adapted to urban habitats, combined with many food resources imported for human use, often produces local species diversity and abundance that is often equal to or greater than the surrounding landscape. With the important exception of low-income areas, urban human populations often inhabit richly cultivated suburban habitats with a relatively high local floral and faunal diversity and/or abundance without awareness of the global impoverishment caused by urbanization. Equally challenging is that, because so many urban species are immigrants adapting to city habitats, urbanites of all income levels become increasingly disconnected from local indigenous species and their natural ecosystems. Urban conservation should therefore focus on promoting preservation and restoration of local indigenous species.},
	number = {3},
	urldate = {2016-03-27TZ},
	journal = {Biological Conservation},
	author = {McKinney, Michael L.},
	month = jan,
	year = {2006},
	keywords = {City, City, Exotic species, Exotic species, Homogenization, Human population, Human population, Non-native species, Non-native species, Urbanization, Urbanization, homogenization},
	pages = {247--260}
}

@article{hutchinson_paradox_1961,
	title = {The {Paradox} of the {Plankton}},
	volume = {95},
	copyright = {Copyright © 1961 The University of Chicago},
	issn = {0003-0147},
	url = {http://www.jstor.org/stable/2458386},
	number = {882},
	urldate = {2015-02-21TZ},
	journal = {The American Naturalist},
	author = {Hutchinson, G. E.},
	month = may,
	year = {1961},
	pages = {137--145}
}

@article{whitley_island_1998,
	title = {The {Island} {Model} {Genetic} {Algorithm}: {On} {Separability}, {Population} {Size} and {Convergence}},
	volume = {7},
	shorttitle = {The {Island} {Model} {Genetic} {Algorithm}},
	abstract = {Parallel Genetic Algorithms have often been reported to yield better performance than Genetic  Algorithms which use a single large panmictic population. In the case of the Island Model  genetic algorithm, it has been informally argued that having multiple subpopulations helps to  preserve genetic diversity, since each island can potentially follow a different search trajectory  through the search space. It is also possible that since linearly separable problems are often  used to test Genetic Algorithms, that Island Models may simply be particularly well suited to  exploiting the separable nature of the test problems. We explore this possibility by using the  infinite population models of simple genetic algorithms to study how Island Models can track  multiple search trajectories. We also introduce a simple model for better understanding when Island  Model genetic algorithms may have an advantage when processing some test problems. We  provide empirical results for both linearly separa...},
	journal = {Journal of Computing and Information Technology},
	author = {Whitley, Darrell and Rana, Soraya and Heckendorn, Robert B.},
	year = {1998},
	pages = {33--47}
}

@article{lenski_evolutionary_2003,
	title = {The evolutionary origin of complex features},
	volume = {423},
	copyright = {© 2003 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v423/n6936/abs/nature01568.html},
	doi = {10.1038/nature01568},
	abstract = {A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.},
	language = {en},
	number = {6936},
	urldate = {2014-04-29TZ},
	journal = {Nature},
	author = {Lenski, Richard E. and Ofria, Charles and Pennock, Robert T. and Adami, Christoph},
	month = may,
	year = {2003},
	pages = {139--144}
}

@article{tilman_resource_1977,
	title = {Resource {Competition} between {Plankton} {Algae}: {An} {Experimental} and {Theoretical} {Approach}},
	volume = {58},
	issn = {00129658},
	shorttitle = {Resource {Competition} between {Plankton} {Algae}},
	url = {http://www.jstor.org/stable/1935608?origin=crossref},
	doi = {10.2307/1935608},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Ecology},
	author = {Tilman, David},
	month = mar,
	year = {1977},
	pages = {338}
}

@inproceedings{harper_spatial_2012,
	address = {New York, NY, USA},
	series = {{GECCO} '12},
	title = {Spatial {Co}-evolution: {Quicker}, {Fitter} and {Less} {Bloated}},
	isbn = {978-1-4503-1177-9},
	shorttitle = {Spatial {Co}-evolution},
	url = {http://doi.acm.org/10.1145/2330163.2330269},
	doi = {10.1145/2330163.2330269},
	urldate = {2014-04-30TZ},
	booktitle = {Proceedings of the 14th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Harper, Robin},
	year = {2012},
	keywords = {Bloat, gp, operator equalisation, spatial co-evolution (scalp)},
	pages = {759--766}
}

@book{jones_scipy:_2001,
	title = {{SciPy}: {Open} source scientific tools for {Python}},
	url = {http://www.scipy.org/},
	author = {Jones, Eric and Oliphant, Travis and Peterson, Pearu and others},
	year = {2001}
}

@article{harpole_grassland_2007,
	title = {Grassland species loss resulting from reduced niche dimension},
	volume = {446},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/doifinder/10.1038/nature05684},
	doi = {10.1038/nature05684},
	number = {7137},
	urldate = {2014-08-13TZ},
	journal = {Nature},
	author = {Harpole, W. Stanley and Tilman, David},
	month = apr,
	year = {2007},
	pages = {791--793}
}

@book{forman_landscape_1986,
	title = {Landscape ecology},
	isbn = {978-0-471-87037-1},
	abstract = {This important new work--the first of its kind--focuses on the distribution patterns of landscape elements or ecosystems; the flows of animals, plants, energy, mineral nutrients and water; and the ecological changes in the landscape over time. Includes over 1,200 references from current ecology, geography, forestry, and wildlife biologcy literature.},
	language = {en},
	publisher = {Wiley},
	author = {Forman, Richard T. T. and Godron, Michel},
	month = feb,
	year = {1986},
	keywords = {Architecture / Landscape, Ecology, Human ecology, Landscape Ecology, Landscape protection, Science / Life Sciences / Ecology}
}

@inproceedings{bongard_guarding_2010,
	address = {New York, NY, USA},
	series = {{GECCO} '10},
	title = {Guarding {Against} {Premature} {Convergence} {While} {Accelerating} {Evolutionary} {Search}},
	isbn = {978-1-4503-0072-8},
	url = {http://doi.acm.org/10.1145/1830483.1830504},
	doi = {10.1145/1830483.1830504},
	abstract = {The fundamental dichotomy in evolutionary algorithms is that between exploration and exploitation. Recently, several algorithms [8, 9, 14, 16, 17, 20] have been introduced that guard against premature convergence by allowing both exploration and exploitation to occur simultaneously. However, continuous exploration greatly increases search time. To reduce the cost of continuous exploration we combine one of these methods (the age-layered population structure (ALPS) algorithm [8, 9]) with an early stopping (ES) method [2] that greatly accelerates the time needed to evaluate a candidate solution during search. We show that this combined method outperforms an equivalent algorithm with neither ALPS nor ES, as well as regimes in which only one of these methods is used, on an evolutionary robotics task.},
	urldate = {2014-08-12TZ},
	booktitle = {Proceedings of the 12th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Bongard, Josh C. and Hornby, Gregory S.},
	year = {2010},
	keywords = {Evolutionary algorithms, Evolutionary algorithms, evolutionary algorithms, evolutionary robotics, evolutionary robotics, premature convergence, premature convergence},
	pages = {111--118}
}

@book{wickham_ggplot2:_2009,
	title = {ggplot2: elegant graphics for data analysis},
	isbn = {978-0-387-98140-6},
	url = {http://had.co.nz/ggplot2/book},
	publisher = {Springer New York},
	author = {Wickham, Hadley},
	year = {2009}
}

@inproceedings{mouret_using_2009,
	address = {New York, NY, USA},
	series = {{GECCO} '09},
	title = {Using {Behavioral} {Exploration} {Objectives} to {Solve} {Deceptive} {Problems} in {Neuro}-evolution},
	isbn = {978-1-60558-325-9},
	url = {http://doi.acm.org/10.1145/1569901.1569988},
	doi = {10.1145/1569901.1569988},
	abstract = {Encouraging exploration, typically by preserving the diversity within the population, is one of the most common method to improve the behavior of evolutionary algorithms with deceptive fitness functions. Most of the published approaches to stimulate exploration rely on a distance between genotypes or phenotypes; however, such distances are difficult to compute when evolving neural networks due to (1) the algorithmic complexity of graph similarity measures, (2) the competing conventions problem and (3) the complexity of most neural-network encodings. In this paper, we introduce and compare two conceptually simple, yet efficient methods to improve exploration and avoid premature convergence when evolving both the topology and the parameters of neural networks. The two proposed methods, respectively called behavioral novelty and behavioral diversity, are built on multiobjective evolutionary algorithms and on a user-defined distance between behaviors. They can be employed with any genotype. We benchmarked them on the evolution of a neural network to compute a Boolean function with a deceptive fitness. The results obtained with the two proposed methods are statistically similar to those of NEAT and substantially better than those of the control experiment and of a phenotype-based diversity mechanism.},
	urldate = {2014-08-12TZ},
	booktitle = {Proceedings of the 11th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Mouret, Jean-Baptiste and Doncieux, Stéphane},
	year = {2009},
	keywords = {deceptive problems, deceptive problems, diversity, diversity, multiobjective evolutionary algorithm, multiobjective evolutionary algorithm, neural networks, neural networks},
	pages = {627--634}
}

@article{hairston_rapid_2005,
	title = {Rapid evolution and the convergence of ecological and evolutionary time},
	volume = {8},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2005.00812.x/abstract},
	doi = {10.1111/j.1461-0248.2005.00812.x},
	abstract = {Recent studies have documented rates of evolution of ecologically important phenotypes sufficiently fast that they have the potential to impact the outcome of ecological interactions while they are underway. Observations of this type go against accepted wisdom that ecological and evolutionary dynamics occur at very different time scales. While some authors have evaluated the rapidity of a measured evolutionary rate by comparing it to the overall distribution of measured evolutionary rates, we believe that ecologists are mainly interested in rapid evolution because of its potential to impinge on ecological processes. We therefore propose that rapid evolution be defined as a genetic change occurring rapidly enough to have a measurable impact on simultaneous ecological change. Using this definition we propose a framework for decomposing rates of ecological change into components driven by simultaneous evolutionary change and by change in a non-evolutionary factor (e.g. density dependent population dynamics, abiotic environmental change). Evolution is judged to be rapid in this ecological context if its contribution to ecological change is large relative to the contribution of other factors. We provide a worked example of this approach based on a theoretical predator–prey interaction [Abrams, P. \& Matsuda, H. (1997). Evolution, 51, 1740], and find that in this system the impact of prey evolution on predator per capita growth rate is 63\% that of internal ecological dynamics. We then propose analytical methods for measuring these contributions in field situations, and apply them to two long-term data sets for which suitable ecological and evolutionary data exist. For both data sets relatively high rates of evolutionary change have been found when measured as character change in standard deviations per generation (haldanes). For Darwin's finches evolving in response to fluctuating rainfall [Grant, P.R. \& Grant, B.R. (2002). Science, 296, 707], we estimate that evolutionary change has been more rapid than ecological change by a factor of 2.2. For a population of freshwater copepods whose life history evolves in response to fluctuating fish predation [Hairston, N.G. Jr \& Dillon, T.A. (1990). Evolution, 44, 1796], we find that evolutionary change has been about one quarter the rate of ecological change – less than in the finch example, but nevertheless substantial. These analyses support the view that in order to understand temporal dynamics in ecological processes it is critical to consider the extent to which the attributes of the system under investigation are simultaneously changing as a result of rapid evolution.},
	language = {en},
	number = {10},
	urldate = {2014-05-01TZ},
	journal = {Ecology Letters},
	author = {Hairston, Nelson G. and Ellner, Stephen P. and Geber, Monica A. and Yoshida, Takehito and Fox, Jennifer A.},
	month = oct,
	year = {2005},
	keywords = {Darwin's finches, Darwin's finches, Geospiza fortis, Geospiza fortis, Onychodiaptomus sanguineus, Onychodiaptomus sanguineus, adaptation, adaptation, bill size, bill size, diapause timing, diapause timing, ecological rate, ecological rate, evolutionary rate, evolutionary rate, haldane, haldane},
	pages = {1114--1127}
}

@article{hunter_matplotlib:_2007,
	title = {Matplotlib: {A} 2D graphics environment},
	volume = {9},
	abstract = {Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.},
	number = {3},
	journal = {Computing In Science \& Engineering},
	author = {Hunter, J. D.},
	year = {2007},
	pages = {90--95}
}

@article{kadmon_integrating_2007,
	title = {Integrating the effects of area, isolation, and habitat heterogeneity on species diversity: a unification of island biogeography and niche theory},
	volume = {170},
	issn = {1537-5323},
	shorttitle = {Integrating the effects of area, isolation, and habitat heterogeneity on species diversity},
	doi = {10.1086/519853},
	abstract = {We present an analytical model that unifies two of the most influential theories in community ecology, namely, island biogeography and niche theory. Our model captures the main elements of both theories by incorporating the combined effects of area, isolation, stochastic colonization and extinction processes, habitat heterogeneity, and niche partitioning in a unified, demographically based framework. While classical niche theory predicts a positive relationship between species richness and habitat heterogeneity, our unified model demonstrates that area limitation and dispersal limitation (the main elements of island biogeography) may create unimodal and even negative relationships between species richness and habitat heterogeneity. We attribute this finding to the fact that increasing heterogeneity increases the potential number of species that may exist in a given area (as predicted by niche theory) but simultaneously reduces the amount of suitable area available for each species and, thus, increases the likelihood of stochastic extinction. Area limitation, dispersal limitation, and low reproduction rates intensify the latter effect by increasing the likelihood of stochastic extinction. These analytical results demonstrate that the integration of island biogeography and niche theory provides new insights about the mechanisms that regulate the diversity of ecological communities and generates unexpected predictions that could not be attained from any single theory.},
	language = {eng},
	number = {3},
	journal = {The American Naturalist},
	author = {Kadmon, Ronen and Allouche, Omri},
	month = sep,
	year = {2007},
	pmid = {17879194},
	keywords = {Ecosystem, Geography, Models, Biological, Population Dynamics, Reproduction, biodiversity},
	pages = {443--454}
}

@article{lavergne_increased_2007,
	title = {Increased genetic variation and evolutionary potential drive the success of an invasive grass},
	volume = {104},
	url = {http://www.pnas.org/content/104/10/3883.short},
	number = {10},
	urldate = {2017-04-16TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Lavergne, Sébastien and Molofsky, Jane},
	year = {2007},
	keywords = {biological invasion, genotypic diversity, multiple immigration, phenotypic plasticity, range expansion},
	pages = {3883--3888}
}

@article{whigham_implicitly_2010,
	title = {Implicitly {Controlling} {Bloat} in {Genetic} {Programming}},
	volume = {14},
	issn = {1089-778X},
	doi = {10.1109/TEVC.2009.2027314},
	abstract = {During the evolution of solutions using genetic programming (GP) there is generally an increase in average tree size without a corresponding increase in fitness-a phenomenon commonly referred to as bloat. Although previously studied from theoretical and practical viewpoints there has been little progress in deriving controls for bloat which do not explicitly refer to tree size. Here, the use of spatial population structure in combination with local elitist replacement is shown to reduce bloat without a subsequent loss of performance. Theoretical concepts regarding inbreeding and the role of elitism are used to support the described approach. The proposed system behavior is confirmed via extensive computer simulations on benchmark problems. The main practical result is that by placing a population on a torus, with selection defined by a Moore neighborhood and local elitist replacement, bloat can be substantially reduced without compromising performance.},
	number = {2},
	journal = {IEEE Transactions on Evolutionary Computation},
	author = {Whigham, P.A. and Dick, G.},
	month = apr,
	year = {2010},
	keywords = {Bloat, Genetic algorithms, Moore neighborhood, benchmark problems, bloat control, elitism, genetic algorithms, genetic programming, inbreeding, local elitist replacement, spatial population structure, spatially-structured evolutionary algorithm, tree data structures, trees (mathematics)},
	pages = {173--190}
}

@article{wilmers_gray_2005,
	title = {Gray {Wolves} as {Climate} {Change} {Buffers} in {Yellowstone}},
	volume = {3},
	url = {http://dx.doi.org/10.1371/journal.pbio.0030092},
	doi = {10.1371/journal.pbio.0030092},
	abstract = {Reintroducing wolves can help ameliorate the negative effects of warmer winters on other species and reveals the importance of maintaining intact food chains in the face of climate change.},
	number = {4},
	urldate = {2014-05-02TZ},
	journal = {PLoS Biol},
	author = {Wilmers, Christopher C and Getz, Wayne M},
	month = mar,
	year = {2005},
	pages = {e92}
}

@article{fortuna_evolving_2013,
	title = {Evolving {Digital} {Ecological} {Networks}},
	volume = {9},
	url = {http://dx.doi.org/10.1371/journal.pcbi.1002928},
	doi = {10.1371/journal.pcbi.1002928},
	abstract = {“It is hard to realize that the living world as we know it is just one among many possibilities” [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms) that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks) that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).},
	number = {3},
	urldate = {2014-05-01TZ},
	journal = {PLoS Comput Biol},
	author = {Fortuna, Miguel A. and Zaman, Luis and Wagner, Aaron P. and Ofria, Charles},
	month = mar,
	year = {2013},
	pages = {e1002928}
}

@inproceedings{goldberg_genetic_1987,
	title = {Genetic algorithms with sharing for multimodal function optimization},
	url = {http://books.google.com/books?hl=en&lr=&id=MYJ_AAAAQBAJ&oi=fnd&pg=PA41&dq=goldberg+richardson+1987&ots=XvmNsn-EBF&sig=a0Y1ydfezWEZJmW1Hg-75hyOEHg},
	urldate = {2014-08-28TZ},
	booktitle = {Genetic algorithms and their applications: {Proceedings} of the {Second} {International} {Conference} on {Genetic} {Algorithms}},
	publisher = {Hillsdale, NJ: Lawrence Erlbaum},
	author = {Goldberg, David E. and Richardson, Jon},
	year = {1987},
	pages = {41--49}
}

@article{pianka_latitudinal_1966,
	title = {Latitudinal {Gradients} in {Species} {Diversity}: {A} {Review} of {Concepts}},
	volume = {100},
	copyright = {Copyright © 1966 The University of Chicago},
	issn = {0003-0147},
	shorttitle = {Latitudinal {Gradients} in {Species} {Diversity}},
	url = {http://www.jstor.org/stable/2459377},
	abstract = {The six major hypotheses of the control of species diversity are restated, examined, and some possible tests suggested. Although several of these mechanisms could be operating simultaneously, it is instructive to consider them separately, as this can serve to clarify our thinking, as well as assist in the choice of the best test situations for future examination.},
	number = {910},
	urldate = {2015-08-13TZ},
	journal = {The American Naturalist},
	author = {Pianka, Eric R.},
	month = jan,
	year = {1966},
	pages = {33--46}
}

@incollection{mcgarigal_landscape_2006,
	title = {Landscape {Pattern} {Metrics}},
	copyright = {Copyright © 2002 John Wiley \& Sons, Ltd},
	isbn = {978-0-470-05733-9},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/9780470057339.val006.pub2/abstract},
	abstract = {Real landscapes contain complex spatial patterns in the distribution of resources that vary over time; quantifying these patterns and their dynamics is the purview of landscape pattern analysis. Landscape pattern analysis involves quantifying the spatial heterogeneity of point patterns, linear networks, continuous surface patterns, and categorical patch mosaics, and sometimes custom hybridizations of these basic models, although the focus in landscape ecology and of this article has been on patch mosaics. In this context, landscape metrics are algorithms that quantify specific spatial characteristics of patches, classes of patches, or entire landscape mosaics, or of the patch mosaic in the neighborhood of each focal cell. These metrics fall into two categories: those that quantify the composition of the map without reference to spatial attributes (i.e., the variety and abundance of patch types), and those that quantify the spatial configuration of the map (i.e., the spatial character and arrangement, position, or orientation of patches within the class or landscape). Metrics are further categorized as structural metrics that measure physical structure of the mosaic without explicit reference to a particular phenomenon, or functional metrics that require additional parameterization and measure the structure of the mosaic as it relates to a specific organism or ecological process. Not surprisingly, landscape metrics are highly sensitive to landscape definition with respect to the thematic content and resolution, spatial grain and extent, and the landscape boundary. The current use and interpretation of landscape metrics is constrained by the lack of a proper theoretical understanding of metric behavior across a wide range of landscape structure gradients, the lack of a proper spatial and/or temporal reference framework for ecologically interpreting the computed value of each metric, and the challenges of choosing a parsimonious suite of metrics for a particular application given the plethora of existing metrics. Ultimately, the definition of the landscape, the establishment of a meaningful reference framework, and the choice of metrics should be based on some hypothesis about the observed landscape pattern and what processes or constraints might be responsible for that pattern. Fortunately, programs like FRAGSTATS make the calculation of landscape metrics practical and accessible to all landscape ecologists.},
	language = {en},
	urldate = {2014-04-28TZ},
	booktitle = {Encyclopedia of {Environmetrics}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {McGarigal, Kevin},
	year = {2006},
	keywords = {FRAGSTATS, landscape heterogeneity, landscape pattern indices, landscape structure, spatial pattern}
}

@inproceedings{walker_evolutionary_2012,
	address = {East Lansing, MI, USA},
	title = {Evolutionary {Potential} is {Maximized} at {Intermediate} {Diversity} {Levels}},
	isbn = {978-0-262-31050-5},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife13/ch017.html},
	doi = {10.7551/978-0-262-31050-5-ch017},
	urldate = {2014-04-29TZ},
	booktitle = {Proceedings of the 13th {International} {Conference} for {Artificial} {Life}},
	publisher = {MIT Press},
	author = {Walker, Bess L. and Ofria, Charles},
	month = jul,
	year = {2012},
	pages = {116--120}
}

@inproceedings{lehman_exploiting_2008,
	title = {Exploiting {Open}-{Endedness} to {Solve} {Problems} {Through} the {Search} for {Novelty}.},
	url = {http://18.7.25.65/sites/default/files/titles/alife/0262287196chap43.pdf},
	urldate = {2014-04-30TZ},
	booktitle = {{ALIFE}},
	author = {Lehman, Joel and Stanley, Kenneth O.},
	year = {2008},
	pages = {329--336}
}

@inproceedings{cooper_evolution_2003,
	title = {Evolution of stable ecosystems in populations of digital organisms},
	url = {http://books.google.com/books?hl=en&lr=&id=si_KlRbL1XoC&oi=fnd&pg=PA227&dq=info:rraWkTOgcVgJ:scholar.google.com&ots=2BF2g6i-m7&sig=b5eaLTS-qoBXy5KyVsYdC8Adp7w},
	urldate = {2016-08-20TZ},
	booktitle = {Artificial {Life} {VIII}: {Proceedings} of the {Eighth} {International} {Conference} on {Artificial} life},
	author = {Cooper, Tim F. and Ofria, Charles},
	year = {2003},
	pages = {227--232}
}

@article{wilke_evolution_2001,
	title = {Evolution of digital organisms at high mutation rates leads to survival of the flattest},
	volume = {412},
	copyright = {© 2001 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v412/n6844/abs/412331a0.html},
	doi = {10.1038/35085569},
	abstract = {Darwinian evolution favours genotypes with high replication rates, a process called 'survival of the fittest'. However, knowing the replication rate of each individual genotype may not suffice to predict the eventual survivor, even in an asexual population. According to quasi-species theory, selection favours the cloud of genotypes, interconnected by mutation, whose average replication rate is highest. Here we confirm this prediction using digital organisms that self-replicate, mutate and evolve. Forty pairs of populations were derived from 40 different ancestors in identical selective environments, except that one of each pair experienced a 4-fold higher mutation rate. In 12 cases, the dominant genotype that evolved at the lower mutation rate achieved a replication rate {\textgreater}1.5-fold faster than its counterpart. We allowed each of these disparate pairs to compete across a range of mutation rates. In each case, as mutation rate was increased, the outcome of competition switched to favour the genotype with the lower replication rate. These genotypes, although they occupied lower fitness peaks, were located in flatter regions of the fitness surface and were therefore more robust with respect to mutations.},
	language = {en},
	number = {6844},
	urldate = {2014-05-01TZ},
	journal = {Nature},
	author = {Wilke, Claus O. and Wang, Jia Lan and Ofria, Charles and Lenski, Richard E. and Adami, Christoph},
	month = jul,
	year = {2001},
	pages = {331--333}
}

@article{stein_environmental_2014,
	title = {Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales},
	copyright = {© 2014 John Wiley \& Sons Ltd/CNRS},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12277/abstract},
	doi = {10.1111/ele.12277},
	abstract = {Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity–richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity–richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity–richness studies. We provide the first quantitative support for the generality of positive heterogeneity–richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity–richness research.},
	language = {en},
	urldate = {2014-04-29TZ},
	journal = {Ecology Letters},
	author = {Stein, Anke and Gerstner, Katharina and Kreft, Holger},
	month = apr,
	year = {2014},
	keywords = {Habitat diversity, habitat structure, meta-analysis, meta-regression, robust variance estimation, spatial scale, species diversity, topographical heterogeneity, vegetation structure},
	pages = {n/a--n/a}
}

@article{haller_evolutionary_2013,
	title = {Evolutionary {Branching} in {Complex} {Landscapes}.},
	volume = {182},
	copyright = {Copyright © 2013 The University of Chicago},
	issn = {0003-0147},
	url = {http://www.jstor.org/stable/10.1086/671907},
	doi = {10.1086/671907},
	abstract = {Abstract Divergent adaptation to different environments can promote speciation, and it is thus important to consider spatial structure in models of speciation. Earlier theoretical work, however, has been limited to particularly simple types of spatial structure (linear environmental gradients and spatially discrete metapopulations), leaving unaddressed the effects of more realistic patterns of landscape heterogeneity, such as nonlinear gradients and spatially continuous patchiness. To elucidate the consequences of such complex landscapes, we adapt an established spatially explicit individual-based model of evolutionary branching. We show that branching is most probable at intermediate levels of various types of heterogeneity and that different types of heterogeneity have, to some extent, additive effects in promoting branching. In contrast to such additivity, we find a novel refugium effect in which refugia in hostile environments provide opportunities for colonization, thus increasing the probability of branching in patchy landscapes. Effects of patchiness depend on the scale of patches relative to dispersal. Providing a needed connection to empirical research on biodiversity and conservation policy, we introduce empirically accessible spatial environmental metrics that quantitatively predict a landscape’s branching propensity.},
	number = {4},
	urldate = {2015-01-10TZ},
	journal = {The American Naturalist},
	author = {Haller, Benjamin C. and Mazzucco, Rupert,  and Dieckmann, Ulf},
	month = oct,
	year = {2013},
	pages = {E127--E141}
}

@inproceedings{grabowski_building_2014,
	title = {Building on {Simplicity}: {Multi}-stage {Evolution} of {Digital} {Organisms}},
	isbn = {978-0-262-32621-6},
	shorttitle = {Building on {Simplicity}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch019.pdf},
	doi = {10.7551/978-0-262-32621-6-ch019},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {Grabowski, Laura and Magaña, Javier},
	month = jul,
	year = {2014},
	pages = {113--120}
}

@article{pianka_convexity_1966,
	title = {Convexity, {Desert} {Lizards}, and {Spatial} {Heterogeneity}},
	volume = {47},
	copyright = {Copyright © 1966 Ecological Society of America},
	issn = {0012-9658},
	url = {http://www.jstor.org/stable/1935656},
	doi = {10.2307/1935656},
	abstract = {The number of lizard species in the flatland desert habitat is correlated with several different structural attributes of the vegetation. It is shown that both the horizontal and vertical components of spatial heterogeneity are correlated with the number of lizard species. The habits of the twelve component species are considered briefly as they relate to the partitioning of the biotope space. Three species are food specialists, eight display various substrate specificities, and only one species appears to be truly "convex." Two tests of the present interpretation of these results are proposed, and some speculations concerning Australian flatland desert lizards are made.},
	number = {6},
	urldate = {2015-08-13TZ},
	journal = {Ecology},
	author = {Pianka, Eric R.},
	month = nov,
	year = {1966},
	pages = {1055--1059}
}

@article{ofria_avida:_2004,
	title = {Avida: {A} {Software} {Platform} for {Research} in {Computational} {Evolutionary} {Biology}},
	volume = {10},
	issn = {1064-5462},
	shorttitle = {Avida},
	url = {http://dx.doi.org/10.1162/106454604773563612},
	doi = {10.1162/106454604773563612},
	abstract = {Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.},
	number = {2},
	urldate = {2014-04-22TZ},
	journal = {Artificial Life},
	author = {Ofria, Charles and Wilke, Claus O.},
	month = mar,
	year = {2004},
	pages = {191--229}
}

@incollection{cantu-paz_are_2003,
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Are {Multiple} {Runs} of {Genetic} {Algorithms} {Better} than {One}?},
	copyright = {©2003 Springer-Verlag Berlin Heidelberg},
	isbn = {978-3-540-40602-0 978-3-540-45105-1},
	url = {http://link.springer.com/chapter/10.1007/3-540-45105-6_94},
	abstract = {There are conflicting reports over whether multiple independent runs of genetic algorithms (GAs) with small populations can reach solutions of higher quality or can find acceptable solutions faster than a single run with a large population. This paper investigates this question analytically using two approaches. First, the analysis assumes that there is a certain fixed amount of computational resources available, and identifies the conditions under which it is advantageous to use multiple small runs. The second approach does not constrain the total cost and examines whether multiple properly-sized independent runs can reach the optimal solution faster than a single run. Although this paper is limited to additively-separable functions, it may be applicable to the larger class of nearly decomposable functions of interest to many GA users. The results suggest that, in most cases under the constant cost constraint, a single run with the largest population possible reaches a better solution than multiple independent runs. Similarly, a single large run reaches the global faster than multiple small runs. The findings are validated with experiments on functions of varying difficulty.},
	language = {en},
	number = {2723},
	urldate = {2014-05-01TZ},
	booktitle = {Genetic and {Evolutionary} {Computation} — {GECCO} 2003},
	publisher = {Springer Berlin Heidelberg},
	author = {Cantú-Paz, Erick and Goldberg, David E.},
	editor = {Cantú-Paz, Erick and Foster, James A. and Deb, Kalyanmoy and Davis, Lawrence David and Roy, Rajkumar and O’Reilly, Una-May and Beyer, Hans-Georg and Standish, Russell and Kendall, Graham and Wilson, Stewart and Harman, Mark and Wegener, Joachim and Dasgupta, Dipankar and Potter, Mitch A. and Schultz, Alan C. and Dowsland, Kathryn A. and Jonoska, Natasha and Miller, Julian},
	month = jan,
	year = {2003},
	keywords = {Algorithm Analysis and Problem Complexity, Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Artificial Intelligence (incl. Robotics), Bioinformatics, Bioinformatics, Computation by Abstract Devices, Computation by Abstract Devices, Computer Appl. in Administrative Data Processing, Computer Appl. in Administrative Data Processing, Programming Techniques, Programming Techniques},
	pages = {801--812}
}

@article{allouche_areaheterogeneity_2012,
	title = {Area–heterogeneity tradeoff and the diversity of ecological communities},
	volume = {109},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/109/43/17495},
	doi = {10.1073/pnas.1208652109},
	abstract = {For more than 50 y ecologists have believed that spatial heterogeneity in habitat conditions promotes species richness by increasing opportunities for niche partitioning. However, a recent stochastic model combining the main elements of niche theory and island biogeography theory suggests that environmental heterogeneity has a general unimodal rather than a positive effect on species richness. This result was explained by an inherent tradeoff between environmental heterogeneity and the amount of suitable area available for individual species: for a given area, as heterogeneity increases, the amount of effective area available for individual species decreases, thereby reducing population sizes and increasing the likelihood of stochastic extinctions. Here we provide a comprehensive evaluation of this hypothesis. First we analyze an extensive database of breeding bird distribution in Catalonia and show that patterns of species richness, species abundance, and extinction rates are consistent with the predictions of the area–heterogeneity tradeoff and its proposed mechanisms. We then perform a metaanalysis of heterogeneity–diversity relationships in 54 published datasets and show that empirical data better fit the unimodal pattern predicted by the area–heterogeneity tradeoff than the positive pattern predicted by classic niche theory. Simulations in which species may have variable niche widths along a continuous environmental gradient are consistent with all empirical findings. The area–heterogeneity tradeoff brings a unique perspective to current theories of species diversity and has important implications for biodiversity conservation.},
	language = {en},
	number = {43},
	urldate = {2015-11-16TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Allouche, Omri and Kalyuzhny, Michael and Moreno-Rueda, Gregorio and Pizarro, Manuel and Kadmon, Ronen},
	month = oct,
	year = {2012},
	pmid = {23045670},
	keywords = {conservation planning, conservation planning, habitat heterogeneity, habitat heterogeneity, neutral theory, neutral theory, stochastic model of community dynamics, stochastic model of community dynamics},
	pages = {17495--17500}
}

@article{de_jong_analysis_1975,
	title = {Analysis of the behavior of a class of genetic adaptive systems},
	url = {http://deepblue.lib.umich.edu/handle/2027.42/4507},
	language = {en\_US},
	urldate = {2014-08-13TZ},
	author = {De Jong, Kenneth Alan},
	year = {1975},
	keywords = {Adaptive control systems., Adaptive control systems., Artificial intelligence., Artificial intelligence., Engineering, Engineering, Genetic algorithms., Genetic algorithms.}
}

@article{friedrich_analysis_2009,
	title = {Analysis of {Diversity}-{Preserving} {Mechanisms} for {Global} {Exploration}*},
	volume = {17},
	issn = {1063-6560},
	url = {http://dx.doi.org/10.1162/evco.2009.17.4.17401},
	doi = {10.1162/evco.2009.17.4.17401},
	abstract = {Maintaining diversity is important for the performance of evolutionary algorithms. Diversity-preserving mechanisms can enhance global exploration of the search space and enable crossover to find dissimilar individuals for recombination. We focus on the global exploration capabilities of mutation-based algorithms. Using a simple bimodal test function and rigorous runtime analyses, we compare well-known diversity-preserving mechanisms like deterministic crowding, fitness sharing, and others with a plain algorithm without diversification. We show that diversification is necessary for global exploration, but not all mechanisms succeed in finding both optima efficiently. Our theoretical results are accompanied by additional experiments for different population sizes.},
	number = {4},
	urldate = {2014-04-30TZ},
	journal = {Evolutionary Computation},
	author = {Friedrich, Tobias and Oliveto, Pietro S. and Sudholt, Dirk and Witt, Carsten},
	month = nov,
	year = {2009},
	pages = {455--476}
}

@article{allouche_general_2009,
	title = {A general framework for neutral models of community dynamics},
	volume = {12},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01379.x/pdf},
	number = {12},
	urldate = {2015-11-16TZ},
	journal = {Ecology letters},
	author = {Allouche, Omri and Kadmon, Ronen},
	year = {2009},
	pages = {1287--1297}
}

@article{chow_adaptive_2004,
	title = {Adaptive {Radiation} from {Resource} {Competition} in {Digital} {Organisms}},
	volume = {305},
	issn = {0036-8075, 1095-9203},
	url = {http://www.sciencemag.org/content/305/5680/84},
	doi = {10.1126/science.1096307},
	abstract = {Species richness often peaks at intermediate productivity and decreases as resources become more or less abundant. The mechanisms that produce this pattern are not completely known, but several previous studies have suggested environmental heterogeneity as a cause. In experiments with evolving digital organisms and populations of fixed size, maximum species richness emerges at intermediate productivity, even in a spatially homogeneous environment, owing to frequency-dependent selection to exploit an influx of mixed resources. A diverse pool of limiting resources is sufficient to cause adaptive radiation, which is manifest by the origin and maintenance of phenotypically and phylogenetically distinct groups of organisms.},
	language = {en},
	number = {5680},
	urldate = {2014-04-22TZ},
	journal = {Science},
	author = {Chow, Stephanie S. and Wilke, Claus O. and Ofria, Charles and Lenski, Richard E. and Adami, Christoph},
	month = jul,
	year = {2004},
	pmid = {15232105},
	pages = {84--86}
}

@article{schluter_evidence_2009,
	title = {Evidence for {Ecological} {Speciation} and {Its} {Alternative}},
	volume = {323},
	issn = {0036-8075},
	url = {http://science.sciencemag.org/content/323/5915/737},
	doi = {10.1126/science.1160006},
	number = {5915},
	journal = {Science},
	author = {Schluter, Dolph},
	year = {2009},
	pages = {737--741}
}

@article{mcdonald_pathogen_2002,
	title = {Pathogen population genetics, evolutionary potential, and durable resistance},
	volume = {40},
	url = {http://dx.doi.org/10.1146/annurev.phyto.40.120501.101443},
	doi = {10.1146/annurev.phyto.40.120501.101443},
	abstract = {We hypothesize that the evolutionary potential of a pathogen population is reflected in its population genetic structure. Pathogen populations with a high evolutionary potential are more likely to overcome genetic resistance than pathogen populations with a low evolutionary potential. We propose a flexible framework to predict the evolutionary potential of pathogen populations based on analysis of their genetic structure. According to this framework, pathogens that pose the greatest risk of breaking down resistance genes have a mixed reproduction system, a high potential for genotype flow, large effective population sizes, and high mutation rates. The lowest risk pathogens are those with strict asexual reproduction, low potential for gene flow, small effective population sizes, and low mutation rates. We present examples of high-risk and low-risk pathogens. We propose general guidelines for a rational approach to breed durable resistance according to the evolutionary potential of the pathogen.},
	number = {1},
	urldate = {2015-03-22},
	journal = {Annual Review of Phytopathology},
	author = {McDonald, Bruce A. and Linde, Celeste},
	year = {2002},
	pmid = {12147764},
	keywords = {major gene resistance, quantitative resistance, risk assessment},
	pages = {349--379}
}

@book{emily_dolson_emilydolson/resource-heterogeneity:_2016,
	title = {emilydolson/resource-heterogeneity: {Journal} {Submission}},
	url = {https://doi.org/10.5281/zenodo.162981},
	author = {Emily Dolson and Samuel Perez and Chaput, Audra},
	month = oct,
	year = {2016},
	note = {DOI: 10.5281/zenodo.162981}
}

@article{craine_global_2013,
	title = {Global diversity of drought tolerance and grassland climate-change resilience},
	volume = {3},
	copyright = {© 2012 Nature Publishing Group},
	issn = {1758-678X},
	url = {http://www.nature.com/nclimate/journal/v3/n1/full/nclimate1634.html},
	doi = {10.1038/nclimate1634},
	abstract = {Drought reduces plant productivity, induces widespread plant mortality and limits the geographic distribution of plant species. As climates warm and precipitation patterns shift in the future, understanding the distribution of the diversity of plant drought tolerance is central to predicting future ecosystem function and resilience to climate change. These questions are especially pressing for the world’s 11,000 grass species, which dominate a large fraction of the terrestrial biosphere, yet are poorly characterized with respect to responses to drought. Here, we show that physiological drought tolerance, which varied tenfold among 426 grass species, is well distributed both climatically and phylogenetically, suggesting most native grasslands are likely to contain a high diversity of drought tolerance. Consequently, local species may help maintain ecosystem functioning in response to changing drought regimes without requiring long-distance migrations of grass species. Furthermore, physiologically drought-tolerant species had higher rates of water and carbon dioxide exchange than intolerant species, indicating that severe droughts may generate legacies for ecosystem functioning. In all, our findings suggest that diverse grasslands throughout the globe have the potential to be resilient to drought in the face of climate change through the local expansion of drought-tolerant species.},
	language = {en},
	number = {1},
	urldate = {2014-05-02},
	journal = {Nature Climate Change},
	author = {Craine, Joseph M. and Ocheltree, Troy W. and Nippert, Jesse B. and Towne, E. Gene and Skibbe, Adam M. and Kembel, Steven W. and Fargione, Joseph E.},
	month = jan,
	year = {2013},
	keywords = {Biodiversity and ecosystems, Biological sciences, Biology, ecology},
	pages = {63--67}
}

@book{cary_conference_ecosystem_2005,
	address = {New York; London},
	title = {Ecosystem function in heterogeneous landscapes},
	isbn = {978-0-387-24091-6 0-387-24091-8 978-0-387-24089-3 0-387-24089-6 0-387-24090-X 978-0-387-24090-9},
	url = {http://dx.doi.org/10.1007/b104357},
	abstract = {Addresses how interactions among ecosystems affect the functioning of individual ecosystems and the larger landscape. This book details challenges of working in spatially heterogeneous systems, approaches used in other disciplines and in different ecosystem types, and the importance of spatial heterogeneity in conservation resource management.},
	language = {English},
	urldate = {2014-05-01},
	publisher = {Springer},
	author = {Cary Conference, Lovett, Gary},
	year = {2005}
}

@article{fraterrigo_interactions_2006,
	title = {Interactions between past land use, life-history traits and understory spatial heterogeneity},
	volume = {21},
	issn = {0921-2973, 1572-9761},
	url = {http://link.springer.com/article/10.1007/s10980-005-5955-z},
	doi = {10.1007/s10980-005-5955-z},
	abstract = {Past land use has contributed to variability in the distribution of herbaceous species by reducing plant abundance and altering species’ chances of recolonizing suitable habitat. Land use may also influence plant heterogeneity by changing environmental conditions within stands. We compared the variability of understory herb abundance in southern Appalachian forests with different land-use histories to examine how past land use influenced plant heterogeneity. The cover of eleven focal species or genera was estimated and mineral soil concentrations were determined during 2001 and 2002 in eight stands that were farmed, logged, or had no disturbance history (reference) in western North Carolina. Analysis of the coefficients of variation revealed that the abundance of understory plants was more heterogeneous in disturbed stands compared with reference stands. However, when nutrient availability differences were accounted for by detrending the plant cover data, understory variability within stands declined, and no differences between disturbed and reference stands could be distinguished. This finding suggests that nutrient availability has important effects on plant heterogeneity, which depend on past land use. Species dispersal, seed size, and phenology also explained variability in the spatial heterogeneity of plants, but generally only before soil nutrient differences were statistically controlled. In addition to demonstrating that past land use has long-term effects on plant heterogeneity, these results indicate that soil nutrients may play different roles in determining vegetation patterns in historically altered and unaltered forests.},
	language = {en},
	number = {5},
	urldate = {2015-03-22},
	journal = {Landscape Ecology},
	author = {Fraterrigo, Jennifer M. and Turner, Monica G. and Pearson, Scott M.},
	month = jul,
	year = {2006},
	keywords = {Dispersal, Forestry, Forestry Management, Herbaceous plants, Land-use history, Landscape Ecology, Plant Ecology, Plant Sciences, Plant abundance, Seed size, Southern Appalachians, USA, ecology},
	pages = {777--790}
}

@article{townsend_species_1997,
	title = {Species traits in relation to temporal and spatial heterogeneity in streams: a test of habitat templet theory},
	volume = {37},
	copyright = {Blackwell Science Ltd, Oxford},
	issn = {1365-2427},
	shorttitle = {Species traits in relation to temporal and spatial heterogeneity in streams},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2427.1997.00166.x/abstract},
	doi = {10.1046/j.1365-2427.1997.00166.x},
	abstract = {1. The habitat templet approach depends on defining templet axes appropriate to the organism(s) of interest, predicting the traits of species associated with different parts of the templet, and testing these predictions in a range of habitats whose positions in the templet have been determined. 2. In this study of thirty-five benthic insect taxa at fifty-four tributary sites of the Taieri River on the South Island of New Zealand, we chose as the temporal axis the intensity/frequency of disturbance, defined in terms of bed movement during high discharge events. As the spatial axis, we postulated that three features would provide refugia and therefore ameliorate disturbance—percentage of the bed with low shear stress, percentage of the bed made up of large substratum particles and availability of interstitial space in the bed—from which we derived a combined multivariate refugium axis. 3. More disturbed communities contained a significantly higher percentage of individuals possessing the following traits: small size, high adult mobility, habitat generalist (each predicted to confer resilience in response to disturbance), clinger, streamlined/flattened and with two or more life stages outside the stream (each predicted to confer resistance in the face of disturbance). When analyses were performed on the percentage of taxa having particular traits, the predicted positive relationships with average bed movement were found for high adult mobility and habitat generalist traits. 4. The percentage of variance in trait scores explained by intensity of disturbance was generally higher in sites with less refugia available and lower in sites further from the headwaters. The percentage of variance explained was higher in sites recently subject to a major high discharge disturbance, suggesting that disturbances tend to strengthen the pattern of preponderance of resilience/resistance traits. 5. We mapped insect taxa onto the two-dimensional templet, following Grime et al.’s triangular terrestrial plant classification. The full variety of resistance and resilience traits were represented in insect species throughout the templet, but taxa associated with more disturbed conditions generally displayed a larger number of resilience and resistance traits, combined, than taxa associated with more stable stream beds.},
	language = {en},
	number = {2},
	urldate = {2015-03-22},
	journal = {Freshwater Biology},
	author = {Townsend, Colin and Dolédec, Sylvain and Scarsbrook, Mike},
	month = apr,
	year = {1997},
	pages = {367--387}
}

@article{noauthor_morphological_nodate,
	title = {Morphological traits and spatial heterogeneity of aquatic plants along sediment and depth gradients, {Lake} {Geneva}, {Switzerland}},
	volume = {55},
	issn = {0304-3770},
	url = {http://www.sciencedirect.com/science/article/pii/S0304377096010789},
	doi = {10.1016/S0304-3770(96)01078-9}
}

@article{barnett_zooplankton_2007,
	title = {Zooplankton biodiversity and lake trophic state: explanations invoking resource abundance and distribution},
	volume = {88},
	issn = {0012-9658},
	shorttitle = {{ZOOPLANKTON} {BIODIVERSITY} {AND} {LAKE} {TROPHIC} {STATE}},
	url = {http://www.esajournals.org/doi/abs/10.1890/06-1056.1},
	doi = {10.1890/06-1056.1},
	language = {en},
	number = {7},
	urldate = {2014-05-01},
	journal = {Ecology},
	author = {Barnett, Allain. and Beisner, Beatrix E.},
	month = jul,
	year = {2007},
	pages = {1675--1686}
}

@article{galloway_nitrogen_2004,
	title = {Nitrogen cycles: past, present, and future},
	volume = {70},
	doi = {10.1007/s10533-004-0370-0},
	journal = {Biogeochemistry},
	author = {Galloway, J. N. and Dentener, F. J. and Capone, D. G. and Boyer, E. W. and Howarth, R. W. and Seitzinger, S. P. and Asner, G. P. and Cleveland, C. C. and Green, P. A. and Holland, E. A. and Karl, D. M. and Michaels, A. F. and Porter, J. H. and Townsend, A. R. and Vorosmarty, C. J.},
	year = {2004},
	pages = {153--226}
}

@article{chesson_mechanisms_2000,
	title = {Mechanisms of {Maintenance} of {Species} {Diversity}},
	volume = {31},
	doi = {10.1146/annurev.ecolsys.31.1.343},
	journal = {Annual Review of Ecology and Systematics},
	author = {Chesson, Peter},
	year = {2000},
	pages = {343--366}
}

@article{jankowski_resource_2014,
	title = {Resource {Availability} and {Spatial} {Heterogeneity} {Control} {Bacterial} {Community} {Response} to {Nutrient} {Enrichment} in {Lakes}},
	volume = {9},
	issn = {1932-6203},
	url = {http://dx.plos.org/10.1371/journal.pone.0086991},
	doi = {10.1371/journal.pone.0086991},
	language = {en},
	number = {1},
	urldate = {2014-05-01},
	journal = {PLoS ONE},
	author = {Jankowski, KathiJo and Schindler, Daniel E. and Horner-Devine, M. Claire},
	editor = {Heil, Martin},
	month = jan,
	year = {2014},
	pages = {e86991}
}

@article{legendre_spatial_1989,
	title = {Spatial {Pattern} and {Ecological} {Analysis}},
	volume = {80},
	doi = {10.1007/BF00048036},
	journal = {Vegetatio},
	author = {Legendre, P. and Fortin, Mj},
	year = {1989},
	pages = {107--138}
}

@article{pacala_limiting_1994,
	title = {Limiting {Similarity} in {Mechanistic} and {Spatial} {Models} of {Plant} {Competition} in {Heterogeneous} {Environments}},
	volume = {143},
	doi = {10.1086/285602},
	journal = {American Naturalist},
	author = {Pacala, Sw and Tilman, D.},
	year = {1994},
	pages = {222--257}
}

@article{arnell_climate_2004,
	title = {Climate change and global water resources: {SRES} emissions and socio-economic scenarios},
	volume = {14},
	doi = {10.1016/j.gloenvcha.2003.10.006},
	journal = {Global Environmental Change},
	author = {Arnell, Nigel W.},
	year = {2004},
	pages = {31--52}
}

@article{kauffman_towards_1987,
	title = {Towards a general theory of adaptive walks on rugged landscapes},
	volume = {128},
	issn = {0022-5193},
	url = {http://www.sciencedirect.com/science/article/pii/S0022519387800292},
	doi = {10.1016/S0022-5193(87)80029-2},
	abstract = {Adaptive evolution, to a large extent, is a complex combinatorial optimization process. In this article we take beginning steps towards developing a general theory of adaptive “walks” via fitter variants in such optimization processes. We introduce the basic idea of a space of entities, each a 1-mutant neighbor of many other entities in the space, and the idea of a fitness ascribed to each entity. Adaptive walks proceed from an initial entity, via fitter neighbors, to locally or globally optimal entities that are fitter than their neighbors. We develop a general theory for the number of local optima, lengths of adaptive walks, and the number of alternative local optima accessible from any given initial entity, for the baseline case of an uncorrelated fitness landscape. Most fitness landscapes are correlated, however. Therefore we develop parts of a universal theory of adaptation on correlated landscapes by adaptive processes that have sufficient numbers of mutations per individual to “jump beyond” the correlation lengths in the underlying landscape. In addition, we explore the statistical character of adaptive walks in two independent complex combinatorial optimization problems, that of evolving a specific cell type in model genetic networks, and that of finding good solutions to the traveling salesman problem. Surprisingly, both show similar statistical features, encouraging the hope that a general theory for adaptive walks on correlated and uncorrelated landscapes can be found. In the final section we explore two limits to the efficacy of selection. The first is new, and surprising: for a wide class of systems, as the complexity of the entities under selection increases, the local optima that are attainable fall progressively closer to the mean properties of the underlying space of entities. This may imply that complex biological systems, such as genetic regulatory systems, are “close” to the mean properties of the ensemble of genomic regulatory systems explored by evolution. The second limit shows that with increasing complexity and a fixed mutation rate, selection often becomes unable to pull an adapting population to those local optima to which connected adaptive walks via fitter variants exist. These beginning steps in theory development are applied to maturation of the immune response, and to the problem of radiation and stasis. Despite the limitations of the adaptive landscape metaphor, we believe that further development along the lines begun here will prove useful.},
	number = {1},
	urldate = {2016-05-16TZ},
	journal = {Journal of Theoretical Biology},
	author = {Kauffman, Stuart and Levin, Simon},
	month = sep,
	year = {1987},
	pages = {11--45}
}

@article{goldsby_task-switching_2012,
	title = {Task-switching costs promote the evolution of division of labor and shifts in individuality},
	volume = {109},
	url = {https://www.pnas.org/content/109/34/13686.full},
	number = {34},
	urldate = {2016-03-14TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Goldsby, Heather J. and Dornhaus, Anna and Kerr, Benjamin and Ofria, Charles},
	year = {2012},
	pages = {13686--13691}
}

@inproceedings{zaman_rapid_2011,
	title = {Rapid host-parasite coevolution drives the production and maintenance of diversity in digital organisms},
	url = {http://dl.acm.org/citation.cfm?id=2001607},
	urldate = {2017-03-09TZ},
	booktitle = {Proceedings of the 13th annual conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Zaman, Luis and Devangam, Suhas and Ofria, Charles},
	year = {2011},
	pages = {219--226}
}

@incollection{channon_passing_2001,
	title = {Passing the {ALife} test: {Activity} statistics classify evolution in {Geb} as unbounded},
	shorttitle = {Passing the {ALife} test},
	url = {http://link.springer.com/chapter/10.1007/3-540-44811-X_45},
	urldate = {2015-10-23TZ},
	booktitle = {Advances in {Artificial} {Life}},
	publisher = {Springer},
	author = {Channon, Alastair},
	year = {2001},
	pages = {417--426}
}

@article{lehman_abandoning_2011,
	title = {Abandoning {Objectives}: {Evolution} {Through} the {Search} for {Novelty} {Alone}},
	volume = {19},
	issn = {1063-6560},
	shorttitle = {Abandoning {Objectives}},
	url = {http://dx.doi.org/10.1162/EVCO_a_00025},
	doi = {10.1162/EVCO_a_00025},
	abstract = {In evolutionary computation, the fitness function normally measures progress toward an objective in the search space, effectively acting as an objective function. Through deception, such objective functions may actually prevent the objective from being reached. While methods exist to mitigate deception, they leave the underlying pathology untreated: Objective functions themselves may actively misdirect search toward dead ends. This paper proposes an approach to circumventing deception that also yields a new perspective on open-ended evolution. Instead of either explicitly seeking an objective or modeling natural evolution to capture open-endedness, the idea is to simply search for behavioral novelty. Even in an objective-based problem, such novelty search ignores the objective. Because many points in the search space collapse to a single behavior, the search for novelty is often feasible. Furthermore, because there are only so many simple behaviors, the search for novelty leads to increasing complexity. By decoupling open-ended search from artificial life worlds, the search for novelty is applicable to real world problems. Counterintuitively, in the maze navigation and biped walking tasks in this paper, novelty search significantly outperforms objective-based search, suggesting the strange conclusion that some problems are best solved by methods that ignore the objective. The main lesson is the inherent limitation of the objective-based paradigm and the unexploited opportunity to guide search through other means.},
	number = {2},
	urldate = {2014-08-12TZ},
	journal = {Evol. Comput.},
	author = {Lehman, Joel and Stanley, Kenneth O.},
	month = jun,
	year = {2011},
	keywords = {Evolutionary algorithms, Evolutionary algorithms, deception, deception, neuroevolution, neuroevolution, novelty search, novelty search, open-ended evolution, open-ended evolution},
	pages = {189--223}
}

@article{tenaillon_tempo_2016,
	title = {Tempo and mode of genome evolution in a 50,000-generation experiment},
	url = {http://biorxiv.org/content/early/2016/01/15/036806.abstract},
	doi = {10.1101/036806},
	abstract = {Adaptation depends on the rates, effects, and interactions of many mutations. We analyzed 264 genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The trajectories for genome evolution in populations that retained the ancestral mutation rate fit a model where most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to lines evolved under a mutation-accumulation regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions, and deletions are overrepresented in the long-term populations, supporting the inference that most fixed mutations are favored by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.},
	journal = {bioRxiv},
	author = {Tenaillon, Olivier and Barrick, Jeffrey E. and Ribeck, Noah and Deatherage, Daniel E. and Blanchard, Jeffrey L. and Dasgupta, Aurko and Wu, Gabriel C. and Wielgoss, Sebastien and Cruveiller, Stephane and Medigue, Claudine and Schneider, Dominique and Lenski, Richard E.},
	month = jan,
	year = {2016}
}

@article{le_gac_ecological_2012,
	title = {Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with {Escherichia} coli},
	volume = {109},
	url = {http://www.pnas.org/content/109/24/9487.abstract},
	doi = {10.1073/pnas.1207091109},
	abstract = {Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.},
	number = {24},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Le Gac, Mickaël and Plucain, Jessica and Hindré, Thomas and Lenski, Richard E. and Schneider, Dominique},
	month = jun,
	year = {2012},
	pages = {9487--9492}
}

@article{turner_evolution_2015,
	title = {Evolution and coexistence in response to a key innovation in a long-term evolution experiment with {Escherichia} coli},
	url = {http://www.biorxiv.org/content/early/2015/06/17/020958.abstract},
	doi = {10.1101/020958},
	abstract = {Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following evolution of a novel function in the long-term evolution experiment (LTEE) with Escherichia coli. A characteristic feature of E. coli is its inability to consume citrate aerobically. However, that ability evolved in one of the LTEE populations. In this population, citrate-utilizing bacteria (Cit+) coexisted stably with another clade of bacteria that lacked the capacity to utilize citrate (Cit−). This coexistence was shaped by the evolution of a cross-feeding relationship in which Cit+ cells released the dicarboxylic acids succinate, fumarate, and malate into the medium, and Cit− cells evolved improved growth on these carbon sources, as did the Cit+ cells. Thus, the evolution of citrate consumption led to a flask-based ecosystem that went from a single limiting resource, glucose, to one with five resources either shared or partitioned between two coexisting clades. Our findings show how evolutionary novelties can change environmental conditions, thereby facilitating diversity and altering both the structure of an ecosystem and the evolutionary trajectories of coexisting organisms.},
	journal = {bioRxiv},
	author = {Turner, Caroline B. and Blount, Zachary D. and Mitchell, Daniel H. and Lenski, Richard E.},
	month = jun,
	year = {2015}
}

@article{lenski_sustained_2015,
	title = {Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with {Escherichia} coli},
	volume = {282},
	url = {http://rspb.royalsocietypublishing.org/content/282/1821/20152292.abstract},
	doi = {10.1098/rspb.2015.2292},
	abstract = {Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10 000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely—or at least for a long time—even in a constant environment.},
	number = {1821},
	journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	author = {Lenski, Richard E. and Wiser, Michael J. and Ribeck, Noah and Blount, Zachary D. and Nahum, Joshua R. and Morris, J. Jeffrey and Zaman, Luis and Turner, Caroline B. and Wade, Brian D. and Maddamsetti, Rohan and Burmeister, Alita R. and Baird, Elizabeth J. and Bundy, Jay and Grant, Nkrumah A. and Card, Kyle J. and Rowles, Maia and Weatherspoon, Kiyana and Papoulis, Spiridon E. and Sullivan, Rachel and Clark, Colleen and Mulka, Joseph S. and Hajela, Neerja},
	month = dec,
	year = {2015}
}

@article{turner_replaying_2015,
	title = {Replaying {Evolution} to {Test} the {Cause} of {Extinction} of {One} {Ecotype} in an {Experimentally} {Evolved} {Population}},
	volume = {10},
	url = {http://dx.doi.org/10.1371%2Fjournal.pone.0142050},
	doi = {10.1371/journal.pone.0142050},
	abstract = {In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit?) ecotypes, with Cit?bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit?lineage went extinct; cells with the Cit?phenotype dropped to levels below detection, and the Cit?clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ ecotype that competitively excluded the Cit?ecotype. We tested this hypothesis by re-evolving the population from a frozen population sample taken within 500 generations of the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit?type did not go extinct in any of these replays, and Cit?cells also persisted in a single replicate that was propagated for 2,500 generations. Even more unexpectedly, we showed that the Cit?ecotype could reinvade the Cit+ population after its extinction. Taken together, these results indicate that the extinction of the Cit?ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ ecotype. The extinction also cannot be explained by demographic stochasticity alone, as the population size of the Cit?ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.},
	number = {11},
	journal = {PLoS ONE},
	author = {Turner, Caroline B. and Blount, Zachary D. and Lenski, Richard E.},
	month = nov,
	year = {2015},
	pages = {e0142050}
}

@article{rozen_longterm_2000,
	title = {Long‐{Term} {Experimental} {Evolution} in {Escherichia} coli. {VIII}. {Dynamics} of a {Balanced} {Polymorphism}.},
	volume = {155},
	copyright = {Copyright © 2000 The University of Chicago},
	issn = {00030147},
	url = {http://www.jstor.org/stable/10.1086/303299},
	doi = {10.1086/303299},
	abstract = {abstract: We describe the short‐ and long‐term dynamics of a phenotypic polymorphism that arose in a population of Escherichia coli while it was serially propagated for almost 20,000 generations in a glucose‐limited minimal medium. The two types, designated L and S, differ conspicuously in the size of the colonies they form on agar plates as well as the size of their individual cells, and these differences are heritable. The S type reached a detectable frequency ({\textbackslash}textgreater1\%) at generation 6,000, and it remained above that frequency throughout the subsequent generations. In addition to morphological differences, L and S diverged in important ecological properties. With clones isolated at 18,000 generations, L has a maximal growth rate in fresh medium that is ∼20\% higher than that of S. However, experiments with conditioned media demonstrate that L and S secrete one or more metabolites that promote the growth of S but not of L. The death rate of L during stationary phase also increases when S is abundant, which suggests that S may either secrete a metabolite that is toxic to L or remove some factor that enables the survival of L. One‐day competition experiments with the clones isolated at generation 18,000 show that their relative fitness is frequency dependent, with each type having an advantage when rare. When these two types are grown together for a period of several weeks, they converge on an equilibrium frequency that is consistent with the 1‐d competition experiments. Over the entire 14,000‐generation period of coexistence, however, the frequency of the S type fluctuated between approximately 10\% and 85\%. We offer several hypotheses that may explain the fluctuations in this balanced polymorphism, including the possibility of coevolution between the two types.},
	number = {1},
	journal = {The American Naturalist},
	author = {Rozen, Daniel E. and Lenski, Richard E.},
	month = jan,
	year = {2000},
	pages = {24--35}
}

@article{blount_genomic_2012,
	title = {Genomic analysis of a key innovation in an experimental {Escherichia} coli population},
	volume = {489},
	issn = {0028-0836},
	url = {http://dx.doi.org/10.1038/nature11514},
	doi = {10.1038/nature11514},
	number = {7417},
	journal = {Nature},
	author = {Blount, Zachary D. and Barrick, Jeffrey E. and Davidson, Carla J. and Lenski, Richard E.},
	month = sep,
	year = {2012},
	pages = {513--518}
}

@article{blount_historical_2008,
	title = {Historical contingency and the evolution of a key innovation in an experimental population of {Escherichia} coli},
	volume = {105},
	url = {http://www.pnas.org/content/105/23/7899.abstract},
	doi = {10.1073/pnas.0803151105},
	abstract = {The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for {\textbackslash}textgreater30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that “replayed” evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 × 1012 ancestral cells, nor among 9 × 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.},
	number = {23},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Blount, Zachary D. and Borland, Christina Z. and Lenski, Richard E.},
	month = jun,
	year = {2008},
	pages = {7899--7906}
}

@article{wielgoss_mutation_2013,
	title = {Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load},
	volume = {110},
	url = {http://www.pnas.org/content/110/1/222.abstract},
	doi = {10.1073/pnas.1219574110},
	abstract = {Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ∼150-fold, whereas the mutY mutations reduced the rate by ∼40–60\%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined.},
	number = {1},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Wielgoss, Sébastien and Barrick, Jeffrey E. and Tenaillon, Olivier and Wiser, Michael J. and Dittmar, W. James and Cruveiller, Stéphane and Chane-Woon-Ming, Béatrice and Médigue, Claudine and Lenski, Richard E. and Schneider, Dominique},
	month = jan,
	year = {2013},
	pages = {222--227}
}

@article{wiser_long-term_2013,
	title = {Long-term dynamics of adaptation in asexual populations},
	volume = {342},
	url = {http://www.sciencemag.org/content/342/6164/1364.abstract},
	doi = {10.1126/science.1243357},
	abstract = {Experimental studies of evolution have increased greatly in number in recent years, stimulated by the growing power of genomic tools. However, organismal fitness remains the ultimate metric for interpreting these experiments, and the dynamics of fitness remain poorly understood over long time scales. Here, we examine fitness trajectories for 12 Escherichia coli populations during 50,000 generations. Mean fitness appears to increase without bound, consistent with a power law. We also derive this power-law relation theoretically by incorporating clonal interference and diminishing-returns epistasis into a dynamical model of changes in mean fitness over time.},
	number = {6164},
	journal = {Science},
	author = {Wiser, Michael J. and Ribeck, Noah and Lenski, Richard E.},
	month = dec,
	year = {2013},
	keywords = {Experiment, Experimental Evolution, LTEE, adaptation, empirical, evolution, fitness},
	pages = {1364--1367}
}

@misc{dolson_whats_2015,
	title = {What's holding artificial life back from open-ended evolution?},
	url = {http://devosoft.org/whats-holding-artificial-life-back-from-open-ended-evolution/},
	urldate = {2016-05-16},
	author = {Dolson, Emily and Vostinar, Anya E. and Ofria, Charles},
	year = {2015}
}

@book{smith_major_1997,
	title = {The major transitions in evolution},
	publisher = {Oxford University Press},
	author = {Smith, John Maynard and Szathmary, Eors},
	year = {1997}
}

@inproceedings{hara_emergence_1999,
	title = {Emergence of cooperative behavior using {ADG}; {Automatically} {Defined} {Groups}},
	booktitle = {Proceedings of the 1999 {Genetic} and {Evolutionary} {\textbackslash}ldots},
	author = {Hara, A and Nagao, T},
	year = {1999}
}
@article{ribeck_modeling_2015,
	title = {Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions},
	volume = {69},
	issn = {1558-5646},
	url = {http://dx.doi.org/10.1111/evo.12645},
	doi = {10.1111/evo.12645},
	number = {5},
	journal = {Evolution},
	author = {Ribeck, Noah and Lenski, Richard E.},
	year = {2015},
	keywords = {Black Queen interaction, cross-feeding interaction, ecological modeling, fitness measurement, frequency dependence, polymorphism},
	pages = {1313--1320}
}

@article{maddamsetti_adaptation_2015,
	title = {Adaptation, {Clonal} {Interference}, and {Frequency}-{Dependent} {Interactions} in a {Long}-{Term} {Evolution} {Experiment} with {Escherichia} coli},
	volume = {200},
	url = {http://www.genetics.org/content/200/2/619.abstract},
	doi = {10.1534/genetics.115.176677},
	abstract = {Twelve replicate populations of Escherichia coli have been evolving in the laboratory for {\textbackslash}textgreater25 years and 60,000 generations. We analyzed bacteria from whole-population samples frozen every 500 generations through 20,000 generations for one well-studied population, called Ara−1. By tracking 42 known mutations in these samples, we reconstructed the history of this population’s genotypic evolution over this period. The evolutionary dynamics of Ara−1 show strong evidence of selective sweeps as well as clonal interference between competing lineages bearing different beneficial mutations. In some cases, sets of several mutations approached fixation simultaneously, often conveying no information about their order of origination; we present several possible explanations for the existence of these mutational cohorts. Against a backdrop of rapid selective sweeps both earlier and later, two genetically diverged clades coexisted for {\textbackslash}textgreater6000 generations before one went extinct. In that time, many additional mutations arose in the clade that eventually prevailed. We show that the clades evolved a frequency-dependent interaction, which prevented the immediate competitive exclusion of either clade, but which collapsed as beneficial mutations accumulated in the clade that prevailed. Clonal interference and frequency dependence can occur even in the simplest microbial populations. Furthermore, frequency dependence may generate dynamics that extend the period of coexistence that would otherwise be sustained by clonal interference alone.},
	number = {2},
	journal = {Genetics},
	author = {Maddamsetti, Rohan and Lenski, Richard E. and Barrick, Jeffrey E.},
	month = jun,
	year = {2015},
	pages = {619--631}
}

@article{lenski_long-term_1991,
	title = {Long-term experimental evolution in {Escherichia} coli. {I}. {Adaptation} and divergence during 2,000 generations},
	volume = {138},
	copyright = {Copyright © 1991 The University of Chicago},
	issn = {00030147},
	url = {http://www.jstor.org/stable/2462549},
	doi = {10.2307/2462549},
	abstract = {We assess the degree to which adaptation to a uniform environment among independently evolving asexual populations is associated with increasing divergence of those populations. In addition, we are concerned with the pattern of adaptation itself, particularly whether the rate of increase in mean fitness tends to decline with the number of generations of selection in a constant environment. The correspondence between the rate of increase in mean fitness and the within-population genetic variance of fitness, as expected from Fisher's fundamental theorem, is also addressed. Twelve Escherichia coli populations were founded from a single clonal ancestor and allowed to evolve for 2,000 generations. Mean fitness increased by about 37\%. However, the rate of increase in mean fitness was slower in later generations. There was no statistically significant within-population genetic variance of fitness, but there was significant between-population variance. Although the estimated genetic variation in fitness within populations was not statistically significant, it was consistent in magnitude with theoretical expectations. Similarly, the variance of mean fitness between populations was consistent with a model that incorporated stochastic variation in the timing and order of substitutions at a finite number of nonepistatic loci, coupled with substitutional delays and interference between substitutions arising from clonality. These results, taken as a whole, are consistent with theoretical expectations that do not invoke divergence due to multiple fitness peaks in a Wrightian evolutionary landscape.},
	number = {6},
	journal = {The American Naturalist},
	author = {Lenski, Richard E. and Rose, Michael R. and Simpson, Suzanne C. and Tadler, Scott C.},
	month = dec,
	year = {1991},
	pages = {1315--1341}
}

@inproceedings{bedau_classification_1998,
	title = {A classification of long-term evolutionary dynamics},
	booktitle = {Artificial life {VI}},
	publisher = {Cambridge: MIT Press},
	author = {Bedau, Mark A and Snyder, Emile and Packard, Norman H},
	year = {1998},
	pages = {228--237}
}

@inproceedings{bedau_bifurcation_1994,
	title = {Bifurcation structure in diversity dynamics},
	booktitle = {Artificial life {IV}},
	author = {Bedau, Mark A and Bahm, Alan},
	year = {1994},
	pages = {258--268}
}

@article{potter_cooperative_2000,
	title = {Cooperative {Coevolution}: {An} {Architecture} for {Evolving} {Coadapted} {Subcomponents}},
	volume = {8},
	number = {1},
	journal = {Evolutionary Computation},
	author = {Potter, Mitchell A and Jong, Kenneth A De},
	month = mar,
	year = {2000},
	pages = {1--29}
}

@article{korb_evolution_2011,
	title = {Evolution unbound: releasing the arrow of complexity},
	volume = {26},
	number = {3},
	journal = {Biology \& Philosophy},
	author = {Korb, Kevin B and Dorin, Alan},
	month = mar,
	year = {2011},
	pages = {317--338}
}

@article{rouzic_evolutionary_2008,
	title = {Evolutionary potential of hidden genetic variation},
	volume = {23},
	issn = {0169-5347},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(07)00333-3},
	doi = {10.1016/j.tree.2007.09.014},
	language = {English},
	number = {1},
	urldate = {2017-04-16TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Rouzic, Arnaud Le and Carlborg, Orjan},
	month = jan,
	year = {2008},
	pmid = {18079017},
	pages = {33--37}
}

@article{forest_preserving_2007,
	title = {Preserving the evolutionary potential of floras in biodiversity hotspots},
	volume = {445},
	copyright = {© 2007 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v445/n7129/full/nature05587.html},
	doi = {10.1038/nature05587},
	abstract = {One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot—the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.},
	language = {en},
	number = {7129},
	urldate = {2016-02-09TZ},
	journal = {Nature},
	author = {Forest, Félix and Grenyer, Richard and Rouget, Mathieu and Davies, T. Jonathan and Cowling, Richard M. and Faith, Daniel P. and Balmford, Andrew and Manning, John C. and Proches, Serban and van der Bank, Michelle and Reeves, Gail and Hedderson, Terry A. J. and Savolainen, Vincent},
	month = feb,
	year = {2007},
	keywords = {conservation, eco-evolutionary dynamics},
	pages = {757--760}
}

@article{ley_ecological_2006,
	title = {Ecological and {Evolutionary} {Forces} {Shaping} {Microbial} {Diversity} in the {Human} {Intestine}},
	volume = {124},
	issn = {0092-8674},
	url = {http://www.sciencedirect.com/science/article/pii/S0092867406001929},
	doi = {10.1016/j.cell.2006.02.017},
	abstract = {The human gut is populated with as many as 100 trillion cells, whose collective genome, the microbiome, is a reflection of evolutionary selection pressures acting at the level of the host and at the level of the microbial cell. The ecological rules that govern the shape of microbial diversity in the gut apply to mutualists and pathogens alike.},
	number = {4},
	urldate = {2017-02-27TZ},
	journal = {Cell},
	author = {Ley, Ruth E. and Peterson, Daniel A. and Gordon, Jeffrey I.},
	month = feb,
	year = {2006},
	pages = {837--848}
}

@article{antwis_fifty_2017,
	title = {Fifty important research questions in microbial ecology},
	volume = {93},
	issn = {0168-6496},
	url = {https://academic.oup.com/femsec/article/93/5/fix044/3098413/Fifty-important-research-questions-in-microbial},
	doi = {10.1093/femsec/fix044},
	number = {5},
	urldate = {2017-05-30TZ},
	journal = {FEMS Microbiology Ecology},
	author = {Antwis, Rachael E. and Griffiths, Sarah M. and Harrison, Xavier A. and Aranega-Bou, Paz and Arce, Andres and Bettridge, Aimee S. and Brailsford, Francesca L. and de Menezes, Alexandre and Devaynes, Andrew and Forbes, Kristian M. and Fry, Ellen L. and Goodhead, Ian and Haskell, Erin and Heys, Chloe and James, Chloe and Johnston, Sarah R. and Lewis, Gillian R. and Lewis, Zenobia and Macey, Michael C. and McCarthy, Alan and McDonald, James E. and Mejia-Florez, Nasmille L. and O’Brien, David and Orland, Chloé and Pautasso, Marco and Reid, William D. K. and Robinson, Heather A. and Wilson, Kenneth and Sutherland, William J.},
	month = may,
	year = {2017}
}

@article{harcombe_metabolic_2014,
	title = {Metabolic {Resource} {Allocation} in {Individual} {Microbes} {Determines} {Ecosystem} {Interactions} and {Spatial} {Dynamics}},
	volume = {7},
	issn = {2211-1247},
	url = {http://www.sciencedirect.com/science/article/pii/S2211124714002800},
	doi = {10.1016/j.celrep.2014.03.070},
	abstract = {Summary
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of microbial communities. This raises the question of whether ecosystem-level behavior of structured communities can be predicted using genome-scale metabolic models for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice and applied it to engineered communities. First, we predicted and experimentally confirmed the species ratio to which a two-species mutualistic consortium converges and the equilibrium composition of a newly engineered three-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the “eclipse dilemma”: does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding that the net outcome is beneficial highlights the complex nature of metabolic interactions in microbial communities while at the same time demonstrating their predictability.
Video Abstract},
	number = {4},
	journal = {Cell Reports},
	author = {Harcombe, William R. and Riehl, William J. and Dukovski, Ilija and Granger, Brian R. and Betts, Alex and Lang, Alex H. and Bonilla, Gracia and Kar, Amrita and Leiby, Nicholas and Mehta, Pankaj and Marx, Christopher J. and Segrè, Daniel},
	month = may,
	year = {2014},
	pages = {1104--1115}
}

@article{dunham_synthetic_2007,
	title = {Synthetic ecology: {A} model system for cooperation},
	volume = {104},
	issn = {0027-8424, 1091-6490},
	shorttitle = {Synthetic ecology},
	url = {http://www.pnas.org/content/104/6/1741},
	doi = {10.1073/pnas.0611067104},
	abstract = {National Academy of Sciences},
	language = {en},
	number = {6},
	urldate = {2017-05-30TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Dunham, Maitreya J.},
	month = feb,
	year = {2007},
	pmid = {17267618},
	pages = {1741--1742}
}

@article{zomorrodi_synthetic_2016,
	series = {Engineering {Tools} and {Prospects} in {Synthetic} {Biology}},
	title = {Synthetic {Ecology} of {Microbes}: {Mathematical} {Models} and {Applications}},
	volume = {428},
	issn = {0022-2836},
	shorttitle = {Synthetic {Ecology} of {Microbes}},
	url = {http://www.sciencedirect.com/science/article/pii/S0022283615006129},
	doi = {10.1016/j.jmb.2015.10.019},
	abstract = {As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.},
	number = {5, Part B},
	journal = {Journal of Molecular Biology},
	author = {Zomorrodi, Ali R. and Segrè, Daniel},
	month = feb,
	year = {2016},
	keywords = {Metabolic engineering, Metabolic network modeling, Microbial communities, Synthetic Biology, systems biology},
	pages = {837--861}
}

@article{scheffer_self-organized_2006,
	title = {Self-organized similarity, the evolutionary emergence of groups of similar species},
	volume = {103},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/103/16/6230},
	doi = {10.1073/pnas.0508024103},
	abstract = {Ecologists have long been puzzled by the fact that there are so many similar species in nature. Here we show that self-organized clusters of look-a-likes may emerge spontaneously from coevolution of competitors. The explanation is that there are two alternative ways to survive together: being sufficiently different or being sufficiently similar. Using a model based on classical competition theory, we demonstrate a tendency for evolutionary emergence of regularly spaced lumps of similar species along a niche axis. Indeed, such lumpy patterns are commonly observed in size distributions of organisms ranging from algae, zooplankton, and beetles to birds and mammals, and could not be well explained by earlier theory. Our results suggest that these patterns may represent self-constructed niches emerging from competitive interactions. A corollary of our findings is that, whereas in species-poor communities sympatric speciation and invasion of open niches is possible, species-saturated communities may be characterized by convergent evolution and invasion by look-a-likes.},
	language = {en},
	number = {16},
	urldate = {2017-05-22TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Scheffer, Marten and Nes, Egbert H. van},
	month = apr,
	year = {2006},
	pmid = {16585519},
	keywords = {biodiversity, coexistence, competition, evolution, niche construction},
	pages = {6230--6235}
}

@incollection{mcphee_using_2016,
	title = {Using graph databases to explore the dynamics of genetic programming runs},
	url = {http://link.springer.com/chapter/10.1007/978-3-319-34223-8_11},
	urldate = {2017-05-20TZ},
	booktitle = {Genetic {Programming} {Theory} and {Practice} {XIII}},
	publisher = {Springer},
	author = {McPhee, Nicholas Freitag and Donatucci, David and Helmuth, Thomas},
	year = {2016},
	pages = {185--201}
}

@inproceedings{helmuth_effects_2016,
	title = {Effects of {Lexicase} and {Tournament} {Selection} on {Diversity} {Recovery} and {Maintenance}},
	isbn = {978-1-4503-4323-7},
	url = {http://dl.acm.org/citation.cfm?doid=2908961.2931657},
	doi = {10.1145/2908961.2931657},
	language = {en},
	urldate = {2017-05-20TZ},
	publisher = {ACM Press},
	author = {Helmuth, Thomas and McPhee, Nicholas Freitag and Spector, Lee},
	year = {2016},
	pages = {983--990}
}

@inproceedings{helmuth_impact_2016,
	title = {The {Impact} of {Hyperselection} on {Lexicase} {Selection}},
	isbn = {978-1-4503-4206-3},
	url = {http://dl.acm.org/citation.cfm?doid=2908812.2908851},
	doi = {10.1145/2908812.2908851},
	language = {en},
	urldate = {2017-05-20TZ},
	publisher = {ACM Press},
	author = {Helmuth, Thomas and McPhee, Nicholas Freitag and Spector, Lee},
	year = {2016},
	pages = {717--724}
}

@incollection{helmuth_lexicase_2016,
	series = {Genetic and {Evolutionary} {Computation}},
	title = {Lexicase {Selection} for {Program} {Synthesis}: {A} {Diversity} {Analysis}},
	copyright = {©2016 Springer International Publishing Switzerland},
	isbn = {978-3-319-34221-4 978-3-319-34223-8},
	shorttitle = {Lexicase {Selection} for {Program} {Synthesis}},
	url = {http://link.springer.com/chapter/10.1007/978-3-319-34223-8_9},
	abstract = {Lexicase selection is a selection method for evolutionary computation in which individuals are selected by filtering the population according to performance on test cases, considered in random order. When used as the parent selection method in genetic programming, lexicase selection has been shown to provide significant improvements in problem-solving power. In this chapter we investigate the reasons for the success of lexicase selection, focusing on measures of population diversity. We present data from eight program synthesis problems and compare lexicase selection to tournament selection and selection based on implicit fitness sharing. We conclude that lexicase selection does indeed produce more diverse populations, which helps to explain the utility of lexicase selection for program synthesis.},
	language = {en},
	urldate = {2017-05-20TZ},
	booktitle = {Genetic {Programming} {Theory} and {Practice} {XIII}},
	publisher = {Springer International Publishing},
	author = {Helmuth, Thomas and McPhee, Nicholas Freitag and Spector, Lee},
	editor = {Riolo, Rick and Worzel, W. P. and Kotanchek, Mark and Kordon, Arthur},
	year = {2016},
	note = {DOI: 10.1007/978-3-319-34223-8\_9},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computational Intelligence, Implicit fitness sharing, Lexicase selection, Operations Research, Management Science, diversity, tournament selection},
	pages = {151--167}
}

@article{mouret_illuminating_2015,
	title = {Illuminating search spaces by mapping elites},
	url = {http://arxiv.org/abs/1504.04909},
	abstract = {Many fields use search algorithms, which automatically explore a search space to find high-performing solutions: chemists search through the space of molecules to discover new drugs; engineers search for stronger, cheaper, safer designs, scientists search for models that best explain data, etc. The goal of search algorithms has traditionally been to return the single highest-performing solution in a search space. Here we describe a new, fundamentally different type of algorithm that is more useful because it provides a holistic view of how high-performing solutions are distributed throughout a search space. It creates a map of high-performing solutions at each point in a space defined by dimensions of variation that a user gets to choose. This Multi-dimensional Archive of Phenotypic Elites (MAP-Elites) algorithm illuminates search spaces, allowing researchers to understand how interesting attributes of solutions combine to affect performance, either positively or, equally of interest, negatively. For example, a drug company may wish to understand how performance changes as the size of molecules and their cost-to-produce vary. MAP-Elites produces a large diversity of high-performing, yet qualitatively different solutions, which can be more helpful than a single, high-performing solution. Interestingly, because MAP-Elites explores more of the search space, it also tends to find a better overall solution than state-of-the-art search algorithms. We demonstrate the benefits of this new algorithm in three different problem domains ranging from producing modular neural networks to designing simulated and real soft robots. Because MAP- Elites (1) illuminates the relationship between performance and dimensions of interest in solutions, (2) returns a set of high-performing, yet diverse solutions, and (3) improves finding a single, best solution, it will advance science and engineering.},
	urldate = {2017-05-18TZ},
	journal = {arXiv:1504.04909 [cs, q-bio]},
	author = {Mouret, Jean-Baptiste and Clune, Jeff},
	month = apr,
	year = {2015},
	note = {arXiv: 1504.04909},
	keywords = {Computer Science - Artificial Intelligence, Computer Science - Neural and Evolutionary Computing, Computer Science - Robotics, Quantitative Biology - Populations and Evolution}
}

@article{spector_genetic_2002,
	title = {Genetic programming and autoconstructive evolution with the push programming language},
	volume = {3},
	url = {http://www.springerlink.com/index/6HEME6VFKXTFV2HY.pdf},
	number = {1},
	urldate = {2017-05-02TZ},
	journal = {Genetic Programming and Evolvable Machines},
	author = {Spector, Lee and Robinson, Alan},
	year = {2002},
	pages = {7--40}
}

@phdthesis{goings_natural_2010,
	address = {United States -- Michigan},
	type = {Ph.{D}.},
	title = {Natural niching: {Applying} ecological principles to evolutionary computation},
	copyright = {Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.},
	shorttitle = {Natural niching},
	url = {http://search.proquest.com/docview/748246734/abstract/BA8FAA8216574AE5PQ/1},
	abstract = {Evolutionary algorithms have shown great promise in evolving novel solutions to real-world problems, but the complexity of those solutions is still limited, unlike the apparently open-ended evolution that occurs in the natural world. The power of traditional evolutionary algorithms is constrained by rapid convergence to a single solution on a sub-optimal local peak, leading to stagnation. In part, nature surmounts these complexity barriers with ecological dynamics that generate a diverse array of raw materials for evolution to build upon.
In this dissertation I focus on one ecological force that increases diversity: frequency-dependent selection that arises from competition among individuals for finite resources. I explore the benefits of incorporating this force into an algorithmic framework, focusing on how this mechanism can increase diversity to provide many evolutionary paths to a problem solution. The use of niching to simultaneously approach a single solution from many directions has not been extensively studied in previous literature. I study competition for limited resources in a digital evolution system and examine the importance of specific resource parameters on population dynamics. I show that my techniques are robust at increasing diversity over a broad range of settings for each parameter, and that the parameter settings are governed by a relatively simple set of equations.
Finally I introduce Eco-EA, a general form of an evolutionary algorithm that associates a limited resource with each trait to be evolved. I apply Eco-EA to several problems, including a real-world software engineering problem, and I show that the Eco-EA yields several advantages over traditional evolutionary algorithm approaches, including: (1) significantly more rapid evolution of targeted complex functions; (2) discovery and maintenance of a diverse set of partial solutions that together solve a problem; (3) maintenance of a selection of high-quality final solutions for the researcher to choose from, often with slightly different properties; and (4) discovery of solutions that are more evolvable when placed in new environments.},
	language = {English},
	urldate = {2017-05-01TZ},
	school = {Michigan State University},
	author = {Goings, Sherri},
	year = {2010},
	keywords = {Applied sciences, Resource sharing, evolutionary computation}
}

@inproceedings{mcdermott_genetic_2012,
	title = {Genetic programming needs better benchmarks},
	isbn = {978-1-4503-1177-9},
	url = {http://dl.acm.org/citation.cfm?doid=2330163.2330273},
	doi = {10.1145/2330163.2330273},
	language = {en},
	urldate = {2017-05-01TZ},
	publisher = {ACM Press},
	author = {McDermott, James and De Jong, Kenneth and O'Reilly, Una-May and White, David R. and Luke, Sean and Manzoni, Luca and Castelli, Mauro and Vanneschi, Leonardo and Jaskowski, Wojciech and Krawiec, Krzysztof and Harper, Robin},
	year = {2012},
	pages = {791}
}

@inproceedings{spector_assessment_2012,
	title = {Assessment of problem modality by differential performance of lexicase selection in genetic programming: a preliminary report},
	shorttitle = {Assessment of problem modality by differential performance of lexicase selection in genetic programming},
	url = {http://dl.acm.org/citation.cfm?id=2330846},
	urldate = {2017-05-01TZ},
	booktitle = {Proceedings of the 14th annual conference companion on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Spector, Lee},
	year = {2012},
	pages = {401--408}
}

@article{rocabert_beware_2017,
	title = {Beware batch culture: {Seasonality} and niche construction predicted to favor bacterial adaptive diversification},
	volume = {13},
	issn = {1553-7358},
	shorttitle = {Beware batch culture},
	url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005459},
	doi = {10.1371/journal.pcbi.1005459},
	abstract = {Author summary Stable bacterial cross-feeding interactions, where one strain feeds on the waste of the other, are important to understand, as they can be a first step toward bacterial speciation. Their emergence is commonly observed in laboratory experiments using Escherichia coli as a model organism. Yet it is not clear how cross-feeding interactions can resist the invasion of a fitter mutant when the environment contains a single resource since there seems to be a single ecological niche. Here, we used another kind of “model organism”, a digital one, allowing for detailed and fast investigations, and providing a way to disentangle generic evolutionary mechanisms from specificities associated with E. coli. Digital organisms with evolvable genomes and metabolic networks compete for resources in conditions mimicking laboratory evolution experiments. In chemostat simulations, although cross-feeding interactions regularly emerged, selective sweeps regularly purged the population of its diversity. By contrast, batch culture allowed for much more stable cross-feeding interactions, because it includes seasons and thus distinct temporal niches, thereby favoring the adaptive diversification of proto-species.},
	number = {3},
	urldate = {2017-04-17TZ},
	journal = {PLOS Computational Biology},
	author = {Rocabert, Charles and Knibbe, Carole and Consuegra, Jessika and Schneider, Dominique and Beslon, Guillaume},
	month = mar,
	year = {2017},
	keywords = {DNA metabolism, Ecological niches, Enzyme metabolism, Metabolic networks, Metabolites, Microbial evolution, Organismal evolution, Phylogenetic analysis},
	pages = {e1005459}
}

@article{avise_role_1989,
	title = {A role for molecular genetics in the recognition and conservation of endangered species},
	volume = {4},
	issn = {0169-5347},
	url = {http://www.sciencedirect.com/science/article/pii/0169534789902036},
	doi = {10.1016/0169-5347(89)90203-6},
	abstract = {Taxonomies based on morphological traits alone sometimes provide inadequate or misleading guides to phylogenetic distinctions at the subspecies and species levels. Yet taxonomic assignments inevitably shape perceptions of biotic diversity, including recognition of endangered species. Case histories are discussed in which the data of molecular genetics revealed prior systematic errors of the two possible kinds: taxonomic recognition of groups showing little evolutionary differentiation, and lack of taxonomic recognition of phylogenetically distinct forms. In such cases, conservation efforts for ‘endangered species’ can be misdirected with respect to the goal of protecting biological diversity.},
	number = {9},
	urldate = {2017-04-17TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Avise, John C.},
	month = sep,
	year = {1989},
	pages = {279--281}
}

@incollection{ripley_mapped_1981,
	title = {Mapped {Point} {Patterns}},
	copyright = {Copyright © 1981 John Wiley \& Sons, Inc. All rights reserved.},
	isbn = {978-0-471-72521-3},
	url = {http://onlinelibrary.wiley.com.proxy1.cl.msu.edu/doi/10.1002/0471725218.ch8/summary},
	abstract = {This chapter includes the following topics:

* Basic Parameters
* Nearest-Neighbor Methods
* Second Moments
* Models
* Comparative Studies
* Examples},
	language = {en},
	urldate = {2017-04-07TZ},
	booktitle = {Spatial {Statistics}},
	publisher = {John Wiley \& Sons, Inc.},
	author = {Ripley, Brian D.},
	year = {1981},
	keywords = {distribution theory, homogeneity, isotropy, mapped point patterns, poisson process},
	pages = {144--190}
}

@article{ripley_second-order_1976,
	title = {The {Second}-{Order} {Analysis} of {Stationary} {Point} {Processes}},
	volume = {13},
	issn = {0021-9002},
	url = {http://www.jstor.org/stable/3212829},
	abstract = {This paper provides a rigorous foundation for the second-order analysis of stationary point processes on general spaces. It illuminates the results of Bartlett on spatial point processes, and covers the point processes of stochastic geometry, including the line and hyperplane processes of Davidson and Krickeberg. The main tool is the decomposition of moment measures pioneered by Krickeberg and Vere-Jones. Finally some practical aspects of the analysis of point processes are discussed.},
	number = {2},
	urldate = {2017-04-07TZ},
	journal = {Journal of Applied Probability},
	author = {Ripley, B. D.},
	year = {1976},
	pages = {255--266}
}

@article{moritz_diversification_2000,
	title = {Diversification of rainforest faunas: an integrated molecular approach},
	volume = {31},
	shorttitle = {Diversification of rainforest faunas},
	url = {http://annualreviews.org/doi/abs/10.1146/annurev.ecolsys.31.1.533},
	number = {1},
	urldate = {2017-04-16TZ},
	journal = {Annual review of ecology and systematics},
	author = {Moritz, C. and Patton, J. L. and Schneider, C. J. and Smith, T. B.},
	year = {2000},
	pages = {533--563}
}

@article{yeaman_regional_2006,
	title = {Regional heterogeneity and gene flow maintain variance in a quantitative trait within populations of lodgepole pine},
	volume = {273},
	issn = {0962-8452},
	doi = {10.1098/rspb.2006.3498},
	abstract = {Genetic variation is of fundamental importance to biological evolution, yet we still know very little about how it is maintained in nature. Because many species inhabit heterogeneous environments and have pronounced local adaptations, gene flow between differently adapted populations may be a persistent source of genetic variation within populations. If this migration-selection balance is biologically important then there should be strong correlations between genetic variance within populations and the amount of heterogeneity in the environment surrounding them. Here, we use data from a long-term study of 142 populations of lodgepole pine (Pinus contorta) to compare levels of genetic variation in growth response with measures of climatic heterogeneity in the surrounding region. We find that regional heterogeneity explains at least 20\% of the variation in genetic variance, suggesting that gene flow and heterogeneous selection may play an important role in maintaining the high levels of genetic variation found within natural populations.},
	language = {eng},
	number = {1594},
	journal = {Proceedings. Biological Sciences},
	author = {Yeaman, Sam and Jarvis, Andy},
	month = jul,
	year = {2006},
	pmid = {16769628},
	pmcid = {PMC1634926},
	keywords = {Climate, Genetic Heterogeneity, Pinus, Quantitative Trait Loci, gene flow},
	pages = {1587--1593}
}

@article{franklin_importance_2009,
	title = {Importance of matrix habitats in maintaining biological diversity},
	volume = {106},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/106/2/349},
	doi = {10.1073/pnas.0812016105},
	abstract = {National Academy of Sciences},
	language = {en},
	number = {2},
	urldate = {2017-04-16TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Franklin, Jerry F. and Lindenmayer, David B.},
	month = jan,
	year = {2009},
	pmid = {19129497},
	pages = {349--350}
}

@article{mcgarigal_surface_2009,
	title = {Surface metrics: an alternative to patch metrics for the quantification of landscape structure},
	volume = {24},
	issn = {0921-2973, 1572-9761},
	shorttitle = {Surface metrics},
	url = {https://link.springer.com/article/10.1007/s10980-009-9327-y},
	doi = {10.1007/s10980-009-9327-y},
	abstract = {Modern landscape ecology is based on the patch mosaic paradigm, in which landscapes are conceptualized and analyzed as mosaics of discrete patches. While this model has been widely successful, there are many situations where it is more meaningful to model landscape structure based on continuous rather than discrete spatial heterogeneity. The growing field of surface metrology offers a variety of surface metrics for quantifying landscape gradients, yet these metrics are largely unknown and/or unused by landscape ecologists. In this paper, we describe a suite of surface metrics with potential for landscape ecological application. We assessed the redundancy among metrics and sought to find groups of similarly behaved metrics by examining metric performance across 264 sample landscapes in western Turkey. For comparative purposes and to evaluate the robustness of the observed patterns, we examined 16 different patch mosaic models and 18 different landscape gradient models of landscape structure. Surface metrics were highly redundant, but less so than patch metrics, and consistently aggregated into four cohesive clusters of similarly behaved metrics representing surface roughness, shape of the surface height distribution, and angular and radial surface texture. While the surface roughness metrics have strong analogs among the patch metrics, the other surface components are largely unique to landscape gradients. We contend that the surface properties we identified are nearly universal and have potential to offer new insights into landscape pattern–process relationships.},
	language = {en},
	number = {3},
	urldate = {2017-04-16TZ},
	journal = {Landscape Ecology},
	author = {McGarigal, Kevin and Tagil, Sermin and Cushman, Samuel A.},
	month = mar,
	year = {2009},
	pages = {433--450}
}

@book{forman_land_1995,
	title = {Land {Mosaics}: {The} {Ecology} of {Landscapes} and {Regions}},
	publisher = {Cambridge University Press},
	author = {Forman, Richard TT},
	year = {1995}
}

@book{ndubisi_ecological_2014,
	title = {The {Ecological} {Design} and {Planning} {Reader}},
	isbn = {9781610914918},
	abstract = {From Henry David Thoreau to Rachel Carson, writers have long examined the effects of industrialization and its potential to permanently alter the world around them. Today, as we experience rapid global urbanization, pressures on the natural environment to accommodate our daily needs for food, work, shelter, and recreation are greatly intensified. Concerted efforts to balance human use with ecological concerns are needed now more than ever.  A rich body of literature on the effect of human actions on the natural environment provides a window into what we now refer to as ecological design and planning. The study and practice of ecological design and planning provide a promising way to manage change in the landscape so that human actions are more in tune with natural processes. In The Ecological Design and Planning Reader Professor Ndubisi offers refreshing insights into key themes that shape the theory and practice of ecological design and planning. He has assembled, synthesized, and framed selected seminal published scholarly works in the field from the past one hundred and fifty years——ranging from Ebenezer Howard’s Garden Cities of To-morrow to Anne Whiston Spirn’s, “Ecological Urbanism: A Framework for the Design of Resilient Cities.” The reader ends with a hopeful look forward, which suggests an agenda for future research and analysis in ecological design and planning.  This is the first volume to bring together classic and contemporary writings on the history, evolution, theory, methods, and exemplary practice of ecological design and planning. The collection provides students, scholars, researchers, and practitioners with a solid foundation for understanding the relationship between human systems and our natural environment.},
	language = {en},
	publisher = {Island Press},
	author = {Ndubisi, Forster O.},
	month = dec,
	year = {2014},
	note = {Google-Books-ID: VXPlBQAAQBAJ},
	keywords = {Architecture / General, Architecture / Urban \& Land Use Planning}
}

@article{losos_adaptive_2010,
	title = {Adaptive {Radiation}, {Ecological} {Opportunity}, and {Evolutionary} {Determinism}.},
	volume = {175},
	issn = {0003-0147},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1086/652433},
	doi = {10.1086/652433},
	abstract = {Adaptive radiation refers to diversification from an ancestral species that produces descendants adapted to use a great variety of distinct ecological niches. In this review, I examine two aspects of adaptive radiation: first, that it results from ecological opportunity and, second, that it is deterministic in terms of its outcome and evolutionary trajectory. Ecological opportunity is usually a prerequisite for adaptive radiation, although in some cases, radiation can occur in the absence of preexisting opportunity. Nonetheless, many clades fail to radiate although seemingly in the presence of ecological opportunity; until methods are developed to identify and quantify ecological opportunity, the concept will have little predictive utility in understanding a priori when a clade might be expected to radiate. Although predicted by theory, replicated adaptive radiations occur only rarely, usually in closely related and poorly dispersing taxa found in the same region on islands or in lakes. Contingencies of a variety of types may usually preclude close similarity in the outcome of evolutionary diversification in other situations. Whether radiations usually unfold in the same general sequence is unclear because of the unreliability of methods requiring phylogenetic reconstruction of ancestral events. The synthesis of ecological, phylogenetic, experimental, and genomic advances promises to make the coming years a golden age for the study of adaptive radiation; natural history data, however, will always be crucial to understanding the forces shaping adaptation and evolutionary diversification.},
	number = {6},
	urldate = {2017-04-16TZ},
	journal = {The American Naturalist},
	author = {Losos, Jonathan B.},
	month = jun,
	year = {2010},
	pages = {623--639}
}

@article{pinto_testing_2008,
	title = {Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in {Caribbean} and mainland {Anolis} lizards},
	volume = {275},
	copyright = {© 2008 The Royal Society},
	issn = {0962-8452, 1471-2954},
	shorttitle = {Testing the island effect in adaptive radiation},
	url = {http://rspb.royalsocietypublishing.org/content/275/1652/2749},
	doi = {10.1098/rspb.2008.0686},
	abstract = {Many of the classic examples of adaptive radiation, including Caribbean Anolis lizards, are found on islands. However, Anolis also exhibits substantial species richness and ecomorphological disparity on mainland Central and South America. We compared patterns and rates of morphological evolution to investigate whether, in fact, island Anolis are exceptionally diverse relative to their mainland counterparts. Quite the contrary, we found that rates and extent of diversification were comparable—Anolis adaptive radiation is not an island phenomenon. However, mainland and Caribbean anoles occupy different parts of morphological space; in independent colonizations of both island and mainland habitats, island anoles have evolved shorter limbs and better-developed toe pads. These patterns suggest that the two areas are on different evolutionary trajectories. The ecological causes of these differences are unknown, but may relate to differences in predation or competition among mainland and island communities.},
	language = {en},
	number = {1652},
	urldate = {2017-04-16TZ},
	journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	author = {Pinto, Gabriel and Mahler, D. Luke and Harmon, Luke J. and Losos, Jonathan B.},
	month = dec,
	year = {2008},
	pmid = {18713721},
	pages = {2749--2757}
}

@book{baddeley_spatial_2015,
	title = {Spatial {Point} {Patterns}: {Methodology} and {Applications} with {R}},
	isbn = {978-1-4822-1021-7},
	shorttitle = {Spatial {Point} {Patterns}},
	abstract = {Modern Statistical Methodology and Software for Analyzing Spatial Point Patterns Spatial Point Patterns: Methodology and Applications with R shows scientific researchers and applied statisticians from a wide range of fields how to analyze their spatial point pattern data. Making the techniques accessible to non-mathematicians, the authors draw on their 25 years of software development experiences, methodological research, and broad scientific collaborations to deliver a book that clearly and succinctly explains concepts and addresses real scientific questions. Practical Advice on Data Analysis and Guidance on the Validity and Applicability of Methods  The first part of the book gives an introduction to R software, advice about collecting data, information about handling and manipulating data, and an accessible introduction to the basic concepts of point processes. The second part presents tools for exploratory data analysis, including non-parametric estimation of intensity, correlation, and spacing properties. The third part discusses model-fitting and statistical inference for point patterns. The final part describes point patterns with additional "structure," such as complicated marks, space-time observations, three- and higher-dimensional spaces, replicated observations, and point patterns constrained to a network of lines. Easily Analyze Your Own Data  Throughout the book, the authors use their spatstat package, which is free, open-source code written in the R language. This package provides a wide range of capabilities for spatial point pattern data, from basic data handling to advanced analytic tools. The book focuses on practical needs from the user’s perspective, offering answers to the most frequently asked questions in each chapter.},
	language = {en},
	publisher = {CRC Press},
	author = {Baddeley, Adrian and Rubak, Ege and Turner, Rolf},
	month = nov,
	year = {2015},
	keywords = {Mathematics / Probability \& Statistics / General, Science / Earth Sciences / Geology}
}

@inproceedings{wright_roles_1932,
	address = {Brooklyn Botanic Garden, Brooklyn, NY},
	title = {The roles of mutation, inbreeding, crossbreeding, and selection in evolution},
	url = {http://www.esp.org/books/6th-congress/facsimile/contents/6th-cong-p356-wright.pdf},
	urldate = {2017-04-04TZ},
	booktitle = {Proceedings of the {Sixth} {International} {Congress} of {Genetics}},
	author = {Wright, Sewall},
	year = {1932},
	pages = {356--366}
}

@book{ferriere_evolutionary_2004,
	title = {Evolutionary conservation biology},
	url = {https://books.google.com/books?hl=en&lr=&id=xfTB7UmQ0N4C&oi=fnd&pg=PP1&dq=evolutionary+conservation+biology&ots=ru9_QLDMaw&sig=ZRj792dm48J_esy-iute7cE6sQY},
	urldate = {2016-02-05TZ},
	publisher = {Cambridge University Press},
	author = {Ferrière, Régis and Dieckmann, Ulf and Couvet, Denis},
	year = {2004}
}

@article{losos_analysis_2000,
	title = {Analysis of an evolutionary species–area relationship},
	volume = {408},
	copyright = {© 2000 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v408/n6814/full/408847a0.html},
	doi = {10.1038/35048558},
	abstract = {Large islands typically have more species than comparable smaller islands. Ecological theories, the most influential being the equilibrium theory of island biogeography, explain the species–area relationship as the outcome of the effect of area on immigration and extinction rates. However, these theories do not apply to taxa on land masses, including continents and large islands, that generate most of their species in situ. In this case, species–area relationships should be driven by higher speciation rates in larger areas, a theory that has never been quantitatively tested. Here we show that Anolis lizards on Caribbean islands meet several expectations of the evolutionary theory. Within-island speciation exceeds immigration as a source of new species on all islands larger than 3,000 km2, whereas speciation is rare on smaller islands. Above this threshold island size, the rate of species proliferation increases with island area, a process that results principally from the positive effects of area on speciation rate. Also as expected, the slope of the species–area relationship jumps sharply above the threshold. Although Anolis lizards have been present on large Caribbean islands for over 30 million years, there are indications that the current number of species still falls below the speciation–extinction equilibrium.},
	language = {en},
	number = {6814},
	urldate = {2016-03-01TZ},
	journal = {Nature},
	author = {Losos, Jonathan B. and Schluter, Dolph},
	month = dec,
	year = {2000},
	pages = {847--850}
}

@book{oldford_qqtest:_2016,
	title = {qqtest: {Self} {Calibrating} {Quantile}-{Quantile} {Plots} for {Visual} {Testing}},
	url = {https://CRAN.R-project.org/package=qqtest},
	author = {Oldford, Wayne},
	year = {2016}
}

@article{proches_how_2006,
	title = {How much evolutionary history in a 10×10 m plot?},
	volume = {273},
	copyright = {© 2006 The Royal Society},
	issn = {0962-8452, 1471-2954},
	url = {http://rspb.royalsocietypublishing.org/content/273/1590/1143},
	doi = {10.1098/rspb.2005.3427},
	abstract = {We use a fully dated phylogenetic tree of the angiosperm families to calculate phylogenetic diversity (PD) in four South African vegetation types with distinct evolutionary histories. Since the branch length values are in this case represented by the ages of plant lineages, PD becomes the cumulative evolutionary age (CEA) of assemblages. Unsurprisingly, total CEA increases with family and with species diversity and observed values are the same as expected from random sampling of family lists. However, when random sampling is done from species lists, observed CEAs are generally lower than expected. In vegetation types which have undergone recent diversification—grassland, fynbos and Nama-karoo—co-occurring species are more closely related than expected, but in subtropical thicket the observed CEAs are well described by random sampling. The use of CEA has great potential for assessing the age of biotic assemblages, particularly as the dating of genus and species-level phylogenies become more accurate.},
	language = {en},
	number = {1590},
	urldate = {2017-04-14TZ},
	journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	author = {Procheş, Şerban and Wilson, John R. U. and Cowling, Richard M.},
	month = may,
	year = {2006},
	pmid = {16600893},
	pages = {1143--1148}
}

@article{latimer_neutral_2005,
	title = {Neutral {Ecological} {Theory} {Reveals} {Isolation} and {Rapid} {Speciation} in a {Biodiversity} {Hot} {Spot}},
	volume = {309},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/309/5741/1722},
	doi = {10.1126/science.1115576},
	abstract = {South Africa's Mediterranean-climate fynbos shrubland is a hot spot of species diversity, but its diversity patterns contrast strongly with other high-diversity areas, including the Amazon rain forest. With its extremely high levels of endemism and species turnover, fynbos is made up of dissimilar local communities that are species-rich but relatively poor in rare species. Using neutral ecological theory, we show that the relative species-abundance distributions in fynbos can be explained by migration rates that are two orders of magnitude lower than they are in tropical rain forests. Speciation rates, which are indexed by the “biodiversity parameter” Θ, are estimated to be higher than they are in any previously examined plant system.
South African shrublands maintain diversity in many distinct regions featuring low migration and high speciation, in contrast to Amazon rain forests where the ranges of diverse species overlap widely.
South African shrublands maintain diversity in many distinct regions featuring low migration and high speciation, in contrast to Amazon rain forests where the ranges of diverse species overlap widely.},
	language = {en},
	number = {5741},
	urldate = {2017-04-14TZ},
	journal = {Science},
	author = {Latimer, Andrew M. and Silander, John A. and Cowling, Richard M.},
	month = sep,
	year = {2005},
	pmid = {16151011},
	pages = {1722--1725}
}

@article{cowling_microevolutionary_2006,
	title = {A microevolutionary perspective on {Mediterranean} plant evolution},
	volume = {21},
	issn = {0169-5347},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(06)00022-X},
	doi = {10.1016/j.tree.2006.01.004},
	language = {English},
	number = {5},
	urldate = {2017-04-14TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Cowling, Richard M.},
	month = may,
	year = {2006},
	pages = {235--236}
}

@article{knight_theory_2009,
	title = {From theory to practice: designing and situating spatial prioritization approaches to better implement conservation action},
	shorttitle = {From theory to practice},
	url = {http://www.academia.edu/download/31663233/14_Knight_A-T_et-al_2009_SCP_Chap18.pdf},
	urldate = {2017-04-14TZ},
	journal = {Spatial conservation prioritization: quantitative methods and computational tools. Oxford University Press Inc., New York, NY},
	author = {Knight, Andrew T. and Cowling, Richard M. and Possingham, Hugh P. and Wilson, Kerrie A.},
	year = {2009},
	pages = {249--259}
}

@article{sutherland_one_2009,
	title = {One hundred questions of importance to the conservation of global biological diversity},
	volume = {23},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2009.01212.x/full},
	number = {3},
	urldate = {2017-04-14TZ},
	journal = {Conservation Biology},
	author = {Sutherland, W. J. and Adams, W. M. and Aronson, R. B. and Aveling, R. and Blackburn, Tim M. and Broad, S. and Ceballos, Germán and Cote, I. M. and Cowling, R. M. and Da Fonseca, G. A. B. and {others}},
	year = {2009},
	pages = {557--567}
}
@article{potts_testing_2013,
	title = {Testing large-scale conservation corridors designed for patterns and processes: comparative phylogeography of three tree species},
	volume = {19},
	shorttitle = {Testing large-scale conservation corridors designed for patterns and processes},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12113/full},
	number = {11},
	urldate = {2017-04-14TZ},
	journal = {Diversity and distributions},
	author = {Potts, Alastair J. and Hedderson, Terry A. and Cowling, Richard M.},
	year = {2013},
	pages = {1418--1428}
}

@article{gillespie_community_2004,
	title = {Community {Assembly} {Through} {Adaptive} {Radiation} in {Hawaiian} {Spiders}},
	volume = {303},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/303/5656/356},
	doi = {10.1126/science.1091875},
	abstract = {Communities arising through adaptive radiation are generally regarded as unique, with speciation and adaptation being quite different from immigration and ecological assortment. Here, I use the chronological arrangement of the Hawaiian Islands to visualize snapshots of evolutionary history and stages of community assembly. Analysis of an adaptive radiation of habitat-associated, polychromatic spiders shows that (i) species assembly is not random; (ii) within any community, similar sets of ecomorphs arise through both dispersal and evolution; and (iii) species assembly is dynamic with maximum species numbers in communities of intermediate age. The similar patterns of species accumulation through evolutionary and ecological processes suggest universal principles underlie community assembly.},
	language = {en},
	number = {5656},
	urldate = {2017-04-13TZ},
	journal = {Science},
	author = {Gillespie, Rosemary},
	month = jan,
	year = {2004},
	pmid = {14726588},
	pages = {356--359}
}

@article{hillebrand_generality_2004,
	title = {On the generality of the latitudinal diversity gradient},
	volume = {163},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1086/381004},
	number = {2},
	urldate = {2017-04-12TZ},
	journal = {The American Naturalist},
	author = {Hillebrand, Helmut},
	year = {2004},
	pages = {192--211}
}

@article{nowak_spatial_1993,
	title = {{THE} {SPATIAL} {DILEMMAS} {OF} {EVOLUTION}},
	volume = {03},
	issn = {0218-1274},
	url = {http://www.worldscientific.com/doi/abs/10.1142/S0218127493000040},
	doi = {10.1142/S0218127493000040},
	abstract = {Evolutionary game theory can be extended to include spatial dimensions. The individual players are placed in a two-dimensional spatial array. In each round every individual “plays the game” with its immediate neighbours. After this, each site is occupied by its original owner or by one of the neighbours, depending on who scored the highest payoff. These rules specify a deterministic cellular automaton. We find that spatial effects can change the outcome of frequency dependent selection. Strategies may coexist that would not coexist in homogeneous populations. Spatial games have interesting mathematical properties. There are static or chaotically changing patterns. For symmetrical starting conditions we find “dynamical fractals” and “evolutionary kaleidoscopes.” There is a new world to be explored.},
	number = {01},
	urldate = {2014-05-05TZ},
	journal = {International Journal of Bifurcation and Chaos},
	author = {NOWAK, MARTIN A. and MAY, ROBERT M.},
	month = feb,
	year = {1993},
	pages = {35--78}
}

@article{odonnell_roles_2014,
	title = {The {Roles} of {Standing} {Genetic} {Variation} and {Evolutionary} {History} in {Determining} the {Evolvability} of {Anti}-{Predator} {Strategies}},
	volume = {9},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100163},
	doi = {10.1371/journal.pone.0100163},
	abstract = {Standing genetic variation and the historical environment in which that variation arises (evolutionary history) are both potentially significant determinants of a population's capacity for evolutionary response to a changing environment. Using the open-ended digital evolution software Avida, we evaluated the relative importance of these two factors in influencing evolutionary trajectories in the face of sudden environmental change. We examined how historical exposure to predation pressures, different levels of genetic variation, and combinations of the two, affected the evolvability of anti-predator strategies and competitive abilities in the presence or absence of threats from new, invasive predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population's capacity to evolve anti-predator traits, i.e. traits effective against novel predators. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations.},
	number = {6},
	urldate = {2017-03-08TZ},
	journal = {PLOS ONE},
	author = {O'Donnell, Daniel R. and Parigi, Abhijna and Fish, Jordan A. and Dworkin, Ian and Wagner, Aaron P.},
	month = jun,
	year = {2014},
	keywords = {Cloning, Evolutionary genetics, Genetic polymorphism, Organismal evolution, Population genetics, Predation, Predator-prey dynamics, Viral evolution},
	pages = {e100163}
}

@article{avise_phylogeography:_2009,
	title = {Phylogeography: {Retrospect} and {Prospect}},
	volume = {36},
	issn = {0305-0270},
	shorttitle = {Phylogeography},
	url = {http://www.jstor.org/stable/20488328},
	abstract = {Phylogeography has grown explosively in the two decades since the word was coined and the discipline was outlined in 1987. Here I summarize the many achievements and novel perspectives that phylogeography has brought to population genetics, phylogenetic biology and biogeography. I also address future directions for the field. From the introduction of mitochondrial DNA assays in the late 1970s, to the key distinction between gene trees and species phylogenies, to the ongoing era of multi-locus coalescent theory, phylogeographic perspectives have consistently challenged conventional genetic and evolutionary paradigms, and they have forged empirical and conceptual bridges between the formerly separate disciplines of population genetics (microevolutionary analysis) and phylogenetic biology (in macroevolution).},
	number = {1},
	urldate = {2017-04-06TZ},
	journal = {Journal of Biogeography},
	author = {Avise, John C. and Riddle, Brett},
	year = {2009},
	pages = {3--15}
}

@inproceedings{school_of_computer_science_university_of_windsor_n_2014,
	title = {n {Enhanced} {Artificial} {Ecosystem}: {Investigating} {Emergence} of {Ecological} {Niches}},
	isbn = {978-0-262-32621-6},
	shorttitle = {n {Enhanced} {Artificial} {Ecosystem}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch111.pdf},
	doi = {10.7551/978-0-262-32621-6-ch111},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Computer Science, University of Windsor} and Mahayekhi, Morteza and Golestani, Abbas and Farahani, Yasaman and Gras, Robin},
	month = jul,
	year = {2014},
	pages = {693--700}
}

@article{liu_insights_2017,
	title = {Insights into resource consumption, cross-feeding, system collapse, stability and biodiversity from an artificial ecosystem},
	volume = {14},
	url = {http://rsif.royalsocietypublishing.org/content/14/126/20160816.abstract},
	number = {126},
	urldate = {2017-03-13TZ},
	journal = {Journal of The Royal Society Interface},
	author = {Liu, Yu and Sumpter, David},
	year = {2017},
	pages = {20160816}
}

@article{watson_how_2016,
	title = {How {Can} {Evolution} {Learn}?},
	volume = {31},
	issn = {0169-5347},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(15)00293-1},
	doi = {10.1016/j.tree.2015.11.009},
	language = {English},
	number = {2},
	urldate = {2017-03-03TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Watson, Richard A. and Szathmáry, Eörs},
	month = feb,
	year = {2016},
	pmid = {26705684},
	pages = {147--157}
}

@misc{noauthor_google_nodate,
	title = {Google {Scholar} {Citations}},
	url = {https://scholar.google.com/citations?view_op=view_citation&hl=en&user=D847cGsAAAAJ&pagesize=100&citation_for_view=D847cGsAAAAJ:SEmTV4UfSqwC},
	urldate = {2017-04-04TZ}
}

@article{fernandez_emergent_2012,
	title = {Emergent {Diversity} in an {Open}-{Ended} {Evolving} {Virtual} {Community}},
	volume = {18},
	issn = {1064-5462},
	url = {http://dx.doi.org/10.1162/artl_a_00059},
	doi = {10.1162/artl_a_00059},
	abstract = {Understanding the dynamics of biodiversity has become an important line of research in theoretical ecology and, in particular, conservation biology. However, studying the evolution of ecological communities under traditional modeling approaches based on differential calculus requires species' characteristics to be predefined, which limits the generality of the results. An alternative but less standardized methodology relies on intensive computer simulation of evolving communities made of simple, explicitly described individuals. We study here the formation, evolution, and diversity dynamics of a community of virtual plants with a novel individual-centered model involving three different scales: the genetic, the developmental, and the physiological scales. It constitutes an original attempt at combining development, evolution, and population dynamics (based on multi-agent interactions) into one comprehensive, yet simple model. In this world, we observe that our simulated plants evolve increasingly elaborate canopies, which are capable of intercepting ever greater amounts of light. Generated morphologies vary from the simplest one-branch structure of promoter plants to a complex arborization of several hundred thousand branches in highly evolved variants. On the population scale, the heterogeneous spatial structuration of the plant community at each generation depends solely on the evolution of its component plants. Using this virtual data, the morphologies and the dynamics of diversity production were analyzed by various statistical methods, based on genotypic and phenotypic distance metrics. The results demonstrate that diversity can spontaneously emerge in a community of mutually interacting individuals under the influence of specific environmental conditions.},
	number = {2},
	urldate = {2017-03-13TZ},
	journal = {Artificial Life},
	author = {Fernández, Jose D. and Lobo, Daniel and Martn, Gema M. and Doursat, René and Vico, Francisco J.},
	month = feb,
	year = {2012},
	pages = {199--222}
}

@article{johnson_evolution_2004,
	title = {Evolution of {Resource} {Competition} between {Mutually} {Dependent} {Digital} {Organisms}},
	volume = {10},
	issn = {1064-5462},
	url = {http://dx.doi.org/10.1162/106454604773563577},
	doi = {10.1162/106454604773563577},
	abstract = {We study the emergence and dynamics of competing strains of digital organisms in a world with two depletable resources. Consumption of one resource produces the other resource as a by-product, and vice versa. As a consequence, two types of mutually dependent organisms emerge that each prey on the waste product of the other. In the absence of mutations, that is, in a purely ecological setting, the abundances of the two types of organisms display a wide range of different types of oscillations, from regular oscillations with large amplitude to irregular oscillations with amplitudes ranging from small to large. In this regime, time-averaged abundance levels seem to be controlled by the relative fitness of the organisms in the absence of resources. Under mutational pressure, on the other hand, populations evolve that seem to avoid the oscillations of intermediate to large amplitudes. In this case, the relative fitness of the organisms in the presence of resources plays an important role in the time-averaged abundance levels as well.},
	number = {2},
	urldate = {2017-03-02TZ},
	journal = {Artificial Life},
	author = {Johnson, Tyler J. and Wilke, Claus O.},
	month = mar,
	year = {2004},
	pages = {145--156}
}

@article{lundh_cross-feeding_2013,
	title = {Cross-feeding dynamics described by a series expansion of the replicator equation},
	volume = {75},
	url = {http://link.springer.com/article/10.1007/s11538-013-9828-3},
	number = {5},
	urldate = {2017-03-13TZ},
	journal = {Bulletin of mathematical biology},
	author = {Lundh, Torbjörn and Gerlee, Philip},
	year = {2013},
	pages = {709--724}
}

@article{wagner_behavioral_2013,
	title = {Behavioral {Strategy} {Chases} {Promote} the {Evolution} of {Prey} {Intelligence}},
	url = {http://arxiv.org/abs/1310.1369},
	abstract = {Predator-prey coevolution is commonly thought to result in reciprocal arms races that produce increasingly extreme and complex traits. However, such directional change is not inevitable. Here, we provide evidence for a previously undemonstrated dynamic that we call "strategy chases," wherein populations explore strategies with similar levels of complexity, but differing behaviorally. Indeed, in populations of evolving digital organisms, as prey evolved more effective predator-avoidance strategies, they explored a wider range of behavioral strategies in addition to exhibiting increased levels of behavioral complexity. Furthermore, coevolved prey became more adept in foraging, evidently through coopting components of explored sense-and-flee avoidance strategies into sense-and-retrieve foraging strategies. Specifically, we demonstrate that coevolution induced non-escalating exploration of behavioral space, corresponding with significant evolutionary advancements, including increasingly intelligent behavioral strategies.},
	urldate = {2014-05-01TZ},
	journal = {arXiv:1310.1369 [q-bio]},
	author = {Wagner, Aaron P. and Zaman, Luis and Dworkin, Ian and Ofria, Charles},
	month = oct,
	year = {2013},
	keywords = {Quantitative Biology - Populations and Evolution}
}

@article{munoz_basking_2016,
	title = {Basking behavior predicts the evolution of heat tolerance in {Australian} rainforest lizards},
	volume = {70},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/evo.13064/full},
	number = {11},
	urldate = {2017-04-09TZ},
	journal = {Evolution},
	author = {Muñoz, Martha M. and Langham, Gary M. and Brandley, Matthew C. and Rosauer, Dan F. and Williams, Stephen E. and Moritz, Craig},
	year = {2016},
	keywords = {biological example},
	pages = {2537--2549}
}

@article{moritz_importance_2013,
	title = {The importance of an evolutionary perspective in conservation policy planning},
	volume = {22},
	issn = {1365-294X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/mec.12565/abstract},
	doi = {10.1111/mec.12565},
	abstract = {Prioritization of taxa for conservation must rest on a foundation of correctly identified species boundaries, enhanced by an understanding of evolutionary history and phylogenetic relationships. Therefore, we can incorporate both evolutionary and ecological processes into efforts to sustain biodiversity. In this issue of Molecular Ecology, Malaney \& Cook () highlight the critical value of an evolutionary biogeographical approach, combining multilocus phylogeography with climatic niche modelling to infer phylogenetically weighted conservation priorities for evolutionary lineages of jumping mice across North America. Remarkably, they find that the Preble's meadow jumping mouse (Zapus hudsonius preblei), long debated as a threatened taxon, in fact represents the southern terminus of a relatively uniform lineage that expanded well into Alaska during the Holocene. By contrast, some other relictual and phylogenetically divergent taxa of jumping mice likely warrant greater conservation priority. This study highlights the value of integrative approaches that place current taxonomy in a broader evolutionary context to identify taxa for conservation assessment, but also highlights the challenges in maintaining potential for adaptive responses to environmental change.},
	language = {en},
	number = {24},
	urldate = {2017-04-09TZ},
	journal = {Molecular Ecology},
	author = {Moritz, Craig C. and Potter, Sally},
	month = dec,
	year = {2013},
	keywords = {Phylogenetics, adaptation, biogeography, conservation, spatial modelling},
	pages = {5969--5971}
}

@article{tonione_high_2011,
	title = {High genetic diversity despite the potential for stepping-stone colonizations in an invasive species of gecko on {Moorea}, {French} {Polynesia}},
	volume = {6},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026874},
	number = {11},
	urldate = {2017-04-09TZ},
	journal = {PLoS One},
	author = {Tonione, Maria A. and Reeder, Natalie and Moritz, Craig C.},
	year = {2011},
	pages = {e26874}
}

@article{moritz_strategies_2002,
	title = {Strategies to protect biological diversity and the evolutionary processes that sustain it},
	volume = {51},
	url = {http://sysbio.oxfordjournals.org/content/51/2/238.short},
	number = {2},
	urldate = {2017-04-09TZ},
	journal = {Systematic biology},
	author = {Moritz, Craig},
	year = {2002},
	pages = {238--254}
}

@article{grant_shallow_1998,
	title = {Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation},
	volume = {89},
	shorttitle = {Shallow population histories in deep evolutionary lineages of marine fishes},
	url = {http://jhered.oxfordjournals.org/content/89/5/415.short},
	number = {5},
	urldate = {2017-04-09TZ},
	journal = {Journal of Heredity},
	author = {Grant, W. A. S. and Bowen, B. W.},
	year = {1998},
	pages = {415--426}
}

@article{frankel_genetic_1974,
	title = {Genetic {Conservation}: {Our} {Evolutionary} {Responsibility}},
	volume = {78},
	issn = {0016-6731},
	shorttitle = {Genetic {Conservation}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1213213/},
	abstract = {The conservation of the crop varieties of traditional agriculture in the centers of genetic diversity is essential to provide genetic resources for plant improvement. These resources are acutely threatened by rapid agricultural development which is essential for the welfare of millions. Methodologies for genetic conservation have been worked out which are both effective and economical. Urgent action is needed to collect and preserve irreplaceable genetic resources., Wild species, increasingly endangered by loss of habitats, will depend on organized protection for their survival. On a long term basis this is feasible only within natural communities in a state of continuing evolution, hence there is an urgent need for exploration and clarification of the genetic principles of conservation. Gene pools of wild species are increasingly needed for various uses, from old and new industries to recreation. But the possibility of a virtual end to the evolution of species of no direct use to man raises questions of responsibility and ethics.},
	number = {1},
	urldate = {2017-04-09TZ},
	journal = {Genetics},
	author = {Frankel, O. H.},
	month = sep,
	year = {1974},
	pmid = {17248668},
	pmcid = {PMC1213213},
	pages = {53--65}
}

@article{pelissier_practical_2001,
	title = {A {Practical} {Approach} to the {Study} of {Spatial} {Structure} in {Simple} {Cases} of {Heterogeneous} {Vegetation}},
	volume = {12},
	issn = {1100-9233},
	url = {http://www.jstor.org/stable/3236678},
	doi = {10.2307/3236678},
	abstract = {Spatial heterogeneity is a characteristic of most natural ecosystems which is difficult to handle analytically, particularly in the absence of knowledge about the exogenous factors responsible for this heterogeneity. While classical methods for analysis of spatial point patterns usually require the hypothesis of homogeneity, we present a practical approach for partitioning heterogeneous vegetation plots into homogeneous subplots in simple cases of heterogeneity without drastically reducing the data. It is based on the detection of endogenous variations of the pattern using local density and second-order local neighbour density functions that allow delineation of irregularly shaped subplots that could be considered as internally homogeneous. Spatial statistics, such as Ripley's K-function adapted to analyse plots of irregular shape, can then be computed for each of the homogeneous subplots. Two applications to forest ecological field data demonstrate that the method, addressed to ecologists, can avoid misinterpretations of the spatial structure of heterogeneous vegetation stands.},
	number = {1},
	urldate = {2017-04-07TZ},
	journal = {Journal of Vegetation Science},
	author = {Pélissier, Raphaël and Goreaud, François},
	year = {2001},
	pages = {99--108}
}

@article{rudman_evosystem_2017,
	title = {Evosystem {Services}: {Rapid} {Evolution} and the {Provision} of {Ecosystem} {Services}},
	volume = {0},
	issn = {0169-5347},
	shorttitle = {Evosystem {Services}},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(17)30058-7},
	doi = {10.1016/j.tree.2017.02.019},
	language = {English},
	number = {0},
	urldate = {2017-04-06TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Rudman, Seth M. and Kreitzman, Maayan and Chan, Kai M. A. and Schluter, Dolph},
	month = mar,
	year = {2017},
	pmid = {28336183}
}

@article{moritz_comparative_1998,
	title = {Comparative phylogeography and the identification of genetically divergent areas for conservation},
	volume = {7},
	issn = {0962-1083, 1365-294X},
	url = {http://doi.wiley.com/10.1046/j.1365-294x.1998.00317.x},
	doi = {10.1046/j.1365-294x.1998.00317.x},
	language = {en},
	number = {4},
	urldate = {2017-04-06TZ},
	journal = {Molecular Ecology},
	author = {Moritz, Craig and Faith, Daniel P.},
	month = apr,
	year = {1998},
	pages = {419--429}
}

@article{hickerson_phylogeographys_2010,
	title = {Phylogeography’s past, present, and future: 10 years after {Avise}, 2000},
	volume = {54},
	issn = {1055-7903},
	shorttitle = {Phylogeography’s past, present, and future},
	url = {http://www.sciencedirect.com/science/article/pii/S105579030900373X},
	doi = {10.1016/j.ympev.2009.09.016},
	abstract = {Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of “likelihood-free” approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology.},
	number = {1},
	urldate = {2017-04-06TZ},
	journal = {Molecular Phylogenetics and Evolution},
	author = {Hickerson, M. J. and Carstens, B. C. and Cavender-Bares, J. and Crandall, K. A. and Graham, C. H. and Johnson, J. B. and Rissler, L. and Victoriano, P. F. and Yoder, A. D.},
	month = jan,
	year = {2010},
	keywords = {Approximate Bayesian computation (ABC), Coalescent theory, Comparative phylogeography, Ecological niche modeling (ENM), Statistical phylogeography},
	pages = {291--301}
}

@article{avise_light_2016,
	title = {In the light of evolution {X}: {Comparative} phylogeography},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	shorttitle = {In the light of evolution {X}},
	url = {http://www.pnas.org/content/113/29/7957},
	doi = {10.1073/pnas.1604338113},
	abstract = {National Academy of Sciences},
	language = {en},
	number = {29},
	urldate = {2017-04-06TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Avise, John C. and Bowen, Brian W. and Ayala, Francisco J.},
	month = jul,
	year = {2016},
	pmid = {27432955},
	pages = {7957--7961}
}

@incollection{avise_epilogue_2014,
	address = {San Diego},
	title = {Epilogue},
	isbn = {978-0-12-420166-8},
	url = {http://www.sciencedirect.com/science/article/pii/B9780124201668000798},
	urldate = {2017-04-06TZ},
	booktitle = {Conceptual {Breakthroughs} in {Evolutionary} {Genetics}},
	publisher = {Academic Press},
	editor = {Avise, John C.},
	year = {2014},
	note = {DOI: 10.1016/B978-0-12-420166-8.00079-8},
	pages = {149}
}

@article{vandergast_are_2008,
	title = {Are hotspots of evolutionary potential adequately protected in southern {California}?},
	volume = {141},
	issn = {0006-3207},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320708001389},
	doi = {10.1016/j.biocon.2008.04.009},
	abstract = {Reserves are often designed to protect rare habitats, or “typical” exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a “multi-species genetic landscape”). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.},
	number = {6},
	urldate = {2017-04-05TZ},
	journal = {Biological Conservation},
	author = {Vandergast, Amy G. and Bohonak, Andrew J. and Hathaway, Stacie A. and Boys, Joshua and Fisher, Robert N.},
	month = jun,
	year = {2008},
	keywords = {Comparative phylogeography, Geographic Information Systems, Reserve design, biogeography, conservation genetics},
	pages = {1648--1664}
}

@book{darwin_voyage_1905,
	title = {The {Voyage} of the {Beagle}: {Journal} of {Researches} into the {Natural} {History} and {Geology} of the {Countries} {Visited} during the {Voyage} {Round} the {World} of {HMS}" {Beagle}" 1839},
	publisher = {London: Amalgamated Press},
	author = {Darwin, Charles},
	year = {1905}
}

@book{darwin_origin_1859,
	title = {On the {Origin} of {Species}},
	url = {https://ncse.com/files/pub/evolution/Illustrated%20Origin--Darwin--small--credit.pdf},
	urldate = {2017-04-04TZ},
	publisher = {London: John Murray},
	author = {Darwin, C. R.},
	year = {1859}
}

@book{waterhouse_zoology_1839,
	title = {The {Zoology} {Of} {The} {Voyage} {Of} {HMS} {Beagle}, {Under} {The} {Command} {Of} {Captain} {Fitzroy}, {RN}, {During} {The} {Years} 1832 {To} 1836: {Mammalia}},
	shorttitle = {The {Zoology} {Of} {The} {Voyage} {Of} {HMS} {Beagle}, {Under} {The} {Command} {Of} {Captain} {Fitzroy}, {RN}, {During} {The} {Years} 1832 {To} 1836},
	publisher = {Smith, Elder \& Company},
	author = {Waterhouse, George Robert and Darwin, Charles Robert},
	year = {1839}
}

@article{silver_spatial_2006,
	title = {Spatial effects favour the evolution of niche construction},
	volume = {70},
	issn = {0040-5809},
	url = {http://www.sciencedirect.com/science/article/pii/S0040580906001109},
	doi = {10.1016/j.tpb.2006.08.003},
	abstract = {We present an individual-based, spatial implementation of an existing two-locus population genetic model of niche construction. Our analysis reveals that, across a broad range of conditions, niche-construction traits can drive themselves to fixation by simultaneously generating selection that favours ‘recipient’ trait alleles and linkage disequilibrium between niche-construction and recipient trait alleles. The effect of spatiality is key, since it is the local, resource-mediated interaction between recipient and niche-constructing loci which gives rise to gene linkage. Spatial clustering effects point to a possible mechanism by which an initially rare recipient trait whose selection depends on niche construction could establish in an otherwise hostile environment. The same mechanism could also lead to the spread of an established niche-constructing colony. Similar phenomena are observed in the spatial modelling of two species ‘engineering webs’. Here, the activities of two niche-constructing species can combine to drive a particular recipient trait to fixation, or in certain circumstances, maintain the presence of polymorphisms through the preservation of otherwise deleterious alleles. This may have some relevance to ecosystem stability and the maintenance of genetic variation, where the frequencies of key resources are affected by the niche-constructing activities of more than one species. Our model suggests that the stability of multi-species webs in natural populations may increase as the complexity of species–environment interactions increases.},
	number = {4},
	urldate = {2017-04-04TZ},
	journal = {Theoretical Population Biology},
	author = {Silver, Matt and Di Paolo, Ezequiel},
	month = dec,
	year = {2006},
	keywords = {Ecosystem stability, Engineering web, Resource-mediated interaction., Spatial effects, individual-based model, niche construction},
	pages = {387--400}
}

@article{geist_paleogeographic_2014,
	title = {A paleogeographic model of the {Galápagos} {Islands} and biogeographical and evolutionary implications},
	url = {https://books.google.com/books?hl=en&lr=&id=TW0HBAAAQBAJ&oi=fnd&pg=PA145&dq=Geist,+D.J.,+Snell,+Howard,+Snell,+Heidi,+Goddard,+Charlotte,+Kurz,+M.D.+(2014).+A+Paleogeographic+Model+of+the+Galapagos+Islands+and+Biogeographical+and+Evolutionary&ots=_5xNKWwdJH&sig=3DYtGm6w95DVvqQvdyEz9Jf7hsg},
	urldate = {2017-04-04TZ},
	journal = {The Galápagos: a natural laboratory for the Earth Sciences. American Geophysical Union, Washington DC, USA},
	author = {Geist, D. and Snell, Howard and Snell, Heidi and Goddard, Charlotte and Kurz, Mark D.},
	year = {2014},
	pages = {145--166}
}

@book{harpp_galapagos:_2014,
	title = {The {Galapagos}: {A} {Natural} {Laboratory} for the {Earth} {Sciences}},
	isbn = {978-1-118-85241-5},
	shorttitle = {The {Galapagos}},
	abstract = {The Galápagos Islands are renown for their unique flora and fauna, inspiring Charles Darwin in the elaboration of his theory of evolution. Yet in his Voyage of the Beagle, published in 1839, Darwin also remarked on the fascinating geology and volcanic origin of these enchanted Islands. Since then, the Galápagos continue to provide scientists with inspiration and invaluable information about ocean island formation and evolution, mantle plumes, and the deep Earth.Motivated by an interdisciplinary Chapman Conference held in the Islands, this AGU volume provides cross-disciplinary collection of recent research into the origin and nature of ocean islands, from their deepest roots in Earth’s mantle, to volcanism, surface processes, and the interface between geology and biodiversity.Volume highlights include:• Case studies in biogeographical, hydrological, and chronological perspective• Understanding the connection between geological processes and biodiversity• Synthesis of decades of interdisciplinary research in physical processes from surface to deep interior of the earth• In-depth discussion of the concept of the island acting as a natural laboratory for earth scientists• Integrated understanding of the Galápagos region from a geological perspectiveCollectively, The Galápagos presents case studies illustrating the Galápagos Archipelago as a dynamic natural laboratory for the earth sciences. This book would be of special interest to a multidisciplinary audience in earth sciences, including petrologists, volcanologists, geochronologists, geochemists, and geobiologists.},
	language = {en},
	publisher = {John Wiley \& Sons},
	author = {Harpp, Karen S. and Mittelstaedt, Eric and d'Ozouville, Noémi and Graham, David W.},
	month = oct,
	year = {2014},
	note = {Google-Books-ID: TW0HBAAAQBAJ},
	keywords = {Science / Earth Sciences / General, Science / Earth Sciences / Geology}
}

@article{rundle_divergent_2005,
	title = {Divergent {Selection} and the {Evolution} of {Signal} {Traits} and {Mating} {Preferences}},
	volume = {3},
	issn = {1545-7885},
	url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0030368},
	doi = {10.1371/journal.pbio.0030368},
	abstract = {Experimentally manipulating the resource environment of Drosophila serrata reveals that mating preferences can evolve, at least in part, as a result of environmentally-based divergent natural selection.},
	number = {11},
	urldate = {2017-04-04TZ},
	journal = {PLOS Biology},
	author = {Rundle, Howard D. and Chenoweth, Stephen F. and Doughty, Paul and Blows, Mark W.},
	month = oct,
	year = {2005},
	keywords = {Evolutionary genetics, Fungal evolution, Maize, Parallel evolution, genetic drift, natural selection, sexual selection, speciation},
	pages = {e368}
}

@article{busby_research_2017,
	title = {Research priorities for harnessing plant microbiomes in sustainable agriculture},
	volume = {15},
	issn = {1545-7885},
	url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001793},
	doi = {10.1371/journal.pbio.2001793},
	abstract = {Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes—i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance—into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host–microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.},
	number = {3},
	urldate = {2017-03-29TZ},
	journal = {PLOS Biology},
	author = {Busby, Posy E. and Soman, Chinmay and Wagner, Maggie R. and Friesen, Maren L. and Kremer, James and Bennett, Alison and Morsy, Mustafa and Eisen, Jonathan A. and Leach, Jan E. and Dangl, Jeffery L.},
	month = mar,
	year = {2017},
	keywords = {Agricultural workers, Agriculture, Community ecology, Flowering plants, Host-pathogen interactions, Microbial ecology, Microbiome, Plant-microbial interactions},
	pages = {e2001793}
}

@article{skelly_evolutionary_2007,
	title = {Evolutionary {Responses} to {Climate} {Change}},
	volume = {21},
	issn = {0888-8892},
	url = {http://www.jstor.org/stable/4620959},
	number = {5},
	urldate = {2017-03-22TZ},
	journal = {Conservation Biology},
	author = {Skelly, David K. and Joseph, Liana N. and Possingham, Hugh P. and Freidenburg, L. Kealoha and Farrugia, Thomas J. and Kinnison, Michael T. and Hendry, Andrew P.},
	year = {2007},
	pages = {1353--1355}
}

@article{gellie_revegetation_2017,
	title = {Revegetation rewilds the soil bacterial microbiome of an old field},
	issn = {09621083},
	url = {http://doi.wiley.com/10.1111/mec.14081},
	doi = {10.1111/mec.14081},
	language = {en},
	urldate = {2017-03-14TZ},
	journal = {Molecular Ecology},
	author = {Gellie, Nicholas J.C. and Mills, Jacob G. and Breed, Martin F. and Lowe, Andrew J.},
	month = mar,
	year = {2017}
}
@article{vessman_pair-wise_nodate,
	title = {From pair-wise interactions to triplet dynamics},
	url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.905.7387&rep=rep1&type=pdf},
	urldate = {2017-03-13TZ},
	author = {Vessman, Björn}
}

@inproceedings{gerlee_urdar-artificial_2011,
	title = {Urdar-an artificial ecology platform.},
	url = {https://mitp-web2.mit.edu/sites/default/files/titles/alife/0262297140chap41.pdf},
	urldate = {2017-03-13TZ},
	booktitle = {{ECAL}},
	author = {Gerlee, Philip and Lundh, Torbjörn},
	year = {2011},
	pages = {258--259}
}

@article{vessman_estimating_2016,
	title = {Estimating the probability of coexistence in cross-feeding communities},
	volume = {408},
	url = {http://www.sciencedirect.com/science/article/pii/S0022519316302260},
	urldate = {2017-03-13TZ},
	journal = {Journal of Theoretical Biology},
	author = {Vessman, Björn and Gerlee, Philip and Lundh, Torbjörn},
	year = {2016},
	pages = {13--21}
}

@article{hummert_evolutionary_2014,
	title = {Evolutionary game theory: cells as players},
	volume = {10},
	shorttitle = {Evolutionary game theory},
	url = {http://pubs.rsc.org/en/content/articlehtml/2014/mb/c3mb70602h},
	number = {12},
	urldate = {2017-03-13TZ},
	journal = {Molecular BioSystems},
	author = {Hummert, Sabine and Bohl, Katrin and Basanta, David and Deutsch, Andreas and Werner, Sarah and Thei{\textbackslash}s sen, Günter and Schroeter, Anja and Schuster, Stefan},
	year = {2014},
	pages = {3044--3065}
}

@article{jonsson_evolution_2011,
	title = {Evolution towards optimality in {Urdar}-an artificial ecosystem},
	url = {http://publications.lib.chalmers.se/records/fulltext/144243.pdf},
	urldate = {2017-03-13TZ},
	author = {Jonsson, Viktor},
	year = {2011}
}

@article{ducharme_simulation_2013,
	title = {Simulation de systèmes chimique et physiologique},
	url = {http://savoirs.usherbrooke.ca/handle/11143/6580},
	urldate = {2017-03-13TZ},
	author = {Ducharme, Vincent},
	year = {2013}
}

@article{ducharme_energy-based_2012,
	title = {Energy-based artificial chemistry simulator},
	volume = {13},
	url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.401.5564&rep=rep1&type=pdf},
	urldate = {2017-03-13TZ},
	journal = {Artificial Life},
	author = {Ducharme, Vincent and Egli, Richard and Legault, Claude Y.},
	year = {2012},
	pages = {449--456}
}

@article{channon_perpetuating_1998,
	title = {Perpetuating evolutionary emergence},
	url = {http://eprints.keele.ac.uk/38/1/Perpetuating%20evolutionary%20emergence%20(AChannon).pdf},
	urldate = {2017-03-09TZ},
	journal = {FROM ANIMALS TO ANIMATS 5},
	author = {Channon, A. D. and Damper, R. I. and {others}},
	year = {1998},
	pages = {534--539}
}

@inproceedings{yaeger_computational_1993,
	title = {Computational genetics, physiology, metabolism, neural systems, learning, vision, and behavior or {PolyWorld}: {Life} in a new context},
	shorttitle = {Computational genetics, physiology, metabolism, neural systems, learning, vision, and behavior or {PolyWorld}},
	url = {http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.38.6719},
	urldate = {2017-03-09TZ},
	booktitle = {Artificial {Life} {III}, {Vol}. {XVII} of {SFI} {Studies} in the {Sciences} of {Complexity}, {Santa} {Fe} {Institute}},
	author = {Yaeger, Larry},
	year = {1993}
}

@inproceedings{connelly_social_2010,
	title = {Social {Structure} and the {Maintenance} of {Biodiversity}.},
	url = {https://mitp-web2.mit.edu/sites/default/files/titles/alife/0262290758chap88.pdf},
	urldate = {2017-03-09TZ},
	booktitle = {{ALIFE}},
	author = {Connelly, Brian D. and Zaman, Luis and Ofria, Charles and McKinley, Philip K.},
	year = {2010},
	pages = {461--468}
}

@phdthesis{zaman_host-symbiont_2014,
	title = {Host-symbiont coevolution in digital and microbial systems},
	url = {http://etd.lib.msu.edu/islandora/object/etd%3A2442/datastream/OBJ/view},
	urldate = {2017-03-09TZ},
	school = {Michigan State University},
	author = {Zaman, Luis},
	year = {2014}
}

@inproceedings{biswas_causes_2014,
	title = {Causes vs {Benefits} in the {Evolution} of {Prey} {Grouping}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch103.pdf},
	doi = {10.7551/978-0-262-32621-6-ch103},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {Biswas, Ritwik and Bryson, David and Ofria, Charles and Wagner, Aaron},
	month = jul,
	year = {2014},
	pages = {641--648}
}

@article{lehmann_cues_2014,
	title = {From {Cues} to {Signals}: {Evolution} of {Interspecific} {Communication} via {Aposematism} and {Mimicry} in a {Predator}-{Prey} {System}},
	volume = {9},
	issn = {1932-6203},
	shorttitle = {From {Cues} to {Signals}},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091783},
	doi = {10.1371/journal.pone.0091783},
	abstract = {Current theory suggests that many signaling systems evolved from preexisting cues. In aposematic systems, prey warning signals benefit both predator and prey. When the signal is highly beneficial, a third species often evolves to mimic the toxic species, exploiting the signaling system for its own protection. We investigated the evolutionary dynamics of predator cue utilization and prey signaling in a digital predator-prey system in which prey could evolve to alter their appearance to mimic poison-free or poisonous prey. In predators, we observed rapid evolution of cue recognition (i.e. active behavioral responses) when presented with sufficiently poisonous prey. In addition, active signaling (i.e. mimicry) evolved in prey under all conditions that led to cue utilization. Thus we show that despite imperfect and dishonest signaling, given a high cost of consuming poisonous prey, complex systems of interspecific communication can evolve via predator cue recognition and prey signal manipulation. This provides evidence supporting hypotheses that cues may serve as stepping-stones in the evolution of more advanced communication and signaling systems that incorporate information about the environment.},
	number = {3},
	urldate = {2017-03-09TZ},
	journal = {PLOS ONE},
	author = {Lehmann, Kenna D. S. and Goldman, Brian W. and Dworkin, Ian and Bryson, David M. and Wagner, Aaron P.},
	month = mar,
	year = {2014},
	keywords = {Animal signaling and communication, Biomimetics, Imitation, Organismal evolution, Predation, Predator-prey dynamics, Toxicity, Toxins},
	pages = {e91783}
}

@inproceedings{walker_evolution_2011,
	address = {New York, NY, USA},
	series = {{GECCO} '11},
	title = {The {Evolution} of {Optimal} {Foraging} {Strategies} in {Populations} of {Digital} {Organisms}},
	isbn = {978-1-4503-0557-0},
	url = {http://doi.acm.org/10.1145/2001576.2001605},
	doi = {10.1145/2001576.2001605},
	abstract = {Foraging strategies in uncertain environments is the subject of a great deal of biological investigation, much of which is grounded in mathematical models. One theoretical prediction with wide empirical support is the ideal free distribution (IFD), where agents distribute themselves among patches of resources in proportion to their suitability. However, the IFD assumes that agents have perfect information of the environment. In nature, this assumption is often violated, yet the IFD is still observed. Insights into evolved mechanisms and behaviors that result in the IFD show how such efficient outcomes may emerge from little information. In this study, the artificial life platform Avida is used to observe populations of digital organisms as they evolved to optimize resource intake in an environment with unpredictable resource distributions. It is shown that the ideal free distribution can emerge from simple foraging strategies that require minimal information. It is demonstrated that this distribution is a result of choices made by the organisms, and not simply due to those in a more advantageous setting producing more offspring. Deviations from the IFD appear to be correlated with reduced information or foraging aggregation. Distributions with organisms of differing abilities are also investigated, demonstrating further correspondence with theoretical predictions.},
	urldate = {2017-03-09TZ},
	booktitle = {Proceedings of the 13th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Walker, Jacob Charles},
	year = {2011},
	keywords = {aggregation, artificial life, digital evolution, ideal free distribution, interference, uncertainty, unequal competitors},
	pages = {203--210}
}

@article{faillace_evolution_2016,
	title = {Evolution alters the consequences of invasions in experimental communities},
	volume = {1},
	copyright = {© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
	issn = {2397-334X},
	url = {http://www.nature.com/articles/s41559-016-0013},
	doi = {10.1038/s41559-016-0013},
	abstract = {Evolved native species with prior experience of invasives consistently perform better than naive invaders, supporting the emergence of increased biotic resistance as one consequence of evolution during invasions.},
	language = {en},
	urldate = {2017-03-08TZ},
	journal = {Nature Ecology \& Evolution},
	author = {Faillace, Cara A. and Morin, Peter J.},
	month = nov,
	year = {2016},
	pages = {0013}
}

@article{wagenaar_influence_2004,
	title = {Influence of chance, history, and adaptation on digital evolution},
	volume = {10},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/106454604773563603},
	number = {2},
	urldate = {2017-03-08TZ},
	journal = {Artificial Life},
	author = {Wagenaar, Daniel A. and Adami, Christoph},
	year = {2004},
	pages = {181--190}
}

@inproceedings{johnson_more_2014,
	title = {More {Bang} {For} {Your} {Buck}: {Quorum}-{Sensing} {Capabilities} {Improve} the {Efficacy} of {Suicidal} {Altruism}},
	isbn = {978-0-262-32621-6},
	shorttitle = {More {Bang} {For} {Your} {Buck}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch020.pdf},
	doi = {10.7551/978-0-262-32621-6-ch020},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {Johnson, Anya and Strauss, Eli and Pickett, Rodney and Adami, Christoph and Dworkin, Ian and Goldsby, Heather},
	month = jul,
	year = {2014},
	pages = {120--128}
}

@inproceedings{beckmann_evolving_2009,
	title = {Evolving quorum sensing in digital organisms},
	url = {http://dl.acm.org/citation.cfm?id=1569916},
	urldate = {2017-03-08TZ},
	booktitle = {Proceedings of the 11th {Annual} conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Beckmann, Benjamin E. and McKinley, Philip K.},
	year = {2009},
	pages = {97--104}
}

@article{guttenberg_cascade_2008,
	title = {Cascade of {Complexity} in {Evolving} {Predator}-{Prey} {Dynamics}},
	volume = {100},
	url = {http://link.aps.org/doi/10.1103/PhysRevLett.100.058102},
	doi = {10.1103/PhysRevLett.100.058102},
	abstract = {We simulate an individual-based model that represents both the phenotype and genome of digital organisms with predator-prey interactions. We show how open-ended growth of complexity arises from the invariance of genetic evolution operators with respect to changes in the complexity, and that the dynamics which emerges shows scaling indicative of a nonequilibrium critical point. The mechanism is analogous to the development of the cascade in fluid turbulence.},
	number = {5},
	urldate = {2017-03-08TZ},
	journal = {Physical Review Letters},
	author = {Guttenberg, Nicholas and Goldenfeld, Nigel},
	month = feb,
	year = {2008},
	pages = {058102}
}

@article{gerlee_productivity_2010,
	title = {{PRODUCTIVITY} {AND} {DIVERSITY} {IN} {A} {CROSS}-{FEEDING} {POPULATION} {OF} {ARTIFICIAL} {ORGANISMS}: {PRODUCTIVITY} {AND} {DIVERSITY} {IN} {A} {CROSS}-{FEEDING} {POPULATION} {OF} {ARTIFICIAL} {ORGANISMS}},
	volume = {64},
	issn = {00143820},
	shorttitle = {{PRODUCTIVITY} {AND} {DIVERSITY} {IN} {A} {CROSS}-{FEEDING} {POPULATION} {OF} {ARTIFICIAL} {ORGANISMS}},
	url = {http://doi.wiley.com/10.1111/j.1558-5646.2010.01020.x},
	doi = {10.1111/j.1558-5646.2010.01020.x},
	language = {en},
	number = {9},
	urldate = {2017-03-08TZ},
	journal = {Evolution},
	author = {Gerlee, Philip and Lundh, Torbjörn},
	month = sep,
	year = {2010},
	pages = {2716--2730}
}

@inproceedings{connelly_seeds_2012,
	address = {New York, NY, USA},
	series = {{GECCO} '12},
	title = {The {SEEDS} {Platform} for {Evolutionary} and {Ecological} {Simulations}},
	isbn = {978-1-4503-1178-6},
	url = {http://doi.acm.org/10.1145/2330784.2330805},
	doi = {10.1145/2330784.2330805},
	abstract = {Over the past few decades, evolutionary computation (EC) has grown substantially in use for biologists and engineers alike. Its transparency makes it an indispensable tool for studying evolutionary- and ecological dynamics, and it has provided researchers with new insights that would be tremendously difficult, if not impossible, to gain using natural systems. In addition, EC has proven to be a powerful search algorithm for engineering applications, and has produced numerous novel and human-competitive solutions to complex problems. Although several well-established packages are readily available, it seems that when most users harness the power of evolutionary computation, they do so using "home-grown" solutions. This can likely be attributed to the ease with which simple models are created, the user's need for customization, and the sizeable learning barrier imposed by available solutions, as well as difficulties in extending them. We present SEEDS, a modular, open-source platform for conducting evolutionary computation experiments. SEEDS provides a simple, flexible, and extensible foundation that enables users with minimal programming experience to perform complex evolutionary and ecological simulations without having to first implement core functionality. In addition, SEEDS provides the tools necessary to make sharing data and reproducing experiments both easy and convenient.},
	urldate = {2017-03-08TZ},
	booktitle = {Proceedings of the 14th {Annual} {Conference} {Companion} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Connelly, Brian D. and Zaman, Luis and McKinley, Philip K.},
	year = {2012},
	keywords = {Ecology, evolution, platform, simulation},
	pages = {133--140}
}

@article{castillo_digital_2014,
	title = {Digital {Organism} {Simulation} {Environment} ({DOSE}): {A} {Library} for {Ecologically}-{Based} {In} {Silico} {Experimental} {Evolution}},
	volume = {3},
	copyright = {Copyright (c) 2015 Advances in Computer Science : an International Journal},
	issn = {2322-5157},
	shorttitle = {Digital {Organism} {Simulation} {Environment} ({DOSE})},
	url = {http://www.acsij.org/acsij/article/view/232},
	number = {1},
	urldate = {2017-03-08TZ},
	journal = {Advances in Computer Science : an International Journal},
	author = {Castillo, Clarence FG and Ling, Maurice HT},
	month = jan,
	year = {2014},
	keywords = {Ecology Simulation, Genetic Distance, Simulation Environment, digital organisms, migration},
	pages = {44--50}
}

@article{zhang_energy_2009,
	title = {Energy flows in complex ecological systems: a review},
	volume = {22},
	issn = {1009-6124, 1559-7067},
	shorttitle = {Energy flows in complex ecological systems},
	url = {http://link.springer.com/10.1007/s11424-009-9169-3},
	doi = {10.1007/s11424-009-9169-3},
	language = {en},
	number = {3},
	urldate = {2017-03-08TZ},
	journal = {Journal of Systems Science and Complexity},
	author = {Zhang, Jiang},
	month = jun,
	year = {2009},
	pages = {345--359}
}

@incollection{gelbukh_chaos_2008,
	address = {Berlin, Heidelberg},
	title = {Chaos and {Budworm} {Dynamics} of {Agent} {Interactions}: {A} {Biologically}-{Inspired} {Approach} to {Digital} {Ecosystems}},
	volume = {5317},
	isbn = {978-3-540-88635-8 978-3-540-88636-5},
	shorttitle = {Chaos and {Budworm} {Dynamics} of {Agent} {Interactions}},
	url = {http://link.springer.com/10.1007/978-3-540-88636-5_84},
	urldate = {2017-03-07TZ},
	booktitle = {{MICAI} 2008: {Advances} in {Artificial} {Intelligence}},
	publisher = {Springer Berlin Heidelberg},
	author = {Lopardo, Gabriel Alejandro and Rateb, Fátima N.},
	editor = {Gelbukh, Alexander and Morales, Eduardo F.},
	year = {2008},
	note = {DOI: 10.1007/978-3-540-88636-5\_84},
	pages = {889--899}
}

@inproceedings{briscoe_biology_2007,
	title = {Biology of {Applied} {Digital} {Ecosystems}},
	doi = {10.1109/DEST.2007.372015},
	abstract = {A primary motivation for research in digital ecosystems is the desire to exploit the self-organising properties of natural ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in digital ecosystem research. Here, we discuss how biological properties contribute to the self-organising features of natural ecosystems. These properties include populations of evolving agents, a complex dynamic environment, and spatial distributions which generate local interactions. The potential for exploiting these properties in artificial systems is then considered. An example architecture, the digital business ecosystem (DBE), is considered in detail. Simulation results imply that the DBE performs better at large scales than a comparable service-oriented architecture. These results suggest that incorporating ideas from theoretical ecology can contribute to useful self-organising properties in digital ecosystems.},
	booktitle = {2007 {Inaugural} {IEEE}-{IES} {Digital} {EcoSystems} and {Technologies} {Conference}},
	author = {Briscoe, G. and Sadedin, S. and Paperin, G.},
	month = feb,
	year = {2007},
	keywords = {Complexity, Computer architecture, Ecosystem, Electronic mail, Environmental factors, Evolution (biology), Humans, Organisms, Paper technology, Robustness, Software design, artificial system, biological property, business data processing, digital business ecosystem, ecosystems, evolution, multi-agent systems, natural ecosystem, self-organising property, service-oriented architecture, software architecture},
	pages = {458--463}
}

@article{ghadri_golestani_individual-based_2014,
	title = {Individual-{Based} {Modeling} and {Nonlinear} {Analysis} for {Complex} {Systems} with {Application} to {Theoretical} {Ecology}},
	url = {http://scholar.uwindsor.ca/etd/5253},
	journal = {Electronic Theses and Dissertations},
	author = {Ghadri Golestani, Abbas},
	month = jan,
	year = {2014}
}

@article{momeni_using_2011,
	title = {Using artificial systems to explore the ecology and evolution of symbioses},
	volume = {68},
	issn = {1420-682X, 1420-9071},
	url = {https://link.springer.com/article/10.1007/s00018-011-0649-y},
	doi = {10.1007/s00018-011-0649-y},
	abstract = {The web of life is weaved from diverse symbiotic interactions between species. Symbioses vary from antagonistic interactions such as competition and predation to beneficial interactions such as mutualism. What are the bases for the origin and persistence of symbiosis? What affects the ecology and evolution of symbioses? How do symbiotic interactions generate ecological patterns? How do symbiotic partners evolve and coevolve? Many of these questions are difficult to address in natural systems. Artificial systems, from abstract to living, have been constructed to capture essential features of natural symbioses and to address these key questions. With reduced complexity and increased controllability, artificial systems can serve as useful models for natural systems. We review how artificial systems have contributed to our understanding of symbioses.},
	language = {en},
	number = {8},
	urldate = {2017-03-07TZ},
	journal = {Cellular and Molecular Life Sciences},
	author = {Momeni, Babak and Chen, Chi-Chun and Hillesland, Kristina L. and Waite, Adam and Shou, Wenying},
	month = apr,
	year = {2011},
	pages = {1353}
}

@article{kawecki_experimental_2012,
	title = {Experimental evolution},
	volume = {27},
	issn = {01695347},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534712001425},
	doi = {10.1016/j.tree.2012.06.001},
	language = {en},
	number = {10},
	urldate = {2017-03-07TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Kawecki, Tadeusz J. and Lenski, Richard E. and Ebert, Dieter and Hollis, Brian and Olivieri, Isabelle and Whitlock, Michael C.},
	month = oct,
	year = {2012},
	pages = {547--560}
}

@article{beckmann_evolution_2012,
	title = {Evolution of resistance to quorum quenching in digital organisms},
	volume = {18},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/artl_a_00066},
	number = {3},
	urldate = {2017-03-07TZ},
	journal = {Artificial life},
	author = {Beckmann, Benjamin E. and Knoester, David B. and Connelly, Brian D. and Waters, Christopher M. and McKinley, Philip K.},
	year = {2012},
	pages = {291--310}
}

@inproceedings{beckmann_evolution_2007,
	title = {Evolution of cooperative information gathering in self-replicating digital organisms},
	url = {http://ieeexplore.ieee.org/abstract/document/4274891/},
	urldate = {2017-03-07TZ},
	booktitle = {Self-{Adaptive} and {Self}-{Organizing} {Systems}, 2007. {SASO}'07. {First} {International} {Conference} on},
	publisher = {IEEE},
	author = {Beckmann, Benjamin E. and McKinley, Philip K. and Knoester, David B. and Ofria, Charles},
	year = {2007},
	pages = {65--76}
}

@article{hamilton_genetical_1964,
	title = {The genetical evolution of social behaviour. {II}},
	volume = {7},
	url = {http://www.sciencedirect.com/science/article/pii/0022519364900396},
	number = {1},
	urldate = {2017-03-06TZ},
	journal = {Journal of theoretical biology},
	author = {Hamilton, William D.},
	year = {1964},
	pages = {17--52}
}

@book{dawkins_selfish_1976,
	address = {New York},
	edition = {British First edition},
	title = {The {Selfish} {Gene}},
	isbn = {978-0-19-857519-1},
	abstract = {This book tells of the selfish gene. A world of savage competition, ruthless exploitation, and deceit. But what of the acts of apparent altruism in nature the bees who commit suicide when they sting to protect the hive, for example? Professor Dawkins holds out the hope that our species has the power to rebel against the designs of the selfish gene.},
	language = {English},
	publisher = {Oxford University Press},
	author = {Dawkins, Richard},
	month = oct,
	year = {1976}
}

@misc{noauthor_book_nodate,
	title = {Book sources},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://en.wikipedia.org/wiki/Special:BookSources/978-0-19-857519-1},
	language = {en},
	urldate = {2017-03-06TZ},
	journal = {Wikipedia}
}

@article{roopnarine_trophic_2007,
	title = {Trophic network models explain instability of {Early} {Triassic} terrestrial communities},
	volume = {274},
	copyright = {© 2007 The Royal Society},
	issn = {0962-8452, 1471-2954},
	url = {http://rspb.royalsocietypublishing.org/content/274/1622/2077},
	doi = {10.1098/rspb.2007.0515},
	abstract = {Studies of the end-Permian mass extinction have emphasized potential abiotic causes and their direct biotic effects. Less attention has been devoted to secondary extinctions resulting from ecological crises and the effect of community structure on such extinctions. Here we use a trophic network model that combines topological and dynamic approaches to simulate disruptions of primary productivity in palaeocommunities. We apply the model to Permian and Triassic communities of the Karoo Basin, South Africa, and show that while Permian communities bear no evidence of being especially susceptible to extinction, Early Triassic communities appear to have been inherently less stable. Much of the instability results from the faster post-extinction diversification of amphibian guilds relative to amniotes. The resulting communities differed fundamentally in structure from their Permian predecessors. Additionally, our results imply that changing community structures over time may explain long-term trends like declining rates of Phanerozoic background extinction},
	language = {en},
	number = {1622},
	urldate = {2017-03-05TZ},
	journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	author = {Roopnarine, Peter D. and Angielczyk, Kenneth D. and Wang, Steve C. and Hertog, Rachel},
	month = sep,
	year = {2007},
	pmid = {17609191},
	pages = {2077--2086}
}

@article{erwin_end_1998,
	title = {The end and the beginning: recoveries from mass extinctions},
	volume = {13},
	issn = {0169-5347},
	shorttitle = {The end and the beginning},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(98)01436-0},
	doi = {10.1016/S0169-5347(98)01436-0},
	language = {English},
	number = {9},
	urldate = {2017-03-05TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Erwin, Douglas H.},
	month = sep,
	year = {1998},
	pmid = {21238338},
	keywords = {biotic recoveries, mass extinction, radiation},
	pages = {344--349}
}

@article{yedid_selective_2009,
	title = {Selective {Press} {Extinctions}, but {Not} {Random} {Pulse} {Extinctions}, {Cause} {Delayed} {Ecological} {Recovery} in {Communities} of {Digital} {Organisms}.},
	volume = {173},
	copyright = {Copyright © 2009 The University of Chicago},
	url = {http://www.jstor.org/stable/10.1086/597228},
	doi = {10.1086/593130},
	abstract = {Abstract: A key issue concerning recovery from mass extinctions is how extinction and diversification mechanisms affect the recovery process. We evolved communities of digital organisms, subjecting them to instantaneous “pulse” extinctions, choosing survivors at random, or to prolonged “press” extinctions involving a period of low resource availability. Functional activity at low trophic levels recovered faster than at higher levels, with the most extensive delays seen at the top level. Postpress communities generally did not fully recover functional activity in the allotted time, which equaled that of their original diversification. We measured recovery of phenotypic diversity, observing considerable variation in outcomes. Communities subjected to pulse extinctions recovered functional activity and phenotypic diversity substantially faster than when subjected to press extinctions. Follow‐up experiments tested whether organisms with shorter generation times and low functional activity contributed to delayed recovery after press extinctions. The results indicate that adaptation during the press episode degraded the organisms’ ability to reevolve preextinction functionality. There are interesting parallels with patterns from the paleontological record. We suggest that some delayed recoveries from mass extinction may reflect the need to both reevolve biological functions and reconstruct ecological interactions lost during the extinction. Adaptation to conditions during an extended disturbance may hinder subsequent recovery.},
	number = {4},
	urldate = {2014-04-22TZ},
	journal = {The American Naturalist},
	author = {Yedid, Gabriel and Ofria, Charles A. and Lenski, Richard E.},
	month = apr,
	year = {2009},
	pages = {E139--E154}
}

@article{yedid_comparison_2012,
	title = {A {Comparison} of the {Effects} of {Random} and {Selective} {Mass} {Extinctions} on {Erosion} of {Evolutionary} {History} in {Communities} of {Digital} {Organisms}},
	volume = {7},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0037233},
	doi = {10.1371/journal.pone.0037233},
	abstract = {The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous “pulse” extinctions, choosing survivors at random, and to prolonged “press” extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse) and strong selective extinction (press) both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself.},
	number = {5},
	urldate = {2017-03-05TZ},
	journal = {PLOS ONE},
	author = {Yedid, Gabriel and Stredwick, Jason and Ofria, Charles A. and Agapow, Paul-Michael},
	month = may,
	year = {2012},
	keywords = {Extinct genomes, Paleoecology, Paleogenetics, Paleontology, Phylogenetic analysis, Phylogenetics, Species extinction, Theoretical ecology},
	pages = {e37233}
}

@article{yedid_historical_2008,
	title = {Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms},
	volume = {21},
	issn = {1420-9101},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2008.01564.x/abstract},
	doi = {10.1111/j.1420-9101.2008.01564.x},
	abstract = {Re-evolution of complex biological features following the extinction of taxa bearing them remains one of evolution’s most interesting phenomena, but is not amenable to study in fossil taxa. We used communities of digital organisms (computer programs that self-replicate, mutate and evolve), subjected to periods of low resource availability, to study the evolution, loss and re-evolution of a complex computational trait, the function EQU (bit-wise logical equals). We focused our analysis on cases where the pre-extinction EQU clade had surviving descendents at the end of the extinction episode. To see if these clades retained the capacity to re-evolve EQU, we seeded one set of multiple subreplicate ‘replay’ populations using the most abundant survivor of the pre-extinction EQU clade, and another set with the actual end-extinction ancestor of the organism in which EQU re-evolved following the extinction episode. Our results demonstrate that stochastic, historical, genomic and ecological factors can lead to constraints on further adaptation, and facilitate or hinder re-evolution of a complex feature.},
	language = {en},
	number = {5},
	urldate = {2017-03-05TZ},
	journal = {Journal of Evolutionary Biology},
	author = {Yedid, G. and Ofria, C. A. and Lenski, R. E.},
	month = sep,
	year = {2008},
	keywords = {Experimental evolution, complex features, contingency, digital organisms, extinction, pre-extinction clade, re-evolution, replay experiment, stochastic factor, structural constraints},
	pages = {1335--1357}
}

@inproceedings{wilke_does_2003,
	title = {Does the {Red} {Queen} reign in the kingdom of digital organisms?},
	url = {http://link.springer.com/chapter/10.1007/978-3-540-39432-7_43},
	urldate = {2017-03-05TZ},
	booktitle = {European {Conference} on {Artificial} {Life}},
	publisher = {Springer},
	author = {Wilke, Claus O.},
	year = {2003},
	pages = {405--414}
}

@article{power_what_2015,
	title = {What can ecosystems learn? {Expanding} evolutionary ecology with learning theory},
	volume = {10},
	issn = {1745-6150},
	shorttitle = {What can ecosystems learn?},
	url = {http://dx.doi.org/10.1186/s13062-015-0094-1},
	doi = {10.1186/s13062-015-0094-1},
	abstract = {The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole?},
	urldate = {2017-03-03TZ},
	journal = {Biology Direct},
	author = {Power, Daniel A. and Watson, Richard A. and Szathmáry, Eörs and Mills, Rob and Powers, Simon T. and Doncaster, C. Patrick and Czapp, BłaŻej},
	year = {2015},
	keywords = {Alternative stable states, Associative learning, Community assembly, Community matrix, Ecological memory, Evolutionary ecology, Lotka-Volterra dynamics, Network structures, Regime shifts, Theoretical ecology},
	pages = {69}
}
@article{adami_ab_2002,
	title = {Ab initio modeling of ecosystems with artificial life},
	volume = {15},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1939-7445.2002.tb00083.x/abstract},
	number = {1},
	urldate = {2017-03-03TZ},
	journal = {Natural Resource Modeling},
	author = {Adami, C.},
	year = {2002},
	pages = {133--145}
}

@article{de_souza_junior_effects_2014,
	title = {Effects of the spatial heterogeneity on the diversity of ecosystems with resource competition},
	volume = {393},
	issn = {0378-4371},
	url = {http://www.sciencedirect.com/science/article/pii/S0378437113007954},
	doi = {10.1016/j.physa.2013.08.045},
	abstract = {The understanding of the mechanisms that promote biodiversity has implications for conservation and extinction of species and has raised the interest of the scientific community in the last decades. It is well established that spatial heterogeneity is an important factor influencing species richness. In this work we use a discrete computer simulation model to survey the impact of spatial heterogeneity on biodiversity patterns of an ecosystem in which species compete for limiting resources. The main feature of the model relies on the assumption that species have different requirements for a given resource. Individuals are arranged over a square lattice, where the sites are occupied by at most one individual. Individuals die at a fixed rate. Empty sites may be recolonized by newborn individuals according to a growth rate which depends on the ability of the individuals in the use of resources. We investigate the species–area relationship (SAR), the species abundance distribution and the dependence of species richness on the number of limiting resources and the degree of spatial heterogeneity. Commonly, the changes in the number of species with area is well approximated by a power law. Here, we show that the SAR displays two power law regimes. By assuming that the species’ abilities to consume resources are uneven, we found that the relationship between species richness and the degree of habitat heterogeneity is described by a unimodal function, being in agreement with experimental data. The dependence of the number of species with the number of resources was also investigated. Remarkably, it is the observation of an optimum value for the number of resources that maximizes the biodiversity.},
	urldate = {2017-02-27TZ},
	journal = {Physica A: Statistical Mechanics and its Applications},
	author = {de Souza Júnior, Misael B. and Ferreira, Fernando F. and de Oliveira, Viviane M.},
	month = jan,
	year = {2014},
	keywords = {Computer simulation model, Resource competition, Species–area relationship, biodiversity, ecosystems, spatial heterogeneity},
	pages = {312--319}
}

@inproceedings{graduate_school_of_information_science_nagoya_university_furo-cho_chikusa-ku_nagoya_464-8601_japan_twitter_2014,
	title = {Twitter as {Social} {Sensor}: {Dynamics} and {Structure} in {Major} {Sporting} {Events}},
	isbn = {978-0-262-32621-6},
	shorttitle = {Twitter as {Social} {Sensor}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch126.pdf},
	doi = {10.7551/978-0-262-32621-6-ch126},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan} and Takeichi, Yuki and Sasahara, Kazutoshi and Suzuki, Reiji and Arita, Takaya},
	month = jul,
	year = {2014},
	pages = {778--784}
}

@inproceedings{department_of_mathematics_and_computer_science_university_of_southern_denmark_denmark_towards_2014,
	title = {Towards an {Optimal} {DNA}-{Templated} {Molecular} {Assembler}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch090.pdf},
	doi = {10.7551/978-0-262-32621-6-ch090},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Mathematics and Computer Science, University of Southern Denmark, Denmark} and Andersen, Jakob and Flamm, Christoph and Hanczyc, Martin and Merkle, Daniel},
	month = jul,
	year = {2014},
	pages = {557--564}
}

@inproceedings{ikegami_laboratory_university_of_tokyo_japan_there_2014,
	title = {There {Can} {Be} {Only} {One}: {Reversible} {Cellular} {Automata} and the {Conservation} of {Genki}},
	isbn = {978-0-262-32621-6},
	shorttitle = {There {Can} {Be} {Only} {One}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch084.pdf},
	doi = {10.7551/978-0-262-32621-6-ch084},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Ikegami Laboratory, University of Tokyo, Japan} and Virgo, Nathaniel and Ikegami, Takashi},
	month = jul,
	year = {2014},
	pages = {530--531}
}

@inproceedings{gamma_ltd_vyborg_russia_kinetic_2014,
	title = {The {Kinetic} {Basis} of {Self}-{Organized} {Pattern} {Formation}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch106.pdf},
	doi = {10.7551/978-0-262-32621-6-ch106},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Gamma Ltd, Vyborg, Russia} and Shalygo, Yuri},
	month = jul,
	year = {2014},
	pages = {665--672}
}

@inproceedings{department_of_computer_and_information_science_norwegian_university_of_science_and_technology_evolution_2014,
	title = {The {Evolution} of {Learning} {Under} {Environmental} {Variability}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch104.pdf},
	doi = {10.7551/978-0-262-32621-6-ch104},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Computer and Information Science, Norwegian University of Science and Technology} and Ellefsen, Kai},
	month = jul,
	year = {2014},
	pages = {649--656}
}

@inproceedings{university_of_washington_tacoma_wa_usa_98402_effect_2014,
	title = {The {Effect} of {Social} {Learning} on {Individual} {Learning}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch118.pdf},
	doi = {10.7551/978-0-262-32621-6-ch118},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Washington, Tacoma, WA, USA 98402} and Marriott, Chris and Chebib, Jobran},
	month = jul,
	year = {2014},
	pages = {736--743}
}

@inproceedings{instituto_de_telecomunicacoes_lisboa_portugal_case_2014,
	title = {The {Case} for {Engineering} the {Evolution} of {Robot} {Controllers}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch113.pdf},
	doi = {10.7551/978-0-262-32621-6-ch113},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Instituto de Telecomunicacoes, Lisboa, Portugal} and Silva, Fernando and Duarte, Miguel and Oliveira, Sancho and Correia, Luís and Christensen, Anders},
	month = jul,
	year = {2014},
	pages = {703--710}
}

@inproceedings{university_of_windsor_testing_2014,
	title = {Testing the {Effects} of {Speciation} and {Mutation} {Rates} on {Distance}-{Based} {Phylogenetic} {Tree} {Construction} {Accuracy} {Using} {EcoSim}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch115.pdf},
	doi = {10.7551/978-0-262-32621-6-ch115},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Windsor} and Scott, Ryan and Gras, Robin},
	month = jul,
	year = {2014},
	pages = {719--725}
}

@inproceedings{biological_cybernetics_lab_school_of_electrical_and_electronic_engineering_yonsei_university_50_yonsei-ro_seodaemun-gu_seoul_120-749_south_korea_task_2014,
	title = {Task {Partitioning} {Based} on {Response} {Threshold} {Model} in {Robot} {Harvesting} {Task}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch122.pdf},
	doi = {10.7551/978-0-262-32621-6-ch122},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Biological Cybernetics Lab, School of Electrical and Electronic Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea} and Lee, Wonki and Kim, DaeEun},
	month = jul,
	year = {2014},
	pages = {759--760}
}

@inproceedings{lesia_team_computer_science_department_university_mohamed_khider_of_biskra_algeria_splittable_2014,
	title = {Splittable {Metamorphic} {Carrier} {Robots}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch129.pdf},
	doi = {10.7551/978-0-262-32621-6-ch129},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{LESIA Team, Computer Science Department University Mohamed Khider of Biskra ALGERIA} and Ababsa, Tarek and Duthen, Yves},
	month = jul,
	year = {2014},
	pages = {801--808}
}

@inproceedings{department_of_computer_science_university_of_new_mexico_albuquerque_nm_87131_self-replicating_2014,
	title = {Self-{Replicating} {Distributed} {Virtual} {Machines}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch114.pdf},
	doi = {10.7551/978-0-262-32621-6-ch114},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Computer Science, University of New Mexico, Albuquerque, NM 87131} and Williams, Lance},
	month = jul,
	year = {2014},
	pages = {711--718}
}

@inproceedings{arizona_state_university_tempe_az_85287_self-referencing_2014,
	title = {Self-{Referencing} {Cellular} {Automata}: {A} {Model} of the {Evolution} of {Information} {Control} in {Biological} {Systems}},
	isbn = {978-0-262-32621-6},
	shorttitle = {Self-{Referencing} {Cellular} {Automata}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch083.pdf},
	doi = {10.7551/978-0-262-32621-6-ch083},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Arizona State University, Tempe, AZ 85287} and Pavlic, Theodore and Adams, Alyssa and Davies, Paul and Walker, Sara},
	month = jul,
	year = {2014},
	pages = {522--529}
}

@inproceedings{department_of_media_and_information_baika_womens_university_2-19-5_shukuno-sho_ibaraki_567-8578_osaka_japan_self-organizing_2014,
	title = {Self-{Organizing} {Process} and {Cluster} {Network} in the {Game} of {Life}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch119.pdf},
	doi = {10.7551/978-0-262-32621-6-ch119},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Media and Information, BAIKA Women’s University 2-19-5 Shukuno-sho, Ibaraki 567-8578, Osaka, Japan} and Kayama, Yoshihiko and Imamura, Yasumasa},
	month = jul,
	year = {2014},
	pages = {744--749}
}

@inproceedings{university_of_toulouse_irit_-_cnrs_umr_5505_2_rue_du_doyen_gabriel_marty_31042_toulouse_france_self-organization_2014,
	title = {Self-{Organization} of {Symbiotic} {Multicellular} {Structures}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch087.pdf},
	doi = {10.7551/978-0-262-32621-6-ch087},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Toulouse, IRIT - CNRS UMR 5505, 2 rue du Doyen Gabriel Marty, 31042 Toulouse, France} and Disset, Jean and Cussat-Blanc, Sylvain and Duthen, Yves},
	month = jul,
	year = {2014},
	pages = {541--548}
}

@inproceedings{ikegami_laboratory_university_of_tokyo_japan_self-organising_2014,
	title = {Self-{Organising} {Autocatalysis}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch080.pdf},
	doi = {10.7551/978-0-262-32621-6-ch080},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Ikegami Laboratory, University of Tokyo, Japan} and Virgo, Nathaniel and McGregor, Simon and Ikegami, Takashi},
	month = jul,
	year = {2014},
	pages = {498--505}
}

@inproceedings{cognitive_science_program_indiana_university_bloomington_in_47406_usa_quantifying_2014,
	title = {Quantifying {Robustness} in a {Spatial} {Model} of {Metabolism}-{Boundary} {Co}-{Construction}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch082.pdf},
	doi = {10.7551/978-0-262-32621-6-ch082},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Cognitive Science Program, Indiana University, Bloomington, IN 47406, USA} and Agmon, Eran and Gates, Alexander and Churavy, Valentin and Beer, Randall},
	month = jul,
	year = {2014},
	pages = {514--521}
}

@inproceedings{department_of_computer_science_university_of_york_york_uk_preserving_2014,
	title = {Preserving {Swarm} {Identity} {Over} {Time}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch116.pdf},
	doi = {10.7551/978-0-262-32621-6-ch116},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Computer Science, University of York York, UK} and Stovold, James and O'Keefe, Simon and Timmis, Jon},
	month = jul,
	year = {2014},
	pages = {726--733}
}

@inproceedings{york_centre_for_complex_systems_analysis_university_of_york_uk_y010_5dd_phenomena_2014,
	title = {Phenomena, {Mechanisms}, {Worlds}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch081.pdf},
	doi = {10.7551/978-0-262-32621-6-ch081},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{York Centre for Complex Systems Analysis, University of York, UK, Y010 5DD} and Nellis, Adam and Stepney, Susan},
	month = jul,
	year = {2014},
	pages = {506--513}
}

@inproceedings{isir_universite_pierre_et_marie_curie_6_cnrs_umr_7222_f-75252_paris_cedex_05_france_optimizing_2014,
	title = {Optimizing the {Crossregulation} {Model} for {Scalable} {Abnormality} {Detection}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch117.pdf},
	doi = {10.7551/978-0-262-32621-6-ch117},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{ISIR, Universite Pierre et Marie Curie 6, CNRS UMR 7222, F-75252, Paris Cedex 05, France} and Tarapore, Danesh and Lima, Pedro and Carneiro, Jorge and Christensen, Anders},
	month = jul,
	year = {2014},
	pages = {734--735}
}

@inproceedings{york_computational_immunology_lab_university_of_york_yo10_5dd_united_kingdom_novel_2014,
	title = {Novel {Approaches} to the {Visualization} and {Quantification} of {Biological} {Simulations} by {Emulating} {Experimental} {Techniques}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch099.pdf},
	doi = {10.7551/978-0-262-32621-6-ch099},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{York Computational Immunology Lab, University of York, YO10 5DD, United Kingdom} and Butler, James and Alden, Kieran and Fernandes, Henrique and Timmis, Jon and Coles, Mark},
	month = jul,
	year = {2014},
	pages = {614--621}
}

@inproceedings{moscow_institute_of_physics_and_technology_state_university_9_institutskiy_per._dolgoprudny_russia_neuroevolution_2014,
	title = {Neuroevolution of {Sequential} {Behavior} in {Multi}-{Goal} {Navigation} {Task}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch125.pdf},
	doi = {10.7551/978-0-262-32621-6-ch125},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, Russia} and Muratov, Sergey and Lakhman, Konstantin and Lakhman, Mikhail},
	month = jul,
	year = {2014},
	pages = {772--777}
}

@inproceedings{fundacion_i+d_del_software_libre_granada_spain_my_2014,
	title = {My {Life} as a {Sim}: {Evolving} {Unique} and {Engaging} {Life} {Stories} {Using} {Virtual} {Worlds}},
	isbn = {978-0-262-32621-6},
	shorttitle = {My {Life} as a {Sim}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch094.pdf},
	doi = {10.7551/978-0-262-32621-6-ch094},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Fundacíon I+D del Software Libre, Granada, Spain} and García, Rubén and García Sánchez, Pablo and Mora, Antonio and Merelo, J.},
	month = jul,
	year = {2014},
	pages = {580--587}
}

@inproceedings{graduate_school_of_information_science_and_technology_osaka_university_yamadaoka_1-5_suita_osaka_japan_mutation_2014,
	title = {Mutation {Accumulation} in {Bacteria} {Exposed} to {UV} {Radiation}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch121.pdf},
	doi = {10.7551/978-0-262-32621-6-ch121},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Graduate School of Information Science and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka, Japan} and Shibai, Atsushi and Tsuru, Saburo and Ying, Bei-Wen and Motooka, Daisuke and Gotoh, Kazuyoshi and Nakamura, Shota and Yomo, Tetsuya},
	month = jul,
	year = {2014},
	pages = {757--758}
}

@inproceedings{cisuc-_centre_for_informatics_and_systems_of_the_university_of_coimbra_multiagent_2014,
	title = {{MultiAgent} {System} {Architecture} in {Orphibs} {II}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch095.pdf},
	doi = {10.7551/978-0-262-32621-6-ch095},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{CISUC- Centre for Informatics and Systems of the University of Coimbra} and Barreto, Nuno and Macedo, Luís and Roque, Licínio},
	month = jul,
	year = {2014},
	pages = {588--595}
}

@inproceedings{school_of_information_and_sciences_nagoya_university_modeling_2014,
	title = {Modeling and {Evaluating} the {Process} of {Creating} {Paintings} with {Evolution} {Computing}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch093.pdf},
	doi = {10.7551/978-0-262-32621-6-ch093},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Information and Sciences, Nagoya University} and Suzuki, Tomohiro and Suzuki, Yasuhiro},
	month = jul,
	year = {2014},
	pages = {572--579}
}

@inproceedings{maastricht_university_p.o._box_616_6200_md_maastricht_the_netherlands_insect-inspired_2014,
	title = {Insect-{Inspired} {Robot} {Coordination}: {Foraging} and {Coverage}},
	isbn = {978-0-262-32621-6},
	shorttitle = {Insect-{Inspired} {Robot} {Coordination}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch123.pdf},
	doi = {10.7551/978-0-262-32621-6-ch123},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands} and Alers, Sjriek and Tuyls, Karl and Ranjbar-Sahraei, Bijan and Claes, Daniel and Weiss, Gerhard},
	month = jul,
	year = {2014},
	pages = {761--768}
}

@inproceedings{beyond_center_for_fundamental_concepts_in_science_arizona_state_university_tempe_az_informational_2014,
	title = {Informational {Architecture} of the {Fission} {Yeast} {Cell} {Cycle} {Regulatory} {Network}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch092.pdf},
	doi = {10.7551/978-0-262-32621-6-ch092},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ} and Kim, Hyunju and Davies, Paul and Walker, Sara},
	month = jul,
	year = {2014},
	pages = {569--570}
}

@inproceedings{university_of_new_mexico_albuquerque_nm_87131_indefinitely_2014,
	title = {Indefinitely {Scalable} {Computing} = {Artificial} {Life} {Engineering}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch098.pdf},
	doi = {10.7551/978-0-262-32621-6-ch098},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of New Mexico, Albuquerque, NM 87131} and Ackley, David and Small, Trent},
	month = jul,
	year = {2014},
	pages = {606--613}
}

@inproceedings{department_of_eecs_computer_science_division_university_of_central_florida_orlando_fl_32816_identifying_2014,
	title = {Identifying {Necessary} {Conditions} for {Open}-{Ended} {Evolution} through the {Artificial} {Life} {World} of {Chromaria}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch128.pdf},
	doi = {10.7551/978-0-262-32621-6-ch128},
	urldate = {2014-08-13TZ},
	publisher = {The MIT Press},
	author = {{Department of EECS (Computer Science Division) University of Central Florida, Orlando, FL 32816} and Soros, L. and Stanley, Kenneth},
	month = jul,
	year = {2014},
	pages = {793--800}
}

@inproceedings{instituto_de_telecomunicacoes_&_instituto_universitario_de_lisboa_iscte-iul_lisboa_portugal_hybrid_2014,
	title = {Hybrid {Control} for {Large} {Swarms} of {Aquatic} {Drones}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch127.pdf},
	doi = {10.7551/978-0-262-32621-6-ch127},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Instituto de Telecomunicacoes \& Instituto Universitario de Lisboa (ISCTE-IUL), Lisboa, Portugal} and Duarte, Miguel and Oliveira, Sancho and Christensen, Anders},
	month = jul,
	year = {2014},
	pages = {785--792}
}

@inproceedings{collective_dynamics_of_complex_systems_research_group_binghamton_university_state_university_of_new_york_binghamton_ny_13902-6000_usa_hierarchical_2014,
	title = {Hierarchical {Heterogeneuous} {Particle} {Swarm} {Optimization}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch101.pdf},
	doi = {10.7551/978-0-262-32621-6-ch101},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Collective Dynamics of Complex Systems Research Group Binghamton University, State University of New York, Binghamton, NY 13902-6000, USA} and Ma, Xinpei and Sayama, Hiroki},
	month = jul,
	year = {2014},
	pages = {629--638}
}

@inproceedings{university_of_toronto_institute_for_aerospace_studies_toronto_ontario_canada_m3h_5t6_evolving_2014,
	title = {Evolving {Autonomous} {Agent} {Controllers} as {Analytical} {Mathematical} {Models}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch108.pdf},
	doi = {10.7551/978-0-262-32621-6-ch108},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Toronto Institute for Aerospace Studies, Toronto, Ontario, Canada M3H 5T6} and Grouchy, Paul and D'Eleuterio, Gabrielle},
	month = jul,
	year = {2014},
	pages = {681--688}
}

@inproceedings{instituto_de_telecomunicacoes_&_instituto_universitario_de_lisboa_iscte-iul_lisbon_portugal_evolution_2014,
	title = {Evolution of {Hierarchical} {Controllers} for {Multirobot} {Systems}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch105.pdf},
	doi = {10.7551/978-0-262-32621-6-ch105},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Instituto de Telecomunicacoes \& Instituto Universitario de Lisboa (ISCTE-IUL), Lisbon, Portugal} and Duarte, Miguel and Oliveira, Sancho and Christensen, Anders},
	month = jul,
	year = {2014},
	pages = {657--664}
}

@inproceedings{natural_and_artificial_cognition_lab_university_of_naples_federico_ii_napoli_italy_evolution_2014,
	title = {Evolution of {Communication}-{Based} {Collaborative} {Behavior} in {Homogeneous} {Robots}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch107.pdf},
	doi = {10.7551/978-0-262-32621-6-ch107},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Natural and Artificial Cognition Lab, University of Naples Federico II, Napoli, Italy} and Gigliotta, Onofrio and Mirolli, Marco},
	month = jul,
	year = {2014},
	pages = {673--680}
}

@inproceedings{york_computational_immunology_laboratory_university_of_york._uk_easing_2014,
	title = {Easing {Parameter} {Sensitivity} {Analysis} of {Netlogo} {Simulations} {Using} {SPARTAN}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch100.pdf},
	doi = {10.7551/978-0-262-32621-6-ch100},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{York Computational Immunology Laboratory, University of York. UK} and Alden, Kieran and Timmis, Jon and Coles, Mark},
	month = jul,
	year = {2014},
	pages = {622--628}
}

@inproceedings{the_university_of_tokyo_designing_2014,
	title = {Designing a {Robotic} {Platform} {Controlled} by {Cultured} {Neural} {Cells}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch124.pdf},
	doi = {10.7551/978-0-262-32621-6-ch124},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{The University of Tokyo} and Maruyama, Norihiro and Masumori, Atsushi and Hubert, Julien and Mita, Takeshi and Bakkum, Douglas and Takahashi, Hirokazu and Ikegami, Takashi},
	month = jul,
	year = {2014},
	pages = {769--770}
}

@inproceedings{comptuer_science_and_engineering_department_egypt-japan_university_of_science_and_technology_e-just_alex_egypt_constrained_2014,
	title = {Constrained {Group} {Counseling} {Optimization}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch102.pdf},
	doi = {10.7551/978-0-262-32621-6-ch102},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Comptuer Science and Engineering Department, Egypt-Japan University of Science and Technology (E-JUST), Alex, Egypt} and Eita, Mohammed and Shoukry, Amine and Iba, Hitoshi},
	month = jul,
	year = {2014},
	pages = {631--638}
}

@inproceedings{institute_for_theoretical_chemistry_university_of_vienna_wahringerstrase_17/3_a-1090_vienna_austria_computational_2014,
	title = {Computational {Design} of a {Circular} {RNA} with {Prion}-{Like} {Behavior}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch091.pdf},
	doi = {10.7551/978-0-262-32621-6-ch091},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Institute for Theoretical Chemistry, University of Vienna, Wahringerstraße 17/3, A-1090 Vienna, Austria} and Badelt, Stefan and Flamm, Christoph and Hofacker, Ivo},
	month = jul,
	year = {2014},
	pages = {565--568}
}

@inproceedings{bar-ilan_university_israel_complex_2014,
	title = {Complex {ALife} {Simulations}: {From} {Generating} {Life}-like {Behaviors} to {Predicting} {Real}-life {Phenomena}},
	isbn = {978-0-262-32621-6},
	shorttitle = {Complex {ALife} {Simulations}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch097.pdf},
	doi = {10.7551/978-0-262-32621-6-ch097},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Bar-Ilan University, Israel} and Stettiner, Orly},
	month = jul,
	year = {2014},
	pages = {602--603}
}

@inproceedings{school_of_biology_georgia_institute_of_technology_atlanta_ga_30332_usa_clonal_2014,
	title = {Clonal {Development} is {Evolutionarily} {Superior} to {Aggregation} in {Wild}-{Collected} {Saccharomyces} cerevisiae},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch088.pdf},
	doi = {10.7551/978-0-262-32621-6-ch088},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA} and Pentz, Jennifer and Travisano, Michael and Ratcliff, William},
	month = jul,
	year = {2014},
	pages = {550--554}
}

@inproceedings{institute_of_matematics_of_the_romanian_academy_p.o._box_1-764_ro_014700_bucharest_romania_chemlambda_2014,
	title = {Chemlambda, {Universality} and {Self}-{Multiplication}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch079.pdf},
	doi = {10.7551/978-0-262-32621-6-ch079},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Institute of Matematics of the Romanian Academy P.O. BOX 1-764, RO 014700, Bucharest, Romania} and Kauffman, Louis and Buliga, Marius},
	month = jul,
	year = {2014},
	pages = {490--497}
}

@inproceedings{center_for_advanced_modeling_johns_hopkins_university_md_21209_chaining_2014,
	title = {Chaining {Distinct} {Tasks} {Drives} the {Evolution} of {Modularity}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch112.pdf},
	doi = {10.7551/978-0-262-32621-6-ch112},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Center for Advanced Modeling, Johns Hopkins University, MD 21209} and Calcott, Brett},
	month = jul,
	year = {2014},
	pages = {701--702}
}

@inproceedings{facultad_de_ingenieria_y_ciencias_universidad_adolfo_ibanez_av._diagonal_las_torres_2640_santiago_chile_attraction_2014,
	title = {Attraction {Basins} in a {Lac} {Operon} {Model} {Under} {Different} {Update} {Schedules}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch109.pdf},
	doi = {10.7551/978-0-262-32621-6-ch109},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Facultad de Ingenierıa y Ciencias, Universidad Adolfo Ibanez, Av. Diagonal Las Torres 2640, Santiago, Chile} and Montalva, Marco and Ruz, Gonzalo and Goles, Eric},
	month = jul,
	year = {2014},
	pages = {689--690}
}

@inproceedings{carnegie_mellon_university_pittsburgh_pa_15213_artificial_2014,
	title = {Artificial {Life} and the {Philosophy} of {Science}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch096.pdf},
	doi = {10.7551/978-0-262-32621-6-ch096},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Carnegie Mellon University, Pittsburgh, PA 15213} and Fahmy, Mostafa},
	month = jul,
	year = {2014},
	pages = {596--601}
}
@inproceedings{keio_university_applying_2014,
	title = {Applying {Self}-{Assembly} and {Self}-{Reconfigurable} {Systems} for {Printer}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch086.pdf},
	doi = {10.7551/978-0-262-32621-6-ch086},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Keio University} and Mitsui, Masayoshi and Masumori, Atsushi and Asakura, Ryo and Tanaka, Hiroya},
	month = jul,
	year = {2014},
	pages = {539--540}
}

@inproceedings{school_of_physics_and_astronomy_university_of_minnesota_116_church_street_se_minneapolis_55455_minnesota_united_states_of_america_novel_2014,
	title = {A {Novel} in {Vitro} {Metabolic} {Scheme} for the {Construction} of a {Minimal} {Biological} {Cell}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch089.pdf},
	doi = {10.7551/978-0-262-32621-6-ch089},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis, 55455 Minnesota, United States of America} and Caschera, Filippo and Noireaux, Vincent},
	month = jul,
	year = {2014},
	pages = {555--556}
}

@article{goings_ecology-based_2012,
	title = {An ecology-based evolutionary algorithm to evolve solutions to complex problems},
	volume = {13},
	url = {http://www.cse.msu.edu/~ofria/pubs/2012GoingsEtAl.pdf},
	urldate = {2017-02-13TZ},
	journal = {Artificial Life},
	author = {Goings, Sherri and Goldsby, Heather J. and Cheng, Betty HC and Ofria, Charles},
	year = {2012},
	pages = {171--177}
}

@inproceedings{department_of_computer_science_portland_state_university_analog_2014,
	title = {An {Analog} {Chemical} {Circuit} with {Parallel}-{Accessible} {Delay} {Line} for {Learning} {Temporal} {Tasks}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch078.pdf},
	doi = {10.7551/978-0-262-32621-6-ch078},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Computer Science, Portland State University} and Banda, Peter and Teuscher, Christof},
	month = jul,
	year = {2014},
	pages = {482--489}
}

@inproceedings{ecole_polytechnique_paris_france__european_erasmus_mundus_masters_in_complex_systems_science_mcss_hybrid_2014,
	title = {A {Hybrid} {Off}/{On}-{Lattice} {Model} of {Emergence} and {Maintenance} {Autopoiesis}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch085.pdf},
	doi = {10.7551/978-0-262-32621-6-ch085},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Ecole Polytechnique, Paris, France – European Erasmus Mundus Master’s in Complex Systems Science (MCSS)} and Wang, Oliver and Doursat, Rene and Bourgine, Paul},
	month = jul,
	year = {2014},
	pages = {532--538}
}

@inproceedings{biological_cybernetics_lab_school_of_electrical_and_electronic_engineering_yonsei_university_50_yonsei-ro_seodaemun-gu_seoul_120-749_south_korea_adaptive_2014,
	title = {Adaptive {Division} of {Labor} in {Multi}-{Robot} {System} with {Minimum} {Task} {Switching}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch120.pdf},
	doi = {10.7551/978-0-262-32621-6-ch120},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Biological Cybernetics Lab, School of Electrical and Electronic Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, South Korea} and Lee, Wonki and Kim, Daeeun},
	month = jul,
	year = {2014},
	pages = {750--756}
}

@inproceedings{payne_takeover_2007,
	address = {New York, NY, USA},
	series = {{GECCO} '07},
	title = {Takeover {Times} on {Scale}-free {Topologies}},
	isbn = {978-1-59593-697-4},
	url = {http://doi.acm.org/10.1145/1276958.1277018},
	doi = {10.1145/1276958.1277018},
	abstract = {The topological properties of a network directly impact the flow of information through a system. In evolving populations, the topology of inter-individual interactions affects the rate of dissemination of advantageous genetic information and thus affects selective pressure. In this study, we investigate the selective pressures induced by several scale-free population structures using takeover time analysis. Previous results have shown that the selective pressures induced by scale-free interaction topologies are at least as strong as those induced by random and panmictic interaction topologies. In contrast, our results show that the selective pressures induced by scale-free interaction topologies are heavily influenced by their underlying topological properties, and can be tuned from a selective pressure close to that of a random or panmictic topology to a selective pressure that is weaker than that of a two-dimensional toroidal lattice with 3x3 rectangular neighborhoods of interactions. We also provide a detailed topological analysis of these population structures and discuss their influence on the observed dynamics in takeover times. We show that the expected takeover times observed on all population structures considered herein can be rapidly estimated using only a few readily computable metrics of the underlying topology, precluding the need to run expensive simulations or recursive probabilistic formulations.},
	urldate = {2017-02-24TZ},
	booktitle = {Proceedings of the 9th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Payne, Joshua L. and Eppstein, Margaret J.},
	year = {2007},
	keywords = {scale-free, selective pressure, spatial structure, takeover time},
	pages = {308--315}
}

@article{hoekstra_strength_2001,
	title = {Strength and tempo of directional selection in the wild},
	volume = {98},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/98/16/9157},
	doi = {10.1073/pnas.161281098},
	abstract = {Directional selection is a major force driving adaptation and evolutionary change. However, the distribution, strength, and tempo of phenotypic selection acting on quantitative traits in natural populations remain unclear across different study systems. We reviewed the literature (1984–1997) that reported the strength of directional selection as indexed by standardized linear selection gradients (β). We asked how strong are viability and sexual selection, and whether strength of selection is correlated with the time scale over which it was measured. Estimates of the magnitude of directional selection ({\textbar}β{\textbar}) were exponentially distributed, with few estimates greater than 0.50 and most estimates less than 0.15. Sexual selection (measured by mating success) appeared stronger than viability selection (measured by survival). Viability selection that was measured over short periods (days) was typically stronger than selection measured over longer periods (months and years), but the strength of sexual selection did not vary with duration of selection episodes; as a result, sexual selection was stronger than viability selection over longer time scales (months and years), but not over short time scales (days).},
	language = {en},
	number = {16},
	urldate = {2017-02-24TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Hoekstra, H. E. and Hoekstra, J. M. and Berrigan, D. and Vignieri, S. N. and Hoang, A. and Hill, C. E. and Beerli, P. and Kingsolver, J. G.},
	month = jul,
	year = {2001},
	pmid = {11470913},
	keywords = {natural populations, natural selection, quantitative traits, selection gradients, sexual selection},
	pages = {9157--9160}
}

@article{kingsolver_strength_2001,
	title = {The {Strength} of {Phenotypic} {Selection} in {Natural} {Populations}.},
	volume = {157},
	issn = {0003-0147},
	url = {http://www.journals.uchicago.edu/doi/full/10.1086/319193},
	doi = {10.1086/319193},
	abstract = {How strong is phenotypic selection on quantitative traits in the wild? We reviewed the literature from 1984 through 1997 for studies that estimated the strength of linear and quadratic selection in terms of standardized selection gradients or differentials on natural variation in quantitative traits for field populations. We tabulated 63 published studies of 62 species that reported over 2,500 estimates of linear or quadratic selection. More than 80\% of the estimates were for morphological traits; there is very little data for behavioral or physiological traits. Most published selection studies were unreplicated and had sample sizes below 135 individuals, resulting in low statistical power to detect selection of the magnitude typically reported for natural populations. The absolute values of linear selection gradients {\textbar}β{\textbar} were exponentially distributed with an overall median of 0.16, suggesting that strong directional selection was uncommon. The values of {\textbar}β{\textbar} for selection on morphological and on life‐history/phenological traits were significantly different: on average, selection on morphology was stronger than selection on phenology/life history. Similarly, the values of {\textbar}β{\textbar} for selection via aspects of survival, fecundity, and mating success were significantly different: on average, selection on mating success was stronger than on survival. Comparisons of estimated linear selection gradients and differentials suggest that indirect components of phenotypic selection were usually modest relative to direct components. The absolute values of quadratic selection gradients {\textbar}γ{\textbar} were exponentially distributed with an overall median of only 0.10, suggesting that quadratic selection is typically quite weak. The distribution of γ values was symmetric about 0, providing no evidence that stabilizing selection is stronger or more common than disruptive selection in nature.},
	number = {3},
	urldate = {2017-02-24TZ},
	journal = {The American Naturalist},
	author = {Kingsolver, J. G. and Hoekstra, H. E. and Hoekstra, J. M. and Berrigan, D. and Vignieri, S. N. and Hill, C. E. and Hoang, A. and Gibert, P. and Beerli, P.},
	month = mar,
	year = {2001},
	pages = {245--261}
}

@inproceedings{guhe_effectiveness_2014,
	title = {The effectiveness of persuasion in {The} {Settlers} of {Catan}},
	doi = {10.1109/CIG.2014.6932861},
	abstract = {We present a method for obtaining a useful symbolic model of persuasion in a complex game, where players' preferences over the outcomes of negotiations over resources are incomplete, uncertain, and dynamic. We focus on the problem of identifying the stage in the game where successfully persuading an agent to perform a particular action will have the most impact on one's chances to win. Our approach exploits empirical data from game simulations, where the set up allows us to investigate individual aspects of the policy in suitably controlled ways. We demonstrate the effectiveness of the approach within the domain of The Settlers of Catan and present some specific lessons that can be learned for this particular game, e.g. that a tipping point in the game occurs for persuasion moves that are made when the leading player reaches 7 Victory Points.},
	booktitle = {2014 {IEEE} {Conference} on {Computational} {Intelligence} and {Games}},
	author = {Guhe, M. and Lascarides, A.},
	month = aug,
	year = {2014},
	keywords = {Computational modeling, Law, Lead, The Settlers of Catan, cognitive agents, computer games, game simulations, multi-agent systems, persuasion symbolic model},
	pages = {1--8}
}

@article{galway_machine_2008,
	title = {Machine learning in digital games: a survey},
	volume = {29},
	shorttitle = {Machine learning in digital games},
	url = {http://dl.acm.org/citation.cfm?id=1612896},
	number = {2},
	urldate = {2017-02-14TZ},
	journal = {Artificial Intelligence Review},
	author = {Galway, Leo and Charles, Darryl and Black, Michaela},
	year = {2008},
	keywords = {Computational Intelligence, Digital games, Game AI, Machine learning},
	pages = {123--161}
}

@article{mayfield_higher-order_2017,
	title = {Higher-order interactions capture unexplained complexity in diverse communities},
	volume = {1},
	copyright = {© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
	issn = {2397-334X},
	url = {http://www.nature.com/articles/s41559-016-0062},
	doi = {10.1038/s41559-016-0062},
	abstract = {Higher-order interactions (HOIs) are often assumed to be negligible in natural communities. Here, the authors present a framework for incorporating HOIs into diversity models and show that their inclusion can dramatically improve explanatory power.},
	language = {en},
	urldate = {2017-02-17TZ},
	journal = {Nature Ecology \& Evolution},
	author = {Mayfield, Margaret M. and Stouffer, Daniel B.},
	month = feb,
	year = {2017},
	pages = {0062}
}

@article{payne_complex_2013,
	title = {Complex and dynamic population structures: synthesis, open questions, and future directions},
	volume = {17},
	issn = {1432-7643, 1433-7479},
	shorttitle = {Complex and dynamic population structures},
	url = {http://link.springer.com/article/10.1007/s00500-013-0994-x},
	doi = {10.1007/s00500-013-0994-x},
	abstract = {The population structure of an evolutionary algorithm influences the dissemination and mixing of advantageous alleles, and therefore affects search performance. Much recent attention has focused on the analysis of complex population structures, characterized by heterogeneous connectivity distributions, non-trivial clustering properties, and degree–degree correlations. Here, we synthesize the results of these recent studies, discuss their limitations, and highlight several open questions regarding (1) unsolved theoretical issues and (2) the practical utility of complex population structures for evolutionary search. In addition, we will discuss an alternative complex population structure that is known to significantly influence dynamical processes, but has yet to be explored for evolutionary optimization. We then shift our attention toward dynamic population structures, which have received markedly less attention than their static counterparts. We will discuss the strengths and limitations of extant techniques and present open theoretical and experimental questions and directions for future research. In particular, we will focus on the prospects of “active linking,” wherein edges are dynamically rewired according to the genotypic or phenotypic properties of individuals, or according to the success of prior inter-individual interactions.},
	language = {en},
	number = {7},
	urldate = {2017-02-10TZ},
	journal = {Soft Computing},
	author = {Payne, Joshua L. and Giacobini, Mario and Moore, Jason H.},
	month = jul,
	year = {2013},
	pages = {1109--1120}
}

@article{bryden_graph-based_2006,
	title = {Graph-based evolutionary algorithms},
	volume = {10},
	issn = {1089-778X},
	url = {http://ieeexplore.ieee.org/document/1705403/},
	doi = {10.1109/TEVC.2005.863128},
	number = {5},
	urldate = {2017-02-24TZ},
	journal = {IEEE Transactions on Evolutionary Computation},
	author = {Bryden, K.M. and Ashlock, D.A. and Corns, S. and Willson, S.J.},
	month = oct,
	year = {2006},
	pages = {550--567}
}

@article{payne_evolutionary_2009,
	title = {Evolutionary {Dynamics} on {Scale}-{Free} {Interaction} {Networks}},
	volume = {13},
	issn = {1941-0026, 1089-778X},
	url = {http://ieeexplore.ieee.org/document/5175362/},
	doi = {10.1109/TEVC.2009.2019825},
	number = {4},
	urldate = {2017-02-24TZ},
	journal = {IEEE Transactions on Evolutionary Computation},
	author = {Payne, J.L. and Eppstein, M.J.},
	month = aug,
	year = {2009},
	pages = {895--912}
}

@inproceedings{ochoa_study_2008,
	title = {A study of {NK} landscapes' basins and local optima networks},
	url = {http://dl.acm.org/citation.cfm?id=1389204},
	urldate = {2017-02-24TZ},
	booktitle = {Proceedings of the 10th annual conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Ochoa, Gabriela and Tomassini, Marco and Vérel, Sebástien and Darabos, Christian},
	year = {2008},
	pages = {555--562}
}

@inproceedings{payne_using_2007,
	title = {Using pair approximations to predict takeover dynamics in spatially structured populations},
	url = {http://dl.acm.org/citation.cfm?id=1274025},
	urldate = {2017-02-24TZ},
	booktitle = {Proceedings of the 9th annual conference companion on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Payne, Joshua L. and Eppstein, Margaret J.},
	year = {2007},
	pages = {2557--2564}
}

@inproceedings{giacobini_takeover_2005,
	title = {Takeover time curves in random and small-world structured populations},
	url = {http://dl.acm.org/citation.cfm?id=1068224},
	urldate = {2017-02-24TZ},
	booktitle = {Proceedings of the 7th annual conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Giacobini, Mario and Tomassini, Marco and Tettamanzi, Andrea},
	year = {2005},
	pages = {1333--1340}
}

@misc{noauthor_hairston:_nodate,
	title = {Hairston: {Rapid} evolution and the convergence of... - {Google} {Scholar}},
	url = {https://scholar.google.com/scholar_lookup?author=N.+G.+Hairston&author=S.+P.+Ellner&author=M.+A.+Geber&author=T.+Yoshida&author=J.+A.+Fox&title=Rapid+evolution+and+the+convergence+of+ecological+and+evolutionary+time&publication_year=2005&journal=Ecol.+Lett.&volume=8},
	urldate = {2017-02-24TZ}
}

@article{weber_evolution_2017,
	title = {Evolution in a {Community} {Context}: {On} {Integrating} {Ecological} {Interactions} and {Macroevolution}},
	volume = {0},
	issn = {0169-5347},
	shorttitle = {Evolution in a {Community} {Context}},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(17)30016-2},
	doi = {10.1016/j.tree.2017.01.003},
	abstract = {Despite a conceptual understanding that evolution and species interactions are inextricably linked, it remains challenging to study ecological and evolutionary dynamics together over long temporal scales. In this review, we argue that, despite inherent challenges associated with reconstructing historical processes, the interplay of ecology and evolution is central to our understanding of macroevolution and community coexistence, and cannot be safely ignored in community and comparative phylogenetic studies. We highlight new research avenues that foster greater consideration of both ecological and evolutionary dynamics as processes that occur along branches of phylogenetic trees. By promoting new ways forward using this perspective, we hope to inspire further integration that creatively co-utilizes phylogenies and ecological data to study eco-evolutionary dynamics over time and space., Ecology and evolution interact over deep time scales, and innovative new research from a variety of fields is expanding our ability to understand these interactions and their effects., New developments in comparative phylogenetic methods incorporate species interactions in models of character change and lineage diversification, enabling direct tests of hypotheses concerning the impacts of ecological interactions on macroevolution., Advances in community phylogenetics improve the study of macroevolutionary constraints on coexistence by using null models that account for the geography of speciation., Although links between ecology and macroevolutionary patterns are difficult to test using a single framework, the synthesis of multiple research approaches makes it increasingly apparent that reciprocal eco-evolutionary dynamics can influence rates of diversification, phenotypic evolution, and community coexistence patterns.},
	language = {English},
	number = {0},
	urldate = {2017-02-23TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Weber, Marjorie G. and Wagner, Catherine E. and Best, Rebecca J. and Harmon, Luke J. and Matthews, Blake},
	month = feb,
	year = {2017},
	pmid = {28215448}
}

@article{pelletier_eco-evolutionary_2009,
	title = {Eco-evolutionary dynamics},
	volume = {364},
	copyright = {Copyright © 2009 The Royal Society.},
	issn = {0962-8436, 1471-2970},
	url = {http://rstb.royalsocietypublishing.org/content/364/1523/1483},
	doi = {10.1098/rstb.2009.0027},
	abstract = {Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.},
	language = {en},
	number = {1523},
	urldate = {2017-02-23TZ},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Pelletier, F. and Garant, D. and Hendry, A. P.},
	month = jun,
	year = {2009},
	pmid = {19414463},
	pages = {1483--1489}
}

@article{porlier_non-random_2009,
	title = {Non-random distribution of individual genetic diversity along an environmental gradient},
	volume = {364},
	copyright = {© 2009 The Royal Society},
	issn = {0962-8436, 1471-2970},
	url = {http://rstb.royalsocietypublishing.org/content/364/1523/1543},
	doi = {10.1098/rstb.2009.0010},
	abstract = {Improving our knowledge of the links between ecology and evolution is especially critical in the actual context of global rapid environmental changes. A critical step in that direction is to quantify how variation in ecological factors linked to habitat modifications might shape observed levels of genetic variability in wild populations. Still, little is known on the factors affecting levels and distribution of genetic diversity at the individual level, despite its vital underlying role in evolutionary processes. In this study, we assessed the effects of habitat quality on population structure and individual genetic diversity of tree swallows (Tachycineta bicolor) breeding along a gradient of agricultural intensification in southern Québec, Canada. Using a landscape genetics approach, we found that individual genetic diversity was greater in poorer quality habitats. This counter-intuitive result was partly explained by the settlement patterns of tree swallows across the landscape. Individuals of higher genetic diversity arrived earlier on their breeding grounds and settled in the first available habitats, which correspond to intensive cultures. Our results highlight the importance of investigating the effects of environmental variability on individual genetic diversity, and of integrating information on landscape structure when conducting such studies.},
	language = {en},
	number = {1523},
	urldate = {2017-02-23TZ},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Porlier, Mélody and Bélisle, Marc and Garant, Dany},
	month = jun,
	year = {2009},
	pmid = {19414469},
	pages = {1543--1554}
}

@article{larue_eco-evolutionary_2017,
	title = {Eco-evolutionary dynamics in restored communities and ecosystems},
	volume = {25},
	issn = {1526-100X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/rec.12458/abstract},
	doi = {10.1111/rec.12458},
	abstract = {Recent ecological studies have revealed that rapid evolution within populations can have significant impacts on the ecological dynamics of communities and ecosystems. These eco-evolutionary dynamics (EED) are likely to have substantial and quantifiable effects in restored habitats over timescales that are relevant for the conservation and restoration of small populations and threatened communities. Restored habitats may serve as “hotspots” for EED due to mismatches between transplanted genotypes and the restored environment, and novel interactions among lineages that do not share a coevolutionary history, both of which can generate strong selection for rapid evolutionary change that has immediate demographic consequences. Rapid evolution that influences population dynamics and community processes is likely to have particularly large effects during the establishment phase of restoration efforts. Finally, restoration activities and their associated long-term monitoring programs provide outstanding opportunities for using eco-evolutionary experimental approaches. Results from such studies will address questions about the effects of rapid evolutionary change on the ecological dynamics of populations and interacting species, while simultaneously providing critical, but currently overlooked, information for conservation practices.},
	language = {en},
	number = {1},
	urldate = {2017-02-21TZ},
	journal = {Restoration Ecology},
	author = {LaRue, Elizabeth A. and Chambers, Sally M. and Emery, Nancy C.},
	month = jan,
	year = {2017},
	keywords = {conservation genetics, evolutionary potential, rapid evolution, reintroduction, restoration genetics, translocation},
	pages = {19--26}
}

@article{kokko_can_2017,
	title = {Can {Evolution} {Supply} {What} {Ecology} {Demands}?},
	volume = {32},
	issn = {0169-5347},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534716302385},
	doi = {10.1016/j.tree.2016.12.005},
	abstract = {A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological ‘demands’ change, evolution ‘supplies’ the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate. In this review, we highlight how complexity in both ecological ‘demands’ and the evolutionary ‘supply’ influences organisms’ ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards ecologically realistic studies of adaptation.},
	number = {3},
	urldate = {2017-02-21TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Kokko, Hanna and Chaturvedi, Anurag and Croll, Daniel and Fischer, Martin C. and Guillaume, Frédéric and Karrenberg, Sophie and Kerr, Ben and Rolshausen, Gregor and Stapley, Jessica},
	month = mar,
	year = {2017},
	pages = {187--197}
}

@article{macpherson_individual-based_2016,
	title = {Individual-based ecological models: {Adjunctive} tools or experimental systems?},
	volume = {323},
	issn = {0304-3800},
	shorttitle = {Individual-based ecological models},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380015005815},
	doi = {10.1016/j.ecolmodel.2015.12.013},
	abstract = {The role that individual-based computer modeling (IBCM) should play in the field of integrative ecology needs to be clarified in light of the continuing concern with the empirical validation of individual-based computer models. Though perfectly legitimate and understandable, the requirement of empirical validation has been taken to extremes. The result of doing so is that potentially useful scientific investigations involving computer simulations risk being thwarted on the grounds that they are not empirically calibrated or perhaps not historically validated. We shall argue that the role that IBCM plays in integrative ecology depends on whether one is doing applied ecology with concerns such as species conservation or whether one is doing theoretical ecology. In the former case, computer modeling should incorporate real-world elements and actual experimental data if the goal is to model existing ecosystems and to make long-term predictions about these systems. In this case, IBCM functions more like an investigative tool for scientific inquiry. On the other hand, if one's concerns are more theoretical, then IBCM has value in its own right in terms of high generality and equally high predictive power. Although the modeling should be realistic in a broad sense that is consistent with species generally that evolve in a world with predation, pathogens and fluctuating resources, simulations for more theoretical investigations need not incorporate experimental data – especially in light of the fact that these are not always obtainable in the field. They are experimental systems in their own right and not merely adjunctive tools.},
	urldate = {2017-02-17TZ},
	journal = {Ecological Modelling},
	author = {MacPherson, Brian and Gras, Robin},
	month = mar,
	year = {2016},
	keywords = {Applied ecology, Individual-based models, Model validation, Theoretical ecology},
	pages = {106--114}
}

@article{noauthor_individual-based_2005,
	title = {Individual-{Based} {Modeling} of {Ecological} and {Evolutionary} {Processes}},
	volume = {36},
	url = {http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152644},
	doi = {10.1146/annurev.ecolsys.36.102003.152644},
	abstract = {Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.},
	number = {1},
	urldate = {2017-02-16TZ},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	year = {2005},
	pages = {147--168}
}

@inproceedings{parunak_agent-based_1998,
	title = {Agent-{Based} {Modeling} vs. {Equation}-{Based} {Modeling}: {A} {Case} {Study} and {Users}’ {Guide}},
	shorttitle = {Agent-{Based} {Modeling} vs. {Equation}-{Based} {Modeling}},
	url = {http://link.springer.com/chapter/10.1007/10692956_2},
	abstract = {In many domains, agent-based system modeling competes with equation-based approaches that identify system variables and evaluate or integrate sets of equations relating these variables. The distinction has been of great interest in a project that applies agent-based modeling to industrial supply networks, since virtually all computer-based modeling of such networks up to this point has used system dynamics, an approach based on ordinary differential equations (ODE’s). This paper summarizes the domain of supply networks and illustrates how they can be modeled both with agents and with equations. It summarizes the similarities and differences of these two classes of models, and develops criteria for selecting one or the other approach.},
	language = {en},
	urldate = {2017-02-16TZ},
	booktitle = {Multi-{Agent} {Systems} and {Agent}-{Based} {Simulation}},
	publisher = {Springer, Berlin, Heidelberg},
	author = {Parunak, H. Van Dyke and Savit, Robert and Riolo, Rick L.},
	month = jul,
	year = {1998},
	note = {DOI: 10.1007/10692956\_2},
	pages = {10--25}
}

@book{hendry_eco-evolutionary_2016,
	title = {Eco-evolutionary {Dynamics}},
	isbn = {978-1-4008-8308-0},
	abstract = {In recent years, scientists have realized that evolution can occur on timescales much shorter than the "long lapse of ages" emphasized by Darwin—in fact, evolutionary change is occurring all around us all the time. This book provides an authoritative and accessible introduction to eco-evolutionary dynamics, a cutting-edge new field that seeks to unify evolution and ecology into a common conceptual framework focusing on rapid and dynamic environmental and evolutionary change.Andrew Hendry covers key aspects of evolution, ecology, and their interactions. Topics range from natural selection, adaptive divergence, ecological speciation, and gene flow to population and community dynamics, ecosystem function, plasticity, and genomics. Hendry evaluates conceptual and methodological approaches, and draws on empirical data from natural populations—including those in human-disturbed environments—to tackle a number of classic and emerging research questions. He also discusses exciting new directions for future research at the intersection of ecology and evolution.An invaluable guide for students and researchers alike, Eco-evolutionary Dynamics reveals how evolution and ecology interact strongly on short timescales to shape the world we see around us.},
	language = {en},
	publisher = {Princeton University Press},
	author = {Hendry, Andrew P.},
	month = nov,
	year = {2016},
	note = {Google-Books-ID: QMtIDAAAQBAJ},
	keywords = {Science / Life Sciences / Biology, Science / Life Sciences / Ecology, Science / Life Sciences / Evolution}
}

@article{schoener_newest_2011,
	title = {The {Newest} {Synthesis}: {Understanding} the {Interplay} of {Evolutionary} and {Ecological} {Dynamics}},
	volume = {331},
	copyright = {Copyright © 2011, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	shorttitle = {The {Newest} {Synthesis}},
	url = {http://science.sciencemag.org/content/331/6016/426},
	doi = {10.1126/science.1193954},
	abstract = {The effect of ecological change on evolution has long been a focus of scientific research. The reverse—how evolutionary dynamics affect ecological traits—has only recently captured our attention, however, with the realization that evolution can occur over ecological time scales. This newly highlighted causal direction and the implied feedback loop—eco-evolutionary dynamics—is invigorating both ecologists and evolutionists and blurring the distinction between them. Despite some recent relevant studies, the importance of the evolution-to-ecology pathway across systems is still unknown. Only an extensive research effort involving multiple experimental approaches—particularly long-term field experiments—over a variety of ecological communities will provide the answer.},
	language = {en},
	number = {6016},
	urldate = {2017-02-15TZ},
	journal = {Science},
	author = {Schoener, Thomas W.},
	month = jan,
	year = {2011},
	pmid = {21273479},
	pages = {426--429}
}

@misc{noauthor_man_2014,
	title = {The {Man} {Who} {Built} {Catan}},
	url = {http://www.newyorker.com/business/currency/the-man-who-built-catan},
	abstract = {Last year, Mayfair Games reported selling more than seven hundred and fifty thousand copies of The Settlers of Catan.},
	urldate = {2017-02-15TZ},
	journal = {The New Yorker},
	month = feb,
	year = {2014}
}

@article{haddad_habitat_2015,
	title = {Habitat fragmentation and its lasting impact on {Earth}’s ecosystems},
	volume = {1},
	url = {http://advances.sciencemag.org/content/1/2/e1500052.abstract},
	doi = {10.1126/sciadv.1500052},
	abstract = {We conducted an analysis of global forest cover to reveal that 70\% of remaining forest is within 1 km of the forest’s edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75\% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.},
	number = {2},
	journal = {Science Advances},
	author = {Haddad, Nick M. and Brudvig, Lars A. and Clobert, Jean and Davies, Kendi F. and Gonzalez, Andrew and Holt, Robert D. and Lovejoy, Thomas E. and Sexton, Joseph O. and Austin, Mike P. and Collins, Cathy D. and Cook, William M. and Damschen, Ellen I. and Ewers, Robert M. and Foster, Bryan L. and Jenkins, Clinton N. and King, Andrew J. and Laurance, William F. and Levey, Douglas J. and Margules, Chris R. and Melbourne, Brett A. and Nicholls, A. O. and Orrock, John L. and Song, Dan-Xia and Townshend, John R.},
	month = mar,
	year = {2015}
}

@inproceedings{guhe_game_2014,
	title = {Game strategies for {The} {Settlers} of {Catan}},
	doi = {10.1109/CIG.2014.6932884},
	abstract = {We present an empirical framework for testing game strategies in The Settlers of Catan, a complex win-lose game that lacks any analytic solution. This framework provides the means to change different components of an autonomous agent's strategy, and to test them in suitably controlled ways via performance metrics in game simulations and via comparisons of the agent's behaviours with those exhibited in a corpus of humans playing the game. We provide changes to the game strategy that not only improve the agent's strength, but corpus analysis shows that they also bring the agent closer to a model of human players.},
	booktitle = {2014 {IEEE} {Conference} on {Computational} {Intelligence} and {Games}},
	author = {Guhe, M. and Lascarides, A.},
	month = aug,
	year = {2014},
	keywords = {Catan settlers, Game theory, Games, Monopoly, autonomous agent strategy, complex win-lose game, corpus analysis, game simulations, game strategies, multi-agent systems, performance metrics},
	pages = {1--8}
}

@inproceedings{pfeiffer_reinforcement_2004,
	title = {Reinforcement learning of strategies for {Settlers} of {Catan}},
	url = {https://www.researchgate.net/profile/Michael_Pfeiffer/publication/228728063_Reinforcement_learning_of_strategies_for_Settlers_of_Catan/links/546ddfb80cf2193b94c5da66.pdf},
	urldate = {2017-02-14TZ},
	booktitle = {Proceedings of the {International} {Conference} on {Computer} {Games}: {Artificial} {Intelligence}, {Design} and {Education}},
	author = {Pfeiffer, Michael},
	year = {2004}
}

@misc{noauthor_effectiveness_nodate,
	title = {The {Effectiveness} of {Persuasion} in {The} {Settlers} of {Catan} - {Google} {Search}},
	url = {https://www.google.com/search?q=The+Effectiveness+of+Persuasion+in+The+Settlers+of+Catan&oq=The+Effectiveness+of+Persuasion+in+The+Settlers+of+Catan&aqs=chrome..69i57.192j0j4&sourceid=chrome&ie=UTF-8},
	urldate = {2017-02-14TZ}
}

@article{mace_preserving_2003,
	title = {Preserving the {Tree} of {Life}},
	volume = {300},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/300/5626/1707},
	doi = {10.1126/science.1085510},
	abstract = {Phylogenies provide new ways to measure biodiversity, to assess conservation priorities, and to quantify the evolutionary history in any set of species. Methodological problems and a lack of knowledge about most species have so far hampered their use. In the future, as techniques improve and more data become accessible, we will have an expanded set of conservation options, including ways to prioritize outcomes from evolutionary and ecological processes.},
	language = {en},
	number = {5626},
	urldate = {2017-02-13TZ},
	journal = {Science},
	author = {Mace, Georgina M. and Gittleman, John L. and Purvis, Andy},
	month = jun,
	year = {2003},
	pmid = {12805539},
	pages = {1707--1709}
}
@inproceedings{whigham_exploring_2008,
	title = {Exploring the use of ancestry as a unified network model of finite population evolution},
	isbn = {978-1-4244-1822-0},
	url = {http://ieeexplore.ieee.org/document/4631303/},
	doi = {10.1109/CEC.2008.4631303},
	urldate = {2017-02-10TZ},
	publisher = {IEEE},
	author = {Whigham, Peter A. and Dick, Grant},
	month = jun,
	year = {2008},
	pages = {3734--3740}
}

@article{laland_extended_2015,
	title = {The extended evolutionary synthesis: its structure, assumptions and predictions},
	volume = {282},
	copyright = {© 2015 The Author(s). Published by the Royal Society. All rights reserved.},
	issn = {0962-8452, 1471-2954},
	shorttitle = {The extended evolutionary synthesis},
	url = {http://rspb.royalsocietypublishing.org/content/282/1813/20151019},
	doi = {10.1098/rspb.2015.1019},
	abstract = {Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.},
	language = {en},
	number = {1813},
	urldate = {2017-01-27TZ},
	journal = {Proc. R. Soc. B},
	author = {Laland, Kevin N. and Uller, Tobias and Feldman, Marcus W. and Sterelny, Kim and Müller, Gerd B. and Moczek, Armin and Jablonka, Eva and Odling-Smee, John},
	month = aug,
	year = {2015},
	pmid = {26246559},
	pages = {20151019}
}

@article{beaume_rapid_2017,
	title = {Rapid adaptation drives invasion of airway donor microbiota by {Pseudomonas} after lung transplantation},
	volume = {7},
	copyright = {© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
	issn = {2045-2322},
	url = {http://www.nature.com/srep/2017/170117/srep40309/full/srep40309.html},
	doi = {10.1038/srep40309},
	abstract = {In cystic fibrosis (CF) patients, chronic airway infection by Pseudomonas leads to progressive lung destruction ultimately requiring lung transplantation (LT).},
	language = {en},
	urldate = {2017-01-25TZ},
	journal = {Scientific Reports},
	author = {Beaume, M. and Köhler, T. and Greub, G. and Manuel, O. and Aubert, J.-D. and Baerlocher, L. and Farinelli, L. and Buckling, A. and Delden, C. van},
	month = jan,
	year = {2017},
	keywords = {evolution, justification, microbiome},
	pages = {40309}
}

@article{makohon-moore_limited_2017,
	title = {Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer},
	copyright = {© 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1061-4036},
	url = {http://www.nature.com.proxy.readcube.com/ng/journal/vaop/ncurrent/full/ng.3764.html?token=amxEYkHVAjPXXsXBvk6me3TnjN6whc4BgLYeNwunPiE=&referrer_url=http://www.nature.com/articles/ng.3764.epdf?shared_access_token=1qktDiXr2QJEc3lZ-3Vc3dRgN0jAjWel9jnR3ZoTv0PL9qm_ZVrkxixeJbskDZfvARU9zf7kuvIsJ5wlbixG-0mg-udWaktAvxMngrjc3Q9bYM7tcsRwqIIojOHBx4J7DPV4_NjZkL9LvwZNArowvekMax9EO49CCrG-6B7YLudcr59NxZIqNaI8AJx1_m4Js8rf5S_vGLXVQhhgAEGtYg%253D%253D},
	doi = {10.1038/ng.3764},
	abstract = {The extent of heterogeneity among driver gene mutations present in naturally occurring metastases—that is, treatment-naive metastatic disease—is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease.},
	language = {en},
	urldate = {2017-01-24TZ},
	journal = {Nature Genetics},
	author = {Makohon-Moore, Alvin P. and Zhang, Ming and Reiter, Johannes G. and Bozic, Ivana and Allen, Benjamin and Kundu, Deepanjan and Chatterjee, Krishnendu and Wong, Fay and Jiao, Yuchen and Kohutek, Zachary A. and Hong, Jungeui and Attiyeh, Marc and Javier, Breanna and Wood, Laura D. and Hruban, Ralph H. and Nowak, Martin A. and Papadopoulos, Nickolas and Kinzler, Kenneth W. and Vogelstein, Bert and Iacobuzio-Donahue, Christine A.},
	year = {2017},
	keywords = {Genome informatics, Metastasis, Pancreatic cancer}
}

@inproceedings{dolson_effects_2016,
	address = {Cancun, Mexico},
	title = {The {Effects} of {Evolution} and {Spatial} {Structure} on {Diversity} in {Biological} {Reserves}},
	copyright = {© 2016, Published by Cold Spring Harbor Laboratory Press. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
	url = {http://www.biorxiv.org/content/early/2016/03/10/043083},
	doi = {10.1101/043083},
	abstract = {Conservation ecologists have long argued over the best way of placing reserves across an environment to maximize population diversity. Many have studied the effect of protecting many small regions of an ecosystem vs. a single large region, with varied results. However, this research tends to ignore evolutionary dynamics under the rationale that the spatiotemporal scale required is prohibitive. We used the Avida digital evolution research platform to overcome this barrier and study the response of phenotypic diversity to eight different reserve placement configurations. The capacity for mutation,and therefore evolution, substantially altered the dynamics of diversity in the population. When mutations were allowed, reserve configurations involving a greater number of consequently smaller reserves were substantially more effective at maintaining existing diversity and generating new diversity. However, when mutations were disallowed, reserve configuration had little effect on diversity generation and maintenance. While further research is necessary before translating these results into policy decisions, this study demonstrates the importance of considering evolution when making such decisions and suggests that a larger number of smaller reserves may have evolutionary benefits.},
	language = {en},
	urldate = {2016-07-16TZ},
	booktitle = {Artificial {Life} {XV}: {Proceedings} of the {Fifteenth} {International} {Conference} on {Artificial} {Life}},
	publisher = {MIT Press},
	author = {Dolson, Emily and Wiser, Michael J. and Ofria, Charles A.},
	year = {2016},
	pages = {434--440}
}

@inproceedings{leas_prisoners_2016,
	address = {Cancun, Mexico},
	title = {The {Prisoner}’s {Dilemma}, {Memory}, and the {Early} {Evolution} of {Intelligence}},
	booktitle = {Artificial {Life} {XV}: {Proceedings} of the {Fifteenth} {International} {Conference} on {Artificial} life},
	publisher = {MIT Press},
	author = {Leas, Mikaela and Dolson, Emily and Annis, Riley and Nahum, Joshua and Grabowski, Laura and Ofria, Charles},
	year = {2016},
	pages = {408--415}
}

@article{taylor_open-ended_2016,
	title = {Open-{Ended} {Evolution}: {Perspectives} from the {OEE} {Workshop} in {York}},
	volume = {22},
	issn = {1064-5462, 1530-9185},
	shorttitle = {Open-{Ended} {Evolution}},
	url = {http://www.mitpressjournals.org/doi/10.1162/ARTL_a_00210},
	doi = {10.1162/ARTL_a_00210},
	language = {en},
	number = {3},
	urldate = {2017-01-11TZ},
	journal = {Artificial Life},
	author = {Taylor, Tim and Bedau, Mark and Channon, Alastair and Ackley, David and Banzhaf, Wolfgang and Beslon, Guillaume and Dolson, Emily and Froese, Tom and Hickinbotham, Simon and Ikegami, Takashi and McMullin, Barry and Packard, Norman and Rasmussen, Steen and Virgo, Nathaniel and Agmon, Eran and Clark, Edward and McGregor, Simon and Ofria, Charles and Ropella, Glen and Spector, Lee and Stanley, Kenneth O. and Stanton, Adam and Timperley, Christopher and Vostinar, Anya and Wiser, Michael},
	month = aug,
	year = {2016},
	pages = {408--423}
}

@article{gibbons_disturbance_2016,
	title = {Disturbance {Regimes} {Predictably} {Alter} {Diversity} in an {Ecologically} {Complex} {Bacterial} {System}},
	volume = {7},
	issn = {, 2150-7511},
	url = {http://mbio.asm.org/content/7/6/e01372-16},
	doi = {10.1128/mBio.01372-16},
	abstract = {Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.
IMPORTANCE The diversity of microbial communities is linked to the functioning and stability of ecosystems. As humanity continues to impact ecosystems worldwide, and as diet and disease perturb our own commensal microbial communities, the ability to predict how microbial diversity will respond to disturbance is of critical importance. Using microbial microcosm experiments, we find that community diversity responds to different disturbance regimes in a reproducible and predictable way. Maximum diversity occurs when two communities, each suited to different environmental conditions, are mixed due to disturbance. This maximum diversity is transient except under specific regimes. Using a simple mathematical model, we show that transient unimodality is likely a common feature of microbial diversity-disturbance relationships in fluctuating environments.},
	language = {en},
	number = {6},
	urldate = {2017-01-06TZ},
	journal = {mBio},
	author = {Gibbons, Sean M. and Scholz, Monika and Hutchison, Alan L. and Dinner, Aaron R. and Gilbert, Jack A. and Coleman, Maureen L.},
	month = dec,
	year = {2016},
	pmid = {27999158},
	pages = {e01372--16}
}

@article{jezkova_what_2017,
	title = {What {Explains} {Patterns} of {Diversification} and {Richness} among {Animal} {Phyla}?},
	issn = {0003-0147},
	url = {http://www.journals.uchicago.edu/doi/10.1086/690194},
	doi = {10.1086/690194},
	abstract = {Animal phyla vary dramatically in species richness (from one species to {\textgreater}1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74\% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67\%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across {\textgreater}80\% of all extant, described species.},
	urldate = {2017-01-06TZ},
	journal = {The American Naturalist},
	author = {Jezkova, Tereza and Wiens, John J. and Heard, Stephen B. and Michalakis, Yannis},
	month = jan,
	year = {2017},
	pages = {000--000}
}

@article{cooper_evolution_2016,
	title = {Evolution at ‘{Sutures}’ and ‘{Centers}’: {Recombination} {Can} {Aid} {Adaptation} of {Spatially} {Structured} {Populations} on {Rugged} {Fitness} {Landscapes}},
	volume = {12},
	issn = {1553-7358},
	shorttitle = {Evolution at ‘{Sutures}’ and ‘{Centers}’},
	url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005247},
	doi = {10.1371/journal.pcbi.1005247},
	abstract = {Author Summary For a novel genotype to establish in a population, it must (1) be created, and (2) not be subsequently lost. Recombination is a double-edged sword in this process, potentially fostering creation, but also hastening loss as the novel genotype is being recombined with other genotypes, especially when rare. In this study, we find that spatial structure may affect both the creative and destructive aspects of recombination in rugged fitness landscapes. By slowing the spread of high-fitness genotypes, spatially restricted mating and dispersal may allow diverse subpopulations to arise. Reproduction across the borders of these subpopulations—at “sutures”—may create genetic novelty. Depending on the topography of the fitness landscape, such novelty may be in the domain of attraction of a new, higher peak; the population may “peak-jump” to an area of genotype space unlikely to be explored by mutation alone. Lineages founded by peak-jumping events are particularly prone to early extinction, as recombination with unlike genotypes may disrupt the rare allele combination and thereby produce low-fitness offspring. However, these fledgling peak lineages may be protected from early extinction by mating within small homotypic clusters—in “centers”. Thus, spatial structure may allow a population to create rare genotypes via recombination, and allow those rare genotypes to persist despite recombination.},
	number = {12},
	urldate = {2016-12-16TZ},
	journal = {PLOS Computational Biology},
	author = {Cooper, Jacob D. and Kerr, Benjamin},
	month = dec,
	year = {2016},
	keywords = {Alleles, Confidence intervals, DNA recombination, Evolutionary adaptation, Evolutionary genetics, Fitness epistasis, Permutation, Variant genotypes},
	pages = {e1005247}
}

@misc{noauthor_spdep_nodate,
	title = {spdep citation info},
	url = {https://cran.r-project.org/web/packages/spdep/citation.html},
	urldate = {2016-12-13TZ}
}

@article{schemske_biotic_2009,
	title = {Biotic interactions and speciation in the tropics},
	journal = {Speciation and patterns of diversity},
	author = {Schemske, DW},
	year = {2009},
	pages = {219--239}
}

@article{mittelbach_evolution_2007,
	title = {Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography},
	volume = {10},
	issn = {1461-023X, 1461-0248},
	shorttitle = {Evolution and the latitudinal diversity gradient},
	url = {http://doi.wiley.com/10.1111/j.1461-0248.2007.01020.x},
	doi = {10.1111/j.1461-0248.2007.01020.x},
	language = {en},
	number = {4},
	urldate = {2016-11-01TZ},
	journal = {Ecology Letters},
	author = {Mittelbach, Gary G. and Schemske, Douglas W. and Cornell, Howard V. and Allen, Andrew P. and Brown, Jonathan M. and Bush, Mark B. and Harrison, Susan P. and Hurlbert, Allen H. and Knowlton, Nancy and Lessios, Harilaos A. and McCain, Christy M. and McCune, Amy R. and McDade, Lucinda A. and McPeek, Mark A. and Near, Thomas J. and Price, Trevor D. and Ricklefs, Robert E. and Roy, Kaustuv and Sax, Dov F. and Schluter, Dolph and Sobel, James M. and Turelli, Michael},
	month = apr,
	year = {2007},
	pages = {315--331}
}

@article{cheney_difficulty_nodate,
	title = {On the {Difficulty} of {Co}-{Optimizing} {Morphology} and {Control} in {Evolved} {Virtual} {Creatures}},
	url = {http://www.sunspiral.org/vytas/cv/2016-alife-cheney.pdf},
	urldate = {2016-10-26TZ},
	author = {Cheney, Nick and Bongard, Josh and SunSpiral, Vytas and Lipson, Hod}
}

@article{nahum_tortoisehare_2015,
	title = {A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria},
	volume = {112},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1410631112},
	doi = {10.1073/pnas.1410631112},
	language = {en},
	number = {24},
	urldate = {2016-10-20TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Nahum, Joshua R. and Godfrey-Smith, Peter and Harding, Brittany N. and Marcus, Joseph H. and Carlson-Stevermer, Jared and Kerr, Benjamin},
	month = jun,
	year = {2015},
	pages = {7530--7535}
}

@article{dunlop_original_2009,
	title = {{ORIGINAL} {ARTICLE}: {Propensity} of marine reserves to reduce the evolutionary effects of fishing in a migratory species},
	volume = {2},
	issn = {1752-4571},
	shorttitle = {{ORIGINAL} {ARTICLE}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1752-4571.2009.00089.x/abstract},
	doi = {10.1111/j.1752-4571.2009.00089.x},
	abstract = {Evolutionary effects of fishing can have unwanted consequences diminishing a fishery’s value and sustainability. Reserves, or no-take areas, have been proposed as a management tool for reducing fisheries-induced selection, but their effectiveness for migratory species has remained unexplored. Here we develop an eco-genetic model to predict the effects of marine reserves on fisheries-induced evolution under migration. To represent a stock that undergoes an annual migration between feeding and spawning grounds, we draw model parameters from Atlantic cod (Gadus morhua) in the northern part of its range. Our analysis leads to the following conclusions: (i) a reserve in a stock’s feeding grounds, protecting immature and mature fish alike, reduces fisheries-induced evolution, even though protected and unprotected population components mix on the spawning grounds; (ii) in contrast, a reserve in a stock’s spawning grounds, protecting only mature fish, has little mitigating effects on fisheries-induced evolution and can sometimes even exacerbate its magnitude; (iii) evolutionary changes that are already underway may be difficult to reverse with a reserve; (iv) directly after a reserve is created or enlarged, most reserve scenarios result in yield losses; and (v) timescale is very important: short-term yield losses immediately after a reserve’s creation can give way to long-term gains.},
	language = {en},
	number = {3},
	urldate = {2016-09-12TZ},
	journal = {Evolutionary Applications},
	author = {Dunlop, Erin S. and Baskett, Marissa L. and Heino, Mikko and Dieckmann, Ulf},
	month = aug,
	year = {2009},
	keywords = {Atlantic cod, contemporary evolution, density-dependent growth, fisheries-induced adaptive change, marine protected area, marine reserve, migration, phenotypic plasticity},
	pages = {371--393}
}

@article{poisot_how_2016,
	title = {How ecological networks evolve},
	copyright = {© 2016, Published by Cold Spring Harbor Laboratory Press. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	url = {http://biorxiv.org/content/early/2016/08/29/071993},
	doi = {10.1101/071993},
	abstract = {Ecological networks represent the backbone of biodiversity. As species diversify over macro-evolutionary time-scales, the structure of these networks changes; this happens because species are gained and lost, and therefore add or remove interactions in their communities. The mechanisms underlying such dynamic changes in ecological network structure, however, remain poorly understood. Here we show that several types of ecological interactions share common evolutionary mechanisms that can be parametrised based on extant interaction data. In particular, we found that a model mimicking birth-death processes for species interactions describes the structure of extant networks remarkably well. Moreover, the various types of ecological interactions we considered--seed dispersal, herbivory, parasitism, bacteriophagy, and pollination--only differed in the position they occupy in the parameters' multi-dimensional space. Notably, we found no clustering of parameters values between antagonistic and mutualistic interactions. Our results provide a common modelling framework for the evolution of ecological networks that we anticipate will contribute to the greater consideration of the explicit role played by species interactions in models of macro-evolution and adaptive radiations.},
	language = {en},
	urldate = {2016-09-12TZ},
	journal = {bioRxiv},
	author = {Poisot, Timothée and Stouffer, Daniel},
	month = aug,
	year = {2016},
	pages = {071993}
}

@article{walter_diversification_2016,
	title = {Diversification across a heterogeneous landscape},
	volume = {70},
	issn = {1558-5646},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/evo.13009/abstract},
	doi = {10.1111/evo.13009},
	abstract = {Adaptation to contrasting environments across a heterogeneous landscape favors the formation of ecotypes by promoting ecological divergence. Patterns of fitness variation in the field can show whether natural selection drives local adaptation and ecotype formation. However, to demonstrate a link between ecological divergence and speciation, local adaptation must have consequences for reproductive isolation. Using contrasting ecotypes of an Australian wildflower, Senecio lautus in common garden experiments, hybridization experiments, and reciprocal transplants, we assessed how the environment shapes patterns of adaptation and the consequences of adaptive divergence for reproductive isolation. Local adaptation was strong between ecotypes, but weaker between populations of the same ecotype. F1 hybrids exhibited heterosis, but crosses involving one native parent performed better than those with two foreign parents. In a common garden experiment, F2 hybrids exhibited reduced fitness compared to parentals and F1 hybrids, suggesting that few genetic incompatibilities have accumulated between populations adapted to contrasting environments. Our results show how ecological differences across the landscape have created complex patterns of local adaptation and reproductive isolation, suggesting that divergent natural selection has played a fundamental role in the early stages of species diversification.},
	language = {en},
	number = {9},
	urldate = {2016-09-12TZ},
	journal = {Evolution},
	author = {Walter, Greg M. and Wilkinson, Melanie J. and James, Maddie E. and Richards, Thomas J. and Aguirre, J. David and Ortiz-Barrientos, Daniel},
	month = sep,
	year = {2016},
	keywords = {adaptation, divergence, diversification, genetic incompatibilities, heterogeneous landscape, natural selection},
	pages = {1979--1992}
}

@article{lurgi_effects_2016,
	title = {The effects of space and diversity of interaction types on the stability of complex ecological networks},
	volume = {9},
	issn = {1874-1738},
	doi = {10.1007/s12080-015-0264-x},
	abstract = {The relationship between structure and stability in ecological networks and the effect of spatial dynamics on natural communities have both been major foci of ecological research for decades. Network research has traditionally focused on a single interaction type at a time (e.g. food webs, mutualistic networks). Networks comprising different types of interactions have recently started to be empirically characterized. Patterns observed in these networks and their implications for stability demand for further theoretical investigations. Here, we employed a spatially explicit model to disentangle the effects of mutualism/antagonism ratios in food web dynamics and stability. We found that increasing levels of plant-animal mutualistic interactions generally resulted in more stable communities. More importantly, increasing the proportion of mutualistic vs. antagonistic interactions at the base of the food web affects different aspects of ecological stability in different directions, although never negatively. Stability is either not influenced by increasing mutualism—for the cases of population stability and species’ spatial distributions—or is positively influenced by it—for spatial aggregation of species. Additionally, we observe that the relative increase of mutualistic relationships decreases the strength of biotic interactions in general within the ecological network. Our work highlights the importance of considering several dimensions of stability simultaneously to understand the dynamics of communities comprising multiple interaction types. © 2015, Springer Science+Business Media Dordrecht.},
	language = {English},
	number = {1},
	journal = {Theoretical Ecology},
	author = {Lurgi, M. and Montoya, D. and Montoya, J.M.},
	year = {2016},
	keywords = {Cellular automata, Food web, Meta-community dynamics, Mutualistic interactions, Network structure, Population Dynamics, Predator-prey, individual-based model},
	pages = {3--13}
}

@article{strona_environmental_2016,
	title = {Environmental change makes robust ecological networks fragile},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/doifinder/10.1038/ncomms12462},
	doi = {10.1038/ncomms12462},
	urldate = {2016-09-12TZ},
	journal = {Nature Communications},
	author = {Strona, Giovanni and Lafferty, Kevin D.},
	month = aug,
	year = {2016},
	pages = {12462}
}

@article{ostrowski_ecological_2007,
	title = {Ecological {Specialization} and {Adaptive} {Decay} in {Digital} {Organisms}},
	volume = {169},
	issn = {0003-0147, 1537-5323},
	url = {http://www.journals.uchicago.edu/doi/10.1086/510211},
	doi = {10.1086/510211},
	language = {en},
	number = {1},
	urldate = {2016-09-12TZ},
	journal = {The American Naturalist},
	author = {Ostrowski, Elizabeth A. and Ofria, Charles and Lenski, Richard E.},
	month = jan,
	year = {2007},
	pages = {E1--E20}
}

@incollection{noauthor_nonconventional_2005,
	series = {Natural {Computing} {Series}},
	title = {Some {Nonconventional} {Models}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_8},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {143--155}
}

@incollection{noauthor_random_2005,
	series = {Natural {Computing} {Series}},
	title = {Random and {Irregular} {Cellular} {Populations}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_6},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {107--124}
}

@incollection{noauthor_lattice_2005,
	series = {Natural {Computing} {Series}},
	title = {Lattice {Cellular} {Models}: {Empirical} {Properties}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	shorttitle = {Lattice {Cellular} {Models}},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_5},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {85--106}
}

@incollection{noauthor_setting_2005,
	series = {Natural {Computing} {Series}},
	title = {Setting the {Stage} for {Structured} {Populations}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_1},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {1--9}
}

@inproceedings{dick_behaviour_2005,
	title = {The behaviour of genetic drift in a spatially-structured evolutionary algorithm},
	volume = {2},
	doi = {10.1109/CEC.2005.1554913},
	abstract = {Spatially-structured evolutionary algorithms (SSEAs) have allowed evolutionary search to be scaled up to increasingly larger and more difficult problems. While their use is becoming more widespread, the basic underlying theory behind them has some omissions. In particular, the effect of random genetic drift on spatial structures is largely unknown. This paper uses models derived from random walk theory to describe the behaviour of a specific class of SSEA. The match between the model and experimental findings is very good. It is the intention that this paper serves as the basis for a more abstract model of drift that encompasses all spatially-structured population models.},
	booktitle = {The 2005 {IEEE} {Congress} on {Evolutionary} {Computation}, 2005},
	author = {Dick, G. and Whigham, P.},
	month = sep,
	year = {2005},
	keywords = {Frequency, Genetic algorithms, Genetics, Information science, Mathematical model, Parallel machines, Sampling methods, Stochastic processes, Topology, evolutionary computation, genetic algorithms, genetic drift, random processes, random walk theory, spatially-structured evolutionary algorithm},
	pages = {1855--1860 Vol. 2}
}

@article{roth_spatial_1976,
	title = {Spatial {Heterogeneity} and {Bird} {Species} {Diversity}},
	volume = {57},
	copyright = {Copyright © 1976 Ecological Society of America},
	url = {http://www.jstor.org/stable/1936190},
	doi = {10.2307/1936190},
	abstract = {A heterogeneity index, D, derived from the point-quarter technique was significantly correlated with bird species diversity (BSD) for several shrub and forest areas. It predicted BSD for a series of similar brushlands where other indices had failed. Species richness increased faster than species overlap in a series of increasing complex habitats up to the forest stage. Species overlap was negatively correlated with patchiness. Additional species may be accommodated in preforest habitats primarily by horizontal spatial segregation facilitate by the presence of additional patches. New patches result from the addition of layers of vegetation. In late shrub or forest stages other kinds of segregation such as vertical segregation become important to species packing. Patchiness, as measured here, has a proximate effect on avian diversity. The extent or existence of latitudinal gradients in habitat patchiness and the effect on bird species diversity is unknown. The need remains for a universal simple, yet meaningful, heterogeneity index which incorporates both horizontal and vertical variability of vegetation.},
	number = {4},
	urldate = {2014-04-29TZ},
	journal = {Ecology},
	author = {Roth, Roland R.},
	month = jul,
	year = {1976},
	pages = {773--782}
}

@article{corriveau_review_2013,
	title = {Review of phenotypic diversity formulations for diagnostic tool},
	volume = {13},
	url = {http://www.sciencedirect.com/science/article/pii/S1568494612004036},
	number = {1},
	urldate = {2014-08-24TZ},
	journal = {Applied Soft Computing},
	author = {Corriveau, Guillaume and Guilbault, Raynald and Tahan, Antoine and Sabourin, Robert},
	year = {2013},
	pages = {9--26}
}

@article{levy_quantitative_2015,
	title = {Quantitative evolutionary dynamics using high-resolution lineage tracking},
	volume = {519},
	copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v519/n7542/abs/nature14279.html?WT.mc_id=TWT_natecolevol},
	doi = {10.1038/nature14279},
	abstract = {Evolution of large asexual cell populations underlies {\textasciitilde}30\% of deaths worldwide, including those caused by bacteria, fungi, parasites, and cancer. However, the dynamics underlying these evolutionary processes remain poorly understood because they involve many competing beneficial lineages, most of which never rise above extremely low frequencies in the population. To observe these normally hidden evolutionary dynamics, we constructed a sequencing-based ultra high-resolution lineage tracking system in Saccharomyces cerevisiae that allowed us to monitor the relative frequencies of {\textasciitilde}500,000 lineages simultaneously. In contrast to some expectations, we found that the spectrum of fitness effects of beneficial mutations is neither exponential nor monotonic. Early adaptation is a predictable consequence of this spectrum and is strikingly reproducible, but the initial small-effect mutations are soon outcompeted by rarer large-effect mutations that result in variability between replicates. These results suggest that early evolutionary dynamics may be deterministic for a period of time before stochastic effects become important.
View full text},
	language = {en},
	number = {7542},
	urldate = {2016-07-14TZ},
	journal = {Nature},
	author = {Levy, Sasha F. and Blundell, Jamie R. and Venkataram, Sandeep and Petrov, Dmitri A. and Fisher, Daniel S. and Sherlock, Gavin},
	month = mar,
	year = {2015},
	keywords = {Evolutionary theory, Experimental evolution, Genome evolution, Mutation},
	pages = {181--186}
}

@incollection{noauthor_island_2005,
	series = {Natural {Computing} {Series}},
	title = {Island {Models}: {Empirical} {Properties}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	shorttitle = {Island {Models}},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_3},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {19--51}
}

@incollection{noauthor_island_2005-1,
	series = {Natural {Computing} {Series}},
	title = {Island {Models}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_2},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {11--18}
}

@incollection{noauthor_lattice_2005-1,
	series = {Natural {Computing} {Series}},
	title = {Lattice {Cellular} {Models}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_4},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {53--84}
}

@article{channon_towards_2000,
	title = {Towards the evolutionary emergence of increasingly complex advantageous behaviours},
	volume = {31},
	url = {http://www.tandfonline.com/doi/abs/10.1080/002077200406570},
	number = {7},
	urldate = {2014-08-13TZ},
	journal = {International Journal of Systems Science},
	author = {Channon, Alastair Daniel and Damper, Robert I.},
	year = {2000},
	pages = {843--860}
}

@article{tjorve_how_2010,
	title = {How to resolve the {SLOSS} debate: {Lessons} from species-diversity models},
	volume = {264},
	issn = {0022-5193},
	shorttitle = {How to resolve the {SLOSS} debate},
	url = {http://www.sciencedirect.com/science/article/pii/S0022519310000767},
	doi = {10.1016/j.jtbi.2010.02.009},
	abstract = {The SLOSS debate – whether a single large reserve will conserve more species than several small – of the 1970s and 1980s never came to a resolution. The first rule of reserve design states that one large reserve will conserve the most species, a rule which has been heavily contested. Empirical data seem to undermine the reliance on general rules, indicating that the best strategy varies from case to case. Modeling has also been deployed in this debate. We may divide the modeling approaches to the SLOSS enigma into dynamic and static approaches. Dynamic approaches, covered by the fields of island equilibrium theory of island biogeography and metapopulation theory, look at immigration, emigration, and extinction. Static approaches, such as the one in this paper, illustrate how several factors affect the number of reserves that will save the most species.

This article approaches the effect of different factors by the application of species-diversity models. These models combine species–area curves for two or more reserves, correcting for the species overlap between them. Such models generate several predictions on how different factors affect the optimal number of reserves. The main predictions are: Fewer and larger reserves are favored by increased species overlap between reserves, by faster growth in number of species with reserve area increase, by higher minimum-area requirements, by spatial aggregation and by uneven species abundances. The effect of increased distance between smaller reserves depends on the two counteracting factors: decreased species density caused by isolation (which enhances minimum-area effect) and decreased overlap between isolates. The first decreases the optimal number of reserves; the second increases the optimal number. The effect of total reserve-system area depends both on the shape of the species–area curve and on whether overlap between reserves changes with scale.

The approach to modeling presented here has several implications for conservational strategies. It illustrates well how the SLOSS enigma can be reduced to a question of the shape of the species–area curve that is expected or generated from reserves of different sizes and a question of overlap between isolates (or reserves).},
	number = {2},
	urldate = {2015-05-12TZ},
	journal = {Journal of Theoretical Biology},
	author = {Tjorve, Even},
	month = may,
	year = {2010},
	keywords = {Minimum-area requirements, Reserve design, Species extinction, Species overlap, Species–area relationship},
	pages = {604--612}
}

@article{farkas_how_nodate,
	title = {How maladaptation can structure biodiversity: eco-evolutionary island biogeography},
	volume = {0},
	issn = {0169-5347},
	shorttitle = {How maladaptation can structure biodiversity},
	url = {http://www.cell.com/article/S016953471500004X/abstract},
	doi = {10.1016/j.tree.2015.01.002},
	abstract = {Current research on eco-evolutionary dynamics is mainly concerned with understanding the role of rapid (or ‘contemporary’) evolution in structuring ecological patterns. We argue that the current eco-evolutionary research program, which focuses largely on natural selection, should be expanded to more explicitly consider other evolutionary processes such as gene flow. Because multiple evolutionary processes interact to generate quantitative variation in the degree of local maladaptation, we focus on how studying the ecological effects of maladaptation will lead to a more comprehensive view of how evolution can influence ecology. We explore how maladaptation can influence ecology through the lens of island biogeography theory, which yields some novel predictions, such as patch isolation increasing species richness.},
	language = {English},
	number = {0},
	urldate = {2015-02-09TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Farkas, Timothy E. and Hendry, Andrew P. and Nosil, Patrik and Beckerman, Andrew P.},
	keywords = {biodiversity, eco-evolutionary dynamics, gene flow, island biogeography, maladaptation, species interactions}
}

@article{petchey_functional_2006,
	title = {Functional diversity: back to basics and looking forward},
	volume = {9},
	issn = {1461-023X, 1461-0248},
	shorttitle = {Functional diversity},
	url = {http://doi.wiley.com/10.1111/j.1461-0248.2006.00924.x},
	doi = {10.1111/j.1461-0248.2006.00924.x},
	language = {en},
	number = {6},
	urldate = {2014-08-13TZ},
	journal = {Ecology Letters},
	author = {Petchey, Owen L. and Gaston, Kevin J.},
	month = jun,
	year = {2006},
	keywords = {Context dependence, ecosystems, functional classification, indirect use value, phenetics, redundancy, species, species richness, traits},
	pages = {741--758}
}

@inproceedings{intelligent_systems_group_department_of_computer_science_university_of_bath_bath_ba1_7ay_u.k._evolving_2014,
	title = {Evolving {Evolvability} in the {Context} of {Environmental} {Change}: {A} {Gene} {Regulatory} {Network} ({GRN}) {Approach}},
	isbn = {978-0-262-32621-6},
	shorttitle = {Evolving {Evolvability} in the {Context} of {Environmental} {Change}},
	url = {http://opus.bath.ac.uk/40017/},
	doi = {10.7551/978-0-262-32621-6-ch010},
	urldate = {2014-10-08TZ},
	publisher = {The MIT Press},
	author = {{Intelligent Systems Group, Department of Computer Science, University of Bath, Bath, BA1 7AY, U.K.} and Wang, Yifei and Bryson, Joanna and Matthews, Stephen},
	month = jul,
	year = {2014},
	pages = {47--53}
}

@article{mace_evolutionary_2008,
	title = {Evolutionary biology and practical conservation: bridging a widening gap},
	volume = {17},
	issn = {1365-294X},
	shorttitle = {Evolutionary biology and practical conservation},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2007.03455.x/abstract},
	doi = {10.1111/j.1365-294X.2007.03455.x},
	abstract = {At the ecosystem, species and population level, available measures suggest that average rates of loss of populations and habitats are now around 1\% per year and seem likely to increase in the future. Habitat conversion continues in most parts of the world, especially in areas of high species richness, and novel threats, especially climate change, will pose new challenges. With this pressure, maintaining evolutionary processes in natural populations will be critical to longer term persistence, and will often require specific planning relevant to the context. However, in many areas of policy and practice, urgent actions tend to focus on pattern-based analyses and considerations of evolutionary and ecological processes are neglected. At a variety of levels, from setting goals to implementing conservation management at the site or species level, there are simple adjustments that can be made. Improved methods for integrating the work of scientists and policymakers is recommended, from the beginning to end of the planning process.},
	language = {en},
	number = {1},
	urldate = {2015-12-10TZ},
	journal = {Molecular Ecology},
	author = {Mace, Georgina M. and Purvis, Andy},
	month = jan,
	year = {2008},
	keywords = {biodiversity goals, conservation planning, evolution, policy},
	pages = {9--19}
}

@inproceedings{goings_ecological_2009,
	title = {Ecological approaches to diversity maintenance in evolutionary algorithms},
	doi = {10.1109/ALIFE.2009.4937703},
	abstract = {Evolutionary algorithms have shown great promise in evolving novel solutions to real-world problems, but the complexity of those solutions is limited, unlike the apparently open-ended evolution that occurs in the natural world. In part, nature surmounts these complexity barriers with natural ecological dynamics that generate an incredibly diverse array of raw materials for the evolutionary process to build upon, the efficacy of which has been demonstrated in the artificial life system Avida [1]. Here, we introduce a method to integrate ecological factors promoting diversity into an EA using limited resources. We show that populations evolving with this method are able to find and cover multiple niches in a simple string-matching problem, and we analyze the conditions that lead to specialists vs. generalists in this environment. These concepts lay a groundwork for building a more comprehensive ecology-based evolutionary algorithm able to achieve higher levels of complexity.},
	booktitle = {{IEEE} {Symposium} on {Artificial} {Life}, 2009. {ALife} '09},
	author = {Goings, S. and Ofria, C.},
	month = mar,
	year = {2009},
	keywords = {Computer Science, Ecology, Evolution (biology), Evolutionary algorithms, Frequency diversity, Organisms, Pareto optimization, Rain, Raw materials, Robustness, biodiversity, diversity maintenance, ecological factors, evolutionary algorithms, evolutionary computation, string matching, string-matching problem},
	pages = {124--130}
}
@incollection{ursem_diversity-guided_2002,
	title = {Diversity-guided evolutionary algorithms},
	url = {http://link.springer.com/chapter/10.1007/3-540-45712-7_45},
	urldate = {2014-08-24TZ},
	booktitle = {Parallel {Problem} {Solving} from {Nature}—{PPSN} {VII}},
	publisher = {Springer},
	author = {Ursem, Rasmus K.},
	year = {2002},
	pages = {462--471}
}

@incollection{green_digital_2006,
	series = {Landscape {Series}},
	title = {{DIGITAL} {ECOLOGY}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_10},
	abstract = {Late in the 1990s, Nick Klomp was studying short-tailed shearwaters, one of the most common bird species along Australia’s eastern coastline. During the breeding season, the shearwaters build their nests on off-shore islands. While one parent tends the nest, the other flies out to sea in search of food. A crucial question in Klomp’s research was how the bird populations interacted with the marine species they feed on. He used a combination of tracking satellites and small transponders attached to the birds to track where they flew within their nesting territories. To everyone’s surprise, data returned by the new technology showed that instead of making short sorties close to their nests, the shearwaters undertake long migrations (Klomp et al. 1997; Klomp and Schultz 2000). They travel several thousand kilometres to and from Antarctica each year during the southern hemisphere summer (Figure 10-1). Klomp’s discovery had many implications, not only about the ecology of shearwaters, but also about species interactions and food webs in Antarctic waters.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {151--168}
}

@incollection{noauthor_coevolutionary_2005,
	series = {Natural {Computing} {Series}},
	title = {Coevolutionary {Structured} {Models}},
	copyright = {©2005 Springer-Verlag},
	isbn = {978-3-540-24193-5 978-3-540-29938-7},
	url = {http://link.springer.com/chapter/10.1007/3-540-29938-6_7},
	urldate = {2014-04-30TZ},
	booktitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	publisher = {Springer Berlin Heidelberg},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Discrete Mathematics in Computer Science, Numeric Computing, Programming Techniques, Theory of Computation},
	pages = {125--142}
}

@inproceedings{adaptive_systems_research_group_university_of_hertfordshire_hatfield_uk_informational_2014,
	title = {An {Informational} {Study} of the {Evolution} of {Codes} in {Different} {Population} {Structures}},
	isbn = {978-0-262-32621-6},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch056.pdf},
	doi = {10.7551/978-0-262-32621-6-ch056},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Adaptive Systems Research Group, University of Hertfordshire, Hatfield, UK} and Burgos, Andrés and Polani, Daniel},
	month = jul,
	year = {2014},
	pages = {352--359}
}

@article{ribeck_competition_2016,
	title = {Competition between continuously evolving lineages in asexual populations},
	copyright = {© 2016, Published by Cold Spring Harbor Laboratory Press. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
	url = {http://biorxiv.org/content/early/2016/07/10/062976},
	doi = {10.1101/062976},
	abstract = {In an asexual population, the fate of a beneficial mutation depends on how its lineage competes against other mutant lineages in the population. With high beneficial mutation rates or large population sizes, competition between contending mutations is strong, and successful lineages can accumulate multiple mutations before any single one achieves fixation. Most current theory about asexual population dynamics either neglects this multiple-mutations regime or introduces simplifying assumptions that may not apply. Here, we develop a theoretical framework that describes the dynamics of adaptation and substitution over all mutation-rate regimes by conceptualizing the population as a collection of continuously adapting lineages. This model of “lineage interference” shows that each new mutant’s advantage over the rest of the population must be above a critical threshold in order to likely achieve fixation, and we derive a simple expression for that threshold. We apply this framework to examine the role of beneficial mutations with different effect sizes across the transition to the multiple-mutations regime.},
	language = {en},
	urldate = {2016-08-04TZ},
	journal = {bioRxiv},
	author = {Ribeck, Noah and Mulka, Joseph S. and Zaman, Luis and Connelly, Brian D. and Lenski, Richard E.},
	month = jul,
	year = {2016},
	pages = {062976}
}

@article{hamilton_population_2007,
	title = {Population genetic consequences of geographic disjunction: a prairie plant isolated on {Great} {Lakes} alvars},
	volume = {16},
	issn = {1365-294X},
	shorttitle = {Population genetic consequences of geographic disjunction},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2007.03241.x/abstract},
	doi = {10.1111/j.1365-294X.2007.03241.x},
	abstract = {Species may often exhibit geographic variation in population genetic structure due to contemporary and historical variation in population size and gene flow. Here, we test the predictions that populations on the margins of a species’ distribution contain less genetic variation and are more differentiated than populations towards the core of the range by comparing patterns of genetic variation at five microsatellite loci between disjunct and core populations of the perennial, allohexaploid herb Geum triflorum. We sampled nine populations isolated on alvar habitat within the eastern Great Lakes region in North America, habitats that include disjunct populations of several plant species, and compared these to 16 populations sampled from prairie habitat throughout the core of the species’ distribution in midwestern Canada and the USA. Alvar populations exhibited much lower within-population diversity and contained only a subset of alleles found in prairie populations. We detected isolation by distance across the species’ range and within alvar and prairie regions separately. As predicted, genetic differentiation was higher among alvar populations than among prairie populations, even after controlling for the geographic distance between sampled populations. Low diversity and high differentiation can be accounted for by the greater contemporary spatial isolation of alvar populations. However, the genetic structure of alvar populations may also have been influenced by postglacial range expansion and contraction. Our results are consistent with alvar populations being founded during an expansion of prairie habitat during the warmer, hypsithermal period ∼5000 bp and subsequently becoming stranded on isolated alvar habitat as the climate grew cooler and wetter.},
	language = {en},
	number = {8},
	urldate = {2016-07-22TZ},
	journal = {Molecular Ecology},
	author = {Hamilton, J. A. and Eckert, C. G.},
	month = apr,
	year = {2007},
	keywords = {alvar, conservation, disjunct populations, genetic differentiation, genetic diversity, polyploidy},
	pages = {1649--1660}
}

@misc{noauthor_proceedings_nodate,
	title = {Proceedings of the {Artificial} {Life} {Conference} 2016},
	url = {https://mitpress.mit.edu/books/proceedings-artificial-life-conference-2016},
	urldate = {2016-07-16TZ},
	journal = {MIT Press}
}

@article{steinberg_environmental_2016,
	title = {Environmental changes bridge evolutionary valleys},
	volume = {2},
	copyright = {Copyright © 2016, The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.},
	issn = {2375-2548},
	url = {http://advances.sciencemag.org/content/2/1/e1500921},
	doi = {10.1126/sciadv.1500921},
	abstract = {In the basic fitness landscape metaphor for molecular evolution, evolutionary pathways are presumed to follow uphill steps of increasing fitness. How evolution can cross fitness valleys is an open question. One possibility is that environmental changes alter the fitness landscape such that low-fitness sequences reside on a hill in alternate environments. We experimentally test this hypothesis on the antibiotic resistance gene TEM-15 β-lactamase by comparing four evolutionary strategies shaped by environmental changes. The strategy that included initial steps of selecting for low antibiotic resistance (negative selection) produced superior alleles compared with the other three strategies. We comprehensively examined possible evolutionary pathways leading to one such high-fitness allele and found that an initially deleterious mutation is key to the allele’s evolutionary history. This mutation is an initial gateway to an otherwise relatively inaccessible area of sequence space and participates in higher-order, positive epistasis with a number of neutral to slightly beneficial mutations. The ability of negative selection and environmental changes to provide access to novel fitness peaks has important implications for natural evolutionary mechanisms and applied directed evolution.
Epistatic interactions and changes in the selection environment facilitate the experimental evolution of β-lactamase.
Epistatic interactions and changes in the selection environment facilitate the experimental evolution of β-lactamase.},
	language = {en},
	number = {1},
	urldate = {2016-07-03TZ},
	journal = {Science Advances},
	author = {Steinberg, Barrett and Ostermeier, Marc},
	month = jan,
	year = {2016},
	pages = {e1500921}
}

@inproceedings{cantu-paz_topologies_1999,
	address = {San Francisco, CA, USA},
	series = {{GECCO}'99},
	title = {Topologies, {Migration} {Rates}, and {Multi}-population {Parallel} {Genetic} {Algorithms}},
	isbn = {9781558606111},
	url = {http://dl.acm.org/citation.cfm?id=2933923.2933933},
	abstract = {This paper presents a study of parallel genetic algorithms (GAs) with multiple populations (also called demes or islands). The study makes explicit the relation between the probability of reaching a desired solution with the deme size, the migration rate, and the degree of the connectivity graph. The paper considers arbitrary topologies with a fixed number of neighbors per deme. The demes evolve in isolation until each converges to a unique solution. Then, the demes exchange an arbitrary number of individuals and restart their execution. An accurate deme-sizing equation is derived, and it is used to determine the optimal configuration of an arbitrary number of demes that minimizes the execution time of the parallel GA.},
	urldate = {2016-05-22TZ},
	booktitle = {Proceedings of the 1st {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation} - {Volume} 1},
	publisher = {Morgan Kaufmann Publishers Inc.},
	author = {Cantú-Paz, Erick},
	year = {1999},
	pages = {91--98}
}

@article{hume_ancestral_2016,
	title = {Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to {Holocene} climate change},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/113/16/4416},
	doi = {10.1073/pnas.1601910113},
	abstract = {Coral communities in the Persian/Arabian Gulf (PAG) withstand unusually high salinity levels and regular summer temperature maxima of up to ∼35 °C that kill conspecifics elsewhere. Due to the recent formation of the PAG and its subsequent shift to a hot climate, these corals have had only {\textless}6,000 y to adapt to these extreme conditions and can therefore inform on how coral reefs may respond to global warming. One key to coral survival in the world’s warmest reefs are symbioses with a newly discovered alga, Symbiodinium thermophilum. Currently, it is unknown whether this symbiont originated elsewhere or emerged from unexpectedly fast evolution catalyzed by the extreme environment. Analyzing genetic diversity of symbiotic algae across {\textgreater}5,000 km of the PAG, the Gulf of Oman, and the Red Sea coastline, we show that S. thermophilum is a member of a highly diverse, ancient group of symbionts cryptically distributed outside the PAG. We argue that the adjustment to temperature extremes by PAG corals was facilitated by the positive selection of preadapted symbionts. Our findings suggest that maintaining the largest possible pool of potentially stress-tolerant genotypes by protecting existing biodiversity is crucial to promote rapid adaptation to present-day climate change, not only for coral reefs, but for ecosystems in general.},
	language = {en},
	number = {16},
	urldate = {2016-05-05TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Hume, Benjamin C. C. and Voolstra, Christian R. and Arif, Chatchanit and D’Angelo, Cecilia and Burt, John A. and Eyal, Gal and Loya, Yossi and Wiedenmann, Jörg},
	month = apr,
	year = {2016},
	pmid = {27044109},
	keywords = {Persian/Arabian Gulf, Symbiodinium, adaptation, climate change, coral},
	pages = {4416--4421}
}

@article{walsh_invasive_2016,
	title = {Invasive species triggers a massive loss of ecosystem services through a trophic cascade},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/113/15/4081},
	doi = {10.1073/pnas.1600366113},
	abstract = {Despite growing recognition of the importance of ecosystem services and the economic and ecological harm caused by invasive species, linkages between invasions, changes in ecosystem functioning, and in turn, provisioning of ecosystem services remain poorly documented and poorly understood. We evaluate the economic impacts of an invasion that cascaded through a food web to cause substantial declines in water clarity, a valued ecosystem service. The predatory zooplankton, the spiny water flea (Bythotrephes longimanus), invaded the Laurentian Great Lakes in the 1980s and has subsequently undergone secondary spread to inland lakes, including Lake Mendota (Wisconsin), in 2009. In Lake Mendota, Bythotrephes has reached unparalleled densities compared with in other lakes, decreasing biomass of the grazer Daphnia pulicaria and causing a decline in water clarity of nearly 1 m. Time series modeling revealed that the loss in water clarity, valued at US\$140 million (US\$640 per household), could be reversed by a 71\% reduction in phosphorus loading. A phosphorus reduction of this magnitude is estimated to cost between US\$86.5 million and US\$163 million (US\$430–US\$810 per household). Estimates of the economic effects of Great Lakes invasive species may increase considerably if cases of secondary invasions into inland lakes, such as Lake Mendota, are included. Furthermore, such extreme cases of economic damages call for increased investment in the prevention and control of invasive species to better maximize the economic benefits of such programs. Our results highlight the need to more fully incorporate ecosystem services into our analysis of invasive species impacts, management, and public policy.},
	language = {en},
	number = {15},
	urldate = {2016-05-05TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Walsh, Jake R. and Carpenter, Stephen R. and Zanden, M. Jake Vander},
	month = apr,
	year = {2016},
	pmid = {27001838},
	keywords = {Bythotrephes, Daphnia, ecosystem service, eutrophication, invasive species},
	pages = {4081--4085}
}

@article{rodriguez-quilon_capturing_2016,
	title = {Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species},
	issn = {1939-5582},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/eap.1361/abstract},
	doi = {10.1002/eap.1361},
	abstract = {Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation - at both neutral molecular markers and quantitative traits - to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 Single Nucleotide Polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control and plasticity were assessed in a multisite clonal common garden experiment (16,544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post-hoc trait distribution comparisons allowed us to define ten genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. This article is protected by copyright. All rights reserved.},
	language = {en},
	urldate = {2016-05-05TZ},
	journal = {Ecological Applications},
	author = {Rodríguez-Quilón, Isabel and Santos-del-Blanco, Luis and Serra-Varela, Mª Jesús and Koskela, Jarkko and González-Martínez, Santiago C. and Alía, Ricardo},
	month = apr,
	year = {2016},
	keywords = {Pinus pinaster, SNPs, conservation genetics, dynamic conservation, microsatellites, phenotypic plasticity, quantitative genetic differentiation},
	pages = {n/a--n/a}
}

@misc{noauthor_small_nodate,
	title = {Small but not forgotten: {New} ideas on pollen's ecology and evolution},
	shorttitle = {Small but not forgotten},
	url = {http://www.eurekalert.org/pub_releases/2016-04/bsoa-sbn040416.php},
	abstract = {Although many only turn their thoughts to pollen as allergy season approaches, a new American Journal of Botany Special Issue shows that a diverse array of researchers are actively pursuing research in pollen performance. The collection of papers gathers together diverse perspectives on pollen performance and lays out clear examples of how to test these ideas. Representing a broad range of taxa and approaches to studying pollen performance, this Special Issue is likely to ignite renewed interest in pollen performance.},
	urldate = {2016-04-13TZ},
	journal = {EurekAlert!}
}

@misc{noauthor_sign_nodate,
	title = {Sign {In}},
	url = {http://www.pnas.org/content/112/51/15636.full.pdf},
	urldate = {2016-04-13TZ},
	pmid = {26644569}
}

@article{coyte_ecology_2015,
	title = {The ecology of the microbiome: {Networks}, competition, and stability},
	volume = {350},
	copyright = {Copyright © 2015, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	shorttitle = {The ecology of the microbiome},
	url = {http://science.sciencemag.org/content/350/6261/663},
	doi = {10.1126/science.aad2602},
	abstract = {What makes the gut microbiome stable?
Classically, we think of our microbiome as stable, benign, and cooperative. Recent experimental work is beginning to unpick essential functions that can be attributed to the stable microbiota of humans. To be able to manipulate the microbiome to improve health, we need to understand community structure and composition and we need models to quantify and predict stability. Coyte et al. applied concepts and tools from community ecology to gut microbiome assembly. Independently developed models converged on a surprising answer: A high diversity of species is likely to coexist stably when the system is dominated by competitive, rather than cooperative, interactions.
Science, this issue p. 663
The human gut harbors a large and complex community of beneficial microbes that remain stable over long periods. This stability is considered critical for good health but is poorly understood. Here we develop a body of ecological theory to help us understand microbiome stability. Although cooperating networks of microbes can be efficient, we find that they are often unstable. Counterintuitively, this finding indicates that hosts can benefit from microbial competition when this competition dampens cooperative networks and increases stability. More generally, stability is promoted by limiting positive feedbacks and weakening ecological interactions. We have analyzed host mechanisms for maintaining stability—including immune suppression, spatial structuring, and feeding of community members—and support our key predictions with recent data.
Diversity and competition are more likely than cooperation to lead to gut microbial community stability.
Diversity and competition are more likely than cooperation to lead to gut microbial community stability.},
	language = {en},
	number = {6261},
	urldate = {2016-04-13TZ},
	journal = {Science},
	author = {Coyte, Katharine Z. and Schluter, Jonas and Foster, Kevin R.},
	month = nov,
	year = {2015},
	pmid = {26542567},
	pages = {663--666}
}

@article{crowley_evolving_1996,
	title = {Evolving cooperation: the role of individual recognition},
	volume = {37},
	issn = {0303-2647},
	shorttitle = {Evolving cooperation},
	url = {http://www.sciencedirect.com/science/article/pii/0303264795015469},
	doi = {10.1016/0303-2647(95)01546-9},
	abstract = {To evaluate the role of individual recognition in the evolution of cooperation, we formulated and analyzed a genetic algorithm model (EvCo) for playing the Iterated Prisoner's Dilemma (IPD) game. Strategies compete against each other during each generation, and successful strategies contribute more of their attributes to the next generation. Each strategy is encoded on a ‘chromosome’ that plays the IPD, responding to the sequences of most recent responses by the interacting individuals (chromosomes). The analysis reported in this paper considered different memory capabilities (one to five previous interactions), pairing continuities (pairs of individuals remain together for about one, two, five, or 1000 consecutive interactions), and types of individual recognition (recognition capability was maximal, nil, or allowed to evolve between these limits). Analysis of the results focused on the frequency of mutual cooperation in pairwise interactions (a good indicator of overall success in the IPD) and on the extent to which previous responses by the focal individual and its partner were associated with the partner's identity (individual recognition). Results indicated that a fixed, substantial amount of individual recognition could maintain high levels of mutual cooperation even at low pairing continuities, and a significant but limited capability for individual recognition evolved under selection. Recognition generally increased mutual cooperation more when the recent responses of individuals other than the current partner were ignored. Titrating recognition memory under selection using a fitness cost suggested that memory of the partner's previous responses was more valuable than memory of the focal's previous responses. The dynamics produced to date by EvCo are a step toward understanding the evolution of social networks, for which additional benefits associated with group interactions must be incorporated.},
	number = {1–2},
	urldate = {2016-04-07TZ},
	journal = {Biosystems},
	author = {Crowley, Philip H. and Provencher, Louis and Sloane, Sarah and Dugatkin, Lee Alan and Spohn, Bryan and Rogers, Lock and Alfieri, Michael},
	year = {1996},
	keywords = {Game theory, Genetic algorithms, Individual recognition, Iterated Prisoner's Dilemma, Reciprocal altruism},
	pages = {49--66}
}

@article{turcotte_impact_2011,
	title = {The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics},
	volume = {14},
	issn = {1461-0248},
	shorttitle = {The impact of rapid evolution on population dynamics in the wild},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2011.01676.x/abstract},
	doi = {10.1111/j.1461-0248.2011.01676.x},
	abstract = {Ecology Letters (2011) 14: 1084–1092 
Abstract
Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of ‘Eco-Evolutionary Dynamics’ or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42\% faster and attained up to 67\% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density.},
	language = {en},
	number = {11},
	urldate = {2016-04-06TZ},
	journal = {Ecology Letters},
	author = {Turcotte, Martin M. and Reznick, David N. and Hare, J. Daniel},
	month = nov,
	year = {2011},
	keywords = {Aphid dynamics, Experimental evolution, brassica pest, clonal selection, contemporary evolution, eco-evolutionary feedback, ecological genetics, evolution enlightened management, population growth rate},
	pages = {1084--1092}
}

@article{fountain_predictable_2016,
	title = {Predictable allele frequency changes due to habitat fragmentation in the {Glanville} fritillary butterfly},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/113/10/2678},
	doi = {10.1073/pnas.1600951113},
	abstract = {Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.},
	language = {en},
	number = {10},
	urldate = {2016-03-23TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Fountain, Toby and Nieminen, Marko and Sirén, Jukka and Wong, Swee Chong and Hanski, Ilkka},
	month = mar,
	year = {2016},
	pmid = {26903642},
	keywords = {adaptive genetic response, contemporary evolution, evolution of dispersal, global change, historical DNA samples},
	pages = {2678--2683}
}

@article{zaman_coevolution_2014,
	title = {Coevolution drives the emergence of complex traits and promotes evolvability},
	volume = {12},
	url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002023},
	number = {12},
	urldate = {2016-03-14TZ},
	journal = {PLoS Biol},
	author = {Zaman, Luis and Meyer, Justin R. and Devangam, Suhas and Bryson, David M. and Lenski, Richard E. and Ofria, Charles},
	year = {2014},
	pages = {e1002023}
}

@article{goldsby_evolution_2012,
	title = {The evolution of temporal polyethism},
	volume = {13},
	url = {https://mitp-web2.mit.edu/sites/default/files/titles/content/alife13/978-0-262-31050-5-ch025.pdf},
	urldate = {2016-03-14TZ},
	journal = {Artificial Life},
	author = {Goldsby, Heather J. and Serra, Neem and Dyer, Fred and Kerr, Benjamin and Ofria, Charles},
	year = {2012},
	pages = {178--185}
}

@article{hassan_ecosystems_2005,
	title = {Ecosystems and human well-being: current state and trends: findings of the {Condition} and {Trends} {Working} {Group}.},
	shorttitle = {Ecosystems and human well-being},
	url = {http://www.sidalc.net/cgi-bin/wxis.exe/?IsisScript=CIMMYT.xis&method=post&formato=2&cantidad=1&expresion=mfn=040256},
	urldate = {2015-12-10TZ},
	journal = {Millennium Ecosystem Assessment},
	author = {Hassan, R. and Scholes, R. and Ash, N.},
	year = {2005}
}

@article{lakens_calculating_2013,
	title = {Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and {ANOVAs}},
	volume = {4},
	issn = {1664-1078},
	shorttitle = {Calculating and reporting effect sizes to facilitate cumulative science},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840331/},
	doi = {10.3389/fpsyg.2013.00863},
	abstract = {Effect sizes are the most important outcome of empirical studies. Most articles on effect sizes highlight their importance to communicate the practical significance of results. For scientists themselves, effect sizes are most useful because they facilitate cumulative science. Effect sizes can be used to determine the sample size for follow-up studies, or examining effects across studies. This article aims to provide a practical primer on how to calculate and report effect sizes for t-tests and ANOVA's such that effect sizes can be used in a-priori power analyses and meta-analyses. Whereas many articles about effect sizes focus on between-subjects designs and address within-subjects designs only briefly, I provide a detailed overview of the similarities and differences between within- and between-subjects designs. I suggest that some research questions in experimental psychology examine inherently intra-individual effects, which makes effect sizes that incorporate the correlation between measures the best summary of the results. Finally, a supplementary spreadsheet is provided to make it as easy as possible for researchers to incorporate effect size calculations into their workflow.},
	urldate = {2016-02-27TZ},
	journal = {Frontiers in Psychology},
	author = {Lakens, Daniël},
	month = nov,
	year = {2013},
	pmid = {24324449},
	pmcid = {PMC3840331},
	pages = {863}
}

@book{gaston_biodiversity:_2004,
	address = {Malden, Mass.},
	title = {Biodiversity: an introduction},
	isbn = {1405118571  9781405118576  1444312324  9781444312324  9786612371127 6612371129},
	shorttitle = {Biodiversity},
	url = {http://site.ebrary.com/lib/alltitles/docDetail.action?docID=10308466},
	language = {English},
	urldate = {2014-08-13TZ},
	publisher = {Blackwell Publishing},
	author = {Gaston, Kevin J and Spicer, John I},
	year = {2004}
}

@article{bates_fitting_2015,
	title = {Fitting {Linear} {Mixed}-{Effects} {Models} {Using} lme4},
	volume = {67},
	doi = {10.18637/jss.v067.i01},
	number = {1},
	journal = {Journal of Statistical Software},
	author = {Bates, Douglas and Machler, Martin and Bolker, Ben and Walker, Steve},
	year = {2015},
	pages = {1--48}
}

@article{sgro_building_2011,
	title = {Building evolutionary resilience for conserving biodiversity under climate change},
	volume = {4},
	copyright = {© 2010 Blackwell Publishing Ltd},
	issn = {1752-4571},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1752-4571.2010.00157.x/abstract},
	doi = {10.1111/j.1752-4571.2010.00157.x},
	abstract = {Evolution occurs rapidly and is an ongoing process in our environments. Evolutionary principles need to be built into conservation efforts, particularly given the stressful conditions organisms are increasingly likely to experience because of climate change and ongoing habitat fragmentation. The concept of evolutionary resilience is a way of emphasizing evolutionary processes in conservation and landscape planning. From an evolutionary perspective, landscapes need to allow in situ selection and capture high levels of genetic variation essential for responding to the direct and indirect effects of climate change. We summarize ideas that need to be considered in planning for evolutionary resilience and suggest how they might be incorporated into policy and management to ensure that resilience is maintained in the face of environmental degradation.},
	language = {en},
	number = {2},
	urldate = {2016-02-09TZ},
	journal = {Evolutionary Applications},
	author = {Sgro, Carla M. and Lowe, Andrew J. and Hoffmann, Ary A.},
	month = mar,
	year = {2011},
	keywords = {adaptive potential, biodiversity, climate change, conservation, evolution, evolutionary resilience, genetic diversity},
	pages = {326--337}
}

@article{biswas_genomic_2006,
	title = {Genomic insights into positive selection},
	volume = {22},
	issn = {0168-9525},
	url = {http://www.cell.com/article/S0168952506001739/abstract},
	doi = {10.1016/j.tig.2006.06.005},
	abstract = {The traditional way of identifying targets of adaptive evolution has been to study a few loci that one hypothesizes a priori to have been under selection. This approach is complicated because of the confounding effects that population demographic history and selection have on patterns of DNA sequence variation. In principle, multilocus analyses can facilitate robust inferences of selection at individual loci. The deluge of large-scale catalogs of genetic variation has stimulated many genome-wide scans for positive selection in several species. Here, we review some of the salient observations of these studies, identify important challenges ahead, consider the limitations of genome-wide scans for selection and discuss the potential significance of a comprehensive understanding of genomic patterns of selection for disease-related research.},
	language = {English},
	number = {8},
	urldate = {2016-03-01TZ},
	journal = {Trends in Genetics},
	author = {Biswas, Shameek and Akey, Joshua M.},
	month = aug,
	year = {2006},
	pmid = {16808986},
	pages = {437--446}
}

@article{stockwell_contemporary_2003,
	title = {Contemporary evolution meets conservation biology},
	volume = {18},
	issn = {0169-5347},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534702000447},
	doi = {10.1016/S0169-5347(02)00044-7},
	abstract = {Recent research has revealed that evolution often occurs on contemporary timescales, often within decades. Contemporary evolution is associated with the same factors that are driving the current extinction crisis: habitat loss and degradation, overharvesting and exotic species. Thus, it is relevant to many conservation situations. First, habitat fragmentation might influence the potential of a population to adapt in response environmental degradation. Second, certain harvesting strategies can result in the evolution of life-history traits, ultimately resulting in negative impacts on harvestable yield. Third, the establishment of exotic species can be influenced by their adaptive potential and our ability to limit that potential. Furthermore, contemporary evolution is of concern for intensively managed species, because it might reduce their fitness in native habitats. Ultimately, contemporary evolution is influenced by complex interactions among population size, genetic variation, the strength of selection, and gene flow, making most management scenarios unique. In a world filled with contemporary evolution, conservation efforts that ignore its implications will be less efficient and perhaps even risk prone.},
	number = {2},
	urldate = {2016-03-01TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Stockwell, Craig A. and Hendry, Andrew P. and Kinnison, Michael T.},
	month = feb,
	year = {2003},
	pages = {94--101}
}

@article{kunin_sample_1997,
	title = {Sample shape, spatial scale and species counts: {Implications} for reserve design},
	volume = {82},
	issn = {0006-3207},
	shorttitle = {Sample shape, spatial scale and species counts},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320797000426},
	doi = {10.1016/S0006-3207(97)00042-6},
	abstract = {The optimal design of nature reserves has been a hotly debated topic for some years. One contentious issue has concerned the ideal shape of reserves, with several researchers suggesting that reserves should be as nearly circular as possible to minimize edge-related degredation and potential ‘peninsularity’ effects. This paper demonstrates an advantage to non-circular reserves: given the spatial autocorrelation of environmental conditions and species ranges, elongated samples should tend to capture a greater diversity of conditions and, consequently, a greater number of species. To test this idea, samples of 16 cells, arranged as 4 × 4 squares, 2 × 8 rectangles and 1 × 16 lines were considered in mapped plant distributions at spatial scales ranging from cells of 1 m2 to 2500 km2. Overall, elongated samples tended to capture significantly larger numbers of species than did their square counterparts, as predicted. The degree of elongated sample advantage was very similar at all but the smallest of the scales considered, suggesting that the pattern of species turnover (β-diversity) is nearly scale-independent or fractal in nature. As the advantages of elongation are largely scale-independent and the only documented disadvantages (edge effects) are very scale-dependent, the optimal shape of a reserve for species sampling should shift as a function of reserve size, with large reserves becoming increasingly elongated.},
	number = {3},
	urldate = {2016-03-01TZ},
	journal = {Biological Conservation},
	author = {Kunin, William E.},
	month = dec,
	year = {1997},
	keywords = {SLOSS, nature reserves, shape effects, spatial autocorrelation, species richness, β-diversity},
	pages = {369--377}
}

@article{tjorve_habitat_2002,
	title = {Habitat size and number in multi-habitat landscapes: a model approach based on species-area curves},
	volume = {25},
	issn = {1600-0587},
	shorttitle = {Habitat size and number in multi-habitat landscapes},
	url = {http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0587.2002.250103.x/abstract},
	doi = {10.1034/j.1600-0587.2002.250103.x},
	abstract = {This paper discusses species diversity in simple multi-habitat environments. Its main purpose is to present simple mathematical and graphical models on how landscape patterns affect species numbers. The idea is to build models of species diversity in multi-habitat landscapes by combining species-area curves for different habitats. Predictions are made about how variables such as species richness and species overlap between habitats influence the proportion of the total landscape each habitat should constitute, and how many habitats it should be divided into in order to be able to sustain the maximal number of species. Habitat size and numbers are the only factors discussed here, not habitat spatial patterns. Among the predictions are: 1) where there are differences in species diversity between habitats, optimal landscape patterns contain larger proportions of species rich habitats. 2) Species overlap between habitats shifts the optimum further towards larger proportions of species rich habitat types. 3) Species overlap also shifts the optimum towards fewer habitat types. 4) Species diversity in landscapes with large species overlap is more resistant to changes in landscape (or reserve) size. This type of model approach can produce theories useful to nature and landscape management in general, and the design of nature reserves and national parks in particular.},
	language = {en},
	number = {1},
	urldate = {2016-03-01TZ},
	journal = {Ecography},
	author = {Tjørve, Even},
	month = feb,
	year = {2002},
	pages = {17--24}
}

@article{connor_statistics_1979,
	title = {The {Statistics} and {Biology} of the {Species}-{Area} {Relationship}},
	volume = {113},
	issn = {0003-0147},
	url = {http://www.jstor.org/stable/2460305},
	number = {6},
	urldate = {2016-03-01TZ},
	journal = {The American Naturalist},
	author = {Connor, Edward F. and McCoy, Earl D.},
	year = {1979},
	pages = {791--833}
}

@article{durrett_approximating_2004,
	title = {Approximating selective sweeps},
	volume = {66},
	issn = {0040-5809},
	url = {http://www.sciencedirect.com/science/article/pii/S0040580904000607},
	doi = {10.1016/j.tpb.2004.04.002},
	abstract = {The fixation of advantageous mutations in a population has the effect of reducing variation in the DNA sequence near that mutation. Kaplan et al. (1989) used a three-phase simulation model to study the effect of selective sweeps on genealogies. However, most subsequent work has simplified their approach by assuming that the number of individuals with the advantageous allele follows the logistic differential equation. We show that the impact of a selective sweep can be accurately approximated by a random partition created by a stick-breaking process. Our simulation results show that ignoring the randomness when the number of individuals with the advantageous allele is small can lead to substantial errors.},
	number = {2},
	urldate = {2016-02-29TZ},
	journal = {Theoretical Population Biology},
	author = {Durrett, Richard and Schweinsberg, Jason},
	month = sep,
	year = {2004},
	keywords = {Coalescent, Hitchhiking, Paintbox construction, Random partition, Selective sweep},
	pages = {129--138}
}

@article{mcvean_structure_2007,
	title = {The {Structure} of {Linkage} {Disequilibrium} {Around} a {Selective} {Sweep}},
	volume = {175},
	copyright = {Copyright © 2007 by the Genetics Society of America},
	issn = {0016-6731, 1943-2631},
	url = {http://www.genetics.org/content/175/3/1395},
	doi = {10.1534/genetics.106.062828},
	abstract = {The fixation of advantageous mutations by natural selection has a profound impact on patterns of linked neutral variation. While it has long been appreciated that such selective sweeps influence the frequency spectrum of nearby polymorphism, it has only recently become clear that they also have dramatic effects on local linkage disequilibrium. By extending previous results on the relationship between genealogical structure and linkage disequilibrium, I obtain simple expressions for the influence of a selective sweep on patterns of allelic association. I show that sweeps can increase, decrease, or even eliminate linkage disequilibrium (LD) entirely depending on the relative position of the selected and neutral loci. I also show the importance of the age of the neutral mutations in predicting their degree of association and describe the consequences of such results for the interpretation of empirical data. In particular, I demonstrate that while selective sweeps can eliminate LD, they generate patterns of genetic variation very different from those expected from recombination hotspots.},
	language = {en},
	number = {3},
	urldate = {2016-02-29TZ},
	journal = {Genetics},
	author = {McVean, Gil},
	month = mar,
	year = {2007},
	pmid = {17194788},
	pages = {1395--1406}
}

@article{storz_invited_2005,
	title = {{INVITED} {REVIEW}: {Using} genome scans of {DNA} polymorphism to infer adaptive population divergence},
	volume = {14},
	issn = {1365-294X},
	shorttitle = {{INVITED} {REVIEW}},
	url = {http://onlinelibrary.wiley.com.proxy2.cl.msu.edu/doi/10.1111/j.1365-294X.2005.02437.x/abstract},
	doi = {10.1111/j.1365-294X.2005.02437.x},
	abstract = {Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome-wide patterns of DNA polymorphism to detect the locus-specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying selection on polygenic traits can be expected to produce predictable patterns of allelic variation at the underlying quantitative trait loci (QTL), and whether the locus-specific effects of selection can be reliably detected against the genome-wide backdrop of stochastic variability. I then review different approaches that have been developed to identify loci involved in adaptive population divergence and I discuss the relative merits of model-based approaches that rely on assumptions about population structure vs. model-free approaches that are based on empirical distributions of summary statistics. Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence.},
	language = {en},
	number = {3},
	urldate = {2016-02-29TZ},
	journal = {Molecular Ecology},
	author = {Storz, Jay F.},
	month = mar,
	year = {2005},
	keywords = {QTL, adaptation, genomics, natural selection, neutral theory, population genomics, positive selection, speciation},
	pages = {671--688}
}

@article{gavrilets_dynamic_2005,
	title = {Dynamic patterns of adaptive radiation},
	volume = {102},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/102/50/18040},
	doi = {10.1073/pnas.0506330102},
	abstract = {Adaptive radiation is defined as the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. When it occurs, adaptive radiation typically follows the colonization of a new environment or the establishment of a “key innovation,” which opens new ecological niches and/or new paths for evolution. Here, we take advantage of recent developments in speciation theory and modern computing power to build and explore a large-scale, stochastic, spatially explicit, individual-based model of adaptive radiation driven by adaptation to multidimensional ecological niches. We are able to model evolutionary dynamics of populations with hundreds of thousands of sexual diploid individuals over a time span of 100,000 generations assuming realistic mutation rates and allowing for genetic variation in a large number of both selected and neutral loci. Our results provide theoretical support and explanation for a number of empirical patterns including “area effect,” “overshooting effect,” and “least action effect,” as well as for the idea of a “porous genome.” Our findings suggest that the genetic architecture of traits involved in the most spectacular radiations might be rather simple. We show that a great majority of speciation events are concentrated early in the phylogeny. Our results emphasize the importance of ecological opportunity and genetic constraints in controlling the dynamics of adaptive radiation.},
	language = {en},
	number = {50},
	urldate = {2016-02-29TZ},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Gavrilets, Sergey and Vose, Aaron},
	month = dec,
	year = {2005},
	pmid = {16330783},
	keywords = {diversification, ecological, modeling, parapatric, speciation},
	pages = {18040--18045}
}

@article{socolar_how_2016,
	title = {How {Should} {Beta}-{Diversity} {Inform} {Biodiversity} {Conservation}?},
	volume = {31},
	issn = {0169-5347},
	url = {http://www.cell.com/article/S016953471500289X/abstract},
	doi = {10.1016/j.tree.2015.11.005},
	language = {English},
	number = {1},
	urldate = {2016-02-12TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Socolar, Jacob B. and Gilroy, James J. and Kunin, William E. and Edwards, David P.},
	month = jan,
	year = {2016},
	keywords = {alpha-diversity, beta-diversity, biodiversity conservation, biotic homogenization, diversity partitioning, gamma-diversity, pairwise dissimilarities, spatial scaling, species–area relationships},
	pages = {67--80}
}

@article{debinski_review:_2000,
	title = {Review: {A} {Survey} and {Overview} of {Habitat} {Fragmentation} {Experiments}},
	volume = {14},
	issn = {0888-8892},
	shorttitle = {Review},
	url = {http://www.jstor.org/stable/2641600},
	abstract = {Habitat destruction and fragmentation are the root causes of many conservation problems. We conducted a literature survey and canvassed the ecological community to identify experimental studies of terrestrial habitat fragmentation and to determine whether consistent themes were emerging from these studies. Our survey revealed 20 fragmentation experiments worldwide. Most studies focused on effects of fragmentation on species richness or on the abundance(s) of particular species. Other important themes were the effect of fragmentation in interspecific interactions, the role of corridors and landscape connectivity in individual movements and species richness, and the influences of dge effects on ecosystem services. Our comparisons showed a remarkable lack of consistency in results across studies, especially with regard to species richness and abundance relative to fragment size. Experiments with arthropods showed the best fit with theoretical expectations of greater species richness on larger fragments. Highly mobile taxa such as birds and mammals, early-successional plant species, long-lived species, and generalist predators did not respond in the "expected" manner. Reasons for these discrepancies included edge effects, competitive release in the habitat fragments, and the spatial scale of the experiments. One of the more consistently supported hypotheses was that movement and species richness are positively affected by corridors and connectivity, respectively. Transient effects dominated many systems; for example, crowding of individuals on fragments commonly was observed after fragmentation, followed by a relaxation toward lower abundance in subsequent years. The three long-term studies (⩾14 years) revealed strong patterns that would have been missed in short-term investigations. Our results emphasize the wide range of species-specific responses to fragmentation, the need for elucidation of behavioral mechanisms affecting these responses, and the potential for changing responses to fragmentation over time.},
	number = {2},
	urldate = {2016-02-12TZ},
	journal = {Conservation Biology},
	author = {Debinski, Diane M. and Holt, Robert D.},
	year = {2000},
	pages = {342--355}
}
@article{rosch_biodiversity_2015,
	title = {Biodiversity conservation across taxa and landscapes requires many small as well as single large habitat fragments},
	volume = {179},
	issn = {0029-8549, 1432-1939},
	url = {http://link.springer.com/article/10.1007/s00442-015-3315-5},
	doi = {10.1007/s00442-015-3315-5},
	abstract = {Agricultural intensification has been shown to reduce biodiversity through processes such as habitat degradation and fragmentation. We tested whether several small or single large habitat fragments (re-visiting the ‘single large or several small’ debate) support more species across a wide range of taxonomic groups (plants, leafhoppers, true bugs, snails). Our study comprised 14 small ({\textless}1 ha) and 14 large (1.5–8 ha) fragments of calcareous grassland in Central Germany along orthogonal gradients of landscape complexity and habitat connectivity. Each taxon was sampled on six plots per fragment. Across taxa, species richness did not differ between large and small fragments, whereas species-area accumulation curves showed that both overall and specialist species richness was much higher on several small fragments of calcareous grassland than on few large fragments. On average, 85 \% of the overall species richness was recorded on all small fragments taken together (4.6 ha), whereas the two largest ones (15.1 ha) only accounted for 37 \% of the species. This could be due to the greater geographic extent covered by many small fragments. However, community composition differed strongly between large and small fragments, and some of the rarest specialist species appeared to be confined to large fragments. The surrounding landscape did not show any consistent effects on species richness and community composition. Our results show that both single large and many small fragments are needed to promote landscape-wide biodiversity across taxa. We therefore question the focus on large fragments only and call for a new diversified habitat fragmentation strategy for biodiversity conservation.},
	language = {en},
	number = {1},
	urldate = {2016-02-12TZ},
	journal = {Oecologia},
	author = {Rösch, Verena and Tscharntke, Teja and Scherber, Christoph and Batáry, Péter},
	month = apr,
	year = {2015},
	keywords = {Calcareous grasslands, Community composition, Ecology, Habitat fragmentation, Hydrology/Water Resources, Invertebrates, Isolation, Plant Sciences},
	pages = {209--222}
}

@article{kinnison_eco-evolutionary_2007,
	title = {Eco-evolutionary conservation biology: contemporary evolution and the dynamics of persistence},
	volume = {21},
	issn = {1365-2435},
	shorttitle = {Eco-evolutionary conservation biology},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2435.2007.01278.x/abstract},
	doi = {10.1111/j.1365-2435.2007.01278.x},
	abstract = {* 1Natural and human mediated perturbations present challenges to the fate of populations but fuel contemporary evolution (evolution over humanly observable time-scales). Here we ask if such evolution is sufficient to make the difference between population extinction and persistence.
* 2To answer this question requires a shift from the usual focus on trait evolution to the emergent ‘eco-evolutionary’ dynamics that arise through interactions of evolution, its fitness consequences and population abundance.
* 3By combining theory, models and insights from empirical studies of contemporary evolution, we provide an assessment of three contexts: persistence of populations in situ, persistence of colonising populations, and persistence under gene flow and in metapopulations.
* 4Contemporary evolution can likely rescue some, but not all, populations facing environmental change. Populations may fail partly because of the demographic cost of selection.
* 5Contemporary evolution that initiates positive population growth, such as selective founding processes, may create a ‘persistence vortex’ that overcomes the problems of small populations.
* 6Complex, even shifting, relationships between gene flow and adaptation may aid the persistence of subpopulations as well as the persistence and expansion of metapopulations.
* 7An eco-evolutionary perspective suggests that we expand our focus beyond the acute problems of threatened populations and growing invasions, to consider how contemporary evolutionary mechanics contribute to such problems in the first place or affect their resolution.},
	language = {en},
	number = {3},
	urldate = {2016-02-10TZ},
	journal = {Functional Ecology},
	author = {Kinnison, Michael T. and Hairston, Nelson G.},
	month = jun,
	year = {2007},
	keywords = {extinction, invasion, metapopulation, rapid evolution, regulation},
	pages = {444--454}
}

@book{whittaker_island_2007,
	title = {Island {Biogeography}: {Ecology}, {Evolution}, and {Conservation}},
	isbn = {9780198566113},
	shorttitle = {Island {Biogeography}},
	abstract = {Island biogeography is the study of the distribution and dynamics of species in island environments. Due to their isolation from more widespread continental species, islands are ideal places for unique species to evolve, but they are also places of concentrated extinction. Not surprisingly, they are widely studied by ecologists, conservationists and evolutionary biologists alike. There is no other recent textbook devoted solely to island biogeography, and a synthesis of the many recent advances is now overdue. This second edition builds on the success and reputation of the first, documenting the recent advances in this exciting field and explaining how islands have been used as natural laboratories in developing and testing ecological and evolutionary theories. In addition, the book describes the main processes of island formation, development and eventual demise, and explains the relevance of island environmental history to island biogeography. The authors demonstrate the huge significance of islands as hotspots of biodiversity, and as places from which disproportionate numbers of species have been extinguished by human action in historical time. Many island species are today threatened with extinction, and this work examines both the chief threats to their persistence and some of the mitigation measures that can be put in play with conservation strategies tailored to islands.},
	language = {en},
	publisher = {OUP Oxford},
	author = {Whittaker, Robert J. and Fernandez-Palacios, Jose Maria},
	year = {2007},
	keywords = {Nature / Environmental Conservation \& Protection, Science / Life Sciences / Biology, Science / Life Sciences / Botany, Science / Life Sciences / Ecology, Science / Life Sciences / Evolution, Science / Life Sciences / Zoology / General}
}

@article{pressey_conservation_2007,
	title = {Conservation planning in a changing world},
	volume = {22},
	issn = {0169-5347},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534707002807},
	doi = {10.1016/j.tree.2007.10.001},
	abstract = {Conservation planning is the process of locating, configuring, implementing and maintaining areas that are managed to promote the persistence of biodiversity and other natural values. Conservation planning is inherently spatial. The science behind it has solved important spatial problems and increasingly influenced practice. To be effective, however, conservation planning must deal better with two types of change. First, biodiversity is not static in time or space but generated and maintained by natural processes. Second, humans are altering the planet in diverse ways at ever faster rates.},
	number = {11},
	urldate = {2016-02-09TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Pressey, Robert L. and Cabeza, Mar and Watts, Matthew E. and Cowling, Richard M. and Wilson, Kerrie A.},
	month = nov,
	year = {2007},
	pages = {583--592}
}

@article{iliopoulos_critical_2010,
	title = {Critical {Dynamics} in the {Evolution} of {Stochastic} {Strategies} for the {Iterated} {Prisoner}'s {Dilemma}},
	volume = {6},
	url = {http://dx.doi.org/10.1371/journal.pcbi.1000948},
	doi = {10.1371/journal.pcbi.1000948},
	abstract = {Author Summary
The observed cooperation between genes, cells, tissues, and higher organisms represents a paradox for Darwinian evolution, because the individual success of cheating is rewarded before its long-term detrimental consequences are felt. The tension between cooperation and defection can be represented by a simple game (the “Prisoner's Dilemma”), which has been used to study the conflicts between decisions to cooperate or defect. Here, we encode these decisions within genes, and allow them to adapt to environments that differ in how well a player can predict how an opponent is going to play. We find that evolutionary paths end at strategies that cooperate if the environment is sufficiently predictable, while they end in defection in uncertain and inconsistent worlds because inconsistency favors defection over cooperation. This work shows that cooperation or defection, in populations of players that use the information from previous moves to plan future ones, can be influenced by changing the environmental parameters.},
	number = {10},
	urldate = {2016-02-09TZ},
	journal = {PLoS Comput Biol},
	author = {Iliopoulos, Dimitris and Hintze, Arend and Adami, Christoph},
	month = oct,
	year = {2010},
	pages = {e1000948}
}

@article{cantu-paz_migration_2001,
	title = {Migration {Policies}, {Selection} {Pressure}, and {Parallel} {Evolutionary} {Algorithms}},
	volume = {7},
	copyright = {Copyright Kluwer Academic Publishers Jul 2001},
	issn = {13811231},
	url = {http://search.proquest.com.proxy2.cl.msu.edu/docview/199224355/abstract/CA9C4247706245FDPQ/1},
	abstract = {This paper investigates how the policy used to select migrants and the individuals they replace affects the selection pressure in parallel evolutionary algorithms (EAs) with multiple populations. The four possible combinations of random and fitness-based emigration and replacement of existing individuals are considered. The investigation follows two approaches. The first is to calculate the takeover time under the four migration policies. This approach makes several simplifying assumptions, but the qualitative conclusions that are derived from the calculations are confirmed by the second approach. The second approach consists on quantifying the increase in the selection intensity. The selection intensity is a domain-independent adimensional quantity that can be used to compare the selection pressure of common selection methods with the pressure caused by migration. The results may help to avoid excessively high (or low) selection pressures that may cause the search to fail, and offer a plausible explanation to the frequent claims of superlinear speedups in parallel EAs. [PUBLICATION ABSTRACT]},
	language = {English},
	number = {4},
	urldate = {2016-02-04TZ},
	journal = {Journal of Heuristics},
	author = {Cantu-Paz, Erick},
	month = jul,
	year = {2001},
	keywords = {Algorithms, Computers--Artificial Intelligence, Methods, Migration, Studies},
	pages = {311}
}

@book{cantu-paz_efficient_2000,
	title = {Efficient and {Accurate} {Parallel} {Genetic} {Algorithms}},
	isbn = {9780792372219},
	abstract = {As genetic algorithms (GAs) become increasingly popular, they are applied to difficult problems that may require considerable computations. In such cases, parallel implementations of GAs become necessary to reach high-quality solutions in reasonable times. But, even though their mechanics are simple, parallel GAs are complex non-linear algorithms that are controlled by many parameters, which are not well understood.  Efficient and Accurate Parallel Genetic Algorithms is about the design of parallel GAs. It presents theoretical developments that improve our understanding of the effect of the algorithm's parameters on its search for quality and efficiency. These developments are used to formulate guidelines on how to choose the parameter values that minimize the execution time while consistently reaching solutions of high quality.  Efficient and Accurate Parallel Genetic Algorithms can be read in several ways, depending on the readers' interests and their previous knowledge about these algorithms. Newcomers to the field will find the background material in each chapter useful to become acquainted with previous work, and to understand the problems that must be faced to design efficient and reliable algorithms. Potential users of parallel GAs that may have doubts about their practicality or reliability may be more confident after reading this book and understanding the algorithms better. Those who are ready to try a parallel GA on their applications may choose to skim through the background material, and use the results directly without following the derivations in detail. These readers will find that using the results can help them to choose the type of parallel GA that best suits their needs, without having to invest the time to implement and test various options. Once that is settled, even the most experienced users dread the long and frustrating experience of configuring their algorithms by trial and error. The guidelines contained herein will shorten dramatically the time spent tweaking the algorithm, although some experimentation may still be needed for fine-tuning.  Efficient and Accurate Parallel Genetic Algorithms is suitable as a secondary text for a graduate level course, and as a reference for researchers and practitioners in industry.},
	language = {en},
	publisher = {Springer Science \& Business Media},
	author = {Cantú-Paz, Erick},
	month = nov,
	year = {2000},
	keywords = {Computers / Computer Science, Computers / Intelligence (AI) \& Semantics, Computers / Programming / Algorithms, Computers / Software Development \& Engineering / General, Computers / Systems Architecture / Distributed Systems \& Computing, Medical / Genetics}
}

@book{tomassini_spatially_2005,
	address = {Berlin, Heidelberg},
	series = {Natural {Computing} {Series}},
	title = {Spatially {Structured} {Evolutionary} {Algorithms}: {Artificial} {Evolution} in {Space} and {Time}},
	copyright = {Springer-Verlag 2005},
	isbn = {364206339X},
	shorttitle = {Spatially {Structured} {Evolutionary} {Algorithms}},
	language = {English},
	publisher = {Springer Berlin Heidelberg},
	author = {Tomassini, Marco},
	month = jan,
	year = {2005},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), COMPUTERS, Computation by Abstract Devices, Computer Science, Discrete Mathematics in Computer Science, Numeric Computing, Programming Algorithms}
}

@inproceedings{dolson_understanding_2015,
	address = {York, United Kingdom},
	title = {Understanding {Complexity} {Barriers} in {Evolving} {Systems}},
	booktitle = {Open-{Ended} {Evolution} {Workshop} at {European} {Conference} on {Artificial} {Life}},
	author = {Dolson, Emily and Vostinar, Anya and Wiser, Michael and Ofria, Charles},
	month = jul,
	year = {2015}
}

@article{paradis_ape:_2004,
	title = {{APE}: analyses of phylogenetics and evolution in {R} language},
	volume = {20},
	journal = {Bioinformatics},
	author = {Paradis, E. and Claude, J. and Strimmer, K.},
	year = {2004},
	pages = {289--290}
}

@article{saunders_biological_1991,
	title = {Biological {Consequences} of {Ecosystem} {Fragmentation}: {A} {Review}},
	volume = {5},
	issn = {0888-8892},
	shorttitle = {Biological {Consequences} of {Ecosystem} {Fragmentation}},
	url = {http://www.jstor.org/stable/2386335},
	abstract = {Research on fragmented ecosystems has focused mostly on the biogeographic consequences of the creation of habitat "islands" of different sizes, and has provided little of practical value to managers. However, ecosystem fragmentation causes large changes in the physical environment as well as biogeographic changes. Fragmentation generally results in a landscape that consists of remnant areas of native vegetation surrounded by a matrix of agricultural or other developed land. As a result, fluxes of radiation, momentum (i.e., wind), water, and nutrients across the landscape are altered significantly. These in turn can have important influences on the biota within remnant areas, especially at or near the edge between the remnant and the surrounding matrix. The isolation of remnant areas by clearing also has important consequences for the biota. These consequences vary with the time since isolation, distance from other remnants, and degree of connectivity with other remnants. The influences of physical and biogeographic changes are modified by the size, shape, and position in the landscape of individual remnants, with larger remnants being less adversely affected by the fragmentation process. The dynamics of remnant areas are predominantly driven by factors arising in the surrounding landscape. Management of, and research on, fragmented ecosystems should be directed at understanding and controlling these external influences as much as at the biota of the remnants themselves. There is a strong need to develop an integrated approach to landscape management that places conservation reserves in the context of the overall landscape.},
	number = {1},
	urldate = {2015-12-10TZ},
	journal = {Conservation Biology},
	author = {Saunders, Denis A. and Hobbs, Richard J. and Margules, Chris R.},
	year = {1991},
	pages = {18--32}
}

@book{noauthor_evolutionary_2009,
	address = {Cambridge, UK},
	edition = {1 edition},
	title = {Evolutionary {Conservation} {Biology}},
	isbn = {9780521116084},
	language = {English},
	publisher = {Cambridge University Press},
	month = jul,
	year = {2009}
}

@article{cowling_rapid_2001,
	title = {Rapid plant diversification: {Planning} for an evolutionary future},
	volume = {98},
	issn = {0027-8424, 1091-6490},
	shorttitle = {Rapid plant diversification},
	url = {http://www.pnas.org/content/98/10/5452},
	doi = {10.1073/pnas.101093498},
	abstract = {Systematic conservation planning is a branch of conservation biology that seeks to identify spatially explicit options for the preservation of biodiversity. Alternative systems of conservation areas are predictions about effective ways of promoting the persistence of biodiversity; therefore, they should consider not only biodiversity pattern but also the ecological and evolutionary processes that maintain and generate species. Most research and application, however, has focused on pattern representation only. This paper outlines the development of a conservation system designed to preserve biodiversity pattern and process in the context of a rapidly changing environment. The study area is the Cape Floristic Region (CFR), a biodiversity hotspot of global significance, located in southwestern Africa. This region has experienced rapid (post-Pliocene) ecological diversification of many plant lineages; there are numerous genera with large clusters of closely related species (flocks) that have subdivided habitats at a very fine scale. The challenge is to design conservation systems that will preserve both the pattern of large numbers of species and various natural processes, including the potential for lineage turnover. We outline an approach for designing a system of conservation areas to incorporate the spatial components of the evolutionary processes that maintain and generate biodiversity in the CFR. We discuss the difficulty of assessing the requirements for pattern versus process representation in the face of ongoing threats to biodiversity, the difficulty of testing the predictions of alternative conservation systems, and the widespread need in conservation planning to incorporate and set targets for the spatial components (or surrogates) of processes.},
	language = {en},
	number = {10},
	urldate = {2015-12-10TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Cowling, R. M. and Pressey, R. L.},
	month = may,
	year = {2001},
	pmid = {11344293},
	pages = {5452--5457}
}

@article{smith_prescriptive_2014,
	title = {Prescriptive {Evolution} to {Conserve} and {Manage} {Biodiversity}},
	volume = {45},
	url = {http://dx.doi.org/10.1146/annurev-ecolsys-120213-091747},
	doi = {10.1146/annurev-ecolsys-120213-091747},
	abstract = {We are witnessing a global, but unplanned, evolutionary experiment with the biodiversity of the planet. Anthropogenic disturbances such as habitat degradation and climate change result in evolutionary mismatch between the environments to which species are adapted and those in which they now exist. The impacts of unmanaged evolution are pervasive, but approaches to address them have received little attention. We review the evolutionary challenges of managing populations in the Anthropocene and introduce the concept of prescriptive evolution, which considers how evolutionary processes may be leveraged to proactively promote wise management. We advocate the planned management of evolutionary processes and explore the advantages of evolutionary interventions to preserve and sustain biodiversity. We show how an evolutionary perspective to conserving biodiversity is fundamental to effective management. Finally, we advocate building frameworks for decision-making, monitoring, and implementation at the boundary between management and evolutionary science to enhance conservation outcomes.},
	number = {1},
	urldate = {2015-12-10TZ},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	author = {Smith, Thomas B. and Kinnison, Michael T. and Strauss, Sharon Y. and Fuller, Trevon L. and Carroll, Scott P.},
	year = {2014},
	keywords = {adaptation, applied evolution, assisted migration, global change, phenotype-environment mismatch, plasticity},
	pages = {1--22}
}

@book{macarthur_theory_1967,
	title = {The {Theory} of {Island} {Biogeography}},
	isbn = {0691088365},
	abstract = {Biogeography was stuck in a "natural history phase" dominated by the collection of data, the young Princeton biologists Robert H. MacArthur and Edward O. Wilson argued in 1967. In this book, the authors developed a general theory to explain the facts of island biogeography. The theory builds on the first principles of population ecology and genetics to explain how distance and area combine to regulate the balance between immigration and extinction in island populations. The authors then test the theory against data. The Theory of Island Biogeography was never intended as the last word on the subject. Instead, MacArthur and Wilson sought to stimulate new forms of theoretical and empirical studies, which will lead in turn to a stronger general theory. Even a third of a century since its publication, the book continues to serve that purpose well. From popular books like David Quammen's Song of the Dodo to arguments in the professional literature, The Theory of Island Biogeography remains at the center of discussions about the geographic distribution of species. In a new preface, Edward O. Wilson reviews the origins and consequences of this classic book.},
	language = {en},
	publisher = {Princeton University Press},
	author = {MacArthur, Robert H. and Wilson, Edward O.},
	year = {1967},
	keywords = {Science / Life Sciences / Biology, Science / Life Sciences / Ecology}
}

@article{diamond_island_1975,
	title = {The island dilemma: {Lessons} of modern biogeographic studies for the design of natural reserves},
	volume = {7},
	issn = {0006-3207},
	shorttitle = {The island dilemma},
	url = {http://www.sciencedirect.com/science/article/pii/000632077590052X},
	doi = {10.1016/0006-3207(75)90052-X},
	abstract = {A system of natural reserves, each surrounded by altered habitat, resembles a system of islands from the point of view of species restricted to natural habitats. Recent advances in island biogeography may provide a detailed basis for understanding what to expect of such a system of reserves. The main conclusions are as follows: The number of species that a reserve can hold at equilibrium is a function of its area and its isolation. Larger reserves, and reserves located close to other reserves, can hold more species. If most of the area of a habitat is destroyed, and a fraction of the area is saved as a reserve, the reserve will initially contain more species than it can hold at equilibrium. The excess will gradually go extinct. The smaller the reserve, the higher will be the extinction rates. Estimates of these extinction rates for bird and mammal species have recently become available in a few cases. Different species require different minimum areas to have a reasonable chance of survival. Some geometric design principles are suggested in order to optimise the function of reserves in saving species.},
	number = {2},
	urldate = {2015-12-10TZ},
	journal = {Biological Conservation},
	author = {Diamond, Jared M.},
	month = feb,
	year = {1975},
	pages = {129--146}
}

@article{simberloff_island_1976,
	title = {Island biogeography theory and conservation practice},
	volume = {191},
	url = {http://planet.botany.uwc.ac.za/NISL/Conservation%20Biology/Chapter1_bak/articles/Simberloff_and_Abele_1976.pdf},
	number = {4224},
	urldate = {2015-12-10TZ},
	journal = {Science},
	author = {Simberloff, Daniel S. and Abele, Lawrence G.},
	year = {1976},
	pages = {285--286}
}

@article{channon_improving_2003,
	title = {Improving and still passing the {ALife} test: {Component}-normalised activity statistics classify evolution in {Geb} as unbounded},
	shorttitle = {Improving and still passing the {ALife} test},
	url = {https://books.google.com/books?hl=en&lr=&id=si_KlRbL1XoC&oi=fnd&pg=PA173&dq=alastair+channon&ots=2BC6f5jTp6&sig=0M-GMq82p6cB-r8Uie3OrvjBrPo},
	urldate = {2015-10-23TZ},
	journal = {Proceedings of Artificial Life VIII, Sydney, RK Standish, MA Bedau, and HA Abbass,(eds.), MIT Press: Cambridge, MA},
	author = {Channon, Alastair and {others}},
	year = {2003},
	pages = {173--181}
}

@article{wiens_speciation_2004,
	title = {Speciation and {Ecology} {Revisited}: {Phylogenetic} {Niche} {Conservatism} and the {Origin} of {Species}},
	volume = {58},
	issn = {1558-5646},
	shorttitle = {Speciation and {Ecology} {Revisited}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2004.tb01586.x/abstract},
	doi = {10.1111/j.0014-3820.2004.tb01586.x},
	abstract = {Abstract Evolutionary biologists have often suggested that ecology is important in speciation, in that natural selection may drive adaptive divergence between lineages that inhabit different environments. I suggest that it is the tendency of lineages to maintain their ancestral ecological niche (phylogenetic niche conservatism) and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation. Niche conservatism may be an important and widespread component of allopatric speciation but is largely unstudied. The perspective outlined here suggests roles for key microevolutionary processes (i.e., natural selection, adaptation) that are strikingly different from those proposed in previous literature on ecology and speciation. Yet, this perspective is complementary to the traditional view because it focuses on a different temporal stage of the speciation process.},
	language = {en},
	number = {1},
	urldate = {2015-10-14TZ},
	journal = {Evolution},
	author = {Wiens, John J.},
	month = jan,
	year = {2004},
	keywords = {Ecology, adaptation, biogeography, natural selection, niche, speciation, vicariance},
	pages = {193--197}
}

@article{macarthur_bird_1961,
	title = {On {Bird} {Species} {Diversity}},
	volume = {42},
	copyright = {Copyright © 1961 Ecological Society of America},
	issn = {0012-9658},
	url = {http://www.jstor.org/stable/1932254},
	doi = {10.2307/1932254},
	number = {3},
	urldate = {2015-08-13TZ},
	journal = {Ecology},
	author = {MacArthur, Robert H. and MacArthur, John W.},
	month = jul,
	year = {1961},
	pages = {594--598}
}

@article{miller_ecologic_1956,
	title = {Ecologic {Factors} that {Accelerate} {Formation} of {Races} and {Species} of {Terrestrial} {Vertebrates}},
	volume = {10},
	copyright = {Copyright © 1956 Society for the Study of Evolution},
	issn = {0014-3820},
	url = {http://www.jstor.org/stable/2406011},
	doi = {10.2307/2406011},
	abstract = {Ecologic determination, working through natural selection, is all-pervasive in the processes of speciation, including the aspects of speed of differentiation. Cycles in numbers of individuals that are ecologically dictated, and other small-population effects that are partly ecological, promote elevation of gene combinations to significant levels of occurrence in the population and permit mass trials and recombinations. The faster and more frequent such exploratory genetic drift, the better the chance of an early attainment of a workable new combination that may be seized upon and perfected by selection. Ecologic contrasts on borders of continents in areas of diverse topography and with pronounced hygrogradients are extraordinarily potent in race formation in terrestrial vertebrates. Without potency there can be no great speed of differentiation. The close proximity of racial differentiates, of differing population densities, greatly favors numerous and quick introgressive contacts resulting from geologic and ecologic disturbances that break down barriers. Races may be modified through exchange to arrive at favorable adaptive and compatible gene complexes and the allopatric semispecies already attained can yield species with important phyletic futures through testing under continental rigor and by borrowing improvements via introgression. Moderate innate ecologic tolerances of species rather than either sharp restriction or eurotopy seem to favor rapid polytypic diversification. Concomitantly, moderate but not full isolation of populations favors prompt initial and subsequent evolutionary progress as made particularly clear by Sewall Wright. These 'middle-ground' interpretations in which balance in the many factors of evolution is stressed might be termed the moderation thesis. Such a thesis is wholly consonant with the view that the diverse topography of continental borders promotes rapid speciation through isolative and selective mechanisms.},
	number = {3},
	urldate = {2015-08-13TZ},
	journal = {Evolution},
	author = {Miller, Alden H.},
	month = sep,
	year = {1956},
	pages = {262--277}
}

@article{knope_limited_2015,
	title = {Limited role of functional differentiation in early diversification of animals},
	volume = {6},
	copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	url = {http://www.nature.com/ncomms/2015/150304/ncomms7455/full/ncomms7455.html},
	doi = {10.1038/ncomms7455},
	abstract = {The origin of most animal phyla and classes during the Cambrian explosion has been hypothesized to represent an ‘early burst’ of evolutionary exploration of functional ecological possibilities. However, the ecological history of marine animals has yet to be fully quantified, preventing an assessment of the early-burst model for functional ecology. Here we use ecological assignments for 18,621 marine animal genera to assess the relative timing of functional differentiation versus taxonomic diversification from the Cambrian to the present day. We find that functional diversity increased more slowly than would be expected given the history of taxonomic diversity. Contrary to previous inferences of rapid ecological differentiation from the early appearances of all well-fossilized phyla and classes, explicit coding of functional characteristics demonstrates that Cambrian genera occupied comparatively few modes of life. Functional diversity increased in the Ordovician and, especially, during the recoveries from the end-Permian and end-Cretaceous mass extinctions. Permanent shifts in the relationship between functional and taxonomic diversity following the era-bounding extinctions indicates a critical role for these biotic crises in coupling taxonomic and functional diversity.},
	language = {en},
	urldate = {2015-06-25TZ},
	journal = {Nature Communications},
	author = {Knope, M. L. and Heim, N. A. and Frishkoff, L. O. and Payne, J. L.},
	month = mar,
	year = {2015},
	keywords = {Biological sciences, Ecology, Palaeontology, evolution}
}

@article{hardin_collective_1971,
	title = {Collective action as an agreeable n-prisoners' dilemma},
	volume = {16},
	copyright = {Copyright © 1971 John Wiley \& Sons, Ltd.},
	issn = {1099-1743},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/bs.3830160507/abstract},
	doi = {10.1002/bs.3830160507},
	abstract = {The problem of collective action to produce a group collective good is analyzed as the game of Individual vs. Collective and then as an n-person game to show that, under the constraints of Mancur Olson's analysis, it is an n-prisoners' dilemma in the cases of latent and intermediate groups. The usual analysis according to which noncooperation is considered the rational strategy for classical 2-prisoners' dilemma is logically similar to Olson's analysis, which suggests that rational members of a latent group should not contribute toward the purchase of the group collective good. However, in the game analysis it is clear that the latent and intermediate groups are not logically different, but rather are distinguishable only statistically. Some prisoners' dilemma experimental results are used to suggest how the difference might arise and how the vast prisoners' dilemma literature can be related to the problem of collective action. The game of collective action is then analyzed not from the view of strategies but of outcomes. There is presented a theorem which states that the outcome in which all player-members of a group pay and all benefit is a Condorcet choice from the set of realizable outcomes for the game. Hence the cooperative outcome in such a game would prevail in election against all other outcomes.},
	language = {en},
	number = {5},
	urldate = {2015-06-18TZ},
	journal = {Behavioral Science},
	author = {Hardin, Russell},
	month = sep,
	year = {1971},
	pages = {472--481}
}

@article{rohde_latitudinal_1992,
	title = {Latitudinal {Gradients} in {Species} {Diversity}: {The} {Search} for the {Primary} {Cause}},
	volume = {65},
	copyright = {Copyright © 1992 Nordic Society Oikos},
	issn = {0030-1299},
	shorttitle = {Latitudinal {Gradients} in {Species} {Diversity}},
	url = {http://www.jstor.org/stable/3545569},
	doi = {10.2307/3545569},
	abstract = {Hypotheses that attempt to explain latitudinal gradients in species diversity are reviewed. Some hypotheses are circular, i.e. they are based on the assumption that some taxa have greater diversity in the tropics. These include explanations assuming different degrees of competition, mutualism, predation, epiphyte load, epidemics, biotic spatial heterogeneity, host diversity, population size, niche width, population growth rate, environmental harshness, and patchiness at different latitudes. Other explanations are not supported by sufficient evidence, i.e. there is no consistent correlation between species diversity and environmental stability, environmental predictability, productivity, abiotic rarefaction, physical heterogeneity, latitudinal decrease in the angle of the sun above the horizon, area, aridity, seasonality, number of habitats, and latitudinal ranges. The ecological and evolutionary time hypotheses, as usually understood, also cannot explain the gradients, nor does the temperature dependence of chemical reactions permit predictions on species richness. Only differences in solar energy are consistently correlated with diversity gradients along latitude, altitude and perhaps depth. It is concluded that greater species diversity is due to greater "effective" evolutionary time (evolutionary speed) in the tropics, probably as the result of shorter generation times, faster mutation rates, and faster selection at greater temperatures. There is an urgent need for experimental studies of temperature effects on speed of selection.},
	number = {3},
	urldate = {2015-05-22TZ},
	journal = {Oikos},
	author = {Rohde, Klaus},
	month = dec,
	year = {1992},
	pages = {514--527}
}

@book{hubbell_unified_2001,
	title = {The unified neutral theory of biodiversity and biogeography ({MPB}-32)},
	volume = {32},
	url = {https://books.google.com/books?hl=en&lr=&id=EIQpFBu84NoC&oi=fnd&pg=PR3&dq=hubbell+neutral+theory&ots=cQIPIZSFn0&sig=esVx2oB42HJF9RxAIXH_LDLGcRs},
	urldate = {2015-05-22TZ},
	publisher = {Princeton University Press},
	author = {Hubbell, Stephen P.},
	year = {2001}
}

@article{winter_phylogenetic_2013,
	title = {Phylogenetic diversity and nature conservation: where are we?},
	volume = {28},
	issn = {0169-5347},
	shorttitle = {Phylogenetic diversity and nature conservation},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534712002881},
	doi = {10.1016/j.tree.2012.10.015},
	abstract = {To date, there is little evidence that phylogenetic diversity has contributed to nature conservation. Here, we discuss the scientific justification of using phylogenetic diversity in conservation and the reasons for its neglect. We show that, apart from valuing the rarity and richness aspect, commonly quoted justifications based on the usage of phylogenetic diversity as a proxy for functional diversity or evolutionary potential are still based on uncertainties. We discuss how a missing guideline through the variety of phylogenetic diversity metrics and their relevance for conservation might be responsible for the hesitation to include phylogenetic diversity in conservation practice. We outline research routes that can help to ease uncertainties and bridge gaps between research and conservation with respect to phylogenetic diversity.},
	number = {4},
	urldate = {2015-05-15TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Winter, Marten and Devictor, Vincent and Schweiger, Oliver},
	month = apr,
	year = {2013},
	pages = {199--204}
}

@article{lausch_understanding_2015,
	series = {Use of ecological indicators in models},
	title = {Understanding and quantifying landscape structure – {A} review on relevant process characteristics, data models and landscape metrics},
	volume = {295},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380014003974},
	doi = {10.1016/j.ecolmodel.2014.08.018},
	abstract = {For quantifying and modelling of landscape patterns, the patch matrix model (PMM) and the gradient model (GM) are fundamental concepts of landscape ecology. While the PMM model has been the backbone for our advances in landscape ecology, it may also hamper truly universal insights into process–pattern relationships.

The PMM describes landscape structures as a mosaic of discretely delineated homogenous areas. This requires simplifications and assumptions which may even result in errors which propagate through subsequent analyses and may reduce our ability to understand effects of landscape structure on ecological processes. Alternative approaches to represent landscape structure should therefore be evaluated. The GM represents continuous surface characteristics without arbitrary vegetation or land-use classification and therefore does not require delineation of discrete areas with sharp boundaries. The GM therefore lends itself to be a more realistic representation of a particular surface characteristic. In the paper PMM and GM are compared regarding their prospects and limitations. Suggestions are made regarding the potential use and implementation of both approaches for process–pattern analysis.

The ecological and anthropogenic process itself and its characteristics under investigation is decisive for: (i) the selection of discrete and/or continuous indicators, (ii) the type of the quantitative pattern analysis approach to be used (PMM/GM) and (iii) the data and the scale required in the analysis. Process characteristics and their effects on pattern characteristics in space and time are decisive for the applicability of the PMM or of the GM approach. A low hemeroby (high naturalness and low human pressure on landscapes) allows for high internal-heterogeneity in space and over time within patterns. Such landscapes can be captured with the GM approach. A high hemeroby reduces heterogeneity in space and time within patterns. For such landscapes we recommend the PMM model.},
	urldate = {2015-04-23TZ},
	journal = {Ecological Modelling},
	author = {Lausch, Angela and Blaschke, Thomas and Haase, Dagmar and Herzog, Felix and Syrbe, Ralf-Uwe and Tischendorf, Lutz and Walz, Ulrich},
	month = jan,
	year = {2015},
	keywords = {Gradient model, Hemeroby, Patch matrix model, Quantitative landscape ecology, Surface metrics, landscape metrics},
	pages = {31--41}
}

@article{mcgarigal_fragstats:_2002,
	title = {{FRAGSTATS}: spatial pattern analysis program for categorical maps},
	author = {McGarigal, Kevin and Cushman, Sam A and Neel, Maile C and Ene, Eduard},
	year = {2002}
}

@article{kanuch_landscape_2012,
	title = {Landscape configuration determines gene flow and phenotype in a flightless forest-edge ground-dwelling bush-cricket, {Pholidoptera} griseoaptera},
	volume = {26},
	issn = {0269-7653, 1573-8477},
	url = {http://link.springer.com/article/10.1007/s10682-012-9571-5},
	doi = {10.1007/s10682-012-9571-5},
	abstract = {Spatial configuration of habitats influences genetic structure and population fitness whereas it affects mainly species with limited dispersal ability. To reveal how habitat fragmentation determines dispersal and dispersal-related morphology in a ground-dispersing insect species we used a bush-cricket (Pholidoptera griseoaptera) which is associated with forest-edge habitat. We analysed spatial genetic patterns together with variability of the phenotype in two forested landscapes with different levels of fragmentation. While spatial configuration of forest habitats did not negatively affect genetic characteristics related to the fitness of sampled populations, genetic differentiation was found higher among populations from an extensive forest. Compared to an agricultural matrix between forest patches, the matrix of extensive forest had lower permeability and posed barriers for the dispersal of this species. Landscape configuration significantly affected also morphological traits that are supposed to account for species dispersal potential; individuals from fragmented forest patches had longer hind femurs and a higher femur to pronotum ratio. This result suggests that selection pressure act differently on populations from both landscape types since dispersal-related morphology was related to the level of habitat fragmentation. Thus observed patterns may be explained as plastic according to the level of landscape configuration; while anthropogenic fragmentation of habitats for this species can lead to homogenization of spatial genetic structure.},
	language = {en},
	number = {6},
	urldate = {2015-04-23TZ},
	journal = {Evolutionary Ecology},
	author = {Kaňuch, Peter and Jarčuška, Benjamín and Schlosserová, Dušana and Sliacka, Anna and Paule, Ladislav and Krištín, Anton},
	month = apr,
	year = {2012},
	keywords = {Evolutionary Biology, Habitat connectivity, Human Genetics, Movement behaviour, Orthoptera, Plant Sciences, Population genetics, Woodland},
	pages = {1331--1343}
}

@article{bonte_evolution_2010,
	title = {Evolution of dispersal polymorphism and local adaptation of dispersal distance in spatially structured landscapes},
	volume = {119},
	copyright = {© 2009 The Authors},
	issn = {1600-0706},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0706.2009.17943.x/abstract},
	doi = {10.1111/j.1600-0706.2009.17943.x},
	abstract = {Many organisms show polymorphism in dispersal distance strategies. This variation is particularly ecological relevant if it encompasses a functional separation of short- (SDD) and long-distance dispersal (LDD). It remains, however, an open question whether both parts of the dispersal kernel are similarly affected by landscape related selection pressures. We implemented an individual-based model to analyze the evolution of dispersal traits in fractal landscapes that vary in the proportion of habitat and its spatial configuration. Individuals are parthenogenetic with dispersal distance determined by two alleles on each individual's genome: one allele coding for the probability of global dispersal and one allele coding for the variance σ of a Gaussian local dispersal with mean value zero. Simulations show that mean distances of local dispersal and the probability of global dispersal, increase with increasing habitat availability, but that changes in the habitat's spatial autocorrelation impose opposing selective pressure: local dispersal distances decrease and global dispersal probabilities increase with decreasing spatial autocorrelation of the available habitat. Local adaptation of local dispersal distance emerges in landscapes with less than 70\% of clumped habitat. These results demonstrate that long and short distance dispersal evolve separately according to different properties of the landscape. The landscape structure may consequently largely affect the evolution of dispersal distance strategies and the level of dispersal polymorphism.},
	language = {en},
	number = {3},
	urldate = {2015-04-21TZ},
	journal = {Oikos},
	author = {Bonte, Dries and Hovestadt, Thomas and Poethke, Hans-Joachim},
	month = mar,
	year = {2010},
	pages = {560--566}
}

@article{adler_persistence_1994,
	title = {Persistence in {Patchy} {Irregular} {Landscapes}},
	volume = {45},
	issn = {0040-5809},
	url = {http://www.sciencedirect.com/science/article/pii/S0040580984710033},
	doi = {10.1006/tpbi.1994.1003},
	abstract = {This paper presents a simulation and three approximations designed to study the effects of spatial clumping of patches in a metapopulation linked by costly dispersal. Assuming that all patches are identical and that each experiences a simple regime of density-independent uncorrelated extinction, we demonstrate that clumping enhances persistence of the population. We find a persistence threshold which depends on the leading eigenvalue of the matrix describing dispersal success between each pair of patches and show that this eigenvalue exceeds the mean dispersal success. An averaged approximation that uses a single statistic to describe each path, rather than the full matrix, successfully predicts the regional population size produced by the simulation and predicts a simple linear relationship between this statistic and the patch immigration rate. An approximation which ignores the detailed spatial structure fails to accurately predict the simulation results.},
	number = {1},
	urldate = {2015-04-21TZ},
	journal = {Theoretical Population Biology},
	author = {Adler, F. R. and Nuernberger, B.},
	month = feb,
	year = {1994},
	pages = {41--75}
}

@article{heinz_adaptive_2006,
	title = {Adaptive {Patch} {Searching} {Strategies} in {Fragmented} {Landscapes}},
	volume = {20},
	issn = {0269-7653, 1573-8477},
	url = {http://link.springer.com/article/10.1007/s10682-005-5378-y},
	doi = {10.1007/s10682-005-5378-y},
	abstract = {The search strategies dispersers employ to search for new habitat patches affect individuals’ search success and subsequently landscape connectivity and metapopulation viability. Some evidence indicates that individuals within the same species may display a variety of behavioural patch searching strategies rather than one species-specific strategy. This may result from landscape heterogeneity. We modelled the evolution of individual patch searching strategies in different landscapes. Specifically, we analysed whether evolution can favour different, co-existing, behavioural search strategies within one population and to what extent this coexistence of multiple strategies was dependent on landscape configuration. Using an individual-based simulation model, we studied the evolution of patch searching strategies in three different landscape configurations: uniform, random and clumped. We found that landscape configuration strongly influenced the evolved search strategy. In uniform landscapes, one fixed search strategy evolved for the entire spatially structured population, while in random and clumped landscapes, a set of different search strategies emerged. The coexistence of several search strategies also strongly depended on the dispersal mortality. We show that our result can affect landscape connectivity and metapopulation dynamics.},
	language = {en},
	number = {2},
	urldate = {2015-04-21TZ},
	journal = {Evolutionary Ecology},
	author = {Heinz, Simone K. and Strand, Espen},
	month = mar,
	year = {2006},
	keywords = {Evolutionary Biology, Human Genetics, Plant Sciences, adaptive modelling, dispersal, evolution, fragmented landscapes, genetic algorithm, individual-based model, metapopulations, patch searching strategies},
	pages = {113--130}
}

@article{baker_r.programs_1992,
	title = {The r.le programs for multiscale analysis of landscape structure using the {GRASS} geographical information system},
	volume = {7},
	issn = {0921-2973, 1572-9761},
	url = {http://link.springer.com/article/10.1007/BF00131258},
	doi = {10.1007/BF00131258},
	abstract = {Geographical information systems (GIS) are well suited to the spatial analysis of landscape data, but generally lack programs for calculating traditional measures of landscape structure (e.g., fractal dimension). Standalone programs for calculating landscape structure measures do exist, but these programs do not enable the user to take advantage of GIS facilities for manipulating and analyzing landscape data. Moreover, these programs lack capabilities for analysis with sampling areas of different size (multiscale analysis) and also lack some needed measures of landscape structure (e.g., texture). We have developed the r.le programs for analyzing landscape structure using the GRASS GIS. The programs can be used to calculate over sixty measures of landscape structure (e.g., distance, size, shape, fractal dimension, perimeters, diversity, texture, juxtaposition, edges) within sampling areas of several sizes simultaneously. Also possible are moving window analyses, which enable the production of new maps of the landscape structure within windows of a particular size. These new maps can then be used in other analyses with the GIS.},
	language = {en},
	number = {4},
	urldate = {2015-04-20TZ},
	journal = {Landscape Ecology},
	author = {Baker, William L. and Cai, Yunming},
	month = dec,
	year = {1992},
	keywords = {Ecology, Forestry, Forestry Management, GIS, Landscape Ecology, Plant Ecology, Plant Sciences, geographical information systems, landscape structure, software},
	pages = {291--302}
}

@article{rosindell_unifying_2015,
	title = {Unifying ecology and macroevolution with individual-based theory},
	volume = {18},
	copyright = {© 2015 The Authors. Ecology Letters published by John Wiley \& Sons Ltd and CNRS., This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12430/abstract},
	doi = {10.1111/ele.12430},
	abstract = {A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage-based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual-based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology.},
	language = {en},
	number = {5},
	urldate = {2015-04-20TZ},
	journal = {Ecology Letters},
	author = {Rosindell, James and Harmon, Luke J. and Etienne, Rampal S.},
	month = may,
	year = {2015},
	keywords = {Ecology, fitness, individual-based model, lineages-through-time, macroevolution, neutral, phylogeny, selection, species abundance, theory},
	pages = {472--482}
}

@article{barrett_population_2008,
	title = {Population structure and diversity in sexual and asexual populations of the pathogenic fungus {Melampsora} lini},
	volume = {17},
	issn = {0962-1083},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653454/},
	doi = {10.1111/j.1365-294X.2008.03843.x},
	abstract = {Many pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale, using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini.},
	number = {14},
	urldate = {2015-04-17TZ},
	journal = {Molecular ecology},
	author = {BARRETT, LUKE G. and THRALL, PETER H. and BURDON, JEREMY J. and NICOTRA, ADRIENNE B. and LINDE, CELESTE C.},
	month = jul,
	year = {2008},
	pmid = {18573166},
	pmcid = {PMC2653454},
	pages = {3401--3415}
}

@article{taper_how_1996,
	title = {How do {Species} {Really} {Divide} {Resources}?},
	volume = {147},
	copyright = {Copyright © 1996 The University of Chicago},
	issn = {0003-0147},
	url = {http://www.jstor.org/stable/2463192},
	abstract = {We show that the relationship between variance in population energy use and variance in species abundance depends critically on the model of causal relationships among metabolic rate, body size, and population density assumed, provided that they specify alternative paths of error propagation. It has been claimed that the allometric relationship between population density and body size indicates that species within communities use resources less equitably than would be inferred from a particular species abundance distribution. Our analysis of 41 local bird communities shows that this claim is supported only if it is assumed that both body size and metabolic rate are a consequence of population density. A more realistic model that assumes a causal role for body size as affecting metabolic rate and population density provides estimates of variance in population energy use that closely match the pattern of variance in population density. This implies that the apportionment of individuals and resources, among species, are equivalent processes.},
	number = {6},
	urldate = {2015-04-11TZ},
	journal = {The American Naturalist},
	author = {Taper, Mark L. and Marquet, Pablo A.},
	month = jun,
	year = {1996},
	pages = {1072--1086}
}
@article{goldsby_evolutionary_2014,
	title = {The {Evolutionary} {Origin} of {Somatic} {Cells} under the {Dirty} {Work} {Hypothesis}},
	volume = {12},
	url = {http://dx.doi.org/10.1371/journal.pbio.1001858},
	doi = {10.1371/journal.pbio.1001858},
	abstract = {Experimental evolution of digital organisms suggests that mutagenic side effects associated with performing valuable metabolic work can produce germ-soma differentiation in multicellular organisms.},
	number = {5},
	urldate = {2015-04-02TZ},
	journal = {PLoS Biol},
	author = {Goldsby, Heather J. and Knoester, David B. and Ofria, Charles and Kerr, Benjamin},
	month = may,
	year = {2014},
	pages = {e1001858}
}

@article{nahum_evolution_2011,
	title = {Evolution of restraint in a structured rock–paper–scissors community},
	volume = {108},
	url = {http://www.pnas.org/content/108/Supplement_2/10831.short},
	number = {Supplement 2},
	urldate = {2015-04-02TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Nahum, Joshua R. and Harding, Brittany N. and Kerr, Benjamin},
	year = {2011},
	pages = {10831--10838}
}

@article{fitzpatrick_locally_2015,
	title = {Locally adapted traits maintained in the face of high gene flow},
	volume = {18},
	copyright = {© 2014 John Wiley \& Sons Ltd/CNRS},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12388/abstract},
	doi = {10.1111/ele.12388},
	abstract = {Gene flow between phenotypically divergent populations can disrupt local adaptation or, alternatively, may stimulate adaptive evolution by increasing genetic variation. We capitalised on historical Trinidadian guppy transplant experiments to test the phenotypic effects of increased gene flow caused by replicated introductions of adaptively divergent guppies, which were translocated from high- to low-predation environments. We sampled two native populations prior to the onset of gene flow, six historic introduction sites, introduction sources and multiple downstream points in each basin. Extensive gene flow from introductions occurred in all streams, yet adaptive phenotypic divergence across a gradient in predation level was maintained. Descendants of guppies from a high-predation source site showed high phenotypic similarity with native low-predation guppies in as few as {\textasciitilde}12 generations after gene flow, likely through a combination of adaptive evolution and phenotypic plasticity. Our results demonstrate that locally adapted phenotypes can be maintained despite extensive gene flow from divergent populations.},
	language = {en},
	number = {1},
	urldate = {2015-03-07TZ},
	journal = {Ecology Letters},
	author = {Fitzpatrick, S. W. and Gerberich, J. C. and Kronenberger, J. A. and Angeloni, L. M. and Funk, W. C.},
	month = jan,
	year = {2015},
	keywords = {Adaptive divergence, Poecilia reticulata, eco-evolutionary dynamics, gene flow, natural selection},
	pages = {37--47}
}

@article{rayfield_connectivity_2010,
	title = {Connectivity for conservation: a framework to classify network measures},
	volume = {92},
	issn = {0012-9658},
	shorttitle = {Connectivity for conservation},
	url = {http://www.esajournals.org/doi/abs/10.1890/09-2190.1},
	doi = {10.1890/09-2190.1},
	abstract = {Graph theory, network theory, and circuit theory are increasingly being used to quantify multiple aspects of habitat connectivity and protected areas. There has been an explosive proliferation of network (connectivity) measures, resulting in over 60 measures for ecologists to now choose from. Conceptual clarification on the ecological meaning of these network measures and their interrelationships is overdue. We present a framework that categorizes network measures based on the connectivity property that they quantify (i.e., route-specific flux, route redundancy, route vulnerability, and connected habitat area) and the structural level of the habitat network to which they apply. The framework reveals a lack of network measures in the categories of “route-specific flux among neighboring habitat patches” and “route redundancy at the level of network components.” We propose that network motif and path redundancy measures can be developed to fill the gaps in these categories. The value of this framework lies in its ability to inform the selection and application of network measures. Ultimately, it will allow a better comparison among graph, network, and circuit analyses, which will improve the design and management of connected landscapes.},
	number = {4},
	urldate = {2015-02-26TZ},
	journal = {Ecology},
	author = {Rayfield, Bronwyn and Fortin, Marie-Josée and Fall, Andrew},
	month = aug,
	year = {2010},
	keywords = {circuit theory, conservation management, corridors, fragmentation, graph theory, habitat resistance, inter-patch movement, landscape connectivity, least-cost path, network theory},
	pages = {847--858}
}

@article{riitters_factor_1995,
	title = {A factor analysis of landscape pattern and structure metrics},
	volume = {10},
	issn = {0921-2973, 1572-9761},
	url = {http://link.springer.com/article/10.1007/BF00158551},
	doi = {10.1007/BF00158551},
	abstract = {Fifty-five metrics of landscape pattern and structure were calculated for 85 maps of land use and land cover. A multivariate factor analysis was used to identify the common axes (or dimensions) of pattern and structure which were measured by a reduced set of 26 metrics. The first six factors explained about 87\% of the variation in the 26 landscape metrics. These factors were interpreted as composite measures of average patch compaction, overall image texture, average patch shape, patch perimeter-area scaling, number of attribute classes, and large-patch density-area scaling. We suggest that these factors can be represented in a simpler way by six univariate metrics - average perimeter-area ratio, contagion, standardized patch shape, patch perimeter-area scaling, number of attribute classes, and large-patch density-area scaling.},
	language = {en},
	number = {1},
	urldate = {2015-02-21TZ},
	journal = {Landscape Ecology},
	author = {Riitters, K. H. and O'Neill, R. V. and Hunsaker, C. T. and Wickham, J. D. and Yankee, D. H. and Timmins, S. P. and Jones, K. B. and Jackson, B. L.},
	month = feb,
	year = {1995},
	keywords = {Ecology, Forestry, Forestry Management, Landscape Ecology, Plant Ecology, Plant Sciences},
	pages = {23--39}
}

@article{henriques-silva_evolution_2015,
	title = {On the evolution of dispersal via heterogeneity in spatial connectivity},
	volume = {282},
	copyright = {© 2015 The Author(s) Published by the Royal Society. All rights reserved.},
	issn = {0962-8452, 1471-2954},
	url = {http://rspb.royalsocietypublishing.org/content/282/1803/20142879},
	doi = {10.1098/rspb.2014.2879},
	abstract = {Dispersal has long been recognized as a mechanism that shapes many observed ecological and evolutionary processes. Thus, understanding the factors that promote its evolution remains a major goal in evolutionary ecology. Landscape connectivity may mediate the trade-off between the forces in favour of dispersal propensity (e.g. kin-competition, local extinction probability) and those against it (e.g. energetic or survival costs of dispersal). It remains, however, an open question how differing degrees of landscape connectivity may select for different dispersal strategies. We implemented an individual-based model to study the evolution of dispersal on landscapes that differed in the variance of connectivity across patches ranging from networks with all patches equally connected to highly heterogeneous networks. The parthenogenetic individuals dispersed based on a flexible logistic function of local abundance. Our results suggest, all else being equal, that landscapes differing in their connectivity patterns will select for different dispersal strategies and that these strategies confer a long-term fitness advantage to individuals at the regional scale. The strength of the selection will, however, vary across network types, being stronger on heterogeneous landscapes compared with the ones where all patches have equal connectivity. Our findings highlight how landscape connectivity can determine the evolution of dispersal strategies, which in turn affects how we think about important ecological dynamics such as metapopulation persistence and range expansion.},
	language = {en},
	number = {1803},
	urldate = {2015-02-18TZ},
	journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	author = {Henriques-Silva, Renato and Boivin, Frédéric and Calcagno, Vincent and Urban, Mark C. and Peres-Neto, Pedro R.},
	month = mar,
	year = {2015},
	pmid = {25673685},
	note = {Dispersal has long been recognized as a mechanism that shapes many observed ecological and evolutionary processes. Thus, understanding the factors that promote its evolution remains a major goal in evolutionary ecology. Landscape connectivity may mediate the trade-off between the forces in favour of dispersal propensity (e.g. kin-competition, local extinction probability) and those against it (e.g. energetic or survival costs of dispersal). It remains, however, an open question how differing degrees of landscape connectivity may select for different dispersal strategies. We implemented an individual-based model to study the evolution of dispersal on landscapes that differed in the variance of connectivity across patches ranging from networks with all patches equally connected to highly heterogeneous networks. The parthenogenetic individuals dispersed based on a flexible logistic function of local abundance. Our results suggest, all else being equal, that landscapes differing in their connectivity patterns will select for different dispersal strategies and that these strategies confer a long-term fitness advantage to individuals at the regional scale. The strength of the selection will, however, vary across network types, being stronger on heterogeneous landscapes compared with the ones where all patches have equal connectivity. Our findings highlight how landscape connectivity can determine the evolution of dispersal strategies, which in turn affects how we think about important ecological dynamics such as metapopulation persistence and range expansion.},
	pages = {20142879}
}

@inproceedings{the_university_of_tokyo_designing_2014,
	title = {Designing a {Passive} {Folding} {String} {Device} with an {Electromagnet}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch161.pdf},
	doi = {10.7551/978-0-262-32621-6-ch161},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{The University of Tokyo} and Masumori, Atsushi and Mitsui, Masayoshi and Tanaka, Hiroya},
	month = jul,
	year = {2014},
	pages = {987--988}
}

@inproceedings{school_of_information_and_sciences_nagoya_university_evolution_2014,
	title = {Evolution of {Chemical} {Signals} in {Ecological} {System} {Evoked} by the "{Cry}-{Wolf}" {Plants}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch160.pdf},
	doi = {10.7551/978-0-262-32621-6-ch160},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Information and Sciences, Nagoya University} and Sakai, Megumi and Suzuki, Yasuhiro},
	month = jul,
	year = {2014},
	pages = {983--986}
}

@inproceedings{flint_center_university_of_southern_denmark_blueprint_2014,
	title = {Blueprint for {Self}-replicating and {Self}-assembling 3D {Printers}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch159.pdf},
	doi = {10.7551/978-0-262-32621-6-ch159},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{FLinT Center, University of Southern Denmark} and Buch, Mads and Rasmussen, Steen},
	month = jul,
	year = {2014},
	pages = {981--982}
}

@inproceedings{university_of_vermont_burlington_vt_05401_improving_2014,
	title = {Improving {Robot} {Behavior} {Optimization} by {Combining} {User} {Preferences}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch158.pdf},
	doi = {10.7551/978-0-262-32621-6-ch158},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Vermont, Burlington, VT 05401} and Bernatskiy, Antonine and Hornby, Gregory and Bongard, Josh},
	month = jul,
	year = {2014},
	pages = {973--980}
}

@inproceedings{biocomputation_research_group_university_of_hertfordshire_hatfield_herts_al10_9ab_uk_volving_2014,
	title = {volving {Spiking} {Neural} {Networks} for {Temporal} {Pattern} {Recognition} in the {Presence} of {Noise}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch157.pdf},
	doi = {10.7551/978-0-262-32621-6-ch157},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Biocomputation Research Group, University of Hertfordshire, Hatfield, Herts AL10 9AB, UK} and Abdelmotaleb, Ahmed and Davey, Neil and Schilstra, Maria and Steuber, Volker and Wróbel, Borys},
	month = jul,
	year = {2014},
	pages = {965--972}
}

@inproceedings{earth-life_science_institute_tokyo_institute_of_technology_vitro_2014,
	title = {In {Vitro} {Reconstruction} of {Functional} {Membrane}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch156.pdf},
	doi = {10.7551/978-0-262-32621-6-ch156},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Earth-Life Science Institute, Tokyo Institute of Technology} and Kuruma, Yutetsu and Matsubayashi, Hideaki and Ueda, Takuya},
	month = jul,
	year = {2014},
	pages = {963--964}
}

@inproceedings{computer_science_department_of_frankfurt_am_main_university_of_applied_sciences_1_nibelungenplatz_60318_frankfurt_am_main_germany_framework_2014,
	title = {Framework for {Adaptive} {Swarm} {Simulation} and {Optimization} {Using} {MapReduce}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch155.pdf},
	doi = {10.7551/978-0-262-32621-6-ch155},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Computer Science Department of Frankfurt am Main University of Applied Sciences, 1 Nibelungenplatz 60318, Frankfurt am Main, Germany} and Canyameres, Sergi and Logofătu, Doina},
	month = jul,
	year = {2014},
	pages = {957--962}
}

@inproceedings{university_of_hertfordshire_hertfordshire_uk_towards_2014,
	title = {Towards {Designing} {Artificial} {Universes} for {Artificial} {Agents} {Under} {Interaction} {Closure}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch154.pdf},
	doi = {10.7551/978-0-262-32621-6-ch154},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Hertfordshire, Hertfordshire, UK} and Biehl, Martin and Salge, Christoph and Polani, Daniel},
	month = jul,
	year = {2014},
	pages = {949--956}
}

@inproceedings{columbia_college_chicago_sounds_2014,
	title = {Sounds {Shadowing} {Agents} {Generating} {Audible} {Features} from {Emergent} {Behaviors}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch153.pdf},
	doi = {10.7551/978-0-262-32621-6-ch153},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Columbia College Chicago} and Choi, Insook and Bargar, Robin},
	month = jul,
	year = {2014},
	pages = {941--948}
}

@inproceedings{dept._of_mathematical_sciences_university_of_delaware_newark_de_19716_continuous-time_2014,
	title = {A {Continuous}-{Time} {Binary} {Consensus} {Protocol} with {Hysteric} {Units} {Applied} to the {Density} {Classification} {Problem}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch152.pdf},
	doi = {10.7551/978-0-262-32621-6-ch152},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Dept. of Mathematical Sciences, University of Delaware, Newark, DE 19716} and Montes de Oca, Marco and Rossi, Louis},
	month = jul,
	year = {2014},
	pages = {932--940}
}

@inproceedings{embodied_emotion_cognition_and_inter-action_lab_school_of_computer_science_university_of_hertfordshire_college_lane_hatfield_herts_al10_9ab_u.k._pleasure_2014,
	title = {Pleasure, {Persistence} and {Opportunism} in {Action} {Selection}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch151.pdf},
	doi = {10.7551/978-0-262-32621-6-ch151},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Embodied Emotion, Cognition and (Inter-)Action Lab School of Computer Science, University of Hertfordshire College Lane, Hatfield, Herts, AL10 9AB, U.K.} and Lewis, Matthew and Hiolle, Antoine and Cañamero, Lola},
	month = jul,
	year = {2014},
	pages = {932--933}
}

@inproceedings{university_of_guelph_ontario_canada_effects_2014,
	title = {The {Effects} of {Elitism} on {Spatial} {Coevolutionary} {GAs}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch150.pdf},
	doi = {10.7551/978-0-262-32621-6-ch150},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Guelph, Ontario, Canada} and McLaughlin, Morgan and Wineberg, Mark},
	month = jul,
	year = {2014},
	pages = {924--931}
}

@inproceedings{school_of_informatics_&_computing_indiana_university_evaluating_2014,
	title = {Evaluating {Topological} {Models} of {Neuromodulation} in {Polyworld}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch149.pdf},
	doi = {10.7551/978-0-262-32621-6-ch149},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Informatics \& Computing, Indiana University} and Yoder, Jason and Yaeger, Larry},
	month = jul,
	year = {2014},
	pages = {916--923}
}

@inproceedings{southern_nazarene_university_bethany_ok_73008_effects_2014,
	title = {Effects of {Personality} {Distribution} on {Collective} {Behavior}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch148.pdf},
	doi = {10.7551/978-0-262-32621-6-ch148},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Southern Nazarene University, Bethany, OK 73008} and Eskridge, Brent and Schlupp, Ingo},
	month = jul,
	year = {2014},
	pages = {908--915}
}

@inproceedings{dept._of_eecs_computer_science_division_university_of_central_florida_orlando_fl_32816_usa_steps_2014,
	title = {Steps {Toward} a {Modular} {Library} for {Turning} {Any} {Evolutionary} {Domain} into an {Online} {Interactive} {Platform}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch147.pdf},
	doi = {10.7551/978-0-262-32621-6-ch147},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Dept. of EECS (Computer Science Division), University of Central Florida, Orlando, FL 32816 USA} and Szerlip, Paul and Stanley, Kenneth},
	month = jul,
	year = {2014},
	pages = {900--907}
}

@inproceedings{the_reilly_center_for_science_technology_and_values_university_of_notre_dame_notre_dame_in_46556_computation_2014,
	title = {Computation and {Scientific} {Discovery}? {A} {Bio}-{Inspired} {Approach}},
	isbn = {9780262326216},
	shorttitle = {Computation and {Scientific} {Discovery}?},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch146.pdf},
	doi = {10.7551/978-0-262-32621-6-ch146},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{The Reilly Center for Science, Technology and Values, University of Notre Dame, Notre Dame, IN 46556} and Muntean, Ioan},
	month = jul,
	year = {2014},
	pages = {892--899}
}

@inproceedings{demo_lab_brandeis_university_waltham_ma_02453_feedback_2014,
	title = {Feedback {Control} of {Evolving} {Swarms}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch145.pdf},
	doi = {10.7551/978-0-262-32621-6-ch145},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{DEMO Lab, Brandeis University, Waltham, MA 02453} and Gold, Jacob and Wang, Adam and Harrington, Kyle},
	month = jul,
	year = {2014},
	pages = {884--891}
}

@inproceedings{school_of_informatics_and_computing_indiana_university_bloomington_in_47406_usa_designing_2014,
	title = {Designing a {Minimalist} {Socially} {Aware} {Robotic} {Agent} for the {Home}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch144.pdf},
	doi = {10.7551/978-0-262-32621-6-ch144},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Informatics and Computing, Indiana University, Bloomington, IN 47406, USA} and Francisco, Matthew and Wood, Ian and Šabanović, Selma and Rocha, Luis},
	month = jul,
	year = {2014},
	pages = {876--883}
}

@inproceedings{bristol_robotics_lab_uwe_bristol_uk_estimating_2014,
	title = {Estimating the {Energy} {Cost} of ({Artificial}) {Evolution}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch143.pdf},
	doi = {10.7551/978-0-262-32621-6-ch143},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Bristol Robotics lab, UWE Bristol, UK} and Winfield, Alan},
	month = jul,
	year = {2014},
	pages = {872--875}
}

@inproceedings{embodied_emotion_cognition_and_inter-action_lab_school_of_computer_science_&_stri_university_of_hertfordshire_united_kingdom_robot_2014,
	title = {A {Robot} that {Uses} {Arousal} to {Detect} {Learning} {Challenges} and {Seek} {Help}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch142.pdf},
	doi = {10.7551/978-0-262-32621-6-ch142},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Embodied Emotion, Cognition, and (Inter-)Action Lab, School of Computer Science \& STRI, University of Hertfordshire, United Kingdom} and Hiolle, Antoine and Lewis, Matthew and Cañamero, Lola},
	month = jul,
	year = {2014},
	pages = {864--871}
}

@inproceedings{university_of_southampton_southampton_uk_pre-template_2014,
	title = {Pre-{Template} {Metabolic} {Replicators}: {Genotype}-{Phenotype} {Decoupling} as a {Route} to {Evolvability}},
	isbn = {9780262326216},
	shorttitle = {Pre-{Template} {Metabolic} {Replicators}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch141.pdf},
	doi = {10.7551/978-0-262-32621-6-ch141},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Southampton, Southampton, UK} and Hurndall, William and Watson, Richard and Brede, Markus},
	month = jul,
	year = {2014},
	pages = {856--863}
}

@inproceedings{universite_du_havre_le_havre_france_76600_close_2014,
	title = {Close {Returns} {Plots} for {Detecting} a {Chaotic} {Source} in an {Interaction} {Network}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch140.pdf},
	doi = {10.7551/978-0-262-32621-6-ch140},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Universite du Havre, Le Havre, France 76600} and Rabai, Haifa and Charrier, Rodolphe and Bertelle, Cyrille},
	month = jul,
	year = {2014},
	pages = {849--855}
}

@inproceedings{androtics_llc_tucson_arizona_85733_usa_evolution_2014,
	title = {Evolution as a {Random} {Walk} on a {High}-{Dimensional} {Manifold} {Defined} by {Physical} {Law}: {Implications} for {Open}-{Ended} {Artificial} {Life}},
	isbn = {9780262326216},
	shorttitle = {Evolution as a {Random} {Walk} on a {High}-{Dimensional} {Manifold} {Defined} by {Physical} {Law}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch139.pdf},
	doi = {10.7551/978-0-262-32621-6-ch139},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Androtics LLC, Tucson, Arizona 85733, USA} and Nelson, Andrew and Bailey, Brenae},
	month = jul,
	year = {2014},
	pages = {847--848}
}

@inproceedings{university_of_guelph_effect_2014,
	title = {The {Effect} of {Network} {Structure} on the {Spatial} {Coevolutionary} {GA}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch138.pdf},
	doi = {10.7551/978-0-262-32621-6-ch138},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Guelph} and McLaughlin, Megan and Wineberg, Mark},
	month = jul,
	year = {2014},
	pages = {845--846}
}

@inproceedings{university_of_hertfordshire_hatfield_uk_dont_2014,
	title = {Don't {Believe} {Everything} {You} {Hear}: {Preserving} {Relevant} {Information} by {Discarding} {Social} {Information}},
	isbn = {9780262326216},
	shorttitle = {Don't {Believe} {Everything} {You} {Hear}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch137.pdf},
	doi = {10.7551/978-0-262-32621-6-ch137},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Hertfordshire, Hatfield, UK} and Salge, Christopher and Polani, Daniel},
	month = jul,
	year = {2014},
	pages = {837--844}
}

@inproceedings{department_of_computer_science_university_of_new_mexico_albuquerque_nm_87131_real-time_2014,
	title = {Real-{Time} {Evolution} of {iAnt} {Robot} {Foraging} {Strategies}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch136.pdf},
	doi = {10.7551/978-0-262-32621-6-ch136},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Computer Science, University of New Mexico, Albuquerque, NM 87131} and Hecker, Joshua and Moses, Melanie},
	month = jul,
	year = {2014},
	pages = {835--836}
}

@inproceedings{demo_lab_school_of_computer_science_brandeis_university_waltham_ma_02453_resistance_2014,
	title = {The {Resistance} of {Swarm} {Ecosystem} {Under} {Environmental} {Variation}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch135.pdf},
	doi = {10.7551/978-0-262-32621-6-ch135},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{DEMO Lab, School of Computer Science, Brandeis University, Waltham, MA 02453} and Lowell, Jessica and Harrington, Kyle and Pollack, Jordan},
	month = jul,
	year = {2014},
	pages = {827--834}
}

@inproceedings{demo_lab_school_of_computer_science_brandeis_university_waltham_ma_02453_effect_2014,
	title = {The {Effect} of {Connection} {Cost} on {Modularity} in {Evolved} {Neural} {Networks}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch134.pdf},
	doi = {10.7551/978-0-262-32621-6-ch134},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{DEMO Lab, School of Computer Science, Brandeis University, Waltham, MA 02453} and Lowell, Jessica and Pollack, Jordan},
	month = jul,
	year = {2014},
	pages = {821--826}
}

@inproceedings{ece_dept._concordia_university_1455_de_maisonneuve_blvd._o._montreal_qc_canada_h3g1m8_coderouge:_2014,
	title = {{CodeRouge}: a {Project} to {Evolve} {Life}-like {Autonomous} {Programs}},
	isbn = {9780262326216},
	shorttitle = {{CodeRouge}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch133.pdf},
	doi = {10.7551/978-0-262-32621-6-ch133},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{ECE Dept., Concordia University, 1455 de Maisonneuve Blvd. O., Montreal, QC, Canada H3G1M8} and Kharma, Nawwaf and Buckley, William},
	month = jul,
	year = {2014},
	pages = {819--820}
}

@inproceedings{mit_computer_science_and_artificial_intelligence_laboratory_spatial_2014,
	title = {Spatial {Patterning} with the {Rule} of {Normal} {Neighbors}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch132.pdf},
	doi = {10.7551/978-0-262-32621-6-ch132},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{MIT Computer Science and Artificial Intelligence Laboratory} and Brodsky, Micah},
	month = jul,
	year = {2014},
	pages = {817--818}
}

@inproceedings{department_of_software_engineering_afeka_-_academic_college_of_engineering_tel_aviv_israel_artificial_2014,
	title = {An {Artificial} {Chemistry} for the '{Lipid} {World}' {Scenario}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch131.pdf},
	doi = {10.7551/978-0-262-32621-6-ch131},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Software Engineering, Afeka - Academic College of Engineering, Tel aviv, Israel} and Shenhav, Barak},
	month = jul,
	year = {2014},
	pages = {815--816}
}

@inproceedings{dept._of_computer_science_and_engineering_graduate_school_of_engineering_nagoya_institute_of_technology_gokiso-cho_showa-ku_nagoya_466-8555_japan_effect_2014,
	title = {The {Effect} of the {Network} {Structure} {Differences} on the {Diffusion} of {Items}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch130.pdf},
	doi = {10.7551/978-0-262-32621-6-ch130},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Dept. of Computer Science and Engineering, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho Showa-ku Nagoya 466-8555 Japan} and Onoda, Shota and Kato, Shohei and Mutoh, Atsuko},
	month = jul,
	year = {2014},
	pages = {809--814}
}

@inproceedings{max-planck-institute_for_dynamics_of_complex_technical_systems_39106_magdeburg_germany_problems_2014,
	title = {Problems {During} {Cell} {Cycle} in {Artificial} {Cell} {Modeling}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch110.pdf},
	doi = {10.7551/978-0-262-32621-6-ch110},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Max-Planck-Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany} and Schneider, Eugenia and Mangold, Michael},
	month = jul,
	year = {2014},
	pages = {691--692}
}
@inproceedings{bangor_university_wales_uk_berry_2014,
	title = {Berry {Eaters}: {Learning} {Color} {Concepts} with {Template} {Based} {Evolution}},
	isbn = {9780262326216},
	shorttitle = {Berry {Eaters}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch077.pdf},
	doi = {10.7551/978-0-262-32621-6-ch077},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Bangor University, Wales, UK} and Headleand, Christopher and Cenydd, Llyr and Teahan, William},
	month = jul,
	year = {2014},
	pages = {473--480}
}

@inproceedings{laboratory_of_intelligent_systems_ecole_polytechnique_federale_de_lausanne_epfl_lausanne_switzerland_online_2014,
	title = {Online {Extreme} {Evolutionary} {Learning} {Machines}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch076.pdf},
	doi = {10.7551/978-0-262-32621-6-ch076},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Laboratory of Intelligent Systems, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland} and Auerbach, Joshua and Fernando, Chrisantha and Floreano, Dario},
	month = jul,
	year = {2014},
	pages = {465--472}
}

@inproceedings{neuromorphic_cognitive_systems_lab_kurchatov_nbics-centre_national_research_center_kurchatov_institute_1_kurchatov_sqr._moscow_russia_evolution_2014,
	title = {Evolution, {Development} and {Learning} with {Predictor} {Neural} {Networks}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch075.pdf},
	doi = {10.7551/978-0-262-32621-6-ch075},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Neuromorphic Cognitive Systems Lab, Kurchatov NBICS-Centre, National Research Center “Kurchatov Institute”, 1 Kurchatov sqr., Moscow, Russia} and Lakhman, Konstantin and Burtsev, Mikhail},
	month = jul,
	year = {2014},
	pages = {457--464}
}

@inproceedings{sorbonne_universites_upmc_univ_paris_06_umr_722_isir_f-75005_paris_france_abstract_2014,
	title = {Abstract of: “{On} the {Relationship} between {Generative} {Encodings}, {Regularity}, and {Learning} {Abilities} when {Evolving} {Plastic} {Artificial} {Networks}”},
	isbn = {9780262326216},
	shorttitle = {Abstract of},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch074.pdf},
	doi = {10.7551/978-0-262-32621-6-ch074},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Sorbonne Universites, UPMC Univ Paris 06, UMR 722, ISIR, F-75005, Paris, France} and Mouret, Jean-Baptiste and Tonelli, Paul},
	month = jul,
	year = {2014},
	pages = {455--456}
}

@inproceedings{evolving_systems_laboratory_faculty_of_biology_adam_mickiewicz_university_poznan_poland_poet:_2014,
	title = {{POET}: {An} {Evo}-{Devo} {Method} to {Optimize} the {Weights} of {Large} {Artificial} {Neural} {Networks}},
	isbn = {9780262326216},
	shorttitle = {{POET}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch073.pdf},
	doi = {10.7551/978-0-262-32621-6-ch073},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Evolving Systems Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland} and Fontana, Alessandro and Soltoggio, Andrea and Wróbel, Borys},
	month = jul,
	year = {2014},
	pages = {447--454}
}

@inproceedings{the_university_of_texas_at_austin_austin_tx_78712_evolving_2014,
	title = {Evolving {Multimodal} {Behavior} {Through} {Subtask} and {Switch} {Neural} {Networks}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch072.pdf},
	doi = {10.7551/978-0-262-32621-6-ch072},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{The University of Texas at Austin, Austin, TX 78712} and Li, Xun and Miikkulainen, Risto},
	month = jul,
	year = {2014},
	pages = {439--446}
}

@inproceedings{csiro_autonomous_systems_program_1_technology_court_pullenvale_qld_4069_australia_evolving_2014,
	title = {Evolving {Spiking} {Networks} for {Turbulence}-{Tolerant} {Quadrotor} {Control}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch071.pdf},
	doi = {10.7551/978-0-262-32621-6-ch071},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{CSIRO, Autonomous Systems Program, 1 Technology Court Pullenvale, QLD 4069 Australia} and Howard, David and Elfes, Alberto},
	month = jul,
	year = {2014},
	pages = {431--438}
}

@inproceedings{school_of_informatics_and_computing_indiana_university_bloomington_in_47406_usa_structure_2014,
	title = {Structure and {Dynamics} {Affect} the {Controlability} of {Complex} {Systems}: {A} {Preliminary} {Study}},
	isbn = {9780262326216},
	shorttitle = {Structure and {Dynamics} {Affect} the {Controlability} of {Complex} {Systems}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch070.pdf},
	doi = {10.7551/978-0-262-32621-6-ch070},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Informatics and Computing, Indiana University, Bloomington, IN 47406, USA} and Gates, Alexander and Rocha, Luis},
	month = jul,
	year = {2014},
	pages = {429--430}
}

@inproceedings{instituto_de_investigaciones_en_matematicas_aplicadas_y_en_sistemas_unam_mexico_d.f._01000_random_2014,
	title = {Random {Fuzzy} {Networks}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch069.pdf},
	doi = {10.7551/978-0-262-32621-6-ch069},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, UNAM, Mexico, D.F. 01000} and Zapata, Octavio and Gershenson, Carlos},
	month = jul,
	year = {2014},
	pages = {427--428}
}

@inproceedings{department_of_earth_&_planetary_sciences_graduate_school_of_science_kobe_university_1-1_rokkodaicho_nada_kobe_657-8501_japan_relationship_2014,
	title = {On the {Relationship} between {Local} {Rewiring} {Rules} and {Stationary} {Out}-{Degree} {Distributions} in {Adaptive} {Random} {Boolean} {Network} {Models}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch068.pdf},
	doi = {10.7551/978-0-262-32621-6-ch068},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Earth \& Planetary Sciences, Graduate School of Science, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501, Japan} and Haruna, Taichi and Tanaka, Sayaka},
	month = jul,
	year = {2014},
	pages = {420--426}
}

@inproceedings{georgetown_university_37th_&_o_st._nw_washington_dc_20057_artificial_2014,
	title = {The {Artificial} {Life}-{Form} {As} {Entrepreneur}: {Synthetic} {Organism}-{Enterprises} and the {Reconceptualization} of {Business}},
	isbn = {9780262326216},
	shorttitle = {The {Artificial} {Life}-{Form} {As} {Entrepreneur}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch067.pdf},
	doi = {10.7551/978-0-262-32621-6-ch067},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Georgetown University, 37th \& O St. NW, Washington, DC 20057} and Gladden, Matthew},
	month = jul,
	year = {2014},
	pages = {417--418}
}

@inproceedings{graduate_school_of_information_science_nagoya_university_gene-culture_2014,
	title = {Gene-{Culture} {Coevolution} of {Language}: {Measurement}-{Interval} {Dependence} of {Evolutionary} {Rate}},
	isbn = {9780262326216},
	shorttitle = {Gene-{Culture} {Coevolution} of {Language}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch066.pdf},
	doi = {10.7551/978-0-262-32621-6-ch066},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Graduate School of Information Science, Nagoya University} and Azumagakito, Tsubasa and Suzuki, Reiji and Arita, Takaya},
	month = jul,
	year = {2014},
	pages = {415--416}
}

@inproceedings{institute_for_complex_systems_simulations_university_of_southampton_uk_so17_1bj_origin_2014,
	title = {The {Origin} of {Culture}: {Selective} {Conditions} for {Horizontal} {Information} {Transfer}},
	isbn = {9780262326216},
	shorttitle = {The {Origin} of {Culture}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch065.pdf},
	doi = {10.7551/978-0-262-32621-6-ch065},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Institute for Complex Systems Simulations, University of Southampton, UK SO17 1BJ} and Gonzalez, Miguel and Watson, Richard and Noble, Jason and Bullock, Seth},
	month = jul,
	year = {2014},
	pages = {408--414}
}

@inproceedings{claremont_graduate_university_agent-based_2014,
	title = {An {Agent}-{Based} {Model} of {Indirect} {Minority} {Influence} on {Social} {Change}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch064.pdf},
	doi = {10.7551/978-0-262-32621-6-ch064},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Claremont Graduate University} and Jung, Jiin and Bramson, Aaron},
	month = jul,
	year = {2014},
	pages = {400--407}
}

@inproceedings{anan_national_college_of_technology_anan_tokushima_japan_invasion_2014,
	title = {Invasion of {Cooperation} in {Scale}-{Free} {Networks}: {Accumulated} vs. {Average} {Payoffs}},
	isbn = {9780262326216},
	shorttitle = {Invasion of {Cooperation} in {Scale}-{Free} {Networks}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch063.pdf},
	doi = {10.7551/978-0-262-32621-6-ch063},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Anan National College of Technology, Anan, Tokushima, Japan} and Ichinose, Genki and Sayama, Hiroki},
	month = jul,
	year = {2014},
	pages = {398--399}
}

@inproceedings{university_of_tokyo_japan_pseudo-static_2014,
	title = {Pseudo-{Static} {Cooperators}: {Moving} {Isn}'t {Always} about {Going} {Somewhere}},
	isbn = {9780262326216},
	shorttitle = {Pseudo-{Static} {Cooperators}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch062.pdf},
	doi = {10.7551/978-0-262-32621-6-ch062},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Tokyo, Japan} and Witkowski, Olaf and Aubert, Nathanael},
	month = jul,
	year = {2014},
	pages = {392--397}
}

@inproceedings{university_of_southampton_southampton_uk_advancing_2014,
	title = {Advancing {Social} {Simulation}: {Lessons} from {Demography}},
	isbn = {9780262326216},
	shorttitle = {Advancing {Social} {Simulation}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch061.pdf},
	doi = {10.7551/978-0-262-32621-6-ch061},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Southampton, Southampton, UK} and Silverman, Eric and Bijak, Jakub and Courgeau, Daniel and Franck, Robert},
	month = jul,
	year = {2014},
	pages = {384--391}
}

@inproceedings{department_of_knowledge_engineering_maastricht_university_the_netherlands_effects_2014,
	title = {Effects of {Evolution} on the {Emergence} of {Scale} {Free} {Networks}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch060.pdf},
	doi = {10.7551/978-0-262-32621-6-ch060},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Knowledge Engineering, Maastricht University, The Netherlands} and Ranjbar-Sahraei, Bijan and Bloembergen, Dean and Ammar, Haitham and Tuyls, Karl and Weiss, Gerhard},
	month = jul,
	year = {2014},
	pages = {376--383}
}

@inproceedings{information_systems_department_faculty_of_business_and_economics_university_of_lausanne_switzerland_reds:_2014,
	title = {{REDS}: {An} {Energy}-{Constrained} {Spatial} {Social} {Network} {Model}},
	isbn = {9780262326216},
	shorttitle = {{REDS}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch059.pdf},
	doi = {10.7551/978-0-262-32621-6-ch059},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Information Systems Department, Faculty of Business and Economics, University of Lausanne, Switzerland} and Antonioni, Alberto and Bullock, Seth and Tomassini, Marco},
	month = jul,
	year = {2014},
	pages = {368--375}
}

@inproceedings{beacon_center_for_the_study_of_evolution_in_action_michigan_state_university_east_lansing_mi_evolution_2014,
	title = {Evolution of {Autonomous} {Hierarchy} {Formation} and {Maintenance}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch058.pdf},
	doi = {10.7551/978-0-262-32621-6-ch058},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI} and Hintze, Arend and Mirmomeni, Masoud},
	month = jul,
	year = {2014},
	pages = {366--367}
}

@inproceedings{iridia/ulb_bruxelles_-_belgium_between_2014,
	title = {In {Between} {Schelling} and {Maynard}-{Smith}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch057.pdf},
	doi = {10.7551/978-0-262-32621-6-ch057},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{IRIDIA/ULB, Bruxelles - Belgium} and Bersini, Hughes},
	month = jul,
	year = {2014},
	pages = {360--364}
}

@inproceedings{department_of_computer_science_university_of_paderborn_germany_evolution_2014,
	title = {Evolution of {Collective} {Behaviors} by {Minimizing} {Surprise}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch055.pdf},
	doi = {10.7551/978-0-262-32621-6-ch055},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Computer Science, University of Paderborn, Germany} and Hamann, Heiko},
	month = jul,
	year = {2014},
	pages = {344--351}
}

@inproceedings{georgia_institute_of_technology_atlanta_ga_30332_inferring_2014,
	title = {Inferring {Social} {Structure} of {Animal} {Groups} from {Tracking} {Data}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch054.pdf},
	doi = {10.7551/978-0-262-32621-6-ch054},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Georgia Institute of Technology, Atlanta, GA 30332} and Hrolenok, Brian and Maddali, Hanuma and Novitzky, Michael and Balch, Tucker},
	month = jul,
	year = {2014},
	pages = {336--343}
}

@inproceedings{beth_israel_deaconess_medical_center_harvard_medical_school_boston_ma_can_2014,
	title = {Can {Active} {Perception} {Generate} {Bistability}? {Heterogeneous} {Collective} {Dynamics} and {Vascular} {Patterning}},
	isbn = {9780262326216},
	shorttitle = {Can {Active} {Perception} {Generate} {Bistability}?},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch053.pdf},
	doi = {10.7551/978-0-262-32621-6-ch053},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Beth Israel Deaconess Medical Center, Harvard Medical School, Boston MA} and Bentley, Katie and Harrington, Kyle and Regan, Erzsébet},
	month = jul,
	year = {2014},
	pages = {328--335}
}

@inproceedings{collective_dynamics_of_complex_systems_research_group_binghamton_university_state_university_of_new_york_binghamton_ny_13902-6000_usa_four_2014,
	title = {Four {Classes} of {Morphogenetic} {Collective} {Systems}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch052.pdf},
	doi = {10.7551/978-0-262-32621-6-ch052},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Collective Dynamics of Complex Systems Research Group Binghamton University, State University of New York, Binghamton, NY 13902-6000, USA} and Sayama, Hiroki},
	month = jul,
	year = {2014},
	pages = {320--327}
}

@inproceedings{organic_computing_university_of_augsburg_bavaria_germany_swarm_2014,
	title = {Swarm {Grammars} {GD}: {Interactive} {Exploration} of {Swarm} {Dynamics} and {Structural} {Development}},
	isbn = {9780262326216},
	shorttitle = {Swarm {Grammars} {GD}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch051.pdf},
	doi = {10.7551/978-0-262-32621-6-ch051},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Organic Computing, University of Augsburg, Bavaria, Germany} and von Mammen, Sebastein and Edenhofer, Sarah},
	month = jul,
	year = {2014},
	pages = {312--319}
}

@inproceedings{the_university_of_texas_at_austin_austin_tx_78712_exploring_2014,
	title = {Exploring {Conditions} {That} {Select} for the {Evolution} of {Cooperative} {Group} {Foraging}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch050.pdf},
	doi = {10.7551/978-0-262-32621-6-ch050},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{The University of Texas at Austin, Austin, TX 78712} and Haley, Patrick and Olson, Randal and Dyer, Fred and Adami, Christoph},
	month = jul,
	year = {2014},
	pages = {310--311}
}

@inproceedings{university_of_tokyo_japan_emergence_2014,
	title = {Emergence of {Signal}-{Based} {Swarmimg}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch049.pdf},
	doi = {10.7551/978-0-262-32621-6-ch049},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Tokyo, Japan} and Witkowski, Olaf and Ikegami, Takashi},
	month = jul,
	year = {2014},
	pages = {302--309}
}

@inproceedings{laboratory_for_entomology_katholieke_universiteit_leuven_59_naamsestraat_-_bus_2466_3000_leuven_belgium_scale-free_2014,
	title = {Scale-{Free} {Correlations} in {Collective} {Motion} with {Position}-{Based} {Interactions}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch048.pdf},
	doi = {10.7551/978-0-262-32621-6-ch048},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Laboratory for Entomology, Katholieke Universiteit Leuven, 59 Naamsestraat - bus 2466, 3000 Leuven, Belgium} and Ferrante, Eliseo and Turgut, Ali and Huepe, Christián},
	month = jul,
	year = {2014},
	pages = {Tom--Wenseleers}
}

@inproceedings{department_of_electronics_university_of_york_relay_2014,
	title = {The {Relay} {Chain}: {A} {Scalable} {Dynamic} {Communication} {Link} between an {Exploratory} {Underwater} {Shoal} and a {Surface} {Vehicle}},
	isbn = {9780262326216},
	shorttitle = {The {Relay} {Chain}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch047.pdf},
	doi = {10.7551/978-0-262-32621-6-ch047},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Electronics, University of York} and Naylor, Becky and Read, Mark and Timmis, Jon and Tyrell, Andy},
	month = jul,
	year = {2014},
	pages = {290--297}
}

@inproceedings{universite_de_lorraine_inria_campus_scientifique_bp_239_vandoeuvre-les-nancy_cedex_f-54506_comparison_2014,
	title = {Comparison of {Selection} {Methods} in {On}-{Line} {Distributed} {Evolutionary} {Robotics}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch046.pdf},
	doi = {10.7551/978-0-262-32621-6-ch046},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Université de Lorraine, INRIA, Campus scientifique BP 239 Vandoeuvre-les-Nancy Cedex, F-54506} and Fernández Pérez, Iñaki and Boumaza, Amine and Charpillet, François},
	month = jul,
	year = {2014},
	pages = {282--289}
}

@inproceedings{texas_a&m_university_college_station_tx_77840_associating_2014,
	title = {Associating {Nearby} {Robots} to {Their} {Voices}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch045.pdf},
	doi = {10.7551/978-0-262-32621-6-ch045},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Texas A\&M University, College Station, TX 77840} and Ivanov, Plamen and Shell, Dylan},
	month = jul,
	year = {2014},
	pages = {274--281}
}

@inproceedings{sorbonne_universites_upmc_univ_paris_06_umr_7222_isir_f-75005_paris_france_embodied_2014,
	title = {Embodied {Evolutionary} {Robotics} with {Large} {Number} of {Robots}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch044.pdf},
	doi = {10.7551/978-0-262-32621-6-ch044},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Sorbonne Universites, UPMC Univ Paris 06, UMR 7222, ISIR, F-75005, Paris, France} and Bredeche, Nicolas},
	month = jul,
	year = {2014},
	pages = {272--273}
}

@inproceedings{institute_for_complex_systems_simulation_and_school_of_electronics_and_computer_science_university_of_southampton_united_kingdom_understanding_2014,
	title = {Understanding the {Role} of {Recruitment} in {Collective} {Robot} {Foraging}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch043.pdf},
	doi = {10.7551/978-0-262-32621-6-ch043},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Institute for Complex Systems Simulation and School of Electronics and Computer Science University of Southampton, United Kingdom} and Pitonakova, Lenka and Crowder, Richard and Bullock, Seth},
	month = jul,
	year = {2014},
	pages = {264--271}
}
@inproceedings{school_of_computing_mathematics_&_digital_technology_manchester_metropolitan_university_evolving_2014,
	title = {Evolving {Morphologies} with {CPPN}-{NEAT} and a {Dynamic} {Substrate}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch042.pdf},
	doi = {10.7551/978-0-262-32621-6-ch042},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Computing, Mathematics \& Digital Technology, Manchester Metropolitan University} and Richards, Daniel and Amos, Martyn},
	month = jul,
	year = {2014},
	pages = {255--262}
}

@inproceedings{the_university_of_texas_at_austin_austin_tx_78712_adopting_2014,
	title = {Adopting {Morphology} to {Multiple} {Tasks} in {Evolved} {Virtual} {Creatures}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch041.pdf},
	doi = {10.7551/978-0-262-32621-6-ch041},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{The University of Texas at Austin, Austin, TX 78712} and Lessin, Dan and Fussell, Don and Miikkulainen, Risto},
	month = jul,
	year = {2014},
	pages = {247--254}
}

@inproceedings{graduate_school_of_information_science_nagoya_university_furo-cho_chikusa-ku_nagoya_464-8601_japan_fine_2014,
	title = {Fine {Grained} {Artificial} {Development} for {Body}-{Controller} {Coevolution} of {Soft}-{Bodied} {Animats}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch040.pdf},
	doi = {10.7551/978-0-262-32621-6-ch040},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan} and Joachimczak, Michal and Suzuki, Reji and Arita, Takaya},
	month = jul,
	year = {2014},
	pages = {239--246}
}

@inproceedings{computer_science_department_union_college_schenectady_ny_12308_evolution_2014,
	title = {Evolution of {Locomotion} on a {Physical} {Tensegrity} {Robot}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch039.pdf},
	doi = {10.7551/978-0-262-32621-6-ch039},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Computer Science Department, Union College, Schenectady NY 12308} and Khazanov, Mark and Jocque, Julian and Rieffel, John},
	month = jul,
	year = {2014},
	pages = {232--238}
}

@inproceedings{the_biorobotics_institute_scuola_superiore_santanna_pisa_italy_model-based_2014,
	title = {A {Model}-{Based} {Framework} to {Investigate} {Morphological} {Computation} in {Muscular} {Hydrostats} and to {Design} {Soft} {Robotic} {Arms}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch038.pdf},
	doi = {10.7551/978-0-262-32621-6-ch038},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{The BioRobotics Institute, Scuola Superiore Sant’Anna, Pisa, Italy} and Cacucciolo, Vito and Cianchetti, Matteo and Laschi, Cecilia},
	month = jul,
	year = {2014},
	pages = {230--231}
}

@inproceedings{creative_machines_lab_cornell_university._ithaca_ny_evolved_2014,
	title = {Evolved {Electrophysiological} {Soft} {Robots}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch037.pdf},
	doi = {10.7551/978-0-262-32621-6-ch037},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Creative Machines Lab, Cornell University. Ithaca, NY} and Cheney, Nicholas and Clune, Jeff and Lipson, Hod},
	month = jul,
	year = {2014},
	pages = {222--229}
}

@inproceedings{instituto_de_telecomunicacoes_lisbon_portugal_systematic_2014,
	title = {Systematic {Derivation} of {Behaviour} {Characterisations} in {Evolutionary} {Robotics}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch036.pdf},
	doi = {10.7551/978-0-262-32621-6-ch036},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Instituto de Telecomunicacoes, Lisbon, Portugal} and Gomes, Jorge and Mariano, Pedro and Christensen, Anders},
	month = jul,
	year = {2014},
	pages = {212--219}
}

@inproceedings{instituto_de_telecomunicacoes_lisboa_portugal_jbotevolver:_2014,
	title = {{JBotEvolver}: {A} {Versatile} {Simulation} {Program} for {Evolutionary} {Robotics}},
	isbn = {9780262326216},
	shorttitle = {{JBotEvolver}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch035.pdf},
	doi = {10.7551/978-0-262-32621-6-ch035},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Instituto de Telecomunicacoes, Lisboa, Portugal} and Duarte, Miguel and Silva, Fernando and Rodrigues, Tiago and Moura Oliveira, Sancho and Christensen, Anders},
	month = jul,
	year = {2014},
	pages = {210--211}
}

@inproceedings{dept._of_eecs_computer_science_division_university_of_central_florida_orlando_fl_32816_usa_real-time_2014,
	title = {Real-time {Hebbian} {Learning} from {Autoencoder} {Features} for {Control} {Tasks}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch034.pdf},
	doi = {10.7551/978-0-262-32621-6-ch034},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Dept. of EECS (Computer Science Division), University of Central Florida, Orlando, FL 32816 USA} and Pugh, Justin and Soltoggio, Andrea and Stanley, Kenneth},
	month = jul,
	year = {2014},
	pages = {202--209}
}

@inproceedings{michigan_state_university_east_lansing_mi_usa_48824_hold_2014,
	title = {Hold the {Spot}: {Evolution} of {Generalized} {Station} {Keeping} for an {Aquatic} {Robot}},
	isbn = {9780262326216},
	shorttitle = {Hold the {Spot}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch033.pdf},
	doi = {10.7551/978-0-262-32621-6-ch033},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Michigan State University, East Lansing, MI, USA 48824} and Moore, Jared and Clark, Anthony},
	month = jul,
	year = {2014},
	pages = {200--201}
}

@inproceedings{university_of_modena_and_reggio_emilia_idiotypic_2014,
	title = {Idiotypic {Networks} for {Evolutionary} {Controllers} in {Virtual} {Creatures}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch032.pdf},
	doi = {10.7551/978-0-262-32621-6-ch032},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Modena and Reggio Emilia} and Capodieci, Nicola and Hart, Emma and Cabri, Giacomo},
	month = jul,
	year = {2014},
	pages = {192--199}
}

@inproceedings{embodied_emotion_cognition_and_inter-action_lab_school_of_computer_science_&_stri_university_of_hertfordshire_hormonal_2014,
	title = {Hormonal {Modulation} of {Development} and {Behaviour} {Permits} a {Robot} to {Adapt} to {Novel} {Interactions}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch031.pdf},
	doi = {10.7551/978-0-262-32621-6-ch031},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Embodied Emotion, Cognition and (Inter-)Action Lab School of Computer Science \& STRI, University of Hertfordshire} and Lones, John and Lewis, Matthew and Cañamero, Lola},
	month = jul,
	year = {2014},
	pages = {184--191}
}

@inproceedings{centre_for_computational_neuroscience_and_robotics_university_of_sussex_active_2014,
	title = {Active {Shape} {Discrimination} with {Physical} {Reservoir} {Computers}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch030.pdf},
	doi = {10.7551/978-0-262-32621-6-ch030},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Centre for Computational Neuroscience and Robotics, University of Sussex} and Johnson, Christopher and Philippides, Andrew and Husbands, Philip},
	month = jul,
	year = {2014},
	pages = {176--183}
}

@inproceedings{embodied_emotion_cognition_and_inter-action_lab_university_of_hertfordshire_school_of_computer_science_hatfield_uk_habit-based_2014,
	title = {Habit-{Based} {Regulation} of {Essential} {Variables}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch029.pdf},
	doi = {10.7551/978-0-262-32621-6-ch029},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Embodied Emotion, Cognition and (Inter-)Action Lab, University of Hertfordshire, School of Computer Science, Hatfield, UK,} and Egbert, Matthew and Cañamero, Lola},
	month = jul,
	year = {2014},
	pages = {168--175}
}

@inproceedings{ubiant_lyon_france_bootstrapping_2014,
	title = {On {Bootstrapping} {Sensori}-{Motor} {Patterns} for a {Constructivist} {Learning} {System} in {Continuous} {Environments}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch028.pdf},
	doi = {10.7551/978-0-262-32621-6-ch028},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{ubiant, Lyon, France} and Mazac, Sébastien and Armetta, Frédéric and Hassas, Salima},
	month = jul,
	year = {2014},
	pages = {160--167}
}

@inproceedings{haasdijk_making_2014,
	title = {Making {MONEE}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch027.pdf},
	doi = {10.7551/978-0-262-32621-6-ch027},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {Haasdijk, Evert and Bredeche, Nicolas and Eiben, A. E.},
	month = jul,
	year = {2014},
	pages = {158--159}
}

@inproceedings{sorbonne_universites_upmc_univ_paris_06_umr_722_isir_f-75005_paris_france_abstract_2014,
	title = {Abstract of: “{Fast} {Damage} {Recovery} in {Robotics} with the {T}-{Resilience} {Algorithm}”},
	isbn = {9780262326216},
	shorttitle = {Abstract of},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch026.pdf},
	doi = {10.7551/978-0-262-32621-6-ch026},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Sorbonne Universites, UPMC Univ Paris 06, UMR 722, ISIR, F-75005, Paris, France} and Koos, Sylvain and Cully, Antoine and Mouret, Jean-Baptiste},
	month = jul,
	year = {2014},
	pages = {156--157}
}

@inproceedings{michigan_state_university_east_lansing_mi_usa_48824_investigating_2014,
	title = {Investigating {Modular} {Coupling} of {Morphology} and {Control} with {Digital} {Muscles}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch025.pdf},
	doi = {10.7551/978-0-262-32621-6-ch025},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Michigan State University, East Lansing, MI, USA 48824} and Moore, Jared and McKinley, Philip},
	month = jul,
	year = {2014},
	pages = {148--155}
}

@inproceedings{sorbonne_universites_upmc_univ_paris_06_umr_722_isir_f-75005_paris_france_learning_2014,
	title = {Learning to {Walk} in {Every} {Direction} with the {TBR}-{Learning} algorithm},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch024.pdf},
	doi = {10.7551/978-0-262-32621-6-ch024},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Sorbonne Universites, UPMC Univ Paris 06, UMR 722, ISIR, F-75005, Paris, France} and Cully, Antoine and Mouret, Jean-Baptiste},
	month = jul,
	year = {2014},
	pages = {146--147}
}

@inproceedings{university_of_vermont_burlington_vt_05401_collective_2014,
	title = {Collective {Design} of {Robot} {Locomotion}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch023.pdf},
	doi = {10.7551/978-0-262-32621-6-ch023},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Vermont, Burlington, VT 05401} and Wagy, Mark and Bongard, Joshua},
	month = jul,
	year = {2014},
	pages = {138--145}
}

@inproceedings{auerbach_robogen:_2014,
	title = {{RoboGen}: {Robot} {Generation} through {Artificial} {Evolution}},
	isbn = {9780262326216},
	shorttitle = {{RoboGen}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch022.pdf},
	doi = {10.7551/978-0-262-32621-6-ch022},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {Auerbach, Joshua and Aydin, Deniz and Maesani, Andrea and Kornatowski, Przemyslaw and Cieslewski, Titus and Heitz, Grégoire and Fernando, Pradeep and Loshchilov, Ilya and Daler, Ludovic and Floreano, Dario},
	month = jul,
	year = {2014},
	pages = {136--137}
}

@inproceedings{university_of_texas_at_austin_center_for_computational_biology_and_bioinfomatics_structured_2014,
	title = {Structured {Populations} with {Limited} {Resources} {Exhibit} {Higher} {Rates} of {Complex} {Function} {Evolution}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch021.pdf},
	doi = {10.7551/978-0-262-32621-6-ch021},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Texas at Austin, Center for Computational Biology and Bioinfomatics} and Covert III, Arthur and McFetridge, Siena and DeLord, Evan},
	month = jul,
	year = {2014},
	pages = {129--134}
}

@inproceedings{graduate_school_of_information_science_nagoya_university_furo-cho_chikusa-ku_nagoya_464-8601_japan_population_2014,
	title = {Population and {Evolutionary} {Dynamics} {Based} on {Predator}-{Prey} {Relationship} in 3D {Physical} {Simulation}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch018.pdf},
	doi = {10.7551/978-0-262-32621-6-ch018},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan} and Ito, Takashi and Pilat, Marcin and Suzuki, Reiji and Arita, Takaya},
	month = jul,
	year = {2014},
	pages = {105--112}
}

@inproceedings{department_of_algorithms_and_system_modelling_gdansk_university_of_technology_gdansk_poland_evolution_2014,
	title = {Evolution of {Animats} {Following} a {Moving} {Target} in an {Artificial} {Ecosystem}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch017.pdf},
	doi = {10.7551/978-0-262-32621-6-ch017},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Department of Algorithms and System Modelling, Gdansk University of Technology, Gdansk, Poland} and Erdei, Joachim and Wróbel, Borys},
	month = jul,
	year = {2014},
	pages = {98--104}
}

@inproceedings{school_of_computing_university_of_kent_ct2_7nf_canterbury_evolving_2014,
	title = {Evolving {Biological} {Systems}: {Evolutionary} {Pressure} to {Inefficiency}},
	isbn = {9780262326216},
	shorttitle = {Evolving {Biological} {Systems}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch016.pdf},
	doi = {10.7551/978-0-262-32621-6-ch016},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Computing, University of Kent, CT2 7NF, Canterbury} and Chu, Dominique and Barnes, David},
	month = jul,
	year = {2014},
	pages = {89--96}
}

@inproceedings{institute_for_complex_systems_simulation_university_of_southampton_u.k._ecosystem_2014,
	title = {Ecosystem {Memory} {Is} {Emergent} from {Local}-{Level} {Natural} {Selection}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch015.pdf},
	doi = {10.7551/978-0-262-32621-6-ch015},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Institute for Complex Systems Simulation, University of Southampton, U.K.} and Power, Daniel and Szathmáry, Eörs and Watson, Richard},
	month = jul,
	year = {2014},
	pages = {87--88}
}

@inproceedings{school_of_computer_science_university_of_manchester_uk_studying_2014,
	title = {Studying the {Evolvability} of of {Self}-{Encoding} {Genotype}-{Phenotype} {Maps}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch014.pdf},
	doi = {10.7551/978-0-262-32621-6-ch014},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{School of Computer Science, University of Manchester, UK} and Webb, Andrew and Knowles, Joshua},
	month = jul,
	year = {2014},
	pages = {79--86}
}

@inproceedings{york_centre_for_complex_systems_analysis_university_of_york_uk_reflective_2014,
	title = {Reflective {Grammatical} {Evolution}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch013.pdf},
	doi = {10.7551/978-0-262-32621-6-ch013},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{York Centre for Complex Systems Analysis, University of York, UK} and Timperley, Christopher and Stepney, Susan},
	month = jul,
	year = {2014},
	pages = {71--78}
}

@inproceedings{university_of_texas_at_austin_austin_tx_evolution_2014,
	title = {The {Evolution} of {General} {Intelligence}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch012.pdf},
	doi = {10.7551/978-0-262-32621-6-ch012},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Texas at Austin, Austin, TX} and Rajagopalan, Padmini and Holekamp, Kay and Miikkulainen, Risto},
	month = jul,
	year = {2014},
	pages = {63--70}
}

@inproceedings{sorbonne_universites_upmc_univ_paris_06_umr_722_isir_f-75005_paris_france_cnrs_umr_7222_isir_f-75005_paris_france_comparing_2014,
	title = {Comparing the {Evolvability} of {Generative} {Encoding} {Schemes}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch011.pdf},
	doi = {10.7551/978-0-262-32621-6-ch011},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Sorbonne Universites, UPMC Univ Paris 06, UMR 722, ISIR, F-75005, Paris, France CNRS, UMR 7222, ISIR, F-75005, Paris, France} and Tarapore, Danesh and Mouret, Jean-Baptiste},
	month = jul,
	year = {2014},
	pages = {55--62}
}

@inproceedings{artificial_life_lab_reed_college_portland_or_identifying_2014,
	title = {Identifying {Adaptations} by {Measuring} the {Trait} {Derivative} of {Fitness}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch009.pdf},
	doi = {10.7551/978-0-262-32621-6-ch009},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Artificial Life Lab, Reed College, Portland, OR} and Blount, Drew},
	month = jul,
	year = {2014},
	pages = {45--46}
}

@inproceedings{simons_institute_for_the_theory_of_computing_stress-induced_2014,
	title = {Stress-{Induced} {Variation} {Can} {Cause} {Average} {Mutation} and {Recombination} {Rates} to {Be} {Positively} {Correlated} with {Fitness}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch008.pdf},
	doi = {10.7551/978-0-262-32621-6-ch008},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Simons Institute for the Theory of Computing} and Weissman, Daniel},
	month = jul,
	year = {2014},
	pages = {43--44}
}

@inproceedings{university_of_wyoming_laramie_wy_usa_summary_2014,
	title = {Summary of “{The} {Evolutionary} {Origins} of {Modularity}”},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch007.pdf},
	doi = {10.7551/978-0-262-32621-6-ch007},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Wyoming, Laramie, WY, USA} and Clune, Jeff and Mouret, Jean-Baptiste and Lipson, Hod},
	month = jul,
	year = {2014},
	pages = {41--42}
}

@inproceedings{nria_rhone-alpes_montbonnot_f-38322_france_what_2014,
	title = {What {Happened} to {My} {Genes}? {Insights} on {Gene} {Family} {Dynamics} from {Digital} {Genetics} {Experiments}},
	isbn = {9780262326216},
	shorttitle = {What {Happened} to {My} {Genes}?},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch006.pdf},
	doi = {10.7551/978-0-262-32621-6-ch006},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{NRIA Rhone-Alpes, Montbonnot F-38322, France} and Knibbe, Carole},
	month = jul,
	year = {2014},
	pages = {33--40}
}

@inproceedings{demo_lab_brandeis_university_waltham_ma_coevolution_2014,
	title = {Coevolution in {Hide} and {Seek}: {Camouflage} and {Vision}},
	isbn = {9780262326216},
	shorttitle = {Coevolution in {Hide} and {Seek}},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch005.pdf},
	doi = {10.7551/978-0-262-32621-6-ch005},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{DEMO Lab, Brandeis University, Waltham, MA} and Harrington, Kyle},
	month = jul,
	year = {2014},
	pages = {25--32}
}

@inproceedings{center_for_research_and_interdisciplinarity_inserm_u1001_universite_paris_descartes_sorbonne_paris_cite_france_constrained_2014,
	title = {Constrained {Genetic} {Architecture} {Promotes} {Cooperation}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch004.pdf},
	doi = {10.7551/978-0-262-32621-6-ch004},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Center for Research and Interdisciplinarity, INSERM U1001, Université Paris Descartes, Sorbonne Paris Cité, France} and Frénoy, Antonine and Taddei, François and Misevic, Dusan},
	month = jul,
	year = {2014},
	pages = {23--24}
}

@inproceedings{university_of_texas_austin_tx_evolution_2014,
	title = {Evolution of {Communication} in {Mate} {Selection}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch003.pdf},
	doi = {10.7551/978-0-262-32621-6-ch003},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{University of Texas, Austin, TX} and Rawal, Aditya and Boughman, Janette and Miikkulainen, Risto},
	month = jul,
	year = {2014},
	pages = {16--22}
}

@inproceedings{nagoya_institute_of_technology_japan_evolution_2014,
	title = {Evolution of {Frequency}-{Dependent} {Sexual} {Selection} {Using} {Agent}-{Based} {Model}},
	isbn = {9780262326216},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/alife14/978-0-262-32621-6-ch002.pdf},
	doi = {10.7551/978-0-262-32621-6-ch002},
	urldate = {2015-02-05TZ},
	publisher = {The MIT Press},
	author = {{Nagoya Institute of Technology, Japan} and Mutoh, Atsuko and Kato, Shohei and Inuzuka, Nobuhiro},
	month = jul,
	year = {2014},
	pages = {10--15}
}
@article{ito_sound_2014,
	title = {Sound source detection robot inspired by water striders},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-014-0180-y},
	number = {4},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Ito, Kazuyuki and Nakatsuka, Hiroki},
	year = {2014},
	pages = {394--399}
}

@article{shimokakimoto_biotoys:_2014,
	title = {{bioToys}: biofeedback toys for playful and self-determined physiotherapeutic activities},
	volume = {19},
	shorttitle = {{bioToys}},
	url = {http://link.springer.com/article/10.1007/s10015-014-0144-2},
	number = {2},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Shimokakimoto, Tomoya and Miura, Asaki and Suzuki, Kenji},
	year = {2014},
	pages = {150--156}
}

@article{nakanishi_facial_2014,
	title = {Facial expression recognition of a speaker using thermal image processing and reject criteria in feature vector space},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-013-0136-7},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Nakanishi, Yuu and Yoshitomi, Yasunari and Asada, Taro and Tabuse, Masayoshi},
	year = {2014},
	pages = {76--88}
}

@article{yan_communication_2014,
	title = {Communication system using {EOG} for persons with disabilities and its judgment by {EEG}},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-013-0139-4},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Yan, Mingmin and Go, Sou and Tamura, Hiroki and Tanno, Koichi},
	year = {2014},
	pages = {89--94}
}

@article{moritoh_evaluation_2014,
	title = {Evaluation for distance learning scheme on distributed multiple server system},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-013-0131-z},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Moritoh, Yoshio and Imai, Yoshiro and Hattori, Tetsuo},
	year = {2014},
	pages = {61--67}
}

@article{kwak_estimating_2014,
	title = {Estimating floodwater from {MODIS} time series and {SRTM} {DEM} data},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-013-0140-y},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Kwak, Youngjoo and Park, Jonggeol and Fukami, Kazuhiko},
	year = {2014},
	pages = {95--102}
}

@article{king_excitability_2014,
	title = {Excitability modulation of oscillating media in 3D-printed structures},
	url = {http://users.minet.uni-jena.de/~dittrich/prj/neuneu/pub/preprints/2013_King_excitability.pdf},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life},
	author = {King, Philip H. and Abraham, Chinnu H. and Zauner, Klaus-Peter and de Planque, Maurits RR},
	year = {2014}
}

@article{lenaerts_special_2014,
	title = {Special {Issue} for the 20th {Anniversary} of the {European} {Conference} on {Artificial} {Life} ({ECAL} 2011)},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/full/10.1162/ARTL_a_00093},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Lenaerts, Tom and Giacobini, Mario and Bersini, Hugues and Bourgine, Paul and Dorigo, Marco and Doursat, René},
	year = {2014},
	pages = {1--3}
}

@article{jones_autonomous_2014,
	title = {Autonomous droplet architectures},
	url = {http://eprints.soton.ac.uk/364114/},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life},
	author = {Jones, Gareth and King, Philip H. and Morgan, Hywel and de Planque, Maurits RR and Zauner, Klaus-Peter},
	year = {2014}
}

@article{zahadat_generation_2014,
	title = {Generation of diversity in a reaction-diffusion-based controller},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00134},
	number = {3},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Zahadat, Payam and Schmickl, Thomas},
	year = {2014},
	pages = {319--342}
}

@article{ouannes_modeling_2014,
	title = {Modeling a bacterial ecosystem through chemotaxis simulation of a single cell},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-014-0187-4},
	number = {4},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Ouannes, Nesrine and Djedi, NourEddine and Luga, Herve and Duthen, Yves},
	year = {2014},
	pages = {382--387}
}

@article{kanada_3d_2014,
	title = {3D printing and simulation of naturally randomized cellular automata},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-014-0182-9},
	number = {4},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Kanada, Yasusi},
	year = {2014},
	pages = {311--316}
}

@article{sawada_model_2014,
	title = {Model following control for continuous-time discrete-valued input systems},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-014-0169-6},
	number = {3},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Sawada, Kenji and Shin, Seiichi},
	year = {2014},
	pages = {277--285}
}

@article{dang_occupancy_2014,
	title = {Occupancy grid map of semi-static objects by mobile observer},
	url = {http://link.springer.com/article/10.1007/s10015-014-0188-3},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Dang, Viet Chau and Kubo, Masao and Sato, Hiroshi and Shirakawa, Tomohiro and Namatame, Akira},
	year = {2014},
	pages = {1--6}
}

@article{lee_development_2014,
	title = {Development and motion control of a biped walking robot based on passive walking theory},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-013-0132-y},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Lee, Jae Hoon and Okamoto, Shingo and Koike, Hisashi and Tani, Keiya},
	year = {2014},
	pages = {68--75}
}

@article{hosokawa_reward_2014,
	title = {A reward allocation method for reinforcement learning in stabilizing control tasks},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-014-0146-0},
	number = {2},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Hosokawa, Shu and Kato, Joji and Nakano, Kazushi},
	year = {2014},
	pages = {109--114}
}

@article{sutrisno_modified_2014,
	title = {Modified fuzzy adaptive controller applied to nonlinear systems modeled under quasi-{ARX} neural network},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-013-0137-6},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Sutrisno, Imam and Jami’in, Mohammad Abu and Hu, Jinglu},
	year = {2014},
	pages = {22--26}
}

@article{suetake_adaptive_2014,
	title = {Adaptive rollover prevention controller for driver–vehicle systems},
	volume = {19},
	url = {http://link.springer.com/article/10.1007/s10015-013-0134-9},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life and Robotics},
	author = {Suetake, Yusuke and Oya, Masahiro and Shu, Panfeng and Zhuo, Jinxin},
	year = {2014},
	pages = {9--15}
}

@article{abdelmotaleb_evolving_2014,
	title = {Evolving spiking neural networks for temporal pattern recognition in the presence of noise},
	url = {http://uhra.herts.ac.uk/handle/2299/14427},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life 2014},
	author = {Abdelmotaleb, Ahmed and Davey, Neil and Schilstra, Maria and Steuber, Volker and Wróbel, Borys},
	year = {2014}
}

@article{bull_evolving_2014,
	title = {Evolving functional and structural dynamism in coupled boolean networks},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00137},
	number = {4},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Bull, Larry},
	year = {2014},
	pages = {441--455}
}

@article{dorin_practice_2014,
	title = {The practice of agent-based model visualization},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00129},
	number = {2},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Dorin, Alan and Geard, Nicholas},
	year = {2014},
	pages = {271--289}
}

@article{pini_task_2014,
	title = {Task partitioning in a robot swarm: {Object} retrieval as a sequence of subtasks with direct object transfer},
	volume = {20},
	shorttitle = {Task partitioning in a robot swarm},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00132},
	number = {3},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Pini, Giovanni and Brutschy, Arne and Scheidler, Alexander and Dorigo, Marco and Birattari, Mauro},
	year = {2014},
	pages = {291--317}
}

@article{bhalla_staging_2014,
	title = {Staging the self-assembly process: {Inspiration} from biological development},
	volume = {20},
	shorttitle = {Staging the self-assembly process},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00095},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Bhalla, Navneet and Bentley, Peter J. and Vize, Peter D. and Jacob, Christian},
	year = {2014},
	pages = {29--53}
}

@article{aguilera_intermittent_2014,
	title = {Intermittent animal behavior: {The} adjustment-deployment dilemma},
	volume = {20},
	shorttitle = {Intermittent animal behavior},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00133},
	number = {4},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Aguilera, Miguel and Bedia, Manuel G. and Seron, Francisco and Barandiaran, Xabier E.},
	year = {2014},
	pages = {471--489}
}

@article{cussat-blanc_cracking_2014,
	title = {Cracking the egg: {Virtual} embryogenesis of real robots},
	volume = {20},
	shorttitle = {Cracking the egg},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00136},
	number = {3},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Cussat-Blanc, Sylvain and Pollack, Jordan},
	year = {2014},
	pages = {361--383}
}

@article{beer_cognitive_2014,
	title = {The cognitive domain of a glider in the game of life},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00125},
	number = {2},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Beer, Randall D.},
	year = {2014},
	pages = {183--206}
}

@article{rieffel_growing_2014,
	title = {Growing and evolving soft robots},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00101},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Rieffel, John and Knox, Davis and Smith, Schuyler and Trimmer, Barry},
	year = {2014},
	pages = {143--162}
}

@article{barandiaran_norm-establishing_2014,
	title = {Norm-establishing and norm-following in autonomous agency},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00094},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life},
	author = {Barandiaran, Xabier E. and Egbert, Matthew D.},
	year = {2014},
	pages = {5--28}
}

@article{pereira_formalization_2014,
	title = {Formalization, implementation, and modeling of institutional controllers for distributed robotic systems},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00100},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Pereira, José N. and Silva, Porfírio and Lima, Pedro U. and Martinoli, Alcherio},
	year = {2014},
	pages = {127--141}
}

@article{demsar_simulated_2014,
	title = {Simulated predator attacks on flocks: a comparison of tactics},
	volume = {20},
	shorttitle = {Simulated predator attacks on flocks},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00135},
	number = {3},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Demšar, Jure and Bajec, Iztok Lebar},
	year = {2014},
	pages = {343--359}
}

@article{gong_exploring_2014,
	title = {Exploring the effect of power law social popularity on language evolution},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00138},
	number = {3},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Gong, Tao and Shuai, Lan},
	year = {2014},
	pages = {385--408}
}

@article{hamann_analysis_2014,
	title = {Analysis of swarm behaviors based on an inversion of the fluctuation theorem},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00097},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Hamann, Heiko and Schmickl, Thomas and Crailsheim, Karl},
	year = {2014},
	pages = {77--93}
}

@article{oohashi_evolutionary_2014,
	title = {Evolutionary acquisition of a mortal genetic program: {The} origin of an altruistic gene},
	volume = {20},
	shorttitle = {Evolutionary acquisition of a mortal genetic program},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00098},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Oohashi, Tsutomu and Maekawa, Tadao and Ueno, Osamu and Kawai, Norie and Nishina, Emi and Honda, Manabu},
	year = {2014},
	pages = {95--110}
}

@article{rano_results_2014,
	title = {Results on the convergence of braitenberg vehicle 3a},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00108},
	number = {2},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Rañó, Iñaki},
	year = {2014},
	pages = {223--235}
}

@article{altenberg_reviewers_2014,
	title = {Reviewers of {Volume} 20},
	volume = {20},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6926030},
	number = {531},
	urldate = {2015-02-04TZ},
	journal = {Artificial Life},
	author = {Altenberg, Lee and Azevedo, Ricardo and Belpaeme, Tony and Bersini, Hugues and Birattari, Mauro and Bourgine, Paul and Czárán, Tamás and De Beule, Joachim and Di Paolo, Ezequiel and Deplazes, Anna and {others}},
	year = {2014}
}

@article{segovia_statistical_2014,
	title = {Statistical thermodynamics concepts and mathematical tools for a multi-agent ecosystem},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00128},
	number = {2},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Segovia, Javier},
	year = {2014},
	pages = {237--270}
}

@article{tomko_many_2014,
	title = {Many hands make light work: {Further} studies in group evolution},
	volume = {20},
	shorttitle = {Many hands make light work},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00102},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Tomko, Nicholas and Harvey, Inman and Virgo, Nathaniel and Philippides, Andrew},
	year = {2014},
	pages = {163--181}
}

@article{payne_robustness_2014,
	title = {Robustness, evolvability, and the logic of genetic regulation},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00099},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Payne, Joshua L. and Moore, Jason H. and Wagner, Andreas},
	year = {2014},
	pages = {111--126}
}

@article{froese_motility_2014,
	title = {Motility at the origin of life: {Its} characterization and a model},
	volume = {20},
	shorttitle = {Motility at the origin of life},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00096},
	number = {1},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Froese, Tom and Virgo, Nathaniel and Ikegami, Takashi},
	year = {2014},
	pages = {55--76}
}

@article{smaldino_institutions_2014,
	title = {Institutions and cooperation in an ecology of games},
	volume = {20},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/ARTL_a_00126},
	number = {2},
	urldate = {2015-02-04TZ},
	journal = {Artificial life},
	author = {Smaldino, Paul E. and Lubell, Mark},
	year = {2014},
	pages = {207--221}
}

@article{model_surface_1982,
	title = {Surface enhanced {Raman} scattering},
	url = {http://link.springer.com/10.1007/978-1-4615-9257-0},
	urldate = {2015-02-04TZ},
	author = {Model, Induced Resonance and Colloids, Metal and by Microlithography, Silver Structures Produced},
	year = {1982}
}

@article{turner_disturbance_2010,
	title = {Disturbance and landscape dynamics in a changing world 1},
	volume = {91},
	url = {http://www.esajournals.org/doi/abs/10.1890/10-0097.1},
	number = {10},
	urldate = {2015-02-04TZ},
	journal = {Ecology},
	author = {Turner, Monica G.},
	year = {2010},
	pages = {2833--2849}
}

@article{guegan_energy_1998,
	title = {Energy availability and habitat heterogeneity predict global riverine fish diversity},
	volume = {391},
	copyright = {© 1998 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v391/n6665/abs/391382a0.html},
	doi = {10.1038/34899},
	abstract = {Processes governing patterns of richness of riverine fish species at the global level can be modelled using artificial neural network (ANN) procedures. These ANNs are the most recent development in computer-aided identification and are very different from conventional techniques,. Here we use the potential of ANNs to deal with some of the persistent fuzzy and nonlinear problems that confound classical statistical methods for species diversity prediction. We show that riverine fish diversity patterns on a global scale can be successfully predicted by geographical patterns in local river conditions. Nonlinear relationships, fitted by ANN methods, adequately describe the data, with up to 93 per cent of the total variation in species richness being explained by our results. These findings highlight the dominant effect of energy availability and habitat heterogeneity on patterns of global fish diversity. Our results reinforce the species-energy theory and contrast with those from a recent study on North American mammal species, but, more interestingly, they demonstrate the applicability of ANN methods in ecology.},
	language = {en},
	number = {6665},
	urldate = {2015-01-15TZ},
	journal = {Nature},
	author = {Guégan, Jean-François and Lek, Sovan and Oberdorff, Thierry},
	month = jan,
	year = {1998},
	pages = {382--384}
}

@article{manel_landscape_2003,
	title = {Landscape genetics: combining landscape ecology and population genetics},
	volume = {18},
	issn = {0169-5347},
	shorttitle = {Landscape genetics},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534703000089},
	doi = {10.1016/S0169-5347(03)00008-9},
	abstract = {Understanding the processes and patterns of gene flow and local adaptation requires a detailed knowledge of how landscape characteristics structure populations. This understanding is crucial, not only for improving ecological knowledge, but also for managing properly the genetic diversity of threatened and endangered populations. For nearly 80 years, population geneticists have investigated how physiognomy and other landscape features have influenced genetic variation within and between populations. They have relied on sampling populations that have been identified beforehand because most population genetics methods have required discrete populations. However, a new approach has emerged for analyzing spatial genetic data without requiring that discrete populations be identified in advance. This approach, landscape genetics, promises to facilitate our understanding of how geographical and environmental features structure genetic variation at both the population and individual levels, and has implications for ecology, evolution and conservation biology. It differs from other genetic approaches, such as phylogeography, in that it tends to focus on processes at finer spatial and temporal scales. Here, we discuss, from a population genetic perspective, the current tools available for conducting studies of landscape genetics.},
	number = {4},
	urldate = {2015-01-14TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Manel, Stéphanie and Schwartz, Michael K. and Luikart, Gordon and Taberlet, Pierre},
	month = apr,
	year = {2003},
	pages = {189--197}
}
@incollection{green_global_2006,
	series = {Landscape {Series}},
	title = {{THE} {GLOBAL} {PICTURE}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_11},
	abstract = {The acid test for any idea is whether it works in practice. As we have seen throughout this book, complexity theory teaches us many lessons that have immediate practical uses in landscape ecology, in conservation and in environmental management. However, if complexity theory teaches us any lessons at all, it teaches that we cannot understand ecosystems by studying them in isolation. To get the full picture, we need to set each ecosystem in the context of its surrounding region. Nor can we understand an entire region without understanding how the elements in its ecological mosaic interact with one another.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {169--202}
}

@incollection{green_virtual_2006,
	series = {Landscape {Series}},
	title = {{VIRTUAL} {WORLDS}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_9},
	abstract = {Some of the biggest questions about life are also the hardest to answer using traditional experimental methods. How did life begin? How did multicellular organisms arise? What are the major transitions in evolution? Why is life so diverse? What might life on other planets be like? These and other big questions deal with processes that occur on massive time and spatial scales. Without a time machine, we cannot directly test our ideas about them empirically. The same problem is faced in other fields of research, from astronomy and geophysics to archaeology and palaeontology.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {133--150}
}

@incollection{green_genetics_2006,
	series = {Landscape {Series}},
	title = {{GENETICS} {AND} {ADAPTATION} {IN} {LANDSCAPES}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_8},
	abstract = {So far in this book, we have looked at populations as if all the individuals comprising them were interchangeable. In reality, this is not so. Walk through an unmown meadow and you will see that different plants of the same species have different sizes, colours and proportions; some may be thornier, have larger leaves, more flowers, or thicker stems than others. Some of these differences are simply attributable to environment: malnourished individuals will usually be relatively small, for example. However, many differences, such as human eye colours, cannot be explained by the environment alone, and instead are influenced by variations in the genetic instructions that regulate development. These instructions tell each cell when and how to construct highly specialised proteins. Genetic instructions are encoded by long strands of deoxyribonucleic acid (DNA). Different sections of a DNA strand are used at different times; each such section is called a gene. Organisms usually have a very large number of genes; for example, the human genome includes around 30,000 genes. Changes in the prevalence of genes are studied by population geneticists. These changes are intimately tied to the ecology of populations at several levels. Evolution, the long-term consequence of changing gene frequencies, generates the diversity of living forms whose interactions are the subject of ecology. Conversely, ecological factors greatly influence evolution. Lastly, the dynamics of genes have much in common at a theoretical level with the ecological dynamics of species.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {115--132}
}

@incollection{green_complexity_2006,
	series = {Landscape {Series}},
	title = {{COMPLEXITY} {AND} {ECOLOGY}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_1},
	abstract = {Covering an area of more than 6 million square kilometres, the Amazon Basin dominates northern Brazil and forms a large part of the South American continent. The richness of its biodiversity, and the hostility of its natural environment, mean that even today we can form no clear picture of the Amazon rainforest ecology. Yet even fragmentary glimpses reveal that the Amazon forms an extravagance of nature beyond the wildest imaginings of taxonomists. When biologist T. L. Erwin examined a single species of Amazonian tree, he found 163 unique species of beetle living in its canopy alone (Erwin 1982). Comparing sites seventy kilometres apart, Erwin found only a 1\% overlap in the beetle species present (Erwin 1988). Brazil has more species of flowering plants and amphibians than any other country, and ranks in the top four countries on earth for mammals, birds, butterflies and reptiles (Fearnside 1999).},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {1--14}
}

@incollection{green_living_2006,
	series = {Landscape {Series}},
	title = {{LIVING} {WITH} {THE} {NEIGHBOURS}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_7},
	abstract = {In the year 1859, Thomas Austin released 24 rabbits into the bush near his farm in the southern Australian colony of Victoria. His aim was to have a regular supply of familiar game to hunt. By the end of the 19th century, the descendants of those rabbits numbered in the tens of millions. Infesting an area nearly the size of Europe, they devastated crops and turned entire regions into wasteland. In the process, they drove many of their marsupial competitors to the brink of extinction.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {99--114}
}

@incollection{green_imbalance_2006,
	series = {Landscape {Series}},
	title = {{THE} {IMBALANCE} {OF} {NATURE}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_5},
	abstract = {It is a quiet spring evening by a lake in eastern Canada. The sun is disappearing behind the distant beech trees. The sound of Loons singing drifts across the water. There is a perfect scene of peace and tranquillity. With everything so still, it is easy to believe it will stay this way forever.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {67--84}
}

@incollection{green_oh_2006,
	series = {Landscape {Series}},
	title = {{OH}, {WHAT} {A} {TANGLED} {WEB}.},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_4},
	abstract = {One of the greatest scientific challenges that nature poses is to understand how the world is put together. How do billions of cells combine to form a living, breathing human being? How does a seed grow into a giant tree? Puzzles such as this have intrigued and frustrated scientists for hundreds of years. The central question is perhaps best captured in the famous saying: “the whole is greater than the sum of its parts.” A tree is more than just a heap of cells. A forest is more than just trees, and an ant colony is more than just thousands of individual ants. All of these systems are organised. The whole emerges out of interactions between many individual parts. But just how does that organisation occur? This is the challenge that complexity theory seeks to answer.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {51--66}
}

@incollection{green_seeing_2006,
	series = {Landscape {Series}},
	title = {{SEEING} {THE} {WOOD} {FOR} {THE} {TREES}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_2},
	abstract = {The whole is greater than the sum of its parts. As we saw in chapter 1, this popular saying captures the essence of complexity. In this chapter, we look briefly at examples of processes in which fine scale functions, at the level of individuals, lead to larger scale organisation. Many other issues (e.g. foraging strategies) arise from individual interactions besides the examples given here. We will meet some of these in later chapters.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {15--32}
}

@incollection{green_complexity_2006-1,
	series = {Landscape {Series}},
	title = {{COMPLEXITY} {IN} {LANDSCAPES}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_3},
	abstract = {In the previous chapter, we saw that interactions between organisms lead to complexity in ecosystems. Interactions between organisms and their environment also contribute. Soil formation, for instance, involves a combination of organic and inorganic processes. Rainforests not only depend on local climate, but also they modify it. Flow of water across a landscape affects the suitability of sites, determining where plants can grow.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {33--50}
}

@incollection{green_populations_2006,
	series = {Landscape {Series}},
	title = {{POPULATIONS} {IN} {LANDSCAPES}},
	copyright = {©2006 Springer},
	isbn = {978-1-4020-4285-0, 978-1-4020-4287-4},
	url = {http://link.springer.com/chapter/10.1007/1-4020-4287-6_6},
	abstract = {Halfway between Sweden and Finland, and separating the Baltic Sea from the Gulf of Bothnia, lies a vast group of islands known as the Åland archipelago. Consisting of more than 6,500 islands, Åland is home to a species of butterfly known as Granville Fritillary (Melitaea cinxia), which inhabits the small patches of dry meadows that are found on many of the islands1. For the most part, the butterflies on each island form a distinct population. About 60-80\% of the butterflies spend their entire lives on the island where they are born. So the butterflies living on each island are almost isolated from the rest of the species.},
	language = {en},
	number = {4},
	urldate = {2015-01-12TZ},
	booktitle = {Complexity in {Landscape} {Ecology}},
	publisher = {Springer Netherlands},
	author = {Green, David G. and Klomp, Nicholas and Rimmington, Glyn and Sadedin, Suzanne},
	month = jan,
	year = {2006},
	keywords = {Complexity, Ecology, Environmental Monitoring/Analysis, Landscape Ecology, Theoretical Ecology/Statistics},
	pages = {85--98}
}

@article{fjellstad_heterogeneity_2001,
	title = {Heterogeneity as a measure of spatial pattern for monitoring agricultural landscapes},
	volume = {55},
	issn = {0029-1951},
	url = {http://dx.doi.org/10.1080/00291950119811},
	doi = {10.1080/00291950119811},
	abstract = {The Norwegian monitoring programme for agricultural landscapes is a sample-based programme that aims to document the current state and patterns of change in the agricultural landscape for the entire country. For this broad geographical coverage an indicator approach is the most cost-effective methodology. Landscape metrics are used as indicators in the monitoring programme based on the assumed importance of landscape composition and spatial pattern for a number of countryside interests. However, although indicators have been used successfully over a long period of time in various disciplines, their use in landscape monitoring is relatively new and there is little empirical data with which to assess their validity. This paper provides information on the performance of landscape diversity and landscape heterogeneity indices as estimated by specific biodiversity measures. Preliminary results show increasing numbers of breeding bird species and numbers of vascular plant species with increasing landscape diversity and heterogeneity, two indices that capture information on landscape content and structure. Overall, the heterogeneity index provided a better surrogate for species richness than the diversity index.},
	number = {2},
	urldate = {2015-01-09TZ},
	journal = {Norsk Geografisk Tidsskrift - Norwegian Journal of Geography},
	author = {Fjellstad, W. J. and Dramstad, W. E. and Strand, G.-H. and Fry, G. L. A.},
	month = jan,
	year = {2001},
	pages = {71--76}
}

@article{vranken_review_2015,
	title = {A review on the use of entropy in landscape ecology: heterogeneity, unpredictability, scale dependence and their links with thermodynamics},
	volume = {30},
	issn = {0921-2973, 1572-9761},
	shorttitle = {A review on the use of entropy in landscape ecology},
	url = {http://link.springer.com/article/10.1007/s10980-014-0105-0},
	doi = {10.1007/s10980-014-0105-0},
	abstract = {The identification of a universal law that can predict the spatiotemporal structure of any entity at any scale has long been pursued. Thermodynamics have targeted this goal, and the concept of entropy has been widely applied for various disciplines and purposes, including landscape ecology. Within this discipline, however, the uses of the entropy concept and its underlying assumptions are various and are seldom described explicitly. In addition, the link between this concept and thermodynamics is unclear. The aim of this paper is to review the various interpretations and applications of entropy in landscape ecology and to sort them into clearly defined categories. First, a retrospective study of the concept genesis from thermodynamics to landscape ecology was conducted. Then, 50 landscape ecology papers that use or discuss entropy were surveyed and classified by keywords, variables and metrics identified as related to entropy. In particular, the thermodynamic component of entropy in landscape ecology and its various interpretations related to landscape structure and dynamics were considered. From the survey results, three major definitions (i.e., spatial heterogeneity, the unpredictability of pattern dynamics and pattern scale dependence) associated with the entropy concept in landscape ecology were identified. The thermodynamic interpretations of these definitions are based on different theories. The thermodynamic interpretation of spatial heterogeneity is not considered relevant. The thermodynamic interpretation related to scale dependence is also questioned by complexity theory. Only unpredictability can be thermodynamically relevant if appropriate measurements are used to test it.},
	language = {en},
	number = {1},
	urldate = {2015-01-09TZ},
	journal = {Landscape Ecology},
	author = {Vranken, Isabelle and Baudry, Jacques and Aubinet, Marc and Visser, Marjolein and Bogaert, Jan},
	month = jan,
	year = {2015},
	keywords = {Complexity, Ecology, Forestry, Forestry Management, Information theory, Landscape Ecology, Pattern dynamics, Plant Ecology, Plant Sciences, Resilience, Scale influence, spatial heterogeneity},
	pages = {51--65}
}

@inproceedings{harper_spatial_2010,
	title = {Spatial co-evolution in {Age} {Layered} {Planes} ({SCALP})},
	isbn = {978-1-4244-6909-3},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5586342&tag=1},
	doi = {10.1109/CEC.2010.5586342},
	urldate = {2015-01-09TZ},
	publisher = {IEEE},
	author = {Harper, Robin},
	month = jul,
	year = {2010},
	pages = {1--8}
}

@article{holtschulte_should_2013,
	title = {Should {Every} {Man} be an {Island}},
	author = {Holtschulte, N. and Moses, M.},
	year = {2013},
	pages = {8}
}

@misc{nahum_unpublished_nodate,
	title = {Unpublished {Data}},
	author = {Nahum, Joshua and Kerr, Benjamin}
}

@article{nahum_improved_nodate,
	title = {Improved adaptation in exogenously and endogenously changing environments},
	journal = {Unpublished},
	author = {Nahum, Joshua and West, Jevin and Althouse, Benjamin and Zaman, Luis and Ofria, Charles and Kerr, Benjamin}
}

@article{whitley_evaluating_1996,
	title = {Evaluating evolutionary algorithms},
	volume = {85},
	issn = {0004-3702},
	url = {http://www.sciencedirect.com/science/article/pii/0004370295001247},
	doi = {10.1016/0004-3702(95)00124-7},
	abstract = {Test functions are commonly used to evaluate the effectiveness of different search algorithms. However, the results of evaluation are as dependent on the test problems as they are on the algorithms that are the subject of comparison. Unfortunately, developing a test suite for evaluating competing search algorithms is difficult without clearly defined evaluation goals. In this paper we discuss some basic principles that can be used to develop test suites and we examine the role of test suites as they have been used to evaluate evolutionary search algorithms. Current test suites include functions that are easily solved by simple search methods such as greedy hill-climbers. Some test functions also have undesirable characteristics that are exaggerated as the dimensionality of the search space is increased. New methods are examined for constructing functions with different degrees of nonlinearity, where the interactions and the cost of evaluation scale with respect to the dimensionality of the search space.},
	number = {1–2},
	urldate = {2014-12-04TZ},
	journal = {Artificial Intelligence},
	author = {Whitley, Darrell and Rana, Soraya and Dzubera, John and Mathias, Keith E.},
	month = aug,
	year = {1996},
	pages = {245--276}
}

@book{jewell_island_1974,
	title = {Island survivors: the ecology of the {Soay} sheep of {St} {Kilda}.},
	shorttitle = {Island survivors},
	url = {http://www.cabdirect.org/abstracts/19740113640.html},
	urldate = {2014-10-14TZ},
	publisher = {Athlone Press.},
	author = {Jewell, Peter Arundel and Milner, Cedric and Boyd, John Morton and {others}},
	year = {1974}
}

@article{noauthor_island_1974,
	title = {Island survivors: the ecology of the {Soay} sheep of {St} {Kilda}.},
	shorttitle = {Island survivors},
	abstract = {The small, deer-like Soay sheep represent the most primitive domestic form of the species in Europe. They may be descended from sheep brought to Britain about 5000 BC or, alternatively, they may have been introduced by the Vikings about the 9th century AD. The present feral population of about 1400 sheep on Hirta, the main island of the St Kilda group, is descended from a flock of 107 sheep which was transferred from the neighbouring island of Soay when the islanders deserted St Kilda in 1932. This book is packed with fascinating and detailed information about the Soay sheep - their physiology, conformation, colour and coat type, their social and sexual behaviour, and the interacting factors which control population size and cause it to fluctuate in a remarkable fashion from year to year. In addition, the habitat, particularly the vegetation and soil, is fully described. The heart of the book is found in those sections by Grubb, and Grubb and Jewell, dealing with social and sexual behaviour, reproduction and population dynamics. These are wide-ranging studies and have a general relevance for all zoologists, ethologists and ecologists quite irrespective of whether they may be interested in Soay sheep. However, these chapters, although of great interest, are excessively detailed. Some data are presented in the form of both tables and diagrams, and descriptive information on the behaviour of individual sheep is extremely lengthy, and perhaps inappropriate in this context. A greater degree of condensation and synthesis would have been welcome. Nevertheless, it is only fair to say that the authors' perceptiveness and enthusiasm are such that they never become tedious. The authoritative studies of Grubb on behaviour and of Gwynn on the vegetation (and its function as the sole food supply of the sheep) result from several years of dedicated work during which they stayed on the island. These, and indeed most of the chapters in this book, are of a high standard. One possible criticism concerns the relative lack of statistical analysis of the data. Quantitative differences are sometimes presented without any indication of their statistical significance or of the degree of variation. The book is fairly well produced for its price, although the standard of reproduction of photographs is disappointing. In general, this book must be rated as an impressive and highly successful record of over 10 years of research under extremely difficult conditions. It cannot fail to be of interest to any biologist. All the contributors and, in particular, the editors, are to be congratulated on completing a daunting but worthwhile task. J. Slee},
	language = {English},
	year = {1974},
	pages = {386 pp.}
}

@article{tanner_order_2010,
	title = {Order {Matters}: {Using} the 5E {Model} to {Align} {Teaching} with {How} {People} {Learn}},
	volume = {9},
	issn = {1931-7913},
	shorttitle = {Order {Matters}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931660/},
	doi = {10.1187/cbe.10-06-0082},
	number = {3},
	urldate = {2014-10-13TZ},
	journal = {CBE Life Sciences Education},
	author = {Tanner, Kimberly D.},
	year = {2010},
	pmid = {20810945},
	pmcid = {PMC2931660},
	pages = {159--164}
}

@article{frenken_fitness_2006,
	title = {A fitness landscape approach to technological complexity, modularity, and vertical disintegration},
	volume = {17},
	issn = {0954-349X},
	url = {http://www.sciencedirect.com/science/article/pii/S0954349X0600004X},
	doi = {10.1016/j.strueco.2006.01.001},
	abstract = {The biological evolution of complex organisms, in which the functioning of genes is interdependent, has been analysed as “hill-climbing” on NK fitness landscapes through random mutation and natural selection [Kauffman, S.A., 1993. The Origins of Order. Self-organization and Selection in Evolution. Oxford University Press, New York \& Oxford]. In evolutionary economics, NK fitness landscapes have been used to simulate the design of complex technological systems as a trial-and-error process towards local optima. Interdependencies among a system's elements do not only render the optimisation of product design a difficult task, but also put constraints on the vertical disintegration of production. In this context, evolutionary economists introduced the concept of “dynamic transaction costs” [Langlois, R.N., 1992. Transaction-cost economics in real time. Industrial and Corporate Change 1 (1), 99–127; Langlois, R.N., 2001. The vanishing hand: the changing dynamics of industrial capitalism, Paper presented at the workshop Reappraising Production Theory: Concepts, Cases and Models, Max Planck Institute, Jena, November 29–December 1]. A system integrator outsourcing the production of elements to supplier firms not only transfers production, but to a large extent looses competence and control to bring about innovations in these elements. This is problematic when the element that is being outsourced is functionally interdependent with other elements in the system. The main aim of the paper is to theorise about modular product architectures that allow for outsourcing while reducing the constraints on possible innovation. The primary way to achieve modular architectures is to introduce elements that function as standards mediating interdependencies between other elements. It is argued that only a generalised version of the NK-model, which is developed in this paper, is able to represent this specific quality of standards that render architectures modular. It is also explained how the model of modular architectures differs from the model of decomposable architectures developed in a previous study [Frenken, K., Marengo, L., Valente, M., 1999. Interdependencies, near-decomposability and adaptation. In: Brenner, T. (Ed.), Computational Techniques for Modelling Learning in Economics. Kluwer, Boston, pp. 209–244]. A number of implications are derived from the generalised NK-model model that can be taken up in empirical studies on patterns of vertical disintegration in the life-cycle evolution of specific products. An evolutionary framework of vertical integration is needed to supplement the theory of the product life-cycle.},
	number = {3},
	urldate = {2014-10-08TZ},
	journal = {Structural Change and Economic Dynamics},
	author = {Frenken, Koen},
	month = sep,
	year = {2006},
	keywords = {Decomposability, NK-model, Transaction costs economics, Vertical integration, modularity},
	pages = {288--305}
}

@inproceedings{oneill_dynamic_2011,
	address = {New York, NY, USA},
	series = {{GECCO} '11},
	title = {Dynamic {Environments} {Can} {Speed} {Up} {Evolution} with {Genetic} {Programming}},
	isbn = {978-1-4503-0690-4},
	url = {http://doi.acm.org/10.1145/2001858.2001965},
	doi = {10.1145/2001858.2001965},
	abstract = {We present a study of dynamic environments with genetic programming to ascertain if a dynamic environment can speed up evolution when compared to an equivalent static environment. We present an analysis of the types of dynamic variation which can occur with a variable-length representation such as adopted in genetic programming identifying modular varying, structural varying and incremental varying goals. An empirical investigation comparing these three types of varying goals on dynamic symbolic regression benchmarks reveals an advantage for goals which vary in terms of increasing structural complexity. This provides evidence to support the added difficulty variable length representations incur due to their requirement to search structural and parametric space concurrently, and how directing search through varying structural goals with increasing complexity can speed up search with genetic programming.},
	urldate = {2014-10-08TZ},
	booktitle = {Proceedings of the 13th {Annual} {Conference} {Companion} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {O'Neill, Michael and Nicolau, Miguel and Brabazon, Anthony},
	year = {2011},
	keywords = {dynamic environments, genetic programming, modular varying goals, structural varying goals},
	pages = {191--192}
}

@article{ovaska_periodical_2009,
	title = {Periodical switching between related goals for improving evolvability to a fixed goal in multi-objective problems},
	volume = {179},
	issn = {0020-0255},
	url = {http://www.sciencedirect.com/science/article/pii/S002002550900365X},
	doi = {10.1016/j.ins.2009.08.019},
	abstract = {Evolutionary computation plays a principal role in intelligent design automation. Evolutionary approaches have discovered novel and patentable designs. Nonetheless, evolutionary techniques may lead to designs that lack robustness. This critical issue is strongly connected to the concept of evolvability. In nature, highly evolvable species tend to be found in rapidly changing environments. Such species can be considered robust against environmental changes. Consequently, to create robust engineering designs it could be beneficial to use variable, rather than fixed, fitness criteria. In this paper, we study the performance of an evolutionary programming algorithm with periodical switching between goals, which are selected randomly from a set of related goals. It is shown by a dual-objective filter optimization example that altering goals may improve evolvability to a fixed goal by enhancing the dynamics of solution population, and guiding the search to areas where improved solutions are likely to be found. Our reference algorithm with a single goal is able to find solutions with competitive fitness, but these solutions are results of premature convergence, because they are poorly evolvable. By using the same algorithm with switching goals, we can extend the productive search length considerably; both the fitness and robustness of such designs are improved.},
	number = {23},
	urldate = {2014-10-08TZ},
	journal = {Information Sciences},
	author = {Ovaska, Seppo J. and Sick, Bernhard and Wright, Alden H.},
	month = nov,
	year = {2009},
	keywords = {Adaptive filtering, Evolutionary programming, Evolvability, Multi-objective optimization, Robustness, Varying environments, evolutionary computation, modularity},
	pages = {4046--4056}
}

@article{parter_facilitated_2008,
	title = {Facilitated {Variation}: {How} {Evolution} {Learns} from {Past} {Environments} {To} {Generalize} to {New} {Environments}},
	volume = {4},
	shorttitle = {Facilitated {Variation}},
	url = {http://dx.doi.org/10.1371/journal.pcbi.1000206},
	doi = {10.1371/journal.pcbi.1000206},
	abstract = {Author Summary
One of the striking features of evolution is the appearance of novel structures in organisms. The origin of the ability to generate novelty is one of the main mysteries in evolutionary theory. The molecular mechanisms that enhance the evolution of novelty were recently integrated by Kirschner and Gerhart in their theory of facilitated variation. This theory suggests that organisms have a design that makes it more likely that random genetic changes will result in organisms with novel shapes that can survive. Here we demonstrate how facilitated variation can arise in computer simulations of evolution. We propose a quantitative approach for studying facilitated variation in computational model systems. We find that the evolution of facilitated variation is enhanced in environments that change from time to time in a systematic way: the varying environments are made of the same set of subgoals, but in different combinations. Under such varying conditions, the simulated organisms store information about past environments in their genome, and develop a special modular design that can readily generate novel modules.},
	number = {11},
	urldate = {2014-10-08TZ},
	journal = {PLoS Comput Biol},
	author = {Parter, Merav and Kashtan, Nadav and Alon, Uri},
	month = nov,
	year = {2008},
	pages = {e1000206}
}

@article{kashtan_varying_2007,
	title = {Varying environments can speed up evolution},
	volume = {104},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/104/34/13711},
	doi = {10.1073/pnas.0611630104},
	abstract = {Simulations of biological evolution, in which computers are used to evolve systems toward a goal, often require many generations to achieve even simple goals. It is therefore of interest to look for generic ways, compatible with natural conditions, in which evolution in simulations can be speeded. Here, we study the impact of temporally varying goals on the speed of evolution, defined as the number of generations needed for an initially random population to achieve a given goal. Using computer simulations, we find that evolution toward goals that change over time can, in certain cases, dramatically speed up evolution compared with evolution toward a fixed goal. The highest speedup is found under modularly varying goals, in which goals change over time such that each new goal shares some of the subproblems with the previous goal. The speedup increases with the complexity of the goal: the harder the problem, the larger the speedup. Modularly varying goals seem to push populations away from local fitness maxima, and guide them toward evolvable and modular solutions. This study suggests that varying environments might significantly contribute to the speed of natural evolution. In addition, it suggests a way to accelerate optimization algorithms and improve evolutionary approaches in engineering.},
	language = {en},
	number = {34},
	urldate = {2014-10-08TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Kashtan, Nadav and Noor, Elad and Alon, Uri},
	month = aug,
	year = {2007},
	pmid = {17698964},
	keywords = {biological physics, modularity, optimization, systems biology},
	pages = {13711--13716}
}

@article{oneill_open_2010,
	title = {Open issues in genetic programming},
	volume = {11},
	url = {http://link.springer.com/article/10.1007/s10710-010-9113-2},
	number = {3-4},
	urldate = {2014-10-08TZ},
	journal = {Genetic Programming and Evolvable Machines},
	author = {O’Neill, Michael and Vanneschi, Leonardo and Gustafson, Steven and Banzhaf, Wolfgang},
	year = {2010},
	pages = {339--363}
}

@inproceedings{shimodaira_dcga:_1997,
	title = {{DCGA}: {A} diversity control oriented genetic algorithm},
	shorttitle = {{DCGA}},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=632277},
	urldate = {2014-09-15TZ},
	booktitle = {Tools with {Artificial} {Intelligence}, 1997. {Proceedings}., {Ninth} {IEEE} {International} {Conference} on},
	publisher = {IEEE},
	author = {Shimodaira, Hisashi},
	year = {1997},
	pages = {367--374}
}

@inproceedings{oppacher_shifting_1999,
	title = {The shifting balance genetic algorithm: {Improving} the {GA} in a dynamic environment},
	volume = {1},
	shorttitle = {The shifting balance genetic algorithm},
	booktitle = {Proceedings of the genetic and evolutionary computation conference},
	publisher = {Citeseer},
	author = {Oppacher, Franz and Wineberg, Mark and {others}},
	year = {1999},
	pages = {504--510}
}

@book{gordon_dataflow_1992,
	title = {Dataflow parallelism in genetic algorithms},
	publisher = {Colorado State University, Department of Computer Science},
	author = {Gordon, V. Scott and Whitley, Darrell and Böhm, Anton Pedro Willem},
	year = {1992}
}

@article{spears_simple_nodate,
	title = {Simple {Subpopulation} {Schemes}},
	url = {http://www.swarmotics.com/uploads/ep94.pdf},
	urldate = {2014-09-14TZ},
	author = {Spears, William M.}
}

@inproceedings{lehman_evolving_2011,
	address = {New York, NY, USA},
	series = {{GECCO} '11},
	title = {Evolving a {Diversity} of {Virtual} {Creatures} {Through} {Novelty} {Search} and {Local} {Competition}},
	isbn = {978-1-4503-0557-0},
	url = {http://doi.acm.org/10.1145/2001576.2001606},
	doi = {10.1145/2001576.2001606},
	abstract = {An ambitious challenge in artificial life is to craft an evolutionary process that discovers a wide diversity of well-adapted virtual creatures within a single run. Unlike in nature, evolving creatures in virtual worlds tend to converge to a single morphology because selection therein greedily rewards the morphology that is easiest to exploit. However, novelty search, a technique that explicitly rewards diverging, can potentially mitigate such convergence. Thus in this paper an existing creature evolution platform is extended with multi-objective search that balances drives for both novelty and performance. However, there are different ways to combine performance-driven search and novelty search. The suggested approach is to provide evolution with both a novelty objective that encourages diverse morphologies and a local competition objective that rewards individuals outperforming those most similar in morphology. The results in an experiment evolving locomoting virtual creatures show that novelty search with local competition discovers more functional morphological diversity within a single run than models with global competition, which are more predisposed to converge. The conclusions are that novelty search with local competition may complement recent advances in evolving virtual creatures and may in general be a principled approach to combining novelty search with pressure to achieve.},
	urldate = {2014-09-12TZ},
	booktitle = {Proceedings of the 13th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Lehman, Joel and Stanley, Kenneth O.},
	year = {2011},
	keywords = {artificial life, natural evolution, novelty search, virtual creatures},
	pages = {211--218}
}

@article{cruz_optimization_2011,
	title = {Optimization in dynamic environments: a survey on problems, methods and measures},
	volume = {15},
	issn = {1432-7643, 1433-7479},
	shorttitle = {Optimization in dynamic environments},
	url = {http://link.springer.com/article/10.1007/s00500-010-0681-0},
	doi = {10.1007/s00500-010-0681-0},
	abstract = {This paper provides a survey of the research done on optimization in dynamic environments over the past decade. We show an analysis of the most commonly used problems, methods and measures together with the newer approaches and trends, as well as their interrelations and common ideas. The survey is supported by a public web repository, located at http://www.dynamic-optimization.org where the collected bibliography is manually organized and tagged according to different categories.},
	language = {en},
	number = {7},
	urldate = {2014-09-12TZ},
	journal = {Soft Computing},
	author = {Cruz, Carlos and González, Juan R. and Pelta, David A.},
	month = jul,
	year = {2011},
	keywords = {Artificial Intelligence (incl. Robotics), Computational Intelligence, Control, Robotics, Mechatronics, Mathematical Logic and Foundations},
	pages = {1427--1448}
}

@incollection{ekart_maintaining_2002,
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Maintaining the {Diversity} of {Genetic} {Programs}},
	copyright = {©2002 Springer-Verlag Berlin Heidelberg},
	isbn = {978-3-540-43378-1, 978-3-540-45984-2},
	url = {http://link.springer.com/chapter/10.1007/3-540-45984-7_16},
	abstract = {The loss of genetic diversity in evolutionary algorithms may lead to suboptimal solutions. Many techniques have been developed for maintaining diversity in genetic algorithms, but few investigations have been done for genetic programs. We define here a diversity measure for genetic programs based on our metric for genetic trees [3]. We use this distance measure for studying the effects of fitness sharing. We then propose a method for adaptively maintaining the diversity of a population during evolution.},
	language = {en},
	number = {2278},
	urldate = {2014-09-10TZ},
	booktitle = {Genetic {Programming}},
	publisher = {Springer Berlin Heidelberg},
	author = {Ekárt, Anikó and Németh, Sandor Z.},
	editor = {Foster, James A. and Lutton, Evelyne and Miller, Julian and Ryan, Conor and Tettamanzi, Andrea},
	month = jan,
	year = {2002},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Pattern Recognition, Programming Techniques},
	pages = {162--171}
}

@inproceedings{deb_investigation_1989,
	title = {An investigation of niche and species formation in genetic function optimization},
	url = {http://dl.acm.org/citation.cfm?id=657099},
	urldate = {2014-09-03TZ},
	booktitle = {Proceedings of the 3rd {International} {Conference} on {Genetic} {Algorithms}},
	publisher = {Morgan Kaufmann Publishers Inc.},
	author = {Deb, Kalyanmoy and Goldberg, David E.},
	year = {1989},
	pages = {42--50}
}

@article{li_species_2002,
	title = {A species conserving genetic algorithm for multimodal function optimization},
	volume = {10},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/106365602760234081},
	number = {3},
	urldate = {2014-09-03TZ},
	journal = {Evolutionary computation},
	author = {Li, Jian-Ping and Balazs, Marton E. and Parks, Geoffrey T. and Clarkson, P. John},
	year = {2002},
	pages = {207--234}
}

@article{mengshoel_crowding_2008,
	title = {The crowding approach to niching in genetic algorithms},
	volume = {16},
	url = {http://dl.acm.org/citation.cfm?id=1450302},
	number = {3},
	urldate = {2014-09-03TZ},
	journal = {Evolutionary computation},
	author = {Mengshoel, Ole J. and Goldberg, David E.},
	year = {2008},
	pages = {315--354}
}

@inproceedings{mengshoel_probabilistic_1999,
	title = {Probabilistic crowding: {Deterministic} crowding with probabilistic replacement},
	shorttitle = {Probabilistic crowding},
	url = {http://works.bepress.com/ole_mengshoel/14/},
	urldate = {2014-09-03TZ},
	booktitle = {Proc. of the {Genetic} and {Evolutionary} {Computation} {Conference} ({GECCO}-99)},
	author = {Mengshoel, Ole J. and Goldberg, David E.},
	year = {1999},
	pages = {409--416}
}

@book{deb_multi-objective_2001,
	title = {Multi-objective optimization using evolutionary algorithms},
	volume = {16},
	url = {http://books.google.com/books?hl=en&lr=&id=OSTn4GSy2uQC&oi=fnd&pg=PR15&ots=tEfxquIkh2&sig=RVqzgqPNSsHsBcGzdDkFKACvYzk},
	urldate = {2014-09-02TZ},
	publisher = {John Wiley \& Sons},
	author = {Deb, Kalyanmoy},
	year = {2001}
}

@article{shannon_mathematical_1963,
	title = {The mathematical theory of communication},
	journal = {The mathematical theory of communication},
	author = {Shannon, C. E. and Weaver, W.},
	year = {1963}
}

@inproceedings{gouvea_diversity_2008,
	title = {Diversity control based on population heterozygosity dynamics},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4631295},
	urldate = {2014-08-24TZ},
	booktitle = {Evolutionary {Computation}, 2008. {CEC} 2008.({IEEE} {World} {Congress} on {Computational} {Intelligence}). {IEEE} {Congress} on},
	publisher = {IEEE},
	author = {Gouvea, M. M. and Araújo, Aluizio FR},
	year = {2008},
	pages = {3671--3678}
}

@article{linhares_structure_2004,
	title = {The structure of local search diversity},
	volume = {3},
	url = {http://www.wseas.us/e-library/conferences/miami2004/papers/484-171.doc},
	number = {1},
	urldate = {2014-08-24TZ},
	journal = {WSEAS Trans Math},
	author = {Linhares, Alexandre},
	year = {2004},
	pages = {216--220}
}
@article{sultan_maintaining_2012,
	title = {Maintaining diversity for genetic algorithm: a case of timetabling problem},
	volume = {44},
	shorttitle = {Maintaining diversity for genetic algorithm},
	url = {http://www.jurnalteknologi.utm.my/index.php/jurnalteknologi/article/view/379},
	number = {1},
	urldate = {2014-08-24TZ},
	journal = {Jurnal Teknologi},
	author = {Sultan, Abu Bakar Md and Mahmod, Ramlan and Sulaiman, Md Nasir and Bakar, Mohd Rizam Abu},
	year = {2012},
	pages = {123--130}
}

@article{alam_diversity_2012,
	title = {Diversity {Guided} {Evolutionary} {Programming}: {A} novel approach for continuous optimization},
	volume = {12},
	shorttitle = {Diversity {Guided} {Evolutionary} {Programming}},
	url = {http://www.sciencedirect.com/science/article/pii/S1568494612000567},
	number = {6},
	urldate = {2014-08-24TZ},
	journal = {Applied soft computing},
	author = {Alam, Mohammad Shafiul and Islam, Md Monirul and Yao, Xin and Murase, Kazuyuki},
	year = {2012},
	pages = {1693--1707}
}

@inproceedings{abdollahzadeh_population_2012,
	title = {On {Population} {Diversity} {Measures} of the {Evolutionary} {Algorithms} used in {History} {Matching}},
	url = {https://www.onepetro.org/conference-paper/SPE-154488-MS},
	urldate = {2014-08-24TZ},
	booktitle = {{SPE} {Europec}/{EAGE} {Annual} {Conference}},
	publisher = {Society of Petroleum Engineers},
	author = {Abdollahzadeh, Asaad and Reynolds, Alan and Christie, Michael A. and Corne, David and Williams, Glyn and Davies, Brian James and {others}},
	year = {2012}
}

@book{grefenstette_genetic_2013,
	title = {Genetic {Algorithms} and {Their} {Applications}: {Proceedings} of the {Second} {International} {Conference} on {Genetic} {Algorithms}},
	isbn = {9781134989737},
	shorttitle = {Genetic {Algorithms} and {Their} {Applications}},
	abstract = {First Published in 1987. Routledge is an imprint of Taylor \& Francis, an informa company.},
	language = {en},
	publisher = {Psychology Press},
	author = {Grefenstette, John J.},
	month = aug,
	year = {2013},
	keywords = {COMPUTERS / General, Psychology / Cognitive Psychology}
}

@inproceedings{ollion_why_2011,
	title = {Why and how to measure exploration in behavioral space},
	url = {http://dl.acm.org/citation.cfm?id=2001613},
	urldate = {2014-08-24TZ},
	booktitle = {Proceedings of the 13th annual conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Ollion, Charles and Doncieux, Stéphane},
	year = {2011},
	pages = {267--274}
}

@incollection{jie_adaptive_2006,
	title = {Adaptive particle swarm optimization with feedback control of diversity},
	url = {http://link.springer.com/chapter/10.1007/11816102_9},
	urldate = {2014-08-24TZ},
	booktitle = {Computational {Intelligence} and {Bioinformatics}},
	publisher = {Springer},
	author = {Jie, Jing and Zeng, Jianchao and Han, Chongzhao},
	year = {2006},
	pages = {81--92}
}

@article{chong_relationship_2009,
	title = {Relationship between generalization and diversity in coevolutionary learning},
	volume = {1},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5286208},
	number = {3},
	urldate = {2014-08-24TZ},
	journal = {Computational Intelligence and AI in Games, IEEE Transactions on},
	author = {Chong, Siang Yew and Tino, Peter and Yao, Xin},
	year = {2009},
	pages = {214--232}
}

@inproceedings{power_promoting_2005,
	title = {Promoting diversity using migration strategies in distributed genetic algorithms},
	volume = {2},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1554910},
	urldate = {2014-08-24TZ},
	booktitle = {Evolutionary {Computation}, 2005. {The} 2005 {IEEE} {Congress} on},
	publisher = {IEEE},
	author = {Power, David and Ryan, Conor and Azad, R. Muhammad Atif},
	year = {2005},
	pages = {1831--1838}
}

@article{linhares_search_2010,
	title = {Search intensity versus search diversity: a false trade off?},
	volume = {32},
	shorttitle = {Search intensity versus search diversity},
	url = {http://link.springer.com/article/10.1007/s10489-008-0145-8},
	number = {3},
	urldate = {2014-08-24TZ},
	journal = {Applied Intelligence},
	author = {Linhares, Alexandre and Yanasse, Horacio Hideki},
	year = {2010},
	pages = {279--291}
}

@inproceedings{friedrich_rigorous_2007,
	title = {Rigorous analyses of simple diversity mechanisms},
	url = {http://dl.acm.org/citation.cfm?id=1277194},
	urldate = {2014-08-24TZ},
	booktitle = {Proceedings of the 9th annual conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Friedrich, Tobias and Hebbinghaus, Nils and Neumann, Frank},
	year = {2007},
	pages = {1219--1225}
}

@article{wang_diversity_2013,
	title = {Diversity enhanced particle swarm optimization with neighborhood search},
	volume = {223},
	url = {http://www.sciencedirect.com/science/article/pii/S0020025512006779},
	urldate = {2014-08-24TZ},
	journal = {Information Sciences},
	author = {Wang, Hui and Sun, Hui and Li, Changhe and Rahnamayan, Shahryar and Pan, Jeng-shyang},
	year = {2013},
	pages = {119--135}
}

@article{porumbel_evolutionary_2010,
	title = {An evolutionary approach with diversity guarantee and well-informed grouping recombination for graph coloring},
	volume = {37},
	url = {http://www.sciencedirect.com/science/article/pii/S0305054810000286},
	number = {10},
	urldate = {2014-08-24TZ},
	journal = {Computers \& Operations Research},
	author = {Porumbel, Daniel Cosmin and Hao, Jin-Kao and Kuntz, Pascale},
	year = {2010},
	pages = {1822--1832}
}

@phdthesis{gustafson_analysis_2004,
	title = {An analysis of diversity in genetic programming},
	url = {http://etheses.nottingham.ac.uk/57/},
	urldate = {2014-08-24TZ},
	school = {University of Nottingham},
	author = {Gustafson, Steven Matt},
	year = {2004}
}

@article{aksela_using_2006,
	title = {Using diversity of errors for selecting members of a committee classifier},
	volume = {39},
	url = {http://www.sciencedirect.com/science/article/pii/S0031320305004309},
	number = {4},
	urldate = {2014-08-24TZ},
	journal = {Pattern Recognition},
	author = {Aksela, Matti and Laaksonen, Jorma},
	year = {2006},
	pages = {608--623}
}

@article{burke_diversity_2004,
	title = {Diversity in genetic programming: {An} analysis of measures and correlation with fitness},
	volume = {8},
	shorttitle = {Diversity in genetic programming},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1266373},
	number = {1},
	urldate = {2014-08-24TZ},
	journal = {Evolutionary Computation, IEEE Transactions on},
	author = {Burke, Edmund K. and Gustafson, Steven and Kendall, Graham},
	year = {2004},
	pages = {47--62}
}

@article{coelho_improved_2009,
	title = {Improved differential evolution approach based on cultural algorithm and diversity measure applied to solve economic load dispatch problems},
	volume = {79},
	url = {http://www.sciencedirect.com/science/article/pii/S0378475409000731},
	number = {10},
	urldate = {2014-08-24TZ},
	journal = {Mathematics and Computers in Simulation},
	author = {Coelho, Leandro dos Santos and Souza, Rodrigo Clemente Thom and Mariani, Viviana Cocco},
	year = {2009},
	pages = {3136--3147}
}

@inproceedings{wineberg_linear_2003,
	title = {A linear time algorithm for determining population diversity in evolutionary computation},
	url = {http://www.actapress.com/PaperInfo.aspx?paperId=13551},
	urldate = {2014-08-24TZ},
	booktitle = {Proceedings of the {IASTED} {International} {Conference} on {Intelligent} {Systems} and {Control}},
	publisher = {Salzburg, Austria: ACTA Press},
	author = {Wineberg, Mark and Oppacher, Franz},
	year = {2003},
	pages = {275--286}
}

@inproceedings{wineberg_enhancing_2000,
	title = {Enhancing the {GA}'s {Ability} to {Cope} with {Dynamic} {Environments}.},
	url = {ftp://ftp.cs.bham.ac.uk/.snapshot/nightly.0/pub/authors/W.B.Langdon/biblio/gecco2000/GA139R.pdf},
	urldate = {2014-08-24TZ},
	booktitle = {{GECCO}},
	author = {Wineberg, Mark and Oppacher, Franz and {others}},
	year = {2000},
	pages = {3--10}
}

@phdthesis{wineberg_improving_2000,
	title = {Improving the behavior of the genetic algorithm in a dynamic environment},
	url = {http://www.cis.uoguelph.ca/~wineberg/publications/theses/mlw_dissertation.pdf},
	urldate = {2014-08-24TZ},
	school = {Carleton University},
	author = {Wineberg, Mark},
	year = {2000}
}

@inproceedings{wineberg_distance_2003,
	title = {Distance between populations},
	url = {http://link.springer.com/chapter/10.1007/3-540-45110-2_20},
	urldate = {2014-08-24TZ},
	booktitle = {Genetic and {Evolutionary} {Computation}—{GECCO} 2003},
	publisher = {Springer},
	author = {Wineberg, Mark and Oppacher, Franz},
	year = {2003},
	pages = {1481--1492}
}

@inproceedings{wineberg_underlying_2003,
	title = {The underlying similarity of diversity measures used in evolutionary computation},
	url = {http://link.springer.com/chapter/10.1007/3-540-45110-2_21},
	urldate = {2014-08-24TZ},
	booktitle = {Genetic and {Evolutionary} {Computation}—{GECCO} 2003},
	publisher = {Springer},
	author = {Wineberg, Mark and Oppacher, Franz},
	year = {2003},
	pages = {1493--1504}
}

@inproceedings{nicholson_maintaining_2008,
	title = {Maintaining population diversity by maintaining family structures},
	url = {http://dl.acm.org/citation.cfm?id=1389198},
	urldate = {2014-08-24TZ},
	booktitle = {Proceedings of the 10th annual conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Nicholson, John and White, Mark},
	year = {2008},
	pages = {533--534}
}

@article{yang_differential_2014,
	title = {Differential {Evolution} with {Auto}-{Enhanced} {Population} {Diversity}},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6868218},
	urldate = {2014-08-24TZ},
	author = {Yang, Ming and Li, Changhe and Cai, Zhihua and Guan, Jing},
	year = {2014}
}

@article{mattiussi_measures_2004,
	title = {Measures of diversity for populations and distances between individuals with highly reorganizable genomes},
	volume = {12},
	url = {http://www.mitpressjournals.org/doi/abs/10.1162/1063656043138923},
	number = {4},
	urldate = {2014-08-24TZ},
	journal = {Evolutionary Computation},
	author = {Mattiussi, Claudio and Waibel, Markus and Floreano, Dario},
	year = {2004},
	pages = {495--515}
}

@article{corriveau_review_2012,
	title = {Review and study of genotypic diversity measures for real-coded representations},
	volume = {16},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6151099},
	number = {5},
	urldate = {2014-08-24TZ},
	journal = {Evolutionary Computation, IEEE Transactions on},
	author = {Corriveau, Guillaume and Guilbault, Raynald and Tahan, Antoine and Sabourin, Robert},
	year = {2012},
	pages = {695--710}
}

@inproceedings{lacevic_population_2010,
	title = {On population diversity measures in {Euclidean} space},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5586498},
	urldate = {2014-08-24TZ},
	booktitle = {Evolutionary {Computation} ({CEC}), 2010 {IEEE} {Congress} on},
	publisher = {IEEE},
	author = {Lacevic, Bakir and Amaldi, Edoardo},
	year = {2010},
	pages = {1--8}
}

@article{nitschke_evolving_2012,
	title = {Evolving behavioral specialization in robot teams to solve a collective construction task},
	volume = {2},
	url = {http://www.sciencedirect.com/science/article/pii/S2210650211000423},
	urldate = {2014-08-24TZ},
	journal = {Swarm and Evolutionary Computation},
	author = {Nitschke, Geoff S. and Schut, Martijn C. and Eiben, A. E.},
	year = {2012},
	pages = {25--38}
}

@article{lacevic_ectropy_2011,
	title = {Ectropy of diversity measures for populations in {Euclidean} space},
	volume = {181},
	url = {http://www.sciencedirect.com/science/article/pii/S0020025510006043},
	number = {11},
	urldate = {2014-08-24TZ},
	journal = {Information Sciences},
	author = {Lacevic, Bakir and Amaldi, Edoardo},
	year = {2011},
	pages = {2316--2339}
}

@article{mahfoud_niching_1995,
	title = {Niching methods for genetic algorithms},
	volume = {51},
	number = {95001},
	journal = {Urbana},
	author = {Mahfoud, Samir W.},
	year = {1995}
}

@article{hutter_fitness_2006,
	title = {Fitness uniform optimization},
	volume = {10},
	issn = {1089-778X},
	doi = {10.1109/TEVC.2005.863127},
	abstract = {In evolutionary algorithms, the fitness of a population increases with time by mutating and recombining individuals and by a biased selection of fitter individuals. The right selection pressure is critical in ensuring sufficient optimization progress on the one hand and in preserving genetic diversity to be able to escape from local optima on the other hand. Motivated by a universal similarity relation on the individuals, we propose a new selection scheme, which is uniform in the fitness values. It generates selection pressure toward sparsely populated fitness regions, not necessarily toward higher fitness, as is the case for all other selection schemes. We show analytically on a simple example that the new selection scheme can be much more effective than standard selection schemes. We also propose a new deletion scheme which achieves a similar result via deletion and show how such a scheme preserves genetic diversity more effectively than standard approaches. We compare the performance of the new schemes to tournament selection and random deletion on an artificial deceptive problem and a range of NP hard problems: traveling salesman, set covering, and satisfiability},
	number = {5},
	journal = {IEEE Transactions on Evolutionary Computation},
	author = {Hutter, M. and Legg, S.},
	month = oct,
	year = {2006},
	keywords = {Convergence, Design optimization, Evolutionary algorithms, Fitness tree model, Genetic algorithms, Genetic mutations, NP hard problems, NP-hard problem, Steady-state, Traveling salesman problems, computability, computational complexity, evolutionary computation, fitness uniform deletion scheme, fitness uniform optimization, fitness uniform selection scheme, genetic diversity, local optima, preserve diversity, random deletion, satisfiability, set covering, tournament selection, traveling salesman, travelling salesman problems},
	pages = {568--589}
}

@inproceedings{hornby_alps:_2006,
	address = {New York, NY, USA},
	series = {{GECCO} '06},
	title = {{ALPS}: {The} {Age}-layered {Population} {Structure} for {Reducing} the {Problem} of {Premature} {Convergence}},
	isbn = {1-59593-186-4},
	shorttitle = {{ALPS}},
	url = {http://doi.acm.org/10.1145/1143997.1144142},
	doi = {10.1145/1143997.1144142},
	abstract = {To reduce the problem of premature convergence we define a new method for measuring an individual's age and propose the Age-Layered Population Structure (ALPS). This new measure of age measures how long the genetic material has been evolving in the population: offspring start with an age of 1 plus the age of their oldest parent instead of starting with an age of 0 as with traditional measures of age. ALPS differs from a typical evolutionary algorithm (EA) by segregating individuals into different age-layers by their age and by regularly introducing new, randomly generated individuals in the youngest layer. The introduction of randomly generated individuals at regular intervals results in an EA that is never completely converged and is always exploring new parts of the fitness landscape. By using age to restrict competition and breeding, younger individuals are able to develop without being dominated by older ones. Analysis of the search behavior of ALPS finds that the offspring of individuals that are randomly generated mid-way through a run are able to move the population out of mediocre local-optima to better parts of the fitness landscape. In comparison against a traditional EA, a multi-start EA and two other EAs with diversity maintenance schemes we find that ALPS produces significantly better designs with a higher reliability than the other EAs.},
	urldate = {2014-08-13TZ},
	booktitle = {Proceedings of the 8th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Hornby, Gregory S.},
	year = {2006},
	keywords = {Evolutionary algorithms, age, computer-automated design, open-ended design, premature convergence},
	pages = {815--822}
}

@inproceedings{risi_how_2009,
	address = {New York, NY, USA},
	series = {{GECCO} '09},
	title = {How {Novelty} {Search} {Escapes} the {Deceptive} {Trap} of {Learning} to {Learn}},
	isbn = {978-1-60558-325-9},
	url = {http://doi.acm.org/10.1145/1569901.1569923},
	doi = {10.1145/1569901.1569923},
	abstract = {A major goal for researchers in neuroevolution is to evolve artificial neural networks (ANNs) that can learn during their lifetime. Such networks can adapt to changes in their environment that evolution on its own cannot anticipate. However, a profound problem with evolving adaptive systems is that if the impact of learning on the fitness of the agent is only marginal, then evolution is likely to produce individuals that do not exhibit the desired adaptive behavior. Instead, because it is easier at first to improve fitness without evolving the ability to learn, they are likely to exploit domain-dependent static (i.e. non-adaptive) heuristics. This paper proposes a way to escape the deceptive trap of static policies based on the novelty search algorithm, which opens up a new avenue in the evolution of adaptive systems because it can exploit the behavioral difference between learning and non-learning individuals. The main idea in novelty search is to abandon objective-based fitness and instead simply search only for novel behavior, which avoids deception entirely and has shown prior promising results in other domains. This paper shows that novelty search significantly outperforms fitness-based search in a tunably deceptive T-Maze navigation domain because it fosters the emergence of adaptive behavior.},
	urldate = {2014-08-13TZ},
	booktitle = {Proceedings of the 11th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Risi, Sebastian and Vanderbleek, Sandy D. and Hughes, Charles E. and Stanley, Kenneth O.},
	year = {2009},
	keywords = {adaptation, learning, neat, neural networks, neuroevolution, neuromodulation, novelty search},
	pages = {153--160}
}

@inproceedings{mouret_overcoming_2009,
	title = {Overcoming the bootstrap problem in evolutionary robotics using behavioral diversity},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4983077},
	urldate = {2014-08-13TZ},
	booktitle = {Evolutionary {Computation}, 2009. {CEC}'09. {IEEE} {Congress} on},
	publisher = {IEEE},
	author = {Mouret, J. and Doncieux, Stéphane},
	year = {2009},
	pages = {1161--1168}
}

@article{mahfoud_niching_2000,
	title = {Niching methods},
	volume = {2},
	url = {http://books.google.com/books?hl=en&lr=&id=Q5viOPDT1ecC&oi=fnd&pg=PA87&dq=Crowding+and+preselection+revisited+mahfoud&ots=2rMGIXQQA5&sig=fYNnP3-_JKYP3BM-Irni4sCGtnI},
	urldate = {2014-08-13TZ},
	journal = {Evolutionary Computation},
	author = {Mahfoud, Samir W.},
	year = {2000},
	pages = {87--92}
}

@article{mahfoud_crowding_1992,
	title = {Crowding and preselection revisited},
	volume = {51},
	journal = {Urbana},
	author = {Mahfoud, Samir W.},
	year = {1992},
	pages = {61801}
}

@article{cavicchio_adaptive_1970,
	title = {Adaptive search using simulated evolution},
	url = {http://deepblue.lib.umich.edu/handle/2027.42/4042},
	language = {en\_US},
	urldate = {2014-08-13TZ},
	author = {Cavicchio, Daniel Joseph},
	year = {1970},
	note = {http://deepblue.lib.umich.edu/bitstream/2027.42/4042/5/bab9712.0001.001.pdf},
	keywords = {Adaptive control systems., Engineering}
}

@article{toffolo_genetic_2003,
	title = {Genetic {Diversity} as an {Objective} in {Multi}-{Objective} {Evolutionary} {Algorithms}},
	volume = {11},
	issn = {1063-6560},
	url = {http://dx.doi.org/10.1162/106365603766646816},
	doi = {10.1162/106365603766646816},
	abstract = {A key feature of an efficient and reliable multi-objective evolutionary algorithm is the ability to maintain genetic diversity within a population of solutions. In this paper, we present a new diversity-preserving mechanism, the Genetic Diversity Evaluation Method (GeDEM), which considers a distance-based measure of genetic diversity as a real objective in fitness assignment. This provides a dual selection pressure towards the exploitation of current non-dominated solutions and the exploration of the search space. We also introduce a new multi-objective evolutionary algorithm, the Genetic Diversity Evolutionary Algorithm (GDEA), strictly designed around GeDEM and then we compare it with other state-of-the-art algorithms on a well-established suite of test problems. Experimental results clearly indicate that the performance of GDEA is top-level.},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Evolutionary Computation},
	author = {Toffolo, Andrea and Benini, Ernesto},
	month = jun,
	year = {2003},
	pages = {151--167}
}
@article{stanley_evolving_2002,
	title = {Evolving {Neural} {Networks} through {Augmenting} {Topologies}},
	volume = {10},
	issn = {1063-6560},
	doi = {10.1162/106365602320169811},
	abstract = {An important question in neuroevolution is how to gain an advantage from evolving neural network topologies along with weights. We present a method, NeuroEvolution of Augmenting Topologies (NEAT), which outperforms the best fixed-topology method on a challenging benchmark reinforcement learning task. We claim that the increased efficiency is due to (1) employing a principled method of crossover of different topologies, (2) protecting structural innovation using speciation, and (3) incrementally growing from minimal structure. We test this claim through a series of ablation studies that demonstrate that each component is necessary to the system as a whole and to each other. What results is signicantly faster learning. NEAT is also an important contribution to GAs because it shows how it is possible for evolution to both optimize and complexify solutions simultaneously, offering the possibility of evolving increasingly complex solutions over generations, and strengthening the analogy with biological evolution.},
	number = {2},
	journal = {Evolutionary Computation},
	author = {Stanley, K and Miikkulainen, R},
	month = jun,
	year = {2002},
	keywords = {Genetic algorithms, competing conventions, network topologies, neural networks, neuroevolution, speciation},
	pages = {99--127}
}

@book{holland_adaptation_1975,
	address = {Oxford,  England},
	title = {Adaptation in natural and artificial systems: {An} introductory analysis with applications to biology, control, and artificial intelligence},
	volume = {viii},
	copyright = {(c) 2012 APA, all rights reserved},
	isbn = {0472084607},
	shorttitle = {Adaptation in natural and artificial systems},
	abstract = {Analyzes and exploits nonadditive system interactions by generalizing the biological concept of "a coadapted set of alleles," and applies a constructive mathematical theory to the full range of adaptive processes, providing both hypotheses for natural systems and algorithms for artificial systems.},
	publisher = {U Michigan Press},
	author = {Holland, John H.},
	year = {1975},
	keywords = {*Adaptation, Mathematical Modeling}
}

@book{jong_reducing_2001,
	title = {Reducing {Bloat} and {Promoting} {Diversity} using {Multi}-{Objective} {Methods}},
	abstract = {Two important problems in genetic programming (GP) are its tendency to find unnecessarily large trees (bloat), and the general evolutionary algorithms problem that diversity in the population can be lost prematurely. The prevention of these problems is frequently an implicit goal of basic GP. We explore the potential of techniques from multi-objective optimization to aid GP by adding explicit objectives to avoid bloat and promote diversity. The even 3, 4, and 5-parity problems were solved efficiently compared to basic GP results from the literature. Even though only non-dominated individuals were selected and populations thus remained extremely small, appropriate diversity was maintained. The size of individuals visited during search consistently remained small, and solutions of what we believe to be the minimum size were found for the 3, 4, and 5-parity problems.},
	author = {Jong, Edwin de and Watson, Richard and Pollack, Jordan},
	year = {2001}
}

@article{standish_open-ended_2003,
	title = {Open-ended artificial evolution},
	volume = {3},
	url = {http://www.worldscientific.com/doi/abs/10.1142/S1469026803000914},
	number = {02},
	urldate = {2014-08-13TZ},
	journal = {International Journal of Computational Intelligence and Applications},
	author = {Standish, Russell K.},
	year = {2003},
	pages = {167--175}
}

@inproceedings{baptista_step_2013,
	title = {Step evolution: {Improving} the performance of open-ended evolution simulations},
	shorttitle = {Step evolution},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6602431},
	urldate = {2014-08-13TZ},
	booktitle = {Artificial {Life} ({ALIFE}), 2013 {IEEE} {Symposium} on},
	publisher = {IEEE},
	author = {Baptista, Tiago and Costa, Ernesto},
	year = {2013},
	pages = {52--59}
}

@inproceedings{standish_visualising_2002,
	title = {Visualising {Tierra}’s tree of life using {Netmap}},
	url = {http://ww.molaah.com/Alife%20NetMap.pdf},
	urldate = {2014-08-13TZ},
	booktitle = {{ALife} {VIII} {Workshop} proceedings},
	author = {Standish, Russell K. and Galloway, John},
	year = {2002},
	pages = {171}
}

@article{kernbach_adaptation_2010,
	title = {Adaptation and self-adaptation of developmental multi-robot systems},
	volume = {3},
	url = {http://www.thinkmind.org/index.php?view=article&articleid=intsys_v3_n12_2010_10},
	number = {1 and 2},
	urldate = {2014-08-13TZ},
	journal = {International Journal On Advances in Intelligent Systems},
	author = {Kernbach, Serge and Meister, Eugen and Schlachter, Florian and Kernbach, Olga},
	year = {2010},
	pages = {121--140}
}

@incollection{lehman_novelty_2011,
	title = {Novelty search and the problem with objectives},
	url = {http://link.springer.com/chapter/10.1007/978-1-4614-1770-5_3},
	urldate = {2014-08-13TZ},
	booktitle = {Genetic {Programming} {Theory} and {Practice} {IX}},
	publisher = {Springer},
	author = {Lehman, Joel and Stanley, Kenneth O.},
	year = {2011},
	pages = {37--56}
}

@phdthesis{miconi_road_2008,
	title = {The road to everywhere: {Evolution}, complexity and progress in natural and artificial systems},
	shorttitle = {The road to everywhere},
	url = {http://etheses.bham.ac.uk/148/},
	urldate = {2014-08-13TZ},
	school = {University of Birmingham},
	author = {Miconi, Thomas},
	year = {2008}
}

@article{oregon_domestic_nodate,
	title = {Domestic {Student} {Health} {Insurance}},
	volume = {474905},
	url = {http://www.eou.edu/student_affairs/documents/08-09_EOU_DOM_AETNA-AETNA.final.8.13.08-1.pdf},
	urldate = {2014-08-13TZ},
	journal = {Policy},
	author = {OREGON, EASTERN},
	pages = {2008--2009}
}

@article{burges_tutorial_1998,
	title = {A {Tutorial} on {Support} {Vector} {Machines} for {Pattern} {Recognition}},
	volume = {2},
	abstract = {. The tutorial starts with an overview of the concepts of VC dimension and structural risk minimization. We then describe linear Support Vector Machines (SVMs) for separable and non-separable data, working through a non-trivial example in detail. We describe a mechanical analogy, and discuss when SVM solutions are unique and when they are global. We describe how support vector training can be practically implemented, and discuss in detail the kernel mapping technique which is used to construct SVM solutions which are nonlinear in the data. We show how Support Vector machines can have very large (even infinite) VC dimension by computing the VC dimension for homogeneous polynomial and Gaussian radial basis function kernels. While very high VC dimension would normally bode ill for generalization performance, and while at present there exists no theory which shows that good generalization performance is guaranteed for SVMs, there are several arguments which support the observed high accura...},
	journal = {Data Mining and Knowledge Discovery},
	author = {Burges, Christopher J. C.},
	year = {1998},
	pages = {121--167}
}

@inproceedings{lee_category-based_2009,
	title = {Category-based intrinsic motivation},
	volume = {146},
	url = {http://www.cs.swarthmore.edu/~meeden/papers/meeden.epirob09.pdf},
	urldate = {2013-08-30TZ},
	booktitle = {Proceedings of the ninth international conference on epigenetic robotics},
	author = {Lee, Rachel and Walker, Ryan and Meeden, Lisa and Marshall, James},
	year = {2009},
	pages = {81--88}
}

@article{niedzwiedzki_tetrapod_2010,
	title = {Tetrapod trackways from the early {Middle} {Devonian} period of {Poland}},
	volume = {463},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/doifinder/10.1038/nature08623},
	doi = {10.1038/nature08623},
	number = {7277},
	urldate = {2014-08-13TZ},
	journal = {Nature},
	author = {Niedźwiedzki, Grzegorz and Szrek, Piotr and Narkiewicz, Katarzyna and Narkiewicz, Marek and Ahlberg, Per E.},
	month = jan,
	year = {2010},
	pages = {43--48}
}

@article{sahney_links_2010,
	title = {Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land},
	volume = {6},
	issn = {1744-9561, 1744-957X},
	url = {http://rsbl.royalsocietypublishing.org/cgi/doi/10.1098/rsbl.2009.1024},
	doi = {10.1098/rsbl.2009.1024},
	language = {en},
	number = {4},
	urldate = {2014-08-13TZ},
	journal = {Biology Letters},
	author = {Sahney, S. and Benton, M. J. and Ferry, P. A.},
	month = aug,
	year = {2010},
	pages = {544--547}
}

@article{kocot_phylogenomics_2011,
	title = {Phylogenomics reveals deep molluscan relationships},
	volume = {477},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/doifinder/10.1038/nature10382},
	doi = {10.1038/nature10382},
	number = {7365},
	urldate = {2014-08-13TZ},
	journal = {Nature},
	author = {Kocot, Kevin M. and Cannon, Johanna T. and Todt, Christiane and Citarella, Mathew R. and Kohn, Andrea B. and Meyer, Achim and Santos, Scott R. and Schander, Christoffer and Moroz, Leonid L. and Lieb, Bernhard and Halanych, Kenneth M.},
	month = sep,
	year = {2011},
	pages = {452--456}
}

@inproceedings{iqbal_salient_2014,
	title = {Salient object detection using learning classifiersystems that compute action mappings},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598371},
	doi = {10.1145/2576768.2598371},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Iqbal, Muhammad and Naqvi, Syed S. and Browne, Will N. and Hollitt, Christopher and Zhang, Mengjie},
	year = {2014},
	pages = {525--532}
}

@article{holloway_what_nodate,
	title = {What is {Paleoneurology}?},
	url = {http://www.springerlink.com/index/H1UU0RV14V5L18U3.html},
	urldate = {2014-08-13TZ},
	author = {Holloway, Ralph L. and Sherwood, Chet C. and Hof, Patrick R. and Rilling, James K.}
}

@article{jablonski_out_2013,
	title = {Out of the tropics, but how? {Fossils}, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient},
	volume = {110},
	issn = {0027-8424, 1091-6490},
	shorttitle = {Out of the tropics, but how?},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1308997110},
	doi = {10.1073/pnas.1308997110},
	language = {en},
	number = {26},
	urldate = {2014-08-13TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Jablonski, D. and Belanger, C. L. and Berke, S. K. and Huang, S. and Krug, A. Z. and Roy, K. and Tomasovych, A. and Valentine, J. W.},
	month = jun,
	year = {2013},
	pages = {10487--10494}
}

@article{jansson_what_2013,
	title = {{WHAT} {CAN} {MULTIPLE} {PHYLOGENIES} {SAY} {ABOUT} {THE} {LATITUDINAL} {DIVERSITY} {GRADIENT}? {A} {NEW} {LOOK} {AT} {THE} {TROPICAL} {CONSERVATISM}, {OUT} {OF} {THE} {TROPICS}, {AND} {DIVERSIFICATION} {RATE} {HYPOTHESES}: {PHYLOGENIES} {AND} {THE} {LATITUDINAL} {DIVERSITY} {GRADIENT}},
	volume = {67},
	issn = {00143820},
	shorttitle = {{WHAT} {CAN} {MULTIPLE} {PHYLOGENIES} {SAY} {ABOUT} {THE} {LATITUDINAL} {DIVERSITY} {GRADIENT}?},
	url = {http://doi.wiley.com/10.1111/evo.12089},
	doi = {10.1111/evo.12089},
	language = {en},
	number = {6},
	urldate = {2014-08-13TZ},
	journal = {Evolution},
	author = {Jansson, Roland and Rodríguez-Castañeda, Genoveva and Harding, Larisa E.},
	month = jun,
	year = {2013},
	pages = {1741--1755}
}

@article{korpimaki_predator-induced_2005,
	title = {Predator-induced synchrony in population oscillations of coexisting small mammal species},
	volume = {272},
	issn = {0962-8452, 1471-2954},
	url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2004.2860},
	doi = {10.1098/rspb.2004.2860},
	language = {en},
	number = {1559},
	urldate = {2014-08-13TZ},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Korpimaki, E. and Norrdahl, K. and Huitu, O. and Klemola, T.},
	month = jan,
	year = {2005},
	pages = {193--202}
}

@article{islam_role_2004,
	title = {Role of metal-reducing bacteria in arsenic release from {Bengal} delta sediments},
	volume = {430},
	issn = {0028-0836, 1476-4679},
	url = {http://www.nature.com/doifinder/10.1038/nature02638},
	doi = {10.1038/nature02638},
	number = {6995},
	urldate = {2014-08-13TZ},
	journal = {Nature},
	author = {Islam, Farhana S. and Gault, Andrew G. and Boothman, Christopher and Polya, David A. and Charnock, John M. and Chatterjee, Debashis and Lloyd, Jonathan R.},
	month = jul,
	year = {2004},
	pages = {68--71}
}

@article{stomp_adaptive_2004,
	title = {Adaptive divergence in pigment composition promotes phytoplankton biodiversity},
	volume = {432},
	url = {http://www.nature.com/nature/journal/v432/n7013/abs/nature03044.html},
	number = {7013},
	urldate = {2014-08-13TZ},
	journal = {Nature},
	author = {Stomp, Maayke and Huisman, Jef and de Jongh, Floris and Veraart, Annelies J. and Gerla, Daan and Rijkeboer, Machteld and Ibelings, Bas W. and Wollenzien, Ute IA and Stal, Lucas J.},
	year = {2004},
	pages = {104--107}
}

@article{minter_between_2007,
	title = {Between a rock and a hard place: arthropod trackways and ichnotaxonomy},
	volume = {40},
	issn = {0024-1164, 1502-3931},
	shorttitle = {Between a rock and a hard place},
	url = {http://doi.wiley.com/10.1111/j.1502-3931.2007.00035.x},
	doi = {10.1111/j.1502-3931.2007.00035.x},
	language = {en},
	number = {4},
	urldate = {2014-08-13TZ},
	journal = {Lethaia},
	author = {Minter, Nicholas J. and Braddy, Simon J. and Davis, Robert B.},
	month = dec,
	year = {2007},
	pages = {365--375}
}

@article{plotnick_invention_2000,
	title = {Invention by evolution: functional analysis in paleobiology},
	volume = {26},
	shorttitle = {Invention by evolution},
	url = {http://www.psjournals.org/doi/abs/10.1666/0094-8373(2000)26%5B305%3AIBEFAI%5D2.0.CO%3B2},
	number = {sp4},
	urldate = {2014-08-13TZ},
	journal = {Paleobiology},
	author = {Plotnick, Roy E. and Baumiller, Tomasz K.},
	year = {2000},
	pages = {305--323}
}

@article{sober_contest_2004,
	title = {The {Contest} {Between} {Parsimony} and {Likelihood}},
	volume = {53},
	issn = {1063-5157, 1076-836X},
	url = {http://sysbio.oxfordjournals.org/cgi/doi/10.1080/10635150490468657},
	doi = {10.1080/10635150490468657},
	number = {4},
	urldate = {2014-08-13TZ},
	journal = {Systematic Biology},
	author = {Sober, Elliott},
	month = aug,
	year = {2004},
	pages = {644--653}
}

@article{willerslev_review_2005,
	title = {Review {Paper}. {Ancient} {DNA}},
	volume = {272},
	issn = {0962-8452, 1471-2954},
	url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2004.2813},
	doi = {10.1098/rspb.2004.2813},
	language = {en},
	number = {1558},
	urldate = {2014-08-13TZ},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Willerslev, E. and Cooper, A.},
	month = jan,
	year = {2005},
	pages = {3--16}
}

@article{bruner_geometric_2004,
	title = {Geometric morphometrics and paleoneurology: brain shape evolution in the genus {Homo}},
	volume = {47},
	issn = {00472484},
	shorttitle = {Geometric morphometrics and paleoneurology},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0047248404001149},
	doi = {10.1016/j.jhevol.2004.03.009},
	language = {en},
	number = {5},
	urldate = {2014-08-13TZ},
	journal = {Journal of Human Evolution},
	author = {Bruner, Emiliano},
	month = nov,
	year = {2004},
	pages = {279--303}
}

@article{kuhner_simulation_1994,
	title = {A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.},
	volume = {11},
	url = {http://mbe.oxfordjournals.org/content/11/3/459.short},
	number = {3},
	urldate = {2014-08-13TZ},
	journal = {Molecular Biology and Evolution},
	author = {Kuhner, Mary K. and Felsenstein, Joseph},
	year = {1994},
	pages = {459--468}
}

@article{ryan_trabecular_2009,
	title = {Trabecular bone structure in the mandibular condyles of gouging and nongouging platyrrhine primates},
	issn = {00029483, 10968644},
	url = {http://doi.wiley.com/10.1002/ajpa.21178},
	doi = {10.1002/ajpa.21178},
	language = {en},
	urldate = {2014-08-13TZ},
	journal = {American Journal of Physical Anthropology},
	author = {Ryan, Timothy M. and Colbert, Matthew and Ketcham, Richard A. and Vinyard, Christopher J.},
	year = {2009},
	pages = {NA--NA}
}

@article{schuenemann_targeted_2011,
	title = {Targeted enrichment of ancient pathogens yielding the {pPCP}1 plasmid of {Yersinia} pestis from victims of the {Black} {Death}},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1105107108},
	doi = {10.1073/pnas.1105107108},
	language = {en},
	number = {38},
	urldate = {2014-08-13TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Schuenemann, V. J. and Bos, K. and DeWitte, S. and Schmedes, S. and Jamieson, J. and Mittnik, A. and Forrest, S. and Coombes, B. K. and Wood, J. W. and Earn, D. J. D. and White, W. and Krause, J. and Poinar, H. N.},
	month = sep,
	year = {2011},
	pages = {E746--E752}
}

@article{thewissen_whales_2007,
	title = {Whales originated from aquatic artiodactyls in the {Eocene} epoch of {India}},
	volume = {450},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/doifinder/10.1038/nature06343},
	doi = {10.1038/nature06343},
	number = {7173},
	urldate = {2014-08-13TZ},
	journal = {Nature},
	author = {Thewissen, J. G. M. and Cooper, Lisa Noelle and Clementz, Mark T. and Bajpai, Sunil and Tiwari, B. N.},
	month = dec,
	year = {2007},
	pages = {1190--1194}
}

@article{trinajstic_microvertebrate_2009,
	title = {{MICROVERTEBRATE} {BIOSTRATIGRAPHY} {OF} {UPPER} {DEVONIAN} ({FRASNIAN}) {CARBONATE} {ROCKS} {IN} {THE} {CANNING} {AND} {CARNARVON} {BASINS} {OF} {WESTERN} {AUSTRALIA}},
	volume = {52},
	issn = {00310239, 14754983},
	url = {http://doi.wiley.com/10.1111/j.1475-4983.2009.00870.x},
	doi = {10.1111/j.1475-4983.2009.00870.x},
	language = {en},
	number = {3},
	urldate = {2014-08-13TZ},
	journal = {Palaeontology},
	author = {Trinajstic, Kate and George, Annette D.},
	month = may,
	year = {2009},
	pages = {641--659}
}

@article{brown_ancient_2013,
	title = {Ancient {DNA} evidence for genetic continuity in arctic dogs},
	volume = {40},
	issn = {03054403},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0305440312004128},
	doi = {10.1016/j.jas.2012.09.010},
	language = {en},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Journal of Archaeological Science},
	author = {Brown, Sarah K. and Darwent, Christyann M. and Sacks, Benjamin N.},
	month = feb,
	year = {2013},
	pages = {1279--1288}
}

@article{butler_anatomy_2012,
	title = {Anatomy and {Cranial} {Functional} {Morphology} of the {Small}-{Bodied} {Dinosaur} {Fruitadens} haagarorum from the {Upper} {Jurassic} of the {USA}},
	volume = {7},
	issn = {1932-6203},
	url = {http://dx.plos.org/10.1371/journal.pone.0031556},
	doi = {10.1371/journal.pone.0031556},
	language = {en},
	number = {4},
	urldate = {2014-08-13TZ},
	journal = {PLoS ONE},
	author = {Butler, Richard J. and Porro, Laura B. and Galton, Peter M. and Chiappe, Luis M.},
	editor = {Farke, Andrew A.},
	month = apr,
	year = {2012},
	pages = {e31556}
}

@article{grine_dental_2012,
	title = {Dental microwear and stable isotopes inform the paleoecology of extinct hominins},
	volume = {148},
	issn = {00029483},
	url = {http://doi.wiley.com/10.1002/ajpa.22086},
	doi = {10.1002/ajpa.22086},
	language = {en},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {American Journal of Physical Anthropology},
	author = {Grine, Frederick E. and Sponheimer, Matt and Ungar, Peter S. and Lee-Thorp, Julia and Teaford, Mark F.},
	month = jun,
	year = {2012},
	pages = {285--317}
}

@article{hillis_approaches_1995,
	title = {Approaches for {Assessing} {Phylogenetic} {Accuracy}},
	volume = {44},
	issn = {10635157},
	url = {http://www.jstor.org/stable/2413480?origin=crossref},
	doi = {10.2307/2413480},
	number = {1},
	urldate = {2014-08-13TZ},
	journal = {Systematic Biology},
	author = {Hillis, David M.},
	month = mar,
	year = {1995},
	pages = {3}
}

@article{joyce_palaeoecology_2004,
	title = {Palaeoecology of {Triassic} stem turtles sheds new light on turtle origins},
	volume = {271},
	issn = {0962-8452, 1471-2954},
	url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2003.2523},
	doi = {10.1098/rspb.2003.2523},
	language = {en},
	number = {1534},
	urldate = {2014-08-13TZ},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Joyce, W. G. and Gauthier, J. A.},
	month = jan,
	year = {2004},
	pages = {1--5}
}

@article{marden_reanalysis_2013,
	title = {{REANALYSIS} {AND} {EXPERIMENTAL} {EVIDENCE} {INDICATE} {THAT} {THE} {EARLIEST} {TRACE} {FOSSIL} {OF} {A} {WINGED} {INSECT} {WAS} {A} {SURFACE}-{SKIMMING} {NEOPTERAN}: {TRACE} {FOSSIL} {OF} {A} {CARBONIFEROUS} {NEOPTERAN} {INSECT}},
	volume = {67},
	issn = {00143820},
	shorttitle = {{REANALYSIS} {AND} {EXPERIMENTAL} {EVIDENCE} {INDICATE} {THAT} {THE} {EARLIEST} {TRACE} {FOSSIL} {OF} {A} {WINGED} {INSECT} {WAS} {A} {SURFACE}-{SKIMMING} {NEOPTERAN}},
	url = {http://doi.wiley.com/10.1111/j.1558-5646.2012.01743.x},
	doi = {10.1111/j.1558-5646.2012.01743.x},
	language = {en},
	number = {1},
	urldate = {2014-08-13TZ},
	journal = {Evolution},
	author = {Marden, James H.},
	month = jan,
	year = {2013},
	pages = {274--280}
}

@article{najarro_high-resolution_2011,
	title = {High-resolution chemo- and biostratigraphic records of the {Early} {Aptian} oceanic anoxic event in {Cantabria} ({N} {Spain}): {Palaeoceanographic} and palaeoclimatic implications},
	volume = {299},
	issn = {00310182},
	shorttitle = {High-resolution chemo- and biostratigraphic records of the {Early} {Aptian} oceanic anoxic event in {Cantabria} ({N} {Spain})},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0031018210006589},
	doi = {10.1016/j.palaeo.2010.10.042},
	language = {en},
	number = {1-2},
	urldate = {2014-08-13TZ},
	journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
	author = {Najarro, María and Rosales, Idoia and Moreno-Bedmar, Josep A. and de Gea, Ginés A. and Barrón, Eduardo and Company, Miguel and Delanoy, Gérard},
	month = jan,
	year = {2011},
	pages = {137--158}
}

@article{stout_neural_2008,
	title = {Neural correlates of {Early} {Stone} {Age} toolmaking: technology, language and cognition in human evolution},
	volume = {363},
	issn = {0962-8436, 1471-2970},
	shorttitle = {Neural correlates of {Early} {Stone} {Age} toolmaking},
	url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2008.0001},
	doi = {10.1098/rstb.2008.0001},
	language = {en},
	number = {1499},
	urldate = {2014-08-13TZ},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Stout, D. and Toth, N. and Schick, K. and Chaminade, T.},
	month = jun,
	year = {2008},
	pages = {1939--1949}
}

@article{bruner_paleoneurology_2008,
	title = {Paleoneurology of an “early” {Neandertal}: endocranial size, shape, and features of {Saccopastore} 1},
	volume = {54},
	issn = {00472484},
	shorttitle = {Paleoneurology of an “early” {Neandertal}},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0047248407002461},
	doi = {10.1016/j.jhevol.2007.08.014},
	language = {en},
	number = {6},
	urldate = {2014-08-13TZ},
	journal = {Journal of Human Evolution},
	author = {Bruner, Emiliano and Manzi, Giorgio},
	month = jun,
	year = {2008},
	pages = {729--742}
}

@article{green_australopithecus_2012,
	title = {Australopithecus afarensis {Scapular} {Ontogeny}, {Function}, and the {Role} of {Climbing} in {Human} {Evolution}},
	volume = {338},
	issn = {0036-8075, 1095-9203},
	url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1227123},
	doi = {10.1126/science.1227123},
	language = {en},
	number = {6106},
	urldate = {2014-08-13TZ},
	journal = {Science},
	author = {Green, D. J. and Alemseged, Z.},
	month = oct,
	year = {2012},
	pages = {514--517}
}

@article{haile_ancient_2009,
	title = {Ancient {DNA} reveals late survival of mammoth and horse in interior {Alaska}},
	volume = {106},
	url = {http://www.pnas.org/content/106/52/22352.short},
	number = {52},
	urldate = {2014-08-13TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Haile, James and Froese, Duane G. and MacPhee, Ross DE and Roberts, Richard G. and Arnold, Lee J. and Reyes, Alberto V. and Rasmussen, Morten and Nielsen, Rasmus and Brook, Barry W. and Robinson, Simon and {others}},
	year = {2009},
	pages = {22352--22357}
}

@article{irmis_high-resolution_2011,
	title = {High-resolution {U}–{Pb} ages from the {Upper} {Triassic} {Chinle} {Formation} ({New} {Mexico}, {USA}) support a diachronous rise of dinosaurs},
	volume = {309},
	issn = {0012821X},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0012821X11004316},
	doi = {10.1016/j.epsl.2011.07.015},
	language = {en},
	number = {3-4},
	urldate = {2014-08-13TZ},
	journal = {Earth and Planetary Science Letters},
	author = {Irmis, Randall B. and Mundil, Roland and Martz, Jeffrey W. and Parker, William G.},
	month = sep,
	year = {2011},
	pages = {258--267}
}

@article{siveter_silurian_2004,
	title = {A {Silurian} sea spider},
	volume = {431},
	issn = {0028-0836, 1476-4679},
	url = {http://www.nature.com/doifinder/10.1038/nature02928},
	doi = {10.1038/nature02928},
	number = {7011},
	urldate = {2014-08-13TZ},
	journal = {Nature},
	author = {Siveter, Derek J. and Sutton, Mark D. and Briggs, Derek E. G. and Siveter, David J.},
	month = oct,
	year = {2004},
	pages = {978--980}
}

@article{noto_broad-scale_2010,
	title = {Broad-{Scale} {Patterns} of {Late} {Jurassic} {Dinosaur} {Paleoecology}},
	volume = {5},
	issn = {1932-6203},
	url = {http://dx.plos.org/10.1371/journal.pone.0012553},
	doi = {10.1371/journal.pone.0012553},
	language = {en},
	number = {9},
	urldate = {2014-08-13TZ},
	journal = {PLoS ONE},
	author = {Noto, Christopher R. and Grossman, Ari},
	editor = {Hector, Andy},
	month = sep,
	year = {2010},
	pages = {e12553}
}
@article{zerjal_genetic_2003,
	title = {The genetic legacy of the {Mongols}},
	volume = {72},
	url = {http://www.sciencedirect.com/science/article/pii/S0002929707605874},
	number = {3},
	urldate = {2014-08-13TZ},
	journal = {The American Journal of Human Genetics},
	author = {Zerjal, Tatiana and Xue, Yali and Bertorelle, Giorgio and Wells, R. Spencer and Bao, Weidong and Zhu, Suling and Qamar, Raheel and Ayub, Qasim and Mohyuddin, Aisha and Fu, Songbin and {others}},
	year = {2003},
	pages = {717--721}
}

@article{voigt_coastal-plain_2013,
	title = {Coastal-plain origin of trace-fossil bearing red beds in the {Early} {Permian} of {Southern} {New} {Mexico}, {U}.{S}.{A}.},
	volume = {369},
	issn = {00310182},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0031018212006244},
	doi = {10.1016/j.palaeo.2012.10.041},
	language = {en},
	urldate = {2014-08-13TZ},
	journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
	author = {Voigt, Sebastian and Lucas, Spencer G. and Krainer, Karl},
	month = jan,
	year = {2013},
	pages = {323--334}
}

@article{falk_hominid_1980,
	title = {Hominid brain evolution: the approach from paleoneurology},
	volume = {23},
	shorttitle = {Hominid brain evolution},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/ajpa.1330230507/full},
	number = {S1},
	urldate = {2014-08-13TZ},
	journal = {American Journal of Physical Anthropology},
	author = {Falk, Dean},
	year = {1980},
	pages = {93--107}
}

@book{arratia_fuentes_recent_2004,
	address = {München},
	title = {Recent advances in the origin and early radiation of vertebrates: honoring {Hans}-{Peter} {Schultze}},
	isbn = {389937052X 9783899370522},
	shorttitle = {Recent advances in the origin and early radiation of vertebrates},
	language = {English},
	publisher = {F. Pfeil},
	editor = {Arratia Fuentes, Gloria and Wilson, Mark V. H and Cloutier, R and Schultze, Hans-Peter},
	year = {2004}
}

@article{behrensmeyer_taphonomy_2000,
	title = {Taphonomy and paleobiology},
	volume = {26},
	url = {http://www.psjournals.org/doi/abs/10.1666/0094-8373(2000)26%5B103%3ATAP%5D2.0.CO%3B2},
	number = {sp4},
	urldate = {2014-08-13TZ},
	journal = {Paleobiology},
	author = {Behrensmeyer, Anna K. and Kidwell, Susan M. and Gastaldo, Robert A.},
	year = {2000},
	pages = {103--147}
}

@article{snitting_morphology_2008,
	title = {Morphology, {Taxonomy} and {Interrelationships} of {Tristichopterid} {Fishes} ({Sarcopterygii}, {Tetrapodomorpha})},
	url = {http://www.diva-portal.org/smash/record.jsf?pid=diva2:171769},
	urldate = {2014-08-13TZ},
	author = {Snitting, Daniel},
	year = {2008}
}

@article{johanson_first_2000,
	title = {First {East} {Gondwanan} record of {Strepsodus} ({Sarcopterygii}, {Rhizodontida}) from the {Lower} {Carboniferous} {Ducabrook} {Formation}, central {Queensland}, {Australia}},
	volume = {22},
	url = {http://www.researchgate.net/publication/213772273_First_East_Gondwanan_record_of_Strepsodus_(Sarcopterygii_Rhizodontida)_from_the_Lower_Carboniferous_Ducabrook_Formation_central_Queensland_Australia/file/79e415116b5c3a4b26.pdf},
	number = {161},
	urldate = {2014-08-13TZ},
	journal = {Geodiversitas},
	author = {Johanson, Zerina and Turner, Susan and Warren, Anne},
	year = {2000},
	pages = {69}
}

@article{janvier_primitive_2007,
	title = {A primitive megalichthyid fish ({Sarcopterygii}, {Tetrapodomorpha}) from the {Upper} {Devonian} of {Turkey} and its biogeographical implications},
	volume = {29},
	url = {http://www.researchgate.net/publication/213772092_A_primitive_megalichthyid_fish_(Sarcopterygii_Tetrapodomorpha)_from_the_Upper_Devonian_of_Turkey_and_its_biogeographical_implications/file/60b7d5203b8d3e0108.pdf},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Geodiversitas},
	author = {Janvier, Philippe and Clement, Gael and Cloutier, Richard},
	year = {2007},
	pages = {249--268}
}

@article{jeffery_mandibles_2002,
	title = {Mandibles of rhizodontids: anatomy, function and evolution within the tetrapod stem-group},
	volume = {93},
	issn = {0263-5933, 1473-7116},
	shorttitle = {Mandibles of rhizodontids},
	url = {http://www.journals.cambridge.org/abstract_S0263593300000432},
	doi = {10.1017/S0263593300000432},
	language = {en},
	number = {03},
	urldate = {2014-08-13TZ},
	journal = {Transactions of the Royal Society of Edinburgh: Earth Sciences},
	author = {Jeffery, Jonathan E.},
	month = sep,
	year = {2002}
}

@article{young_phyllolepid_2005,
	title = {Phyllolepid placoderm fish remains from the {Devonian} {Aztec} {Siltstone}, southern {Victoria} {Land}, {Antarctica}},
	volume = {17},
	issn = {0954-1020, 1365-2079},
	url = {http://www.journals.cambridge.org/abstract_S095410200500283X},
	doi = {10.1017/S095410200500283X},
	language = {en},
	number = {03},
	urldate = {2014-08-13TZ},
	journal = {Antarctic Science},
	author = {Young, Gavin C. and Long, John A.},
	month = aug,
	year = {2005},
	pages = {387}
}

@article{wang_confidence_2012,
	title = {Confidence intervals for the duration of a mass extinction},
	volume = {38},
	url = {http://www.psjournals.org/doi/abs/10.1666/11016.1},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Paleobiology},
	author = {Wang, Steve C. and Zimmerman, Aaron E. and McVeigh, Brendan S. and Everson, Philip J. and Wong, Heidi},
	year = {2012},
	pages = {265--277}
}

@article{hara_growth_1993,
	title = {Growth {Dynamics} and {Size} {Structure} of {Shoots} of {Phragmites} {Australis}, a {Clonal} {Plant}},
	volume = {81},
	issn = {00220477},
	url = {http://www.jstor.org/stable/2261223?origin=crossref},
	doi = {10.2307/2261223},
	number = {1},
	urldate = {2014-08-13TZ},
	journal = {The Journal of Ecology},
	author = {Hara, T. and van Der Toorn, J. and Mook, J. H.},
	month = mar,
	year = {1993},
	pages = {47}
}

@article{mech_users_1998,
	title = {User’s {Manual} for {Environmental} programs},
	url = {http://www.usna.edu/Users/cs/stahl/SI462/Spring2007/Papers/Instructor/submitted_materials/graftals/L-studio-4.2.12/Help/enviro.pdf},
	urldate = {2014-08-13TZ},
	journal = {Calguary, Canada: University of Calguary},
	author = {Mech, Radomır and Prusinkiewicz, Przemyslaw},
	year = {1998}
}

@article{bellingham_resprouting_2000,
	title = {Resprouting as a life history strategy in woody plant communities},
	volume = {89},
	url = {http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0706.2000.890224.x/full},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Oikos},
	author = {Bellingham, Peter J. and Sparrow, Ashley D.},
	year = {2000},
	pages = {409--416}
}

@article{mcglynn_test_2013,
	title = {A test of species-energy theory: patch occupancy and colony size in tropical rainforest litter-nesting ants},
	volume = {122},
	issn = {00301299},
	shorttitle = {A test of species-energy theory},
	url = {http://doi.wiley.com/10.1111/j.1600-0706.2013.00102.x},
	doi = {10.1111/j.1600-0706.2013.00102.x},
	language = {en},
	number = {9},
	urldate = {2014-08-13TZ},
	journal = {Oikos},
	author = {McGlynn, Terrence P. and Alonso-Rodríguez, Aura M. and Weaver, Melinda},
	month = sep,
	year = {2013},
	pages = {1357--1361}
}

@article{buddemeier_coastal_2008,
	title = {Coastal typology: {An} integrative “neutral” technique for coastal zone characterization and analysis},
	volume = {77},
	issn = {02727714},
	shorttitle = {Coastal typology},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0272771407004441},
	doi = {10.1016/j.ecss.2007.09.021},
	language = {en},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Buddemeier, Robert W. and Smith, Stephen V. and Swaney, Dennis P. and Crossland, Christopher J. and Maxwell, Bruce A.},
	month = apr,
	year = {2008},
	pages = {197--205}
}

@article{winkler_modelling_1999,
	title = {Modelling the {Competitiveness} of {Clonal} {Plants} by {Complementary} {Analytical} and {Simulation} {Approaches}},
	volume = {85},
	issn = {00301299},
	url = {http://www.jstor.org/stable/3546488?origin=crossref},
	doi = {10.2307/3546488},
	number = {2},
	urldate = {2014-08-13TZ},
	journal = {Oikos},
	author = {Winkler, Eckart and Fischer, Markus and Schmid, Bernhard},
	month = may,
	year = {1999},
	pages = {217}
}

@inproceedings{moraglio_geometric_2006,
	title = {Geometric unification of evolutionary algorithms},
	url = {http://www.cs.bham.ac.uk/~wbl/biblio/cache/http___www.vanhemert.co.uk_publications_EvoPhD2006.pdf#page=53},
	urldate = {2014-08-13TZ},
	booktitle = {European {Graduate} {Student} {Workshop} on {Evolutionary} {Computation}},
	author = {Moraglio, Alberto},
	year = {2006},
	pages = {45}
}

@article{imasheva_growth_2000,
	title = {Growth temperature and genetic variability of wing dimensions in {Drosophila}: opposite trends in two sibling species},
	volume = {76},
	shorttitle = {Growth temperature and genetic variability of wing dimensions in {Drosophila}},
	url = {http://journals.cambridge.org/abstract_S0016672300004717},
	number = {03},
	urldate = {2014-08-13TZ},
	journal = {Genetical research},
	author = {IMASHEVA, ALEXANDRA G. and MORETEAU, BRIGITTE and DAVID, JEAN R.},
	year = {2000},
	pages = {237--247}
}

@article{sintes_modeling_2006,
	title = {Modeling nonlinear seagrass clonal growth: assessing the efficiency of space occupation across the seagrass flora},
	volume = {29},
	shorttitle = {Modeling nonlinear seagrass clonal growth},
	url = {http://link.springer.com/article/10.1007/BF02784700},
	number = {1},
	urldate = {2014-08-13TZ},
	journal = {Estuaries and coasts},
	author = {Sintes, Tomàs and Marbà, Núria and Duarte, Carlos M.},
	year = {2006},
	pages = {72--80}
}

@article{suykens_least_1999,
	title = {Least squares support vector machine classifiers},
	volume = {9},
	url = {http://link.springer.com/article/10.1023/A:1018628609742},
	number = {3},
	urldate = {2014-08-13TZ},
	journal = {Neural processing letters},
	author = {Suykens, Johan AK and Vandewalle, Joos},
	year = {1999},
	pages = {293--300}
}

@article{erhan_why_2010,
	title = {Why does unsupervised pre-training help deep learning?},
	volume = {11},
	url = {http://dl.acm.org/citation.cfm?id=1756025},
	urldate = {2014-08-13TZ},
	journal = {The Journal of Machine Learning Research},
	author = {Erhan, Dumitru and Bengio, Yoshua and Courville, Aaron and Manzagol, Pierre-Antoine and Vincent, Pascal and Bengio, Samy},
	year = {2010},
	pages = {625--660}
}

@inproceedings{choi_data_2011,
	title = {From {Data} {Streams} to {Information} {Flow}: {Information} {Exchange} in {Child}-{Parent} {Interaction}},
	shorttitle = {From {Data} {Streams} to {Information} {Flow}},
	url = {http://palm.mindmodeling.org/cogsci2011/papers/0192/paper0192.pdf},
	urldate = {2014-08-13TZ},
	booktitle = {The {Annual} {Meeting} of the {Cognitive} {Science} {Society} ({CogSci}2011), {Boston}, {MA}},
	author = {Choi, Heeyoul and Yu, Chen and Smith, Linda B. and Sporns, Olaf},
	year = {2011}
}

@article{chattopadhyay_inverse_2013,
	title = {Inverse {Gillespie} for inferring stochastic reaction mechanisms from intermittent samples},
	volume = {110},
	url = {http://www.pnas.org/content/110/32/12990.short},
	number = {32},
	urldate = {2014-08-13TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Chattopadhyay, Ishanu and Kuchina, Anna and Süel, Gürol M. and Lipson, Hod},
	year = {2013},
	pages = {12990--12995}
}

@article{hsieh_nonlinear_2004,
	title = {Nonlinear multivariate and time series analysis by neural network methods},
	volume = {42},
	issn = {8755-1209},
	url = {http://doi.wiley.com/10.1029/2002RG000112},
	doi = {10.1029/2002RG000112},
	language = {en},
	number = {1},
	urldate = {2014-08-13TZ},
	journal = {Reviews of Geophysics},
	author = {Hsieh, William W.},
	year = {2004}
}

@article{zhu_semi-supervised_2005,
	title = {Semi-supervised learning literature survey},
	author = {Zhu, Xiaojin},
	year = {2005}
}

@inproceedings{tang_multidimensional_2012,
	title = {Multidimensional analysis of atypical events in cyber-physical data},
	url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6228153},
	urldate = {2014-08-13TZ},
	booktitle = {Data {Engineering} ({ICDE}), 2012 {IEEE} 28th {International} {Conference} on},
	publisher = {IEEE},
	author = {Tang, Lu-An and Yu, Xiao and Kim, Sangkyum and Han, Jiawei and Peng, Wen-Chih and Sun, Yizhou and Gonzalez, Hector and Seith, Sebastian},
	year = {2012},
	pages = {1025--1036}
}

@book{world_congress_on_engineering_world_2009,
	title = {World {Congress} on {Engineering} 2009. {Volume} 2 {Volume} 2},
	isbn = {9789881821010  9881821010},
	url = {https://ezproxy.siast.sk.ca:443/login?url=http://search.ebscohost.com/direct.asp?db=a9h&jid=AWDF&scope=site},
	language = {English},
	urldate = {2014-08-13TZ},
	author = {{World Congress on Engineering}},
	year = {2009}
}

@article{loreau_biodiversity_2001,
	title = {Biodiversity and ecosystem functioning: current knowledge and future challenges},
	volume = {294},
	shorttitle = {Biodiversity and ecosystem functioning},
	url = {http://www.sciencemag.org/content/294/5543/804.short},
	number = {5543},
	urldate = {2014-08-13TZ},
	journal = {science},
	author = {Loreau, Michel and Naeem, Shahid and Inchausti, Pablo and Bengtsson, J. and Grime, J. P. and Hector, A. and Hooper, D. U. and Huston, M. A. and Raffaelli, D. and Schmid, B. and {others}},
	year = {2001},
	pages = {804--808}
}

@article{montoya_emerging_2012,
	title = {Emerging perspectives in the restoration of biodiversity-based ecosystem services},
	volume = {27},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534712001656},
	number = {12},
	urldate = {2014-08-13TZ},
	journal = {Trends in ecology \& evolution},
	author = {Montoya, Daniel and Rogers, Lucy and Memmott, Jane},
	year = {2012},
	pages = {666--672}
}

@article{alvarado_role_2002,
	title = {The role of emotion in an architecture of mind},
	journal = {IBM Research},
	author = {Alvarado, Nancy and Adams, S. and Burbeck, S.},
	year = {2002}
}

@article{holroyd_neural_2002,
	title = {The neural basis of human error processing: {Reinforcement} learning, dopamine, and the error-related negativity.},
	volume = {109},
	issn = {0033-295X},
	shorttitle = {The neural basis of human error processing},
	url = {http://doi.apa.org/getdoi.cfm?doi=10.1037/0033-295X.109.4.679},
	doi = {10.1037//0033-295X.109.4.679},
	language = {en},
	number = {4},
	urldate = {2014-08-13TZ},
	journal = {Psychological Review},
	author = {Holroyd, Clay B. and Coles, Michael G.H.},
	year = {2002},
	pages = {679--709}
}

@article{maxwell_coastal_2002,
	title = {Coastal typology development with heterogeneous data sets},
	volume = {3},
	issn = {1436-3798},
	url = {http://link.springer.com/10.1007/s10113-001-0034-8},
	doi = {10.1007/s10113-001-0034-8},
	number = {1-3},
	urldate = {2014-08-13TZ},
	journal = {Regional Environmental Change},
	author = {Maxwell, Bruce and Buddemeier, Robert},
	month = dec,
	year = {2002},
	pages = {77--87}
}

@inproceedings{oudeyer_playground_2005,
	title = {The playground experiment: {Task}-independent development of a curious robot},
	shorttitle = {The playground experiment},
	url = {http://www.cs.swarthmore.edu/~meeden/DevelopmentalRobotics/oudeyer.pdf},
	urldate = {2014-08-13TZ},
	booktitle = {Proceedings of the {AAAI} {Spring} {Symposium} on {Developmental} {Robotics}},
	publisher = {Stanford, California},
	author = {Oudeyer, Pierre-Yves and Kaplan, Frédéric and Hafner, Verena V. and Whyte, Andrew},
	year = {2005},
	pages = {42--47}
}

@inproceedings{bonyadi_spso_2014,
	title = {{SPSO} 2011: analysis of stability; local convergence; and rotation sensitivity},
	isbn = {9781450326629},
	shorttitle = {{SPSO} 2011},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598263},
	doi = {10.1145/2576768.2598263},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Bonyadi, Mohammad Reza and Michalewicz, Zbigniew},
	year = {2014},
	pages = {9--16}
}

@inproceedings{tinos_use_2014,
	title = {Use of explicit memory in the dynamic traveling salesman problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598247},
	doi = {10.1145/2576768.2598247},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Tinós, Renato and Whitley, Darrell and Howe, Adele},
	year = {2014},
	pages = {999--1006}
}

@inproceedings{rodrigues_novel_2014,
	title = {A novel population-based multi-objective {CMA}-{ES} and the impact of different constraint handling techniques},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598329},
	doi = {10.1145/2576768.2598329},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Rodrigues, Silvio and Bauer, Pavol and Bosman, Peter A.N.},
	year = {2014},
	pages = {991--998}
}

@inproceedings{khayrattee_derivative_2014,
	title = {Derivative free optimization using a population-based stochastic gradient estimator},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598365},
	doi = {10.1145/2576768.2598365},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Khayrattee, Azhar and Anagnostopoulos, Georgios C.},
	year = {2014},
	pages = {983--990}
}

@inproceedings{chelly_two-leveled_2014,
	title = {A two-leveled hybrid dendritic cell algorithm under imprecise reasoning},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598217},
	doi = {10.1145/2576768.2598217},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Chelly, Zeineb and Elouedi, Zied},
	year = {2014},
	pages = {97--104}
}

@inproceedings{jansen_evolutionary_2014,
	title = {Evolutionary algorithms and artificial immune systems on a bi-stable dynamic optimisation problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598344},
	doi = {10.1145/2576768.2598344},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Jansen, Thomas and Zarges, Christine},
	year = {2014},
	pages = {975--982}
}

@inproceedings{aulig_neuro-evolutionary_2014,
	title = {Neuro-evolutionary topology optimization of structures by utilizing local state features},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598314},
	doi = {10.1145/2576768.2598314},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Aulig, Nikola and Olhofer, Markus},
	year = {2014},
	pages = {967--974}
}

@inproceedings{wong_grammar-based_2014,
	title = {Grammar-based genetic programming with dependence learning and bayesian network classifier},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598256},
	doi = {10.1145/2576768.2598256},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Wong, Pak-Kan and Lo, Leung-Yau and Wong, Man-Leung and Leung, Kwong-Sak},
	year = {2014},
	pages = {959--966}
}

@inproceedings{langdon_improving_2014,
	title = {Improving 3D medical image registration {CUDA} software with genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598244},
	doi = {10.1145/2576768.2598244},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Langdon, William B. and Modat, Marc and Petke, Justyna and Harman, Mark},
	year = {2014},
	pages = {951--958}
}

@inproceedings{kren_utilization_2014,
	title = {Utilization of reductions and abstraction elimination in typed genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598361},
	doi = {10.1145/2576768.2598361},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Křen, Tomáš and Neruda, Roman},
	year = {2014},
	pages = {943--950}
}

@inproceedings{krawiec_behavioral_2014,
	title = {Behavioral programming: a broader and more detailed take on semantic {GP}},
	isbn = {9781450326629},
	shorttitle = {Behavioral programming},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598288},
	doi = {10.1145/2576768.2598288},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Krawiec, Krzysztof and O'Reilly, Una-May},
	year = {2014},
	pages = {935--942}
}

@inproceedings{hunt_evolving_2014,
	title = {Evolving "less-myopic" scheduling rules for dynamic job shop scheduling with genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598224},
	doi = {10.1145/2576768.2598224},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Hunt, Rachel and Johnston, Mark and Zhang, Mengjie},
	year = {2014},
	pages = {927--934}
}

@inproceedings{helmuth_word_2014,
	title = {Word count as a traditional programming benchmark problem for genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598230},
	doi = {10.1145/2576768.2598230},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Helmuth, Thomas and Spector, Lee},
	year = {2014},
	pages = {919--926}
}
@inproceedings{harada_asynchronously_2014,
	title = {Asynchronously evolving solutions with excessively different evaluation time by reference-based evaluation},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598330},
	doi = {10.1145/2576768.2598330},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Harada, Tomohiro and Takadama, Keiki},
	year = {2014},
	pages = {911--918}
}

@inproceedings{fitzgerald_size_2014,
	title = {On size, complexity and generalisation error in {GP}},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598346},
	doi = {10.1145/2576768.2598346},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Fitzgerald, Jeannie and Ryan, Conor},
	year = {2014},
	pages = {903--910}
}

@inproceedings{zhang_automatic_2014,
	title = {Automatic path planning for autonomous underwater vehicles based on an adaptive differential evolution},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598267},
	doi = {10.1145/2576768.2598267},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Zhang, Chuan-Bin and Gong, Yue-Jiao and Li, Jing-Jing and Lin, Ying},
	year = {2014},
	pages = {89--96}
}

@inproceedings{de_melo_kaizen_2014,
	title = {Kaizen programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598264},
	doi = {10.1145/2576768.2598264},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {De Melo, Vinícius Veloso},
	year = {2014},
	pages = {895--902}
}

@inproceedings{cano_gpu-parallel_2014,
	title = {{GPU}-parallel subtree interpreter for genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598272},
	doi = {10.1145/2576768.2598272},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Cano, Alberto and Ventura, Sebastian},
	year = {2014},
	pages = {887--894}
}

@inproceedings{arnaldo_multiple_2014,
	title = {Multiple regression genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598291},
	doi = {10.1145/2576768.2598291},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Arnaldo, Ignacio and Krawiec, Krzysztof and O'Reilly, Una-May},
	year = {2014},
	pages = {879--886}
}

@inproceedings{zaefferer_efficient_2014,
	title = {Efficient global optimization for combinatorial problems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598282},
	doi = {10.1145/2576768.2598282},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Zaefferer, Martin and Stork, Jörg and Friese, Martina and Fischbach, Andreas and Naujoks, Boris and Bartz-Beielstein, Thomas},
	year = {2014},
	pages = {871--878}
}

@inproceedings{vafaee_among-site_2014,
	title = {Among-site rate variation: adaptation of genetic algorithm mutation rates at each single site},
	isbn = {9781450326629},
	shorttitle = {Among-site rate variation},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598216},
	doi = {10.1145/2576768.2598216},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Vafaee, Fatemeh and Turan, Gyorgy and Nelson, Peter C. and Berger-Wolf, Tanya Y.},
	year = {2014},
	pages = {863--870}
}

@inproceedings{vafaee_learning_2014,
	title = {Learning the structure of large-scale bayesian networks using genetic algorithm},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598223},
	doi = {10.1145/2576768.2598223},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Vafaee, Fatemeh},
	year = {2014},
	pages = {855--862}
}

@inproceedings{sinha_bilevel_2014,
	title = {A bilevel optimization approach to automated parameter tuning},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598221},
	doi = {10.1145/2576768.2598221},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Sinha, Ankur and Malo, Pekka and Xu, Peng and Deb, Kalyanmoy},
	year = {2014},
	pages = {847--854}
}

@inproceedings{shi_feedback_2014,
	title = {Feedback control for multi-modal optimization using genetic algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598231},
	doi = {10.1145/2576768.2598231},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Shi, Jun and Mengshoel, Ole J. and Pal, Dipan K.},
	year = {2014},
	pages = {839--846}
}

@inproceedings{ruiz_search_2014,
	title = {Search for maximal snake-in-the-box using new genetic algorithm},
	url = {http://dl.acm.org/citation.cfm?id=2598296},
	urldate = {2014-08-13TZ},
	booktitle = {Proceedings of the 2014 conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Ruiz, Kim-Hang},
	year = {2014},
	pages = {831--838}
}

@inproceedings{ray_evolving_2014,
	title = {Evolving {QWOP} gaits},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598248},
	doi = {10.1145/2576768.2598248},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Ray, Steven and Gordon, Vahl Scott and Vaucher, Laurent},
	year = {2014},
	pages = {823--830}
}

@inproceedings{zapotecas_martinez_constrained_2014,
	title = {Constrained multi-objective aerodynamic shape optimization via swarm intelligence},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598372},
	doi = {10.1145/2576768.2598372},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Zapotecas Martinez, Saul and Arias Montano, Alfredo and Coello Coello, Carlos A.},
	year = {2014},
	pages = {81--88}
}

@inproceedings{picek_fitness_2014,
	title = {From fitness landscape to crossover operator choice},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598320},
	doi = {10.1145/2576768.2598320},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Picek, Stjepan and Jakobovic, Domagoj},
	year = {2014},
	pages = {815--822}
}

@inproceedings{nallaperuma_fixed_2014,
	title = {A fixed budget analysis of randomized search heuristics for the traveling salesperson problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598302},
	doi = {10.1145/2576768.2598302},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Nallaperuma, Samadhi and Neumann, Frank and Sudholt, Dirk},
	year = {2014},
	pages = {807--814}
}

@inproceedings{mayer_stochastic_2014,
	title = {Stochastic tunneling transformation during selection in genetic algorithm},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598243},
	doi = {10.1145/2576768.2598243},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Mayer, Benjamin E. and Hamacher, Kay},
	year = {2014},
	pages = {801--806}
}

@inproceedings{kromer_genetic_2014,
	title = {Genetic algorithm for sampling from scale-free data and networks},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598391},
	doi = {10.1145/2576768.2598391},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Krömer, Pavel and Platoš, Jan},
	year = {2014},
	pages = {793--800}
}

@inproceedings{gao_runtime_2014,
	title = {Runtime analysis for maximizing population diversity in single-objective optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598251},
	doi = {10.1145/2576768.2598251},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Gao, Wanru and Neumann, Frank},
	year = {2014},
	pages = {777--784}
}

@inproceedings{doerr_unbiased_2014,
	title = {Unbiased black-box complexities of jump functions: how to cross large plateaus},
	isbn = {9781450326629},
	shorttitle = {Unbiased black-box complexities of jump functions},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598341},
	doi = {10.1145/2576768.2598341},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Doerr, Benjamin and Doerr, Carola and Kötzing, Timo},
	year = {2014},
	pages = {769--776}
}

@inproceedings{cruz-vega_adaptive-surrogate_2014,
	title = {Adaptive-surrogate based on a neuro-fuzzy network and granular computing},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598376},
	doi = {10.1145/2576768.2598376},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Cruz-Vega, Israel and Garcia-Limon, Mauricio and Escalante, Hugo Jair},
	year = {2014},
	pages = {761--768}
}

@inproceedings{colin_monotonic_2014,
	title = {Monotonic functions in {EC}: anything but monotone!},
	isbn = {9781450326629},
	shorttitle = {Monotonic functions in {EC}},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598338},
	doi = {10.1145/2576768.2598338},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Colin, `Sylvain and Doerr, Benjamin and Férey, Gaspard},
	year = {2014},
	pages = {753--760}
}

@inproceedings{wilson_continuous_2014,
	title = {A continuous developmental model for wind farm layout optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598383},
	doi = {10.1145/2576768.2598383},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Wilson, Dennis and Cussat-Blanc, Sylvain and Veeramachaneni, Kalyan and O'Reilly, Una-May and Luga, Hervé},
	year = {2014},
	pages = {745--752}
}

@inproceedings{yu_differential_2014,
	title = {Differential evolution using mutation strategy with adaptive greediness degree control},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598236},
	doi = {10.1145/2576768.2598236},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Yu, Wei-Jie and Li, Jing-Jing and Zhang, Jun and Wan, Meng},
	year = {2014},
	pages = {73--80}
}

@inproceedings{velez_novelty_2014,
	title = {Novelty search creates robots with general skills for exploration},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598225},
	doi = {10.1145/2576768.2598225},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Velez, Roby and Clune, Jeff},
	year = {2014},
	pages = {737--744}
}

@inproceedings{smalikho_growth_2014,
	title = {Growth in co-evolution of sensory system and signal processing for optimal wing control},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598318},
	doi = {10.1145/2576768.2598318},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Smalikho, Olga and Olhofer, Markus},
	year = {2014},
	pages = {729--736}
}

@inproceedings{samuelsen_distance_2014,
	title = {Some distance measures for morphological diversification in generative evolutionary robotics},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598325},
	doi = {10.1145/2576768.2598325},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Samuelsen, Eivind and Glette, Kyrre},
	year = {2014},
	pages = {721--728}
}

@inproceedings{risi_guided_2014,
	title = {Guided self-organization in indirectly encoded and evolving topographic maps},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598369},
	doi = {10.1145/2576768.2598369},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Risi, Sebastian and Stanley, Kenneth O.},
	year = {2014},
	pages = {713--720}
}

@inproceedings{lessin_trading_2014,
	title = {Trading control intelligence for physical intelligence: muscle drives in evolved virtual creatures},
	isbn = {9781450326629},
	shorttitle = {Trading control intelligence for physical intelligence},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598290},
	doi = {10.1145/2576768.2598290},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Lessin, Dan and Fussell, Don and Miikkulainen, Risto},
	year = {2014},
	pages = {705--712}
}

@inproceedings{huizinga_evolving_2014,
	title = {Evolving neural networks that are both modular and regular: {HyperNEAT} plus the connection cost technique},
	isbn = {9781450326629},
	shorttitle = {Evolving neural networks that are both modular and regular},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598232},
	doi = {10.1145/2576768.2598232},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Huizinga, Joost and Clune, Jeff and Mouret, Jean-Baptiste},
	year = {2014},
	pages = {697--704}
}

@inproceedings{bryson_there_2014,
	title = {There and back again: gene-processing hardware for the evolution and robotic deployment of robust navigation strategies},
	isbn = {9781450326629},
	shorttitle = {There and back again},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598363},
	doi = {10.1145/2576768.2598363},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Bryson, David M. and Wagner, Aaron P. and Ofria, Charles},
	year = {2014},
	pages = {689--696}
}

@inproceedings{yuan_evolutionary_2014,
	title = {Evolutionary many-objective optimization using ensemble fitness ranking},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598345},
	doi = {10.1145/2576768.2598345},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Yuan, Yuan and Xu, Hua and Wang, Bo},
	year = {2014},
	pages = {669--676}
}

@inproceedings{yuan_improved_2014,
	title = {An improved {NSGA}-{III} procedure for evolutionary many-objective optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598342},
	doi = {10.1145/2576768.2598342},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Yuan, Yuan and Xu, Hua and Wang, Bo},
	year = {2014},
	pages = {661--668}
}

@inproceedings{von_der_osten_anticipatory_2014,
	title = {Anticipatory stigmergic collision avoidance under noise},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598389},
	doi = {10.1145/2576768.2598389},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {von der Osten, Friedrich Burkhard and Kirley, Michael and Miller, Tim},
	year = {2014},
	pages = {65--72}
}

@inproceedings{xiao_hybridization_2014,
	title = {Hybridization of electromagnetism with multi-objective evolutionary algorithms for {RCPSP}},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598228},
	doi = {10.1145/2576768.2598228},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Xiao, Jing and Wu, Zhou and Tang, Jian-Chao},
	year = {2014},
	pages = {653--660}
}

@inproceedings{sato_inverted_2014,
	title = {Inverted {PBI} in {MOEA}/{D} and its impact on the search performance on multi and many-objective optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598297},
	doi = {10.1145/2576768.2598297},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Sato, Hiroyuki},
	year = {2014},
	pages = {645--652}
}

@inproceedings{pilat_hypervolume-based_2014,
	title = {Hypervolume-based local search in multi-objective evolutionary optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598332},
	doi = {10.1145/2576768.2598332},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Pilát, Martin and Neruda, Roman},
	year = {2014},
	pages = {637--644}
}

@inproceedings{miyakawa_controlling_2014,
	title = {Controlling selection area of useful infeasible solutions and their archive for directed mating in evolutionary constrained multiobjective optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598313},
	doi = {10.1145/2576768.2598313},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Miyakawa, Minami and Takadama, Keiki and Sato, Hiroyuki},
	year = {2014},
	pages = {629--636}
}

@inproceedings{iordache_framework_2014,
	title = {A framework for the study of preference incorporation in multiobjective evolutionary algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598380},
	doi = {10.1145/2576768.2598380},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Iordache, Raluca and Iordache, Serban and Moldoveanu, Florica},
	year = {2014},
	pages = {621--628}
}

@inproceedings{huo_parameter_2014,
	title = {The parameter optimization of kalman filter based on multi-objective memetic algorithm},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598242},
	doi = {10.1145/2576768.2598242},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Huo, Yu Dan and Cai, Zhi Hua and Gong, Wen Yin and Liu, Qin},
	year = {2014},
	pages = {613--620}
}

@inproceedings{fieldsend_efficiently_2014,
	title = {Efficiently identifying pareto solutions when objective values change},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598279},
	doi = {10.1145/2576768.2598279},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Fieldsend, Jonathan E. and Everson, Richard M.},
	year = {2014},
	pages = {605--612}
}

@inproceedings{dohr_improving_2014,
	title = {Improving many-objective optimization performance by sequencing evolutionary algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598326},
	doi = {10.1145/2576768.2598326},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Dohr, Martin and Eichberger, Bernd},
	year = {2014},
	pages = {597--604}
}

@inproceedings{bringmann_two-dimensional_2014,
	title = {Two-dimensional subset selection for hypervolume and epsilon-indicator},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598276},
	doi = {10.1145/2576768.2598276},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Bringmann, Karl and Friedrich, Tobias and Klitzke, Patrick},
	year = {2014},
	pages = {589--596}
}

@inproceedings{azzouz_steady_2014,
	title = {Steady state {IBEA} assisted by {MLP} neural networks for expensive multi-objective optimization problems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598271},
	doi = {10.1145/2576768.2598271},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Azzouz, Nessrine and Bechikh, Slim and Ben Said, Lamjed},
	year = {2014},
	pages = {581--588}
}

@inproceedings{volkel_ant_2014,
	title = {Ant colony optimization with group learning},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598214},
	doi = {10.1145/2576768.2598214},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Völkel, Gunnar and Maucher, Markus and Schöning, Uwe and Kestler, Hans A.},
	year = {2014},
	pages = {57--64}
}

@inproceedings{nalepa_memetic_2014,
	title = {A memetic algorithm to select training data for support vector machines},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598370},
	doi = {10.1145/2576768.2598370},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Nalepa, Jakub and Kawulok, Michal},
	year = {2014},
	pages = {573--580}
}

@inproceedings{nakata_modified_2014,
	title = {A modified {XCS} classifier system for sequence labeling},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598352},
	doi = {10.1145/2576768.2598352},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Nakata, Masaya and Kovacs, Tim and Takadama, Keiki},
	year = {2014},
	pages = {565--572}
}

@inproceedings{nakata_complete_2014,
	title = {Complete action map or best action map in accuracy-based reinforcement learning classifier systems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598351},
	doi = {10.1145/2576768.2598351},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Nakata, Masaya and Lanzi, Pier Luca and Kovacs, Tim and Takadama, Keiki},
	year = {2014},
	pages = {557--564}
}

@inproceedings{koutnik_evolving_2014,
	title = {Evolving deep unsupervised convolutional networks for vision-based reinforcement learning},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598358},
	doi = {10.1145/2576768.2598358},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Koutník, Jan and Schmidhuber, Juergen and Gomez, Faustino},
	year = {2014},
	pages = {541--548}
}

@inproceedings{kamath_sax-efg:_2014,
	title = {{SAX}-{EFG}: an evolutionary feature generation framework for time series classification},
	isbn = {9781450326629},
	shorttitle = {{SAX}-{EFG}},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598321},
	doi = {10.1145/2576768.2598321},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Kamath, Uday and Lin, Jessica and De Jong, Kenneth},
	year = {2014},
	pages = {533--540}
}
@inproceedings{garcia-limon_simultaneous_2014,
	title = {Simultaneous generation of prototypes and features through genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598356},
	doi = {10.1145/2576768.2598356},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Garcia-Limon, Mauricio and Escalante, Hugo Jair and Morales, Eduardo and Morales-Reyes, Alicia},
	year = {2014},
	pages = {517--524}
}

@inproceedings{witt_revised_2014,
	title = {Revised analysis of the (1+1) ea for the minimum spanning tree problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598237},
	doi = {10.1145/2576768.2598237},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Witt, Carsten},
	year = {2014},
	pages = {509--516}
}

@inproceedings{tinos_generalized_2014,
	title = {Generalized asymmetric partition crossover ({GAPX}) for the asymmetric {TSP}},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598245},
	doi = {10.1145/2576768.2598245},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Tinós, Renato and Whitley, Darrell and Ochoa, Gabriela},
	year = {2014},
	pages = {501--508}
}

@inproceedings{solum_consensus_2014,
	title = {Consensus costs and conflict in a collective movement},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598357},
	doi = {10.1145/2576768.2598357},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Solum, Timothy and Eskridge, Brent E. and Schlupp, Ingo},
	year = {2014},
	pages = {49--56}
}

@inproceedings{tantar_asymmetric_2014,
	title = {Asymmetric quadratic landscape approximation model},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598381},
	doi = {10.1145/2576768.2598381},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Tantar, Alexandru-Adrian and Tantar, Emilia and Schütze, Oliver},
	year = {2014},
	pages = {493--500}
}

@inproceedings{shenoy_k_b_performance_2014,
	title = {Performance of metropolis algorithm for the minimum weight code word problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598274},
	doi = {10.1145/2576768.2598274},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Shenoy K B, Ajitha and Biswas, Somenath and Kurur, Piyush P.},
	year = {2014},
	pages = {485--492}
}

@inproceedings{polyakovskiy_comprehensive_2014,
	title = {A comprehensive benchmark set and heuristics for the traveling thief problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598249},
	doi = {10.1145/2576768.2598249},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Polyakovskiy, Sergey and Bonyadi, Mohammad Reza and Wagner, Markus and Michalewicz, Zbigniew and Neumann, Frank},
	year = {2014},
	pages = {477--484}
}

@inproceedings{monical_static_2014,
	title = {Static vs. dynamic populations in genetic algorithms for coloring a dynamic graph},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598233},
	doi = {10.1145/2576768.2598233},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Monical, Cara and Stonedahl, Forrest},
	year = {2014},
	pages = {469--476}
}

@inproceedings{meignan_heuristic_2014,
	title = {A heuristic approach to schedule reoptimization in the context of interactive optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598213},
	doi = {10.1145/2576768.2598213},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Meignan, David},
	year = {2014},
	pages = {461--468}
}

@inproceedings{iclanzan_data-driven_2014,
	title = {Data-driven local optima network characterization of {QAPLIB} instances},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598275},
	doi = {10.1145/2576768.2598275},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Iclanzan, David and Daolio, Fabio and Tomassini, Marco},
	year = {2014},
	pages = {453--460}
}

@inproceedings{choi_hybrid_2014,
	title = {A hybrid incremental genetic algorithm for subgraph isomorphism problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598382},
	doi = {10.1145/2576768.2598382},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Choi, HyukGeun and Kim, JinHyun and Moon, Byung-Ro},
	year = {2014},
	pages = {445--452}
}

@inproceedings{chicano_efficient_2014,
	title = {Efficient identification of improving moves in a ball for pseudo-boolean problems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598304},
	doi = {10.1145/2576768.2598304},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Chicano, Francisco and Whitley, Darrell and Sutton, Andrew M.},
	year = {2014},
	pages = {437--444}
}

@inproceedings{cunha_campos_nsga-ii_2014,
	title = {{NSGA}-{II} with iterated greedy for a bi-objective three-stage assembly flowshop scheduling problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598324},
	doi = {10.1145/2576768.2598324},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Cunha Campos, Saulo and Claudio Arroyo, José Elias},
	year = {2014},
	pages = {429--436}
}

@inproceedings{bonyadi_socially_2014,
	title = {Socially inspired algorithms for the travelling thief problem},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598367},
	doi = {10.1145/2576768.2598367},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Bonyadi, Mohammad Reza and Michalewicz, Zbigniew and Roman Przybyŏek, Michaŏ and Wierzbicki, Adam},
	year = {2014},
	pages = {421--428}
}

@inproceedings{liu_energy_2014,
	title = {Energy aware virtual machine placement scheduling in cloud computing based on ant colony optimization approach},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598265},
	doi = {10.1145/2576768.2598265},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Liu, Xiao-Fang and Zhan, Zhi-Hui and Du, Ke-Jing and Chen, Wei-Neng},
	year = {2014},
	pages = {41--48}
}

@inproceedings{basseur_efficiency_2014,
	title = {On the efficiency of worst improvement for climbing {NK}-landscapes},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598268},
	doi = {10.1145/2576768.2598268},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Basseur, Matthieu and Goëffon, Adrien},
	year = {2014},
	pages = {413--420}
}

@inproceedings{andrade_evolutionary_2014,
	title = {Evolutionary algorithms for overlapping correlation clustering},
	url = {http://dl.acm.org/citation.cfm?id=2598284},
	urldate = {2014-08-13TZ},
	booktitle = {Proceedings of the 2014 conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Andrade, Carlos E. and Resende, Mauricio GC and Karloff, Howard J. and Miyazawa, Flávio K.},
	year = {2014},
	pages = {405--412}
}

@inproceedings{loshchilov_computationally_2014,
	title = {A computationally efficient limited memory {CMA}-{ES} for large scale optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598294},
	doi = {10.1145/2576768.2598294},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Loshchilov, Ilya},
	year = {2014},
	pages = {397--404}
}

@inproceedings{glasmachers_handling_2014,
	title = {Handling sharp ridges with local supremum transformations},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598215},
	doi = {10.1145/2576768.2598215},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Glasmachers, Tobias},
	year = {2014},
	pages = {389--396}
}

@inproceedings{au_halfspace_2014,
	title = {Halfspace sampling in evolution strategies},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598335},
	doi = {10.1145/2576768.2598335},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Au, Chun-Kit and Leung, Ho-Fung},
	year = {2014},
	pages = {381--388}
}

@inproceedings{akimoto_comparison-based_2014,
	title = {Comparison-based natural gradient optimization in high dimension},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598258},
	doi = {10.1145/2576768.2598258},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Akimoto, Youhei and Auger, Anne and Hansen, Nikolaus},
	year = {2014},
	pages = {373--380}
}

@inproceedings{martins_multimodality_2014,
	title = {Multimodality and the linkage-learning difficulty of additively separable functions},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598281},
	doi = {10.1145/2576768.2598281},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Martins, Jean P. and Delbem, Alexandre C.B.},
	year = {2014},
	pages = {365--372}
}

@inproceedings{luong_multi-objective_2014,
	title = {Multi-objective gene-pool optimal mixing evolutionary algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598261},
	doi = {10.1145/2576768.2598261},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Luong, Ngoc Hoang and La Poutré, Han and Bosman, Peter A.N.},
	year = {2014},
	pages = {357--364}
}

@inproceedings{helmi_estimation_2014,
	title = {Estimation of distribution algorithm using factor graph and {Markov} blanket canonical factorization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598266},
	doi = {10.1145/2576768.2598266},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Helmi, Bentolhoda and Rahmani, Adel Torkaman},
	year = {2014},
	pages = {349--356}
}

@inproceedings{cox_solving_2014,
	title = {Solving building block problems using generative grammar},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598259},
	doi = {10.1145/2576768.2598259},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Cox, Chris R. and Watson, Richard A.},
	year = {2014},
	pages = {341--348}
}

@inproceedings{lin_tribal_2014,
	title = {A tribal ecosystem inspired algorithm ({TEA}) for global optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598253},
	doi = {10.1145/2576768.2598253},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Lin, Ying and Li, Jing-Jing and Zhang, Jun and Wan, Meng},
	year = {2014},
	pages = {33--40}
}

@inproceedings{christie_minimal_2014,
	title = {Minimal walsh structure and ordinal linkage of monotonicity-invariant function classes on bit strings},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598240},
	doi = {10.1145/2576768.2598240},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Christie, Lee A. and McCall, John A.W. and Lonie, David P.},
	year = {2014},
	pages = {333--340}
}

@inproceedings{schrum_evolving_2014,
	title = {Evolving multimodal behavior with modular neural networks in {Ms}. {Pac}-{Man}},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598234},
	doi = {10.1145/2576768.2598234},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Schrum, Jacob and Miikkulainen, Risto},
	year = {2014},
	pages = {325--332}
}

@inproceedings{nallaperuma_evor:_2014,
	title = {{EVOR}: an online evolutionary algorithm for car racing games},
	isbn = {9781450326629},
	shorttitle = {{EVOR}},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598298},
	doi = {10.1145/2576768.2598298},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Nallaperuma, Samadhi and Neumann, Frank and Bonyadi, Mohammad Reza and Michalewicz, Zbigniew},
	year = {2014},
	pages = {317--324}
}

@inproceedings{macret_automatic_2014,
	title = {Automatic design of sound synthesizers as pure data patches using coevolutionary mixed-typed cartesian genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598303},
	doi = {10.1145/2576768.2598303},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Macret, Matthieu and Pasquier, Philippe},
	year = {2014},
	pages = {309--316}
}

@inproceedings{machado_semantic_2014,
	title = {Semantic aware methods for evolutionary art},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598293},
	doi = {10.1145/2576768.2598293},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Machado, Penousal and Correia, João},
	year = {2014},
	pages = {301--308}
}

@inproceedings{jacobsen_monte_2014,
	title = {Monte {Mario}: platforming with {MCTS}},
	isbn = {9781450326629},
	shorttitle = {Monte {Mario}},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598392},
	doi = {10.1145/2576768.2598392},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Jacobsen, Emil Juul and Greve, Rasmus and Togelius, Julian},
	year = {2014},
	pages = {293--300}
}

@inproceedings{barry_virtual_2014,
	title = {Virtual photography using multi-objective particle swarm optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598210},
	doi = {10.1145/2576768.2598210},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Barry, William and Ross, Brian J.},
	year = {2014},
	pages = {285--292}
}

@inproceedings{ibragimov_multiple_2014,
	title = {Multiple graph edit distance: simultaneous topological alignment of multiple protein-protein interaction networks with an evolutionary algorithm},
	isbn = {9781450326629},
	shorttitle = {Multiple graph edit distance},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598390},
	doi = {10.1145/2576768.2598390},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Ibragimov, Rashid and Malek, Maximilian and Baumbach, Jan and Guo, Jiong},
	year = {2014},
	pages = {277--284}
}

@inproceedings{golan_predicting_2014,
	title = {Predicting patterns of gene expression during drosophila embryogenesis},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598250},
	doi = {10.1145/2576768.2598250},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Golan, Rotem and Jacob, Christian and Grewal, Savraj and Denzinger, Jörg},
	year = {2014},
	pages = {269--276}
}

@inproceedings{carter_ga-based_2014,
	title = {{GA}-based selection of vaginal microbiome features associated with bacterial vaginosis},
	url = {http://dl.acm.org/citation.cfm?id=2598378},
	urldate = {2014-08-13TZ},
	booktitle = {Proceedings of the 2014 conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Carter, Joi and Beck, Daniel and Williams, Henry and Dozier, Gerry and Foster, James A.},
	year = {2014},
	pages = {265--268}
}

@inproceedings{hernandez-ocana_stepsize_2014,
	title = {Stepsize control on the modified bacterial foraging algorithm for constrained numerical optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598379},
	doi = {10.1145/2576768.2598379},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Hernández-Ocaña, Betania and Pozos-Parra, Ma. Del Pilar and Mezura-Montes, Efrén},
	year = {2014},
	pages = {25--32}
}

@inproceedings{bautista_enhancing_2014,
	title = {Enhancing genetic algorithm-based genome-scale metabolic network curation efficiency},
	url = {http://dl.acm.org/citation.cfm?id=2598218},
	urldate = {2014-08-13TZ},
	booktitle = {Proceedings of the 2014 conference on {Genetic} and evolutionary computation},
	publisher = {ACM},
	author = {Bautista, Eddy J. and Srivastava, Ranjan},
	year = {2014},
	pages = {257--264}
}

@inproceedings{ahmed_multiple_2014,
	title = {Multiple feature construction for effective biomarker identification and classification using genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598292},
	doi = {10.1145/2576768.2598292},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Ahmed, Soha and Zhang, Mengjie and Peng, Lifeng and Xue, Bing},
	year = {2014},
	pages = {249--256}
}

@inproceedings{zahadat_wolfpack-inspired_2014,
	title = {Wolfpack-inspired evolutionary algorithm and a reaction-diffusion-based controller are used for pattern formation},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598262},
	doi = {10.1145/2576768.2598262},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Zahadat, Payam and Schmickl, Thomas},
	year = {2014},
	pages = {241--248}
}

@inproceedings{woolley_novel_2014,
	title = {A novel human-computer collaboration: combining novelty search with interactive evolution},
	isbn = {9781450326629},
	shorttitle = {A novel human-computer collaboration},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598353},
	doi = {10.1145/2576768.2598353},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Woolley, Brian G. and Stanley, Kenneth O.},
	year = {2014},
	pages = {233--240}
}

@inproceedings{shorten_generational_2014,
	title = {Generational neuro-evolution: restart and retry for improvement},
	isbn = {9781450326629},
	shorttitle = {Generational neuro-evolution},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598295},
	doi = {10.1145/2576768.2598295},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Shorten, David Peter and Nitschke, Geoff Stuart},
	year = {2014},
	pages = {225--232}
}

@inproceedings{pugh_directional_2014,
	title = {Directional communication in evolved multiagent teams},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598299},
	doi = {10.1145/2576768.2598299},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Pugh, Justin K. and Goodell, Skyler and Stanley, Kenneth O.},
	year = {2014},
	pages = {217--224}
}

@inproceedings{moore_evolving_2014,
	title = {Evolving joint-level control with digital muscles},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598373},
	doi = {10.1145/2576768.2598373},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Moore, Jared M. and McKinley, Philip K.},
	year = {2014},
	pages = {209--216}
}

@inproceedings{li_coevolutionary_2014,
	title = {Coevolutionary learning of swarm behaviors without metrics},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598349},
	doi = {10.1145/2576768.2598349},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Li, Wei and Gauci, Melvin and Gross, Roderich},
	year = {2014},
	pages = {201--208}
}

@inproceedings{li_encouraging_2014,
	title = {Encouraging creative thinking in robots improves their ability to solve challenging problems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598222},
	doi = {10.1145/2576768.2598222},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Li, Jingyu and Storie, Jed and Clune, Jeff},
	year = {2014},
	pages = {193--200}
}

@inproceedings{lehman_overcoming_2014,
	title = {Overcoming deception in evolution of cognitive behaviors},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598300},
	doi = {10.1145/2576768.2598300},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Lehman, Joel and Miikkulainen, Risto},
	year = {2014},
	pages = {185--192}
}

@inproceedings{gonzalez-fernandez_identifying_2014,
	title = {Identifying and exploiting the scale of a search space in particle swarm optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598280},
	doi = {10.1145/2576768.2598280},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Gonzalez-Fernandez, Yasser and Chen, Stephen},
	year = {2014},
	pages = {17--24}
}

@inproceedings{johnson_evolution_2014,
	title = {The evolution of kin inclusivity levels},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598283},
	doi = {10.1145/2576768.2598283},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Johnson, Anya E. and Goldsby, Heather J. and Goings, Sherri and Ofria, Charles},
	year = {2014},
	pages = {177--184}
}
@inproceedings{fairey_evolution_2014,
	title = {Evolution of communication and cooperation},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598377},
	doi = {10.1145/2576768.2598377},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Fairey, Jason and Soule, Terence},
	year = {2014},
	pages = {169--176}
}

@inproceedings{coleman_automated_2014,
	title = {Automated generation of environments to test the general learning capabilities of {AI} agents},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598257},
	doi = {10.1145/2576768.2598257},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Coleman, Oliver J. and Blair, Alan D. and Clune, Jeff},
	year = {2014},
	pages = {161--168}
}

@inproceedings{catteeuw_evolution_2014,
	title = {Evolution of honest signaling by social punishment},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598312},
	doi = {10.1145/2576768.2598312},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Catteeuw, David and Han, The Anh and Manderick, Bernard},
	year = {2014},
	pages = {153--160}
}

@inproceedings{asher_evolution_2014,
	title = {Evolution of biologically plausible neural networks performing a visually guided reaching task},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598368},
	doi = {10.1145/2576768.2598368},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Asher, Derrik E. and Krichmar, Jeffrey L. and Oros, Nicolas},
	year = {2014},
	pages = {145--152}
}

@inproceedings{wei_runtime_2014,
	title = {Runtime analysis to compare best-improvement and first-improvement in memetic algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598386},
	doi = {10.1145/2576768.2598386},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Wei, Kuai and Dinneen, Michael J.},
	year = {2014},
	pages = {1439--1446}
}

@inproceedings{sutton_superpolynomial_2014,
	title = {Superpolynomial lower bounds for the (1+1) {EA} on some easy combinatorial problems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598278},
	doi = {10.1145/2576768.2598278},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Sutton, Andrew M.},
	year = {2014},
	pages = {1431--1438}
}

@inproceedings{song_gaussian_2014,
	title = {Gaussian mixture model of evolutionary algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598252},
	doi = {10.1145/2576768.2598252},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Song, Bo and Li, Victor O.K.},
	year = {2014},
	pages = {1423--1430}
}

@inproceedings{shukla_theoretical_2014,
	title = {A theoretical analysis of volume based {Pareto} front approximations},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598348},
	doi = {10.1145/2576768.2598348},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Shukla, Pradyumn Kumar and Doll, Nadja and Schmeck, Hartmut},
	year = {2014},
	pages = {1415--1422}
}

@inproceedings{lockett_model-optimal_2014,
	title = {Model-optimal optimization by solving bellman equations},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598306},
	doi = {10.1145/2576768.2598306},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Lockett, Alan J.},
	year = {2014},
	pages = {1407--1414}
}

@inproceedings{lissovoi_mmas_2014,
	title = {{MMAS} vs. population-based {EA} on a family of dynamic fitness functions},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598301},
	doi = {10.1145/2576768.2598301},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Lissovoi, Andrei and Witt, Carsten},
	year = {2014},
	pages = {1399--1406}
}

@inproceedings{kotzing_concentration_2014,
	title = {Concentration of first hitting times under additive drift},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598364},
	doi = {10.1145/2576768.2598364},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Kötzing, Timo},
	year = {2014},
	pages = {1391--1398}
}

@inproceedings{giesen_robustness_2014,
	title = {Robustness of populations in stochastic environments},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598227},
	doi = {10.1145/2576768.2598227},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Gießen, Christian and Kötzing, Timo},
	year = {2014},
	pages = {1383--1390}
}

@inproceedings{acre_adapting_2014,
	title = {Adapting to a changing environment using winner and loser effects},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598355},
	doi = {10.1145/2576768.2598355},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Acre, Jeremy and Eskridge, Brent E. and Zoller, Nicholas and Schlupp, Ingo},
	year = {2014},
	pages = {137--144}
}

@inproceedings{doerr_impact_2014,
	title = {The impact of random initialization on the runtime of randomized search heuristics},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598359},
	doi = {10.1145/2576768.2598359},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Doerr, Benjamin and Doerr, Carola},
	year = {2014},
	pages = {1375--1382}
}

@inproceedings{dang_refined_2014,
	title = {Refined upper bounds on the expected runtime of non-elitist populations from fitness-levels},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598374},
	doi = {10.1145/2576768.2598374},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Dang, Duc-Cuong and Lehre, Per Kristian},
	year = {2014},
	pages = {1367--1374}
}

@inproceedings{dang_evolution_2014,
	title = {Evolution under partial information},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598375},
	doi = {10.1145/2576768.2598375},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Dang, Duc-Cuong and Lehre, Per Kristian},
	year = {2014},
	pages = {1359--1366}
}

@inproceedings{zhang_online_2014,
	title = {Online model racing based on extreme performance},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598336},
	doi = {10.1145/2576768.2598336},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Zhang, Tiantian and Georgiopoulos, Michael and Anagnostopoulos, Georgios C.},
	year = {2014},
	pages = {1351--1358}
}

@inproceedings{ugolotti_analysis_2014,
	title = {Analysis of evolutionary algorithms using multi-objective parameter tuning},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598226},
	doi = {10.1145/2576768.2598226},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Ugolotti, Roberto and Cagnoni, Stefano},
	year = {2014},
	pages = {1343--1350}
}

@inproceedings{tanabe_pathological_2014,
	title = {On the pathological behavior of adaptive differential evolution on hybrid objective functions},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598322},
	doi = {10.1145/2576768.2598322},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Tanabe, Ryoji and Fukunaga, Alex S.},
	year = {2014},
	pages = {1335--1342}
}

@inproceedings{soria_alcaraz_evolvability_2014,
	title = {Evolvability metrics in adaptive operator selection},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598220},
	doi = {10.1145/2576768.2598220},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Soria Alcaraz, Jorge A. and Ochoa, Gabriela and Carpio, Martin and Puga, Hector},
	year = {2014},
	pages = {1327--1334}
}

@inproceedings{karafotias_generic_2014,
	title = {Generic parameter control with reinforcement learning},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598360},
	doi = {10.1145/2576768.2598360},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Karafotias, Giorgos and Eiben, Agoston Endre and Hoogendoorn, Mark},
	year = {2014},
	pages = {1319--1326}
}

@inproceedings{basgalupp_grammatical_2014,
	title = {A grammatical evolution based hyper-heuristic for the automatic design of split criteria},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598327},
	doi = {10.1145/2576768.2598327},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Basgalupp, Márcio Porto and Barros, Rodrigo Coelho and Barabasz, Tiago},
	year = {2014},
	pages = {1311--1318}
}

@inproceedings{adriaensen_fair-share_2014,
	title = {Fair-share {ILS}: a simple state-of-the-art iterated local search hyperheuristic},
	isbn = {9781450326629},
	shorttitle = {Fair-share {ILS}},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598285},
	doi = {10.1145/2576768.2598285},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Adriaensen, Steven and Brys, Tim and Nowé, Ann},
	year = {2014},
	pages = {1303--1310}
}

@inproceedings{textor_generic_2014,
	title = {A generic finite automata based approach to implementing lymphocyte repertoire models},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598331},
	doi = {10.1145/2576768.2598331},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Textor, Johannes and Dannenberg, Katharina and Liśkiewicz, Macie},
	year = {2014},
	pages = {129--136}
}

@inproceedings{yue_applying_2014,
	title = {Applying search algorithms for optimizing stakeholders familiarity and balancing workload in requirements assignment},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598309},
	doi = {10.1145/2576768.2598309},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Yue, Tao and Ali, Shaukat},
	year = {2014},
	pages = {1295--1302}
}

@inproceedings{ramirez_performance_2014,
	title = {On the performance of multiple objective evolutionary algorithms for software architecture discovery},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598310},
	doi = {10.1145/2576768.2598310},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Ramírez, Aurora and Romero, José Raúl and Ventura, Sebastián},
	year = {2014},
	pages = {1287--1294}
}

@inproceedings{poulding_generating_2014,
	title = {Generating structured test data with specific properties using nested {Monte}-{Carlo} search},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598339},
	doi = {10.1145/2576768.2598339},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Poulding, Simon and Feldt, Robert},
	year = {2014},
	pages = {1279--1286}
}

@inproceedings{omar_comparing_2014,
	title = {Comparing search techniques for finding subtle higher order mutants},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598286},
	doi = {10.1145/2576768.2598286},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Omar, Elmahdi and Ghosh, Sudipto and Whitley, Darrell},
	year = {2014},
	pages = {1271--1278}
}

@inproceedings{mkaouer_high_2014,
	title = {High dimensional search-based software engineering: finding tradeoffs among 15 objectives for automating software refactoring using {NSGA}-{III}},
	isbn = {9781450326629},
	shorttitle = {High dimensional search-based software engineering},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598366},
	doi = {10.1145/2576768.2598366},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Mkaouer, Mohamed Wiem and Kessentini, Marouane and Bechikh, Slim and Deb, Kalyanmoy and Ó Cinnéide, Mel},
	year = {2014},
	pages = {1263--1270}
}

@inproceedings{lopez-herrejon_parallel_2014,
	title = {A parallel evolutionary algorithm for prioritized pairwise testing of software product lines},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598305},
	doi = {10.1145/2576768.2598305},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Lopez-Herrejon, Roberto Erick and Javier Ferrer, Javier and Chicano, Francisco and Haslinger, Evelyn Nicole and Egyed, Alexander and Alba, Enrique},
	year = {2014},
	pages = {1255--1262}
}

@inproceedings{li_robust_2014,
	title = {Robust next release problem: handling uncertainty during optimization},
	isbn = {9781450326629},
	shorttitle = {Robust next release problem},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598334},
	doi = {10.1145/2576768.2598334},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Li, Lingbo and Harman, Mark and Letier, Emmanuel and Zhang, Yuanyuan},
	year = {2014},
	pages = {1247--1254}
}

@inproceedings{efstathiou_surrogate-assisted_2014,
	title = {Surrogate-assisted optimisation of composite applications in mobile ad hoc networks},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598307},
	doi = {10.1145/2576768.2598307},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Efstathiou, Dionysios and McBurney, Peter and Zschaler, Steffen and Bourcier, Johann},
	year = {2014},
	pages = {1239--1246}
}

@inproceedings{ali_improved_2014,
	title = {Improved heuristics for solving {OCL} constraints using search algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598308},
	doi = {10.1145/2576768.2598308},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Ali, Shaukat and Iqbal, Muhammad Zohaib and Arcuri, Andrea},
	year = {2014},
	pages = {1231--1238}
}

@inproceedings{zaefferer_tuning_2014,
	title = {Tuning multi-objective optimization algorithms for cyclone dust separators},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598260},
	doi = {10.1145/2576768.2598260},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Zaefferer, Martin and Breiderhoff, Beate and Naujoks, Boris and Friese, Martina and Stork, Jörg and Fischbach, Andreas and Flasch, Oliver and Bartz-Beielstein, Thomas},
	year = {2014},
	pages = {1223--1230}
}

@inproceedings{sim_improved_2014,
	title = {An improved immune inspired hyper-heuristic for combinatorial optimisation problems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598241},
	doi = {10.1145/2576768.2598241},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Sim, Kevin and Hart, Emma},
	year = {2014},
	pages = {121--128}
}

@inproceedings{yliniemi_evolutionary_2014,
	title = {Evolutionary agent-based simulation of the introduction of new technologies in air traffic management},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598388},
	doi = {10.1145/2576768.2598388},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Yliniemi, Logan and Agogino, Adrian K. and Tumer, Kagan},
	year = {2014},
	pages = {1215--1222}
}

@inproceedings{stolfi_eco-friendly_2014,
	title = {Eco-friendly reduction of travel times in european smart cities},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598317},
	doi = {10.1145/2576768.2598317},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Stolfi, Daniel H. and Alba, Enrique},
	year = {2014},
	pages = {1207--1214}
}

@inproceedings{shukla_homogenization_2014,
	title = {On homogenization of coal in longitudinal blending beds},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598316},
	doi = {10.1145/2576768.2598316},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Shukla, Pradyumn Kumar and Cipold, Michael P. and Bachmann, Claus and Schmeck, Hartmut},
	year = {2014},
	pages = {1199--1206}
}

@inproceedings{sholomon_genetic_2014,
	title = {Genetic algorithm-based solver for very large multiple jigsaw puzzles of unknown dimensions and piece orientation},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598289},
	doi = {10.1145/2576768.2598289},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Sholomon, Dror and David, Omid E. and Netanyahu, Ramat-Gan S.},
	year = {2014},
	pages = {1191--1198}
}

@inproceedings{sato_applying_2014,
	title = {Applying {GA} with local search by taking hamming distances into consideration to credit erasure processing problems},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598229},
	doi = {10.1145/2576768.2598229},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Sato, Yuji and Oku, Yusuke and Fukuda, Masanori},
	year = {2014},
	pages = {1183--1190}
}

@inproceedings{rahat_multi-objective_2014,
	title = {Multi-objective routing optimisation for battery-powered wireless sensor mesh networks},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598311},
	doi = {10.1145/2576768.2598311},
	language = {en},
	urldate = {2014-08-13TZ},
	publisher = {ACM Press},
	author = {Rahat, Alma As-Aad Mohammad and Everson, Richard M. and Fieldsend, Jonathan E.},
	year = {2014},
	pages = {1175--1182}
}

@inproceedings{rafique_evolutionary_2014,
	title = {Evolutionary algorithms for classification of malware families through different network behaviors},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598238},
	doi = {10.1145/2576768.2598238},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Rafique, M. Zubair and Chen, Ping and Huygens, Christophe and Joosen, Wouter},
	year = {2014},
	pages = {1167--1174}
}

@inproceedings{purshouse_evolutionary_2014,
	title = {Evolutionary parameter estimation for a theory of planned behaviour microsimulation of alcohol consumption dynamics in an {English} birth cohort 2003 to 2010},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598239},
	doi = {10.1145/2576768.2598239},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Purshouse, Robin C. and Ally, Abdallah K. and Brennan, Alan and Moyo, Daniel and Norman, Paul},
	year = {2014},
	pages = {1159--1166}
}

@inproceedings{praxedes_lithology_2014,
	title = {Lithology discrimination using seismic elastic attributes: a genetic fuzzy classifier approach},
	isbn = {9781450326629},
	shorttitle = {Lithology discrimination using seismic elastic attributes},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598319},
	doi = {10.1145/2576768.2598319},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Praxedes, Eric da Silva and Koshiyama, Adriano Soares and Abreu, Elita Selmara and Dias, Douglas Mota and Vellasco, Marley Maria Bernardes Rebuzzi and Pacheco, Marco Aurélio Cavalcanti},
	year = {2014},
	pages = {1151--1158}
}

@inproceedings{levy_genetic_2014,
	title = {Genetic algorithms and deep learning for automatic painter classification},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598287},
	doi = {10.1145/2576768.2598287},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Levy, Erez and David, Omid E. and Netanyahu, Nathan S.},
	year = {2014},
	pages = {1143--1150}
}

@inproceedings{oliveto_runtime_2014,
	title = {On the runtime analysis of stochastic ageing mechanisms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598328},
	doi = {10.1145/2576768.2598328},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Oliveto, Pietro S. and Sudholt, Dirk},
	year = {2014},
	pages = {113--120}
}

@inproceedings{hudson_dynamic_2014,
	title = {Dynamic multi-dimensional {PSO} with indirect encoding for proportional fair constrained resource allocation},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598387},
	doi = {10.1145/2576768.2598387},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Hudson, Jonathan and Ghaderi, Majid and Denzinger, Jörg},
	year = {2014},
	pages = {1135--1142}
}

@inproceedings{hinckley_evolved_2014,
	title = {Evolved spacecraft trajectories for low earth orbit},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598246},
	doi = {10.1145/2576768.2598246},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Hinckley, David W. and Zieba, Karol and Hitt, Darren L. and Eppstein, Margaret J.},
	year = {2014},
	pages = {1127--1134}
}

@inproceedings{gupta_quantum_2014,
	title = {Quantum inspired genetic algorithm for community structure detection in social networks},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598277},
	doi = {10.1145/2576768.2598277},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Gupta, Shikha and Taneja, Sheetal and Kumar, Naveen},
	year = {2014},
	pages = {1119--1126}
}

@inproceedings{gholami_passive_2014,
	title = {Passive solar building design using genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598211},
	doi = {10.1145/2576768.2598211},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Gholami, Mohammad M.O. and Ross, Brian J.},
	year = {2014},
	pages = {1111--1118}
}
@inproceedings{eicholtz_recognizing_2014,
	title = {Recognizing planar kinematic mechanisms from a single image using evolutionary computation},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598354},
	doi = {10.1145/2576768.2598354},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Eicholtz, Matthew and Kara, Levent Burak and Lohn, Jason},
	year = {2014},
	pages = {1103--1110}
}

@inproceedings{de_falco_using_2014,
	title = {Using an adaptive invasion-based model for fast range image registration},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598340},
	doi = {10.1145/2576768.2598340},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {De Falco, Ivanoe and Della Cioppa, Antonio and Maisto, Domenico and Scafuri, Umberto and Tarantino, Ernesto},
	year = {2014},
	pages = {1095--1102}
}

@inproceedings{curran_hierarchical_2014,
	title = {Hierarchical simulation for complex domains: air traffic flow management},
	isbn = {9781450326629},
	shorttitle = {Hierarchical simulation for complex domains},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598385},
	doi = {10.1145/2576768.2598385},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Curran, William and Agogino, Adrian and Tumer, Kagan},
	year = {2014},
	pages = {1087--1094}
}

@inproceedings{cheney_automated_2014,
	title = {Automated vibrational design and natural frequency tuning of multi-material structures},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598362},
	doi = {10.1145/2576768.2598362},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Cheney, Nicholas and Ritz, Ethan and Lipson, Hod},
	year = {2014},
	pages = {1079--1086}
}

@inproceedings{bucur_tradeoffs_2014,
	title = {The tradeoffs between data delivery ratio and energy costs in wireless sensor networks: a multi-objectiveevolutionary framework for protocol analysis},
	isbn = {9781450326629},
	shorttitle = {The tradeoffs between data delivery ratio and energy costs in wireless sensor networks},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598384},
	doi = {10.1145/2576768.2598384},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Bucur, Doina and Iacca, Giovanni and Squillero, Giovanni and Tonda, Alberto},
	year = {2014},
	pages = {1071--1078}
}

@inproceedings{bartoli_playing_2014,
	title = {Playing regex golf with genetic programming},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598333},
	doi = {10.1145/2576768.2598333},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Bartoli, Alberto and De Lorenzo, Andrea and Medvet, Eric and Tarlao, Fabiano},
	year = {2014},
	pages = {1063--1070}
}

@inproceedings{ludwig_clonal_2014,
	title = {Clonal selection based fuzzy {C}-means algorithm for clustering},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598270},
	doi = {10.1145/2576768.2598270},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Ludwig, Simone A.},
	year = {2014},
	pages = {105--112}
}

@inproceedings{probst_implicitly_2014,
	title = {An implicitly parallel {EDA} based on restricted boltzmann machines},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598273},
	doi = {10.1145/2576768.2598273},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Probst, Malte and Rothlauf, Franz and Grahl, Jörn},
	year = {2014},
	pages = {1055--1062}
}

@inproceedings{mambrini_design_2014,
	title = {Design and analysis of adaptive migration intervals in parallel evolutionary algorithms},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598347},
	doi = {10.1145/2576768.2598347},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Mambrini, Andrea and Sudholt, Dirk},
	year = {2014},
	pages = {1047--1054}
}

@inproceedings{luque_enhancing_2014,
	title = {Enhancing parallel cooperative trajectory based metaheuristics with path relinking},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598337},
	doi = {10.1145/2576768.2598337},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Luque, Gabriel and Alba, Enrique},
	year = {2014},
	pages = {1039--1046}
}

@inproceedings{ludwig_mapreduce-based_2014,
	title = {{MapReduce}-based optimization of overlay networks using particle swarm optimization},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598269},
	doi = {10.1145/2576768.2598269},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Ludwig, Simone A.},
	year = {2014},
	pages = {1031--1038}
}

@inproceedings{jaros_gpu-accelerated_2014,
	title = {{GPU}-accelerated evolutionary design of the complete exchange communication on wormhole networks},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598315},
	doi = {10.1145/2576768.2598315},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Jaros, Jiri and Tyrala, Radek},
	year = {2014},
	pages = {1023--1030}
}

@inproceedings{hrbacek_towards_2014,
	title = {Towards highly optimized cartesian genetic programming: from sequential via {SIMD} and thread to massive parallel implementation},
	isbn = {9781450326629},
	shorttitle = {Towards highly optimized cartesian genetic programming},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598343},
	doi = {10.1145/2576768.2598343},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Hrbacek, Radek and Sekanina, Lukas},
	year = {2014},
	pages = {1015--1022}
}

@inproceedings{hidalgo_solving_2014,
	title = {Solving {GA}-hard problems with {EMMRS} and {GPGPUs}},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598219},
	doi = {10.1145/2576768.2598219},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {hidalgo, J. Ignacio and Colmenar, J. Manuel and Risco-Martín, Jose L. and Sánchez-Lacruz, Carlos and Lanchares, Juan and Garnica, Oscar and Díaz, Josefa},
	year = {2014},
	pages = {1007--1014}
}

@inproceedings{goldman_parameter-less_2014,
	title = {Parameter-less population pyramid},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598350},
	doi = {10.1145/2576768.2598350},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Goldman, Brian W. and Punch, William F.},
	year = {2014},
	pages = {785--792}
}

@inproceedings{ahmed_improved_2014,
	title = {An improved multi-start particle swarm-based algorithm for protein structure comparison},
	isbn = {9781450326629},
	url = {http://dl.acm.org/citation.cfm?doid=2576768.2598212},
	doi = {10.1145/2576768.2598212},
	language = {en},
	urldate = {2014-08-12TZ},
	publisher = {ACM Press},
	author = {Ahmed, Hazem Radwan and Glasgow, Janice I.},
	year = {2014},
	pages = {1--8}
}

@inproceedings{burke_survey_2002,
	title = {A {Survey} {And} {Analysis} {Of} {Diversity} {Measures} {In} {Genetic} {Programming}.},
	volume = {2},
	url = {ftp://ftp.cs.bham.ac.uk/.snapshot/hourly.3/pub/authors/W.B.Langdon/biblio/gecco2002/GP125.pdf},
	urldate = {2014-08-12TZ},
	booktitle = {{GECCO}},
	author = {Burke, Raymond and Gustafson, Steven M. and Kendall, Graham},
	year = {2002},
	pages = {716--723}
}

@inproceedings{bui_multiobjective_2005,
	title = {Multiobjective optimization for dynamic environments},
	volume = {3},
	doi = {10.1109/CEC.2005.1554987},
	abstract = {This paper investigates the use of evolutionary multi-objective optimization methods (EMOs) for solving single-objective optimization problems in dynamic environments. A number of authors proposed the use of EMOs for maintaining diversity in a single objective optimization task, where they transform the single objective optimization problem into a multi-objective optimization problem by adding an artificial objective function. We extend this work by looking at the dynamic single objective task and examine a number of different possibilities for the artificial objective function. We adopt the non-dominated sorting genetic algorithm version 2 (NSGA2). The results show that the resultant formulations are promising and competitive to other methods for handling dynamic environments.},
	booktitle = {The 2005 {IEEE} {Congress} on {Evolutionary} {Computation}, 2005},
	author = {Bui, Lam Thu and Abbass, H.A and Branke, J.},
	month = sep,
	year = {2005},
	keywords = {Australia, Benchmark testing, Biological cells, Genetic algorithms, NSGA2, Optimization methods, Portfolios, Robots, Sorting, Stock markets, artificial objective function, distributed processing, dynamic environments, evolutionary computation, evolutionary multi-objective optimization, genetic algorithms, nondominated sorting genetic algorithm version 2, single-objective optimization problems},
	pages = {2349--2356 Vol. 3}
}

@incollection{abbass_searching_2003,
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Searching under {Multi}-evolutionary {Pressures}},
	copyright = {©2003 Springer-Verlag Berlin Heidelberg},
	isbn = {978-3-540-01869-8, 978-3-540-36970-7},
	url = {http://link.springer.com/chapter/10.1007/3-540-36970-8_28},
	abstract = {A number of authors made the claim that a multiobjective approach preserves genetic diversity better than a single objective approach. Sofar, none of these claims presented a thorough analysis to the effect of multiobjective approaches. In this paper, we provide such analysis and show that a multiobjective approach does preserve reproductive diversity. We make our case by comparing a pareto multiobjective approach against a single objective approach for solving single objective global optimization problems in the absence of mutation. We show that the fitness landscape is different in both cases and the multiobjective approach scales faster and produces better solutions than the single objective approach.},
	language = {en},
	number = {2632},
	urldate = {2014-08-12TZ},
	booktitle = {Evolutionary {Multi}-{Criterion} {Optimization}},
	publisher = {Springer Berlin Heidelberg},
	author = {Abbass, Hussein A. and Deb, Kalyanmoy},
	editor = {Fonseca, Carlos M. and Fleming, Peter J. and Zitzler, Eckart and Thiele, Lothar and Deb, Kalyanmoy},
	month = jan,
	year = {2003},
	keywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computer Appl. in Administrative Data Processing, Discrete Mathematics in Computer Science, Numeric Computing, optimization},
	pages = {391--404}
}

@article{hu_hierarchical_2005,
	title = {The {Hierarchical} {Fair} {Competition} ({HFC}) {Framework} for {Sustainable} {Evolutionary} {Algorithms}},
	volume = {13},
	issn = {1063-6560},
	url = {http://dx.doi.org/10.1162/1063656054088530},
	doi = {10.1162/1063656054088530},
	abstract = {Many current Evolutionary Algorithms (EAs) suffer from a tendency to converge prematurely or stagnate without progress for complex problems. This may be due to the loss of or failure to discover certain valuable genetic material or the loss of the capability to discover new genetic material before convergence has limited the algorithm's ability to search widely. In this paper, the Hierarchical Fair Competition (HFC) model, including several variants, is proposed as a generic framework for sustainable evolutionary search by transforming the convergent nature of the current EA framework into a non-convergent search process. That is, the structure of HFC does not allow the convergence of the population to the vicinity of any set of optimal or locally optimal solutions. The sustainable search capability of HFC is achieved by ensuring a continuous supply and the incorporation of genetic material in a hierarchical manner, and by culturing and maintaining, but continually renewing, populations of individuals of intermediate fitness levels. HFC employs an assembly-line structure in which subpopulations are hierarchically organized into different fitness levels, reducing the selection pressure within each subpopulation while maintaining the global selection pressure to help ensure the exploitation of the good genetic material found. Three EAs based on the HFC principle are tested - two on the even-10-parity genetic programming benchmark problem and a real-world analog circuit synthesis problem, and another on the HIFF genetic algorithm (GA) benchmark problem. The significant gain in robustness, scalability and efficiency by HFC, with little additional computing effort, and its tolerance of small population sizes, demonstrates its effectiveness on these problems and shows promise of its potential for improving other existing EAs for difficult problems. A paradigm shift from that of most EAs is proposed: rather than trying to escape from local optima or delay convergence at a local optimum, HFC allows the emergence of new optima continually in a bottom-up manner, maintaining low local selection pressure at all fitness levels, while fostering exploitation of high-fitness individuals through promotion to higher levels.},
	number = {2},
	urldate = {2014-08-12TZ},
	journal = {Evolutionary Computation},
	author = {Hu, Jianjun and Goodman, Erik and Seo, Kisung and Fan, Zhun and Rosenberg, Rondal},
	month = jun,
	year = {2005},
	pages = {241--277}
}

@inproceedings{hornby_steady-state_2009,
	address = {New York, NY, USA},
	series = {{GECCO} '09},
	title = {Steady-state {ALPS} for {Real}-valued {Problems}},
	isbn = {978-1-60558-325-9},
	url = {http://doi.acm.org/10.1145/1569901.1570011},
	doi = {10.1145/1569901.1570011},
	abstract = {The objectives of this paper are to describe a steady-state version of the Age-Layered Population Structure (ALPS) Evolutionary Algorithm (EA) and to compare it against other GAs on real-valued problems. Motivation for this work comes from our previous success in demonstrating that a generational version of ALPS greatly improves search performance on a Genetic Programming problem. In making steady-state ALPS, some modifications were made to the method for calculating age and the method for moving individuals up age layers. To demonstrate that ALPS works well on real-valued problems we compare it against CMA-ES and Differential Evolution (DE) on five challenging, real-valued functions and on one real-world problem. While CMA-ES and DE outperform ALPS on the two unimodal test functions, ALPS is much better on the three multimodal test problems and on the real-world problem. Further examination shows that, unlike the other GAs, ALPS maintains a genotypically diverse population throughout the entire search process. These findings strongly suggest that the ALPS paradigm is better able to avoid premature convergence then the other GAs.},
	urldate = {2014-08-12TZ},
	booktitle = {Proceedings of the 11th {Annual} {Conference} on {Genetic} and {Evolutionary} {Computation}},
	publisher = {ACM},
	author = {Hornby, Gregory S.},
	year = {2009},
	keywords = {age, evolutionary algorithm, numerical optimization, premature convergence},
	pages = {795--802}
}

@article{campbell_quantity_2013,
	title = {Quantity is {Nothing} without {Quality}: {Automated} {QA}/{QC} for {Streaming} {Environmental} {Sensor} {Data}},
	volume = {63},
	issn = {0006-3568, 1525-3244},
	shorttitle = {Quantity is {Nothing} without {Quality}},
	url = {http://bioscience.oxfordjournals.org/content/63/7/574},
	doi = {10.1525/bio.2013.63.7.10},
	abstract = {Sensor networks are revolutionizing environmental monitoring by producing massive quantities of data that are being made publically available in near real time. These data streams pose a challenge for ecologists because traditional approaches to quality assurance and quality control are no longer practical when confronted with the size of these data sets and the demands of real-time processing. Automated methods for rapidly identifying and (ideally) correcting problematic data are essential. However, advances in sensor hardware have outpaced those in software, creating a need for tools to implement automated quality assurance and quality control procedures, produce graphical and statistical summaries for review, and track the provenance of the data. Use of automated tools would enhance data integrity and reliability and would reduce delays in releasing data products. Development of community-wide standards for quality assurance and quality control would instill confidence in sensor data and would improve interoperability across environmental sensor networks.},
	language = {en},
	number = {7},
	urldate = {2014-06-13TZ},
	journal = {BioScience},
	author = {Campbell, John L. and Rustad, Lindsey E. and Porter, John H. and Taylor, Jeffrey R. and Dereszynski, Ethan W. and Shanley, James B. and Gries, Corinna and Henshaw, Donald L. and Martin, Mary E. and Sheldon, Wade M. and Boose, Emery R.},
	month = jul,
	year = {2013},
	keywords = {computers in biology, environmental science, informatics, instrumentation},
	pages = {574--585}
}

@article{whigham_exploring_2006,
	series = {Selected {Papers} from the {Third} {Conference} of the {International} {Society} for {Ecological} {Informatics} ({ISEI}), {August} 26--30, 2002, {Grottaferrata}, {Rome}, {Italy}},
	title = {Exploring seasonal patterns using process modelling and evolutionary computation},
	volume = {195},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380005005867},
	doi = {10.1016/j.ecolmodel.2005.11.017},
	abstract = {Process models of chlorophyll-a concentration for freshwater systems, and in particular lake environments, have been developed over many years. Previous work has demonstrated that the optimisation of constants within these models has been able to significantly improve the quality of the resulting model on unseen data. This paper explores two properties of one particular process model: can the model predictions be improved by optimising the constants over different temporal scales; and can seasonal patterns be identified, based on monthly training scales, that allow further understanding of the response of the freshwater system to changing environmental conditions. The results show that there is some improvement on the prediction of unseen data when using constants of the process model optimised for individual months, versus constants trained over a yearly cycle. Additionally, by studying the patterns of the constants over various time scales some underlying seasonal patterns can be observed. These patterns can be further studied by exploring how the various elements of the process model vary with monthly versus yearly training constants. This work demonstrates some possible directions for understanding how the behaviour of freshwater systems at different time scales can be used to understand the properties of these complexes, non-linear systems. The results also suggest that local models of ecological time series data can be used to extract information that may not be obtainable from a single, global model.},
	number = {1–2},
	urldate = {2014-05-05TZ},
	journal = {Ecological Modelling},
	author = {Whigham, P. A. and Dick, G. and Recknagel, F.},
	month = may,
	year = {2006},
	keywords = {Chlorophyll-a, Local model, Optimisation, Process model, evolutionary computation},
	pages = {146--152}
}

@article{covert_experiments_2013,
	title = {Experiments on the role of deleterious mutations as stepping stones in adaptive evolution},
	volume = {110},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/110/34/E3171},
	doi = {10.1073/pnas.1313424110},
	abstract = {Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions.},
	language = {en},
	number = {34},
	urldate = {2014-05-01TZ},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Covert, Arthur W. and Lenski, Richard E. and Wilke, Claus O. and Ofria, Charles},
	month = aug,
	year = {2013},
	pmid = {23918358},
	keywords = {Experimental evolution, epistasis, genetic drift},
	pages = {E3171--E3178}
}

@article{aguilera_impacts_2009,
	title = {Impacts of the invasive plant {Fallopia} japonica ({Houtt}.) on plant communities and ecosystem processes},
	volume = {12},
	issn = {1387-3547},
	url = {http://www.springerlink.com/index/10.1007/s10530-009-9543-z},
	doi = {10.1007/s10530-009-9543-z},
	number = {5},
	urldate = {2011-06-11TZ},
	journal = {Biological Invasions},
	author = {Aguilera, Anna G. and Alpert, Peter and Dukes, Jeffrey S. and Harrington, Robin},
	month = aug,
	year = {2009},
	keywords = {Clonal growth, Developmental Biology, Ecology, Fallopia japonica, Freshwater \& Marine Ecology, Japanese knotweed, Nitrogen mineralization, Plant Sciences, diversity, diversity, general, invasions, invasive species, japonica, litter, observational, plot comparisons, soil},
	pages = {1243--1252}
}

@article{matsui_evolution_1990,
	title = {Evolution of the {Feminist} {Movement} in {Japan}},
	volume = {2},
	copyright = {Copyright © 1990 The Johns Hopkins University Press},
	issn = {1040-0656},
	url = {http://www.jstor.org/stable/4316048},
	doi = {10.2307/4316048},
	number = {3},
	urldate = {2012-12-11TZ},
	journal = {NWSA Journal},
	author = {Matsui, Machiko},
	month = jul,
	year = {1990},
	note = {ArticleType: research-article / Full publication date: Summer, 1990 / Copyright © 1990 The Johns Hopkins University Press},
	pages = {435--449}
}

@article{shin_womens_1999,
	title = {Women's {Political} {Activism} {In} {Japan} {And} {Other} {Late} {Developing} {Asian} {Countries}, 1870–1945},
	volume = {27},
	copyright = {© 1999 Policy Studies Organization},
	issn = {1747-1346},
	url = {http://onlinelibrary.wiley.com.proxy.swarthmore.edu/doi/10.1111/j.1747-1346.1999.tb00524.x/abstract},
	doi = {10.1111/j.1747-1346.1999.tb00524.x},
	abstract = {The main thrust of this paper is that countries at different industrial and developmental stages experience different pressure from both within and without. And these differences largely shape the nature of women's political activities. This paper examines the nature of Japanese women's political activities in initial stages, between 1868–1945, as an example to shed some light on where there exist differences between political activities of advanced Western industrial countries, especially the United States, and the late developing countries such as Japan and some other Asian countries. The paper asserts that the study of women's political consciousness and participation should be approached from the larger issue of international political environment in which internal politics of a country takes place. That is, the presence and absence of feminism in women's political activities should be understood in the context of the world historical time.},
	language = {en},
	number = {1},
	urldate = {2012-12-22TZ},
	journal = {Southeastern Political Review},
	author = {Shin, Youngtae},
	year = {1999},
	pages = {81--102}
}

@article{nkurunziza_carbohydrate_2011,
	title = {Carbohydrate dynamics in roots and rhizomes of {Cirsium} arvense and {Tussilago} farfara},
	issn = {1365-3180},
	url = {http://dx.doi.org/10.1111/j.1365-3180.2011.00866.x},
	doi = {10.1111/j.1365-3180.2011.00866.x},
	journal = {Weed Research},
	author = {Nkurunziza, L and Streibig, J C},
	year = {2011},
	keywords = {carbohydrates, carbohydrates, carbon, coltsfoot, coltsfoot, compensation point, compensation point, creeping thistle, creeping thistle, perennial weeds, perennial weeds, source and sink, source and sink, translocation},
	pages = {no}
}

@article{noauthor_effects_nodate,
	title = {Effects of reducing sugar concentration on in vitro tuber formation and sprouting in yam ({Dioscorea} cayenensis–{D}. rotundata complex) - {Springer}},
	url = {http://link.springer.com/article/10.1007/s11240-009-9575-1/fulltext.html},
	urldate = {2013-01-22TZ}
}

@article{price_seasonal_2001,
	title = {Seasonal patterns of partitioning and remobilization of $^{\textrm{14}}${C} in the invasive rhizomatous perennial {Japanese} knotweed (\textit{{Fallopia} japonica} ({Houtt}.) {Ronse} {Decraene})},
	volume = {15},
	issn = {0269-7653},
	url = {http://dx.doi.org/10.1023/A:1016036916017},
	doi = {10.1023/A:1016036916017},
	abstract = {Resource partitioning between shoot growth, storage and reproduction is poorly understood in many clonal plant species. This study documents seasonal patterns of growth, 14C-labelled photoassimilate distribution and remobilization in the invasive rhizomatous species Fallopia japonica (Japanese knotweed). Biomass accumulation above- and below-ground in F. japonica was rapid. By September, rhizome biomass had increased 18-fold from the initial harvest in May (representing 48\% of total plant biomass) and this was maintained over winter. Patterns of 14C allocation from F. japonica shoots labelled at different times of year show that as the season progressed, the rhizomes became an increasingly important sink for current assimilate (the percentage of 14C recovered from rhizomes was 35\% in August and 67\% in September) and the corresponding retention of assimilate by established shoots declined. The percentage of 14C exported to roots was greatest in August. Relatively little photoassimilate was exported to other shoots on the plant, or to flowers. Recycling of photoassimilate was fairly tight in this species and 14C fixed by shoots in early May 1999 or September 1999 was remobilized to the rhizome prior to shoot senescence and death. Some of this 14C was then remobilized to new shoots early the following spring. These characteristics may contribute to the success of F. japonica in colonizing a variety of contrasting habitats, often with serious management implications.},
	number = {4},
	journal = {Evolutionary Ecology},
	author = {Price, Elizabeth A.C. and Gamble, Rebecca and Williams, Gareth G. and Marshall, Christopher},
	month = jul,
	year = {2001},
	keywords = {Biomedical and Life Sciences, Evolutionary Biology, Human Genetics, Japanese knotweed, Plant Sciences, assimilate partitioning, carbon, experimental, glucose, growth, japonica, nutrient allocation, remobilization of 14C, rhizome, translocation},
	pages = {347--362}
}

@misc{ncdc_climate_2013,
	title = {Climate {Data} {Online} ({CDO}) {Web} {Services}},
	url = {http://www.ncdc.noaa.gov/cdo-web/webservices/ncdcwebservices},
	abstract = {Climate Data Online (CDO) is the web access application for the National Climatic Data Center's (NCDC) archive of weather and climate data.},
	language = {eng},
	urldate = {2013-04-30TZ},
	author = {(NCDC), National Climatic Data Center},
	month = apr,
	year = {2013},
	note = {Climate Data Online (CDO) Web Services documentation and help pages},
	keywords = {Climate Data Online (CDO) Web Services}
}
@inproceedings{olson_evolved_2013,
	title = {Evolved digital ecosystems: {Dynamic} steady state, not optimal fixed point},
	isbn = {9780262317092},
	shorttitle = {Evolved digital ecosystems},
	url = {http://mitpress.mit.edu/sites/default/files/titles/content/ecal13/ch019.html},
	doi = {10.7551/978-0-262-31709-2-ch019},
	urldate = {2014-04-29TZ},
	publisher = {MIT Press},
	author = {Olson, Randal and Mirmomeni, Masoud and Brom, Tim and Bruger, Eric and Hintze, Arend and Knoester, David and Adami, Christoph},
	month = sep,
	year = {2013},
	pages = {126--133}
}

@article{tan_introduction_2006,
	title = {Introduction to data mining},
	journal = {WP Co},
	author = {Tan, Pang-Ning and Steinbach, Michael and Kumar, Vipin},
	year = {2006}
}

@article{rousseeuw_silhouettes:_1987,
	title = {Silhouettes: a graphical aid to the interpretation and validation of cluster analysis},
	volume = {20},
	shorttitle = {Silhouettes},
	url = {http://www.sciencedirect.com/science/article/pii/0377042787901257},
	urldate = {2014-04-22TZ},
	journal = {Journal of computational and applied mathematics},
	author = {Rousseeuw, Peter J.},
	year = {1987},
	pages = {53--65}
}

@article{benton_how_2007,
	title = {How {Did} {Life} {Become} so {Diverse}? the {Dynamics} of {Diversification} {According} to the {Fossil} {Record} and {Molecular} {Phylogenetics}},
	volume = {50},
	issn = {1475-4983},
	shorttitle = {How {Did} {Life} {Become} so {Diverse}?},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1475-4983.2006.00612.x/abstract},
	doi = {10.1111/j.1475-4983.2006.00612.x},
	abstract = {Abstract:  The long-term diversification of life probably cannot be modelled as a simple equilibrial process: the time scales are too long, the potential for exploring new ecospace is too large and it is unlikely that ecological controls can act at global scales. The sum of many clade expansions and reductions, each of which happens according to its own dynamic, probably approximates more a damped exponential curve when translated into a global-scale species diversification curve. Unfortunately, it is not possible to plot such a meaningful global-scale species diversification curve through time, but curves at higher taxonomic levels have been produced. These curves are subject to the vagaries of the fossil record, but it is unlikely that the sources of error entirely overwhelm the biological signal. Clades radiate when the external and internal conditions are right: a new territory or ecospace becomes available, and the lineage has acquired a number of characters that open up a new diet or mode of life. Modern high levels of diversity in certain speciose clades may depend on such ancient opportunities taken. Dramatic climatic changes through the Quaternary must have driven extinctions and originations, but many species responded simply by moving to more favourable locations. Ecological communities appear to be no more than merely chance associations of species, but there may be real interactions among species. Ironically, high species diversity may lead to more speciation, not, as had been assumed, less: more species create more opportunities and selective pressures for other species to respond to, rather than capping diversity at a fixed equilibrium level. Studies from the scale of modern ecosystems to global long-term patterns in the fossil record support a model for the exponential diversification of life, and one explanation for a pattern of exponential diversification is that as diversity increases, new forms become ever more refinements of existing forms. In a sense the world becomes increasingly divided into finer niche space. Organisms have a propensity to speciate freely, species richness within ecosystems appears to generate opportunities for more speciation, clades show all kinds of patterns from sluggish speciation rates and constant diversity through time to apparently explosive speciation, and there is no evidence that rapidly speciating clades have reached a limit, nor that they are driving other clades to extinction. A corollary of this view is that current biodiversity must be higher than it has ever been. Limits to infinite growth are clearly local, regional, and global turnover and extinction events, when climate change and physical catastrophes knock out species and whole clades, and push the rising exponential curve down a notch or two.},
	language = {en},
	number = {1},
	urldate = {2014-04-22TZ},
	journal = {Palaeontology},
	author = {Benton, Michael J. and Emerson, Brent C.},
	month = jan,
	year = {2007},
	keywords = {biodiversity, diversification, diversity, molecular phylogeny, phylogeography, speciation},
	pages = {23--40}
}

@article{gruner_does_2008,
	title = {Does species richness drive speciation? {A} reassessment with the {Hawaiian} biota},
	volume = {31},
	copyright = {© 2008 The Authors},
	issn = {1600-0587},
	shorttitle = {Does species richness drive speciation?},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2008.5289.x/abstract},
	doi = {10.1111/j.0906-7590.2008.5289.x},
	language = {en},
	number = {2},
	urldate = {2014-04-22TZ},
	journal = {Ecography},
	author = {Gruner, Daniel S. and Gotelli, Nicholas J. and Price, Jonathan P. and Cowie, Robert H.},
	month = apr,
	year = {2008},
	pages = {279--285}
}

@article{buckling_role_2002,
	title = {The role of parasites in sympatric and allopatric host diversification},
	volume = {420},
	copyright = {© 2002 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v420/n6915/abs/nature01164.html},
	doi = {10.1038/nature01164},
	abstract = {Exploiters (parasites and predators) are thought to play a significant role in diversification, and ultimately speciation, of their hosts or prey. Exploiters may drive sympatric (within-population) diversification if there are a variety of exploiter-resistance strategies or fitness costs associated with exploiter resistance. Exploiters may also drive allopatric (between-population) diversification by creating different selection pressures and increasing the rate of random divergence. We examined the effect of a virulent viral parasite (phage) on the diversification of the bacterium Pseudomonas fluorescens in spatially structured microcosms. Here we show that in the absence of phages, bacteria rapidly diversified into spatial niche specialists with similar patterns of diversity across replicate populations. In the presence of phages, sympatric diversity was greatly reduced, as a result of phage-imposed reductions in host density decreasing competition for resources. In contrast, allopatric diversity was greatly increased as a result of phage-imposed selection for resistance, which caused populations to follow divergent evolutionary trajectories. These results show that exploiters can drive diversification between populations, but may inhibit diversification within populations by opposing diversifying selection that arises from resource competition.},
	language = {en},
	number = {6915},
	urldate = {2014-04-22TZ},
	journal = {Nature},
	author = {Buckling, Angus and Rainey, Paul B.},
	month = dec,
	year = {2002},
	pages = {496--499}
}

@article{whittaker_island_2007,
	title = {The island immaturity–speciation pulse model of island evolution: an alternative to the “diversity begets diversity” model},
	volume = {30},
	shorttitle = {The island immaturity–speciation pulse model of island evolution},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2007.04761.x/full},
	number = {3},
	urldate = {2014-04-22TZ},
	journal = {Ecography},
	author = {Whittaker, Robert J. and Ladle, Richard J. and Araújo, Miguel B. and María Fernández-Palacios, José and Domingo Delgado, Juan and Ramón Arévalo, José},
	year = {2007},
	pages = {321--327}
}

@article{emerson_species_2005,
	title = {Species diversity can drive speciation},
	volume = {434},
	copyright = {© 2005 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v434/n7036/abs/nature03450.html},
	doi = {10.1038/nature03450},
	abstract = {A fundamental question in evolutionary ecology and conservation biology is: why do some areas contain greater species diversity than others? Island biogeographic theory has identified the roles of immigration and extinction in relation to area size and proximity to source areas, and the role of speciation is also recognized as an important factor. However, one as yet unexplored possibility is that species diversity itself might help to promote speciation, and indeed the central tenets of island biogeographic theory support such a prediction. Here we use data for plants and arthropods of the volcanic archipelagos of the Canary and Hawaiian Islands to address whether there is a positive relationship between species diversity and rate of diversification. Our index of diversification for each island is the proportion of species that are endemic, and we test our prediction that this increases with increasing species number. We show that even after controlling for several important physical features of islands, diversification is strongly related to species number.},
	language = {en},
	number = {7036},
	urldate = {2014-04-21TZ},
	journal = {Nature},
	author = {Emerson, Brent C. and Kolm, Niclas},
	month = apr,
	year = {2005},
	pages = {1015--1017}
}

@article{brockhurst_niche_2007,
	title = {Niche {Occupation} {Limits} {Adaptive} {Radiation} in {Experimental} {Microcosms}},
	volume = {2},
	url = {http://dx.plos.org/10.1371/journal.pone.0000193},
	doi = {10.1371/journal.pone.0000193},
	abstract = {Adaptive radiations have played a key role in the evolution of biological diversity. The breadth of adaptive radiation in an invading lineage is likely to be influenced by the availability of ecological niches, which will be determined to some extent by the diversity of the resident community. High resident diversity may result in existing ecological niches being filled, inhibiting subsequent adaptive radiation. Conversely, high resident diversity could result in the creation of novel ecological niches or an increase in within niche competition driving niche partitioning, thus promoting subsequent diversification. We tested the role of resident diversity on adaptive radiations in experimental populations of the bacterium Pseudomonas fluorescens that readily diversify into a range of niche specialists when grown in a heterogeneous environment. We allowed an undiversified strain to invade resident communities that varied in the number of niche specialists. The breadth of adaptive radiation attainable by an invading lineage decreased with increasing niche occupation of the resident community. Our results highlight the importance of niche occupation as a constraint on adaptive radiation.},
	number = {2},
	urldate = {2014-04-21TZ},
	journal = {PLoS ONE},
	author = {Brockhurst, Michael A. and Colegrave, Nick and Hodgson, David J. and Buckling, Angus},
	month = feb,
	year = {2007},
	pages = {e193}
}

@article{cadena_ecology:_2005,
	title = {Ecology: {Is} speciation driven by species diversity?},
	volume = {438},
	shorttitle = {Ecology},
	url = {http://www.nature.com/nature/journal/v438/n7064/abs/nature04308.html},
	number = {7064},
	urldate = {2014-04-21TZ},
	journal = {Nature},
	author = {Cadena, Carlos Daniel and Ricklefs, Robert E. and Jimenez, Ivan and Bermingham, Eldredge},
	year = {2005},
	pages = {E1--E2}
}

@article{tews_animal_2004,
	title = {Animal species diversity driven by habitat heterogeneity/diversity: the importance of keystone structures},
	volume = {31},
	issn = {1365-2699},
	shorttitle = {Animal species diversity driven by habitat heterogeneity/diversity},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.0305-0270.2003.00994.x/abstract},
	doi = {10.1046/j.0305-0270.2003.00994.x},
	abstract = {Aim In a selected literature survey we reviewed studies on the habitat heterogeneity–animal species diversity relationship and evaluated whether there are uncertainties and biases in its empirical support.Location World-wide.Methods We reviewed 85 publications for the period 1960–2003. We screened each publication for terms that were used to define habitat heterogeneity, the animal species group and ecosystem studied, the definition of the structural variable, the measurement of vegetation structure and the temporal and spatial scale of the study.Main conclusions The majority of studies found a positive correlation between habitat heterogeneity/diversity and animal species diversity. However, empirical support for this relationship is drastically biased towards studies of vertebrates and habitats under anthropogenic influence. In this paper, we show that ecological effects of habitat heterogeneity may vary considerably between species groups depending on whether structural attributes are perceived as heterogeneity or fragmentation. Possible effects may also vary relative to the structural variable measured. Based upon this, we introduce a classification framework that may be used for across-studies comparisons. Moreover, the effect of habitat heterogeneity for one species group may differ in relation to the spatial scale. In several studies, however, different species groups are closely linked to ‘keystone structures’ that determine animal species diversity by their presence. Detecting crucial keystone structures of the vegetation has profound implications for nature conservation and biodiversity management.},
	language = {en},
	number = {1},
	urldate = {2014-02-03TZ},
	journal = {Journal of Biogeography},
	author = {Tews, J. and Brose, U. and Grimm, V. and Tielbörger, K. and Wichmann, M. C. and Schwager, M. and Jeltsch, F.},
	year = {2004},
	keywords = {Habitat fragmentation, Habitat heterogeneity hypothesis, biodiversity, foliage height diversity, spatial scale, species richness, structural diversity, structural heterogeneity},
	pages = {79--92}
}

@article{kumar_spatial_2006,
	title = {{SPATIAL} {HETEROGENEITY} {INFLUENCES} {NATIVE} {AND} {NONNATIVE} {PLANT} {SPECIES} {RICHNESS}},
	volume = {87},
	issn = {0012-9658},
	url = {http://www.esajournals.org/doi/abs/10.1890/0012-9658(2006)87%5B3186:SHINAN%5D2.0.CO%3B2},
	doi = {10.1890/0012-9658(2006)87[3186:SHINAN]2.0.CO;2},
	abstract = {Spatial heterogeneity may have differential effects on the distribution of native and nonnative plant species richness. We examined the effects of spatial heterogeneity on native and nonnative plant species richness distributions in the central part of Rocky Mountain National Park, Colorado, USA. Spatial heterogeneity around vegetation plots was characterized using landscape metrics, environmental/topographic variables (slope, aspect, elevation, and distance from stream or river), and soil variables (nitrogen, clay, and sand). The landscape metrics represented five components of landscape heterogeneity and were measured at four spatial extents (within varying radii of 120, 240, 480, and 960 m) using the FRAGSTATS landscape pattern analysis program. Akaike's Information Criterion adjusted for small sample size (AICc) was used to select the best models from a set of multiple linear regression models developed for native and nonnative plant species richness at four spatial extents and three levels of ecological hierarchy (i.e., landscape, land cover, and community). Both native and nonnative plant species richness were positively correlated with edge density, Simpson's diversity index and interspersion/juxtaposition index, and were negatively correlated with mean patch size. The amount of variation explained at four spatial extents and three hierarchical levels ranged from 30\% to 70\%. At the landscape level, the best models explained 43\% of the variation in native plant species richness and 70\% of the variation in nonnative plant species richness (240-m extent). In general, the amount of variation explained was always higher for nonnative plant species richness, and the inclusion of landscape metrics always significantly improved the models. The best models explained 66\% of the variation in nonnative plant species richness for both the conifer land cover type and lodgepole pine community. The relative influence of the components of spatial heterogeneity differed for native and nonnative plant species richness and varied with the spatial extent of analysis and levels of ecological hierarchy. The study offers an approach to quantify spatial heterogeneity to improve models of plant biodiversity. The results demonstrate that ecologists must recognize the importance of spatial heterogeneity in managing native and nonnative plant species.},
	number = {12},
	urldate = {2014-02-03TZ},
	journal = {Ecology},
	author = {Kumar, Sunil and Stohlgren, Thomas J. and Chong, Geneva W.},
	month = dec,
	year = {2006},
	keywords = {AIC, FRAGSTATS, Rocky Mountains, landscape metrics, model selection, native and nonnative plant species richness, spatial autocorrelation, spatial heterogeneity, spatial scales},
	pages = {3186--3199}
}

@article{chaparro_effect_2013,
	title = {Effect of {Spatial} {Heterogeneity} on {Zooplankton} {Diversity}: {A} {Multi}-{Scale} {Habitat} {Approximation} in a {Floodplain} {Lake}},
	copyright = {Copyright © 2013 John Wiley \& Sons, Ltd.},
	issn = {1535-1467},
	shorttitle = {Effect of {Spatial} {Heterogeneity} on {Zooplankton} {Diversity}},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/rra.2711/abstract},
	doi = {10.1002/rra.2711},
	abstract = {Environmental heterogeneity is an essential quality of ecosystems as it has important implications in community structure. Macrophytes are a main component of environmental heterogeneity in floodplain lakes, and their dynamics are highly influenced by water level changes. In this context, we analysed at different spatial scales the relationship among hydrological variations, environmental heterogeneity associated to macrophytes and zooplankton regional diversity (γ diversity) in a South American floodplain lake adjacent to the Paraná River, and we also compared the local zooplankton diversity (α diversity) among the different environments that comprised the lake heterogeneity. At very low waters, the environmental heterogeneity was reduced as the lake was mainly limited to open water areas with low zooplankton diversity. At high waters, the profuse vegetation development (emergent and free-floating), in mixed or homogeneous patches, determined a higher lake environmental heterogeneity with enhanced regional zooplankton diversity; littoral species increased over limnetic ones. Zooplankton α diversity was higher in environments with free-floating macrophytes than in those without these plants. The structural complexity in the water column provided by plant roots would be closely related to the enhanced diversity found under free-floating mats. This study contributes to the knowledge on the effects of strong water level variations on environmental heterogeneity, which is strongly associated to macrophytes and on zooplankton diversity, and highlights the role of free-floating plants as diversity hosts and ‘key structures’ in floodplain lakes. Copyright © 2013 John Wiley \& Sons, Ltd.},
	language = {en},
	urldate = {2014-02-03TZ},
	journal = {River Research and Applications},
	author = {Chaparro, G. and Kandus, P. and O'Farrell, I.},
	year = {2013},
	keywords = {diversity, macrophytes, remote sensing, spatial patterns, water level, zooplankton},
	pages = {n/a--n/a}
}

@article{brown_spatial_2003,
	title = {Spatial heterogeneity reduces temporal variability in stream insect communities},
	volume = {6},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2003.00431.x/abstract},
	doi = {10.1046/j.1461-0248.2003.00431.x},
	abstract = {Although all natural systems are heterogeneous, the direct influence of spatial heterogeneity on most ecological variables is unknown. In many systems, spatial heterogeneity is positively correlated with both microhabitat refugia and species richness. Both an increased number of microhabitat refugia and the effects of statistical averaging via increased species richness should lead to an inverse relationship between spatial heterogeneity and variability in community composition. To test this prediction, I measured diversity and temporal variability of invertebrate communities in a northern New Hampshire stream along a natural gradient of spatial heterogeneity formed by variation in stream substrates. On average, there was a 42\% decrease in community variability along a gradient of increasing heterogeneity. This pattern was robust to changes in metrics of both heterogeneity and community variability. There was also a significant positive relationship between taxon richness and spatial heterogeneity with predicted taxon richness increasing c. 1.5× along the heterogeneity gradient. By resampling community abundance data, I estimated that statistical averaging accounted for only 4\% of the observed decrease in community variability in this study. I concluded that the remaining decrease was very likely explained by a greater number of refugia from predation and/or flooding in high-heterogeneity habitats. The results of this study suggest that maximizing heterogeneity in ecological restoration programmes may promote temporally stable and diverse communities and may aid in responsible management of aquatic resources.},
	language = {en},
	number = {4},
	urldate = {2014-02-03TZ},
	journal = {Ecology Letters},
	author = {Brown, Bryan L.},
	year = {2003},
	keywords = {Temporal variability, benthic macroinvertebrates, community structure, refugia, spatial heterogeneity, species richness, statistical averaging, stream},
	pages = {316--325}
}

@article{golestani_speciation_2012,
	title = {Speciation with gene flow in a heterogeneous virtual world: can physical obstacles accelerate speciation?},
	volume = {279},
	issn = {0962-8452, 1471-2954},
	shorttitle = {Speciation with gene flow in a heterogeneous virtual world},
	url = {http://rspb.royalsocietypublishing.org/content/279/1740/3055},
	doi = {10.1098/rspb.2012.0466},
	abstract = {The origin of species remains one of the most controversial and least understood topics in evolution. While it is being widely accepted that complete cessation of gene-flow between populations owing to long-lasting geographical barriers results in a steady, irreversible increase of divergence and eventually speciation, the extent to which various degrees of habitat heterogeneity influences speciation rates is less well understood. Here, we investigate how small, randomly distributed physical obstacles influence the distribution of populations and species, the level of population connectivity (e.g. gene flow), as well as the mode and tempo of speciation in a virtual ecosystem composed of prey and predator species. We adapted an existing individual-based platform, EcoSim, to allow fine tuning of the gene flow's level between populations by adding various numbers of obstacles in the world. The platform implements a simple food chain consisting of primary producers, herbivores (prey) and predators. It allows complex intra- and inter-specific interactions, based on individual evolving behavioural models, as well as complex predator–prey dynamics and coevolution in spatially homogenous and heterogeneous worlds. We observed a direct and continuous increase in the speed of evolution (e.g. the rate of speciation) with the increasing number of obstacles in the world. The spatial distribution of species was also more compact in the world with obstacles than in the world without obstacles. Our results suggest that environmental heterogeneity and other factors affecting demographic stochasticity can directly influence speciation and extinction rates.},
	language = {en},
	number = {1740},
	urldate = {2014-01-13TZ},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Golestani, Abbas and Gras, Robin and Cristescu, Melania},
	month = aug,
	year = {2012},
	pmid = {22513856},
	keywords = {gene flow, heterogeneity, individual-based simulation, predator–prey system, speciation},
	pages = {3055--3064}
}

@article{silvertown_new_2009,
	title = {A new dawn for citizen science},
	volume = {24},
	issn = {0169-5347},
	url = {http://www.sciencedirect.com/science/article/pii/S016953470900175X},
	doi = {10.1016/j.tree.2009.03.017},
	abstract = {A citizen scientist is a volunteer who collects and/or processes data as part of a scientific enquiry. Projects that involve citizen scientists are burgeoning, particularly in ecology and the environmental sciences, although the roots of citizen science go back to the very beginnings of modern science itself.},
	number = {9},
	urldate = {2013-12-10TZ},
	journal = {Trends in Ecology \& Evolution},
	author = {Silvertown, Jonathan},
	month = sep,
	year = {2009},
	pages = {467--471}
}

@book{fiedler_environmental_2013,
	title = {The {Environmental} {Legacy} of the {UC} {Natural} {Reserve} {System}},
	isbn = {9780520953642},
	abstract = {The UC Natural Reserve System, established in 1965 to support field research, teaching, and public service in natural environments, has become a prototype of conservation and land stewardship looked to by natural resource managers throughout the world. From its modest beginnings of seven sites, the UC NRS has grown to encompass more than 750,000 wildland acres. This book tells the story of how a few forward-thinking UC faculty, who’d had their research plots and teaching spots destroyed by development and habitat degradation, devised a way to save representative examples of many of California’s major ecosystems. Working together with conservation-minded donors and landowners, with state and federal agencies, and with land trusts and private conservation organizations, they founded what would become the world’s largest university-administered natural reserve system—a legacy of lasting significance and utility. This lavishly illustrated volume, which includes images by famed photographers Ansel Adams and Galen Rowell, describes the natural and human histories of the system’s many reserves. Located throughout California, these wildland habitats range from coastal tide pools to inland deserts, from lush wetlands to ancient forests, and from vernal pools to oak savannas. By supporting teaching, research, and public service within such protected landscapes, the UC NRS contributes to the understanding and wise stewardship of the Earth.},
	language = {en},
	publisher = {University of California Press},
	author = {Fiedler, Peggy L. and Rumsey, Susan Gee and Wong, Kathleen M.},
	month = jan,
	year = {2013},
	keywords = {Nature / Ecology}
}

@misc{dolson_incorporating_2012,
	address = {Swarthmore College, Swarthmore, PA},
	type = {Poster},
	title = {Incorporating domain knowledge into {ACMI} ({Automated} {Crystallographic} {Map} {Interpretation})},
	author = {Dolson, Emily and Cho, Stella and Soni, Ameet},
	month = oct,
	year = {2012}
}

@misc{dolson_towards_2013,
	address = {Swarthmore College},
	type = {Poster},
	title = {Towards a unified model of {Fallopia} japonica ({Japanese} knotweed) 
growth and control by mechanical techniques},
	author = {Dolson, Emily},
	month = mar,
	year = {2013}
}

@misc{dolson_detecting_2013,
	address = {North Woodstock, NH},
	title = {Detecting errors and rare events in data streams from multiple sensors: insights from adaptive robotics},
	author = {Dolson,  Emily},
	month = jul,
	year = {2013}
}

@misc{dolson_introduction_2013,
	title = {Introduction},
	url = {http://intelligentecosystems.blogspot.com/b/layout-preview},
	urldate = {2013-07-04TZ},
	journal = {Intelligent (eco)systems},
	author = {Dolson, Emily},
	month = jul,
	year = {2013}
}

@article{drake_modelling_2006,
	title = {Modelling ecological niches with support vector machines},
	volume = {43},
	issn = {1365-2664},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2664.2006.01141.x/abstract},
	doi = {10.1111/j.1365-2664.2006.01141.x},
	abstract = {* 1The ecological niche is a fundamental biological concept. Modelling species’ niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species’ ranges. * 2A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species’ environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. * 3We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. * 4Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species’ potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.},
	language = {en},
	number = {3},
	urldate = {2013-05-18TZ},
	journal = {Journal of Applied Ecology},
	author = {Drake, John M. and Randin, Christophe and Guisan, Antoine},
	year = {2006},
	keywords = {ecological modelling, habitat, presence-only data, species distribution},
	pages = {424--432}
}

@article{snitting_heddleichthys_2009,
	title = {Heddleichthys– a new tristichopterid genus from the {Dura} {Den} {Formation}, {Midland} {Valley}, {Scotland} ({Famennian}, {Late} {Devonian})},
	volume = {90},
	copyright = {© 2009 The Author. Journal compilation © 2009 The Royal Swedish Academy of Sciences},
	issn = {1463-6395},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1463-6395.2008.00376.x/abstract},
	doi = {10.1111/j.1463-6395.2008.00376.x},
	abstract = {A new tristichopterid genus, Heddleichthys, from the Famennian of Scotland is described based on material previously assigned to a number of different genera, including Glyptopomus, Gyroptychius and Eusthenopteron. The validity of the new genus is established by a discussion of the reasons for the invalidity of the previous assignments. Heddleichthys is characterized by a combination of derived and primitive tristichopterid features. Derived features include the presence of symphyseal dentary fangs and premaxillary pseudofangs, a diamond-shaped symmetric caudal fin, a low posterodorsal expansion of the maxilla, and a posteriorly positioned kite-shaped pineal series. Primitive features include a postorbital and jugal contribution to the orbital margin and a parasphenoid with a ventral keel. External dermal bones are rather poorly preserved in the referred material, with few easily discernible sutures. The holotype specimen, a three-dimensionally preserved skull, was scanned by computed tomography to reveal well-preserved internal dermal bones, including entopterygoids, vomers and parasphenoid. There is no preserved endoskeletal material. As the first representative of derived tristichopterids described from Britain, Heddleichthys lends support to the idea that faunal dispersion between Gondwana and Laurussia in the Late Devonian was widespread. Derived tristichopterids have been described from all continents except South America. In contrast, the basal tristichopterids Eusthenopteron and Tristichopterus are still only described from Laurussia.},
	language = {en},
	urldate = {2013-05-18TZ},
	journal = {Acta Zoologica},
	author = {Snitting, Daniel},
	year = {2009},
	keywords = {Dura Den, Famennian, Heddleichthys, Late Devonian, Tristichopteridae},
	pages = {273--284}
}

@article{clement_new_2009,
	title = {A {New} {Tristichopterid} (sarcopterygii, {Tetrapodomorpha}) from the {Upper} {Famennian} {Evieux} {Formation} (upper {Devonian}) of {Belgium}},
	volume = {52},
	copyright = {© The Palaeontological Association},
	issn = {1475-4983},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1475-4983.2009.00876.x/abstract},
	doi = {10.1111/j.1475-4983.2009.00876.x},
	abstract = {Abstract: Additional material of a large specimen of tristichopterid fish from the Upper Famennian Evieux Formation of Belgium is described. This large fish was previously assigned to Tristichopteridae gen. et sp. indet. due to the lack of diagnostic anatomical data. New available material consists of the internal surface of the parietal shield, vomers and anterior part of the parasphenoid, subopercular and submandibulo-branchiostegal bones, and an internal view of the anterior part of the mandible. A possible autapomorphy of the new form from Belgium, Langlieria socqueti gen. nov. et sp. nov., is the absence of marginal teeth on the vomer except on its most lateral part. Apart from these features, it only differs from the genus Mandageria from Australia in the absence of marginal teeth between the dentary fang and the mandibular symphysis, in the presence of a raised marginal crest lateral to the anterior coronoid fang, and in the presence of numerous small marginal teeth on the premaxilla. It differs from the cosmopolitan genus Eusthenodon in a number of respects: the supratemporal, tabular, and postparietal bones are superficially fused, as are the intertemporal and parietal bones, the dermal ornament is proportionally very fine, and the denticulated field of the parasphenoid stands proud rather than being recessed into the body of the bone.},
	language = {en},
	number = {4},
	urldate = {2013-05-17TZ},
	journal = {Palaeontology},
	author = {Clement, Gaël and Snitting, Daniel and Ahlberg, Per Erik},
	year = {2009},
	keywords = {Belgium, Late Devonian, Tetrapodomorpha, Tristichopteridae, biogeography, phylogeny},
	pages = {823--836}
}

@article{bashtanova_physiological_2009,
	title = {Physiological approaches to the improvement of chemical control of {Japanese} knotweed ({Fallopia} japonica).},
	volume = {57},
	doi = {10.1614/WS-09-069.1},
	abstract = {Japanese knotweed is an aggressive alien species in Europe, North America, and Australia, causing a range of environmental problems. Eradication of Japanese knotweed is proving to be a difficult task, because the plant is able to propagate generatively by intra- and interspecific hybridization, and vegetatively from shoot and tiny rhizome pieces. Despite the economic consequences of Japanese knotweed on natural and built environments, its physiology is not yet fully understood; especially important are sink-source relations between old and young parts of the rhizome and growth of lateral and latent rhizome buds. Current methods of chemical control include three types of phloem-mobile herbicides, such as glyphosate, imazapyr, and synthetic auxins. These herbicides have limitations on their use, and all fail to eradicate the plant completely, for the reasons discussed in this review. Our aim is to suggest prospective approaches to enable chemical eradication: use of signals to induce controlled growth and development of quiescent rhizome buds; use of phytohormones, sugars, and light to increase allocation of phloem-mobile herbicides to the rhizome; use of xylem-mobile herbicides to exterminate the old rhizome parts; and use of different phloem-mobile herbicides at different growth stages.},
	language = {English},
	number = {6},
	journal = {Weed Science},
	author = {Bashtanova, U. B. and Beckett, K. P. and Flowers, T. J.},
	year = {2009},
	pages = {584--592}
}

@article{pedregosa_scikit-learn:_2011,
	title = {Scikit-learn: {Machine} {Learning} in {Python}},
	volume = {12},
	journal = {Journal of Machine Learning Research},
	author = {Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
	year = {2011},
	pages = {2825--2830}
}

@article{monsi_factor_2005,
	title = {On the {Factor} {Light} in {Plant} {Communities} and its {Importance} for {Matter} {Production}},
	volume = {95},
	issn = {0305-7364, 1095-8290},
	url = {http://aob.oxfordjournals.org/content/95/3/549},
	doi = {10.1093/aob/mci052},
	language = {en},
	number = {3},
	urldate = {2013-04-25TZ},
	journal = {Annals of Botany},
	author = {Monsi, Masami and Saeki, Toshiro},
	month = feb,
	year = {2005},
	pages = {549--567}
}

@misc{bochkanov_alglib_nodate,
	title = {{ALGLIB}},
	url = {www.alglib.net},
	author = {Bochkanov, Sergey and Bystritsky, Vladimir}
}

@article{perez_ipython:_2007,
	title = {{IPython}: a {System} for {Interactive} {Scientific} {Computing}},
	volume = {9},
	url = {http://ipython.org},
	number = {3},
	journal = {Comput. Sci. Eng.},
	author = {Pérez, Fernando and Granger, Brian E.},
	month = may,
	year = {2007},
	pages = {21--29}
}

@article{velleman_datadesk:_2012,
	title = {{DataDesk}: an interactive package for data exploration, display, model building, and data analysis},
	volume = {4},
	copyright = {Copyright © 2012 Wiley Periodicals, Inc.},
	issn = {1939-0068},
	shorttitle = {{DataDesk}},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/wics.1208/abstract},
	doi = {10.1002/wics.1208},
	abstract = {DataDesk is an interactive package for exploration, display, and analysis of data that runs on a variety of desktop computers. Because it has been designed from the ground up for the purpose of data exploration, it incorporates several global design principles not found together in other data analysis software. This article discusses those design principles and illustrates how they lead to innovative approaches to regression model building. WIREs Comput Stat 2012. doi: 10.1002/wics.1208},
	language = {en},
	number = {4},
	urldate = {2013-04-25TZ},
	journal = {Wiley Interdisciplinary Reviews: Computational Statistics},
	author = {Velleman, Paul F.},
	year = {2012},
	keywords = {exploratory data analysis, plot brushing, plot rotation, regression model building},
	pages = {407--414}
}

@article{thomson_faunal_1976,
	title = {The {Faunal} {Relationships} of {Rhipidistian} {Fishes} ({Crossopterygii}) from the {Catskill} ({Upper} {Devonian}) of {Pennsylvania}},
	volume = {50},
	copyright = {Copyright © 1976 SEPM Society for Sedimentary Geology},
	issn = {0022-3360},
	url = {http://www.jstor.org/stable/1303562},
	doi = {10.2307/1303562},
	abstract = {Comparison of the occurrence and distribution of rhipidistian fishes from the Upper Old Red Sandstone ("Catskill") of Pennsylvania confirms that they belong to a widely distributed fauna common to North America, Greenland, Scotland and the Baltic Province. Holoptychius, Eusthenodon and Glyptopomus are the most widely distributed genera, whereas Hyneria, Sterropterygion and Sauripterus are not known outside the Appalachian Basin. Eusthenopteron does not occur in North America after the Frasnian. New records are given for Eusthenodon wängsö, material tentatively referred to Eusthenodon, Holoptychius sp., cf. Sterropterygion and an undetermined osteolepid taxon. It is possible that the presence or absence of cosmine-bearing fishes in rhipidistian assemblages may reflect the nature of the environment.},
	number = {6},
	urldate = {2013-02-18TZ},
	journal = {Journal of Paleontology},
	author = {Thomson, Keith Stewart},
	month = nov,
	year = {1976},
	note = {ArticleType: research-article / Full publication date: Nov., 1976 / Copyright © 1976 SEPM Society for Sedimentary Geology},
	pages = {1203--1208}
}

@inproceedings{bulusu_scalable_2001,
	title = {Scalable coordination for wireless sensor networks: self-configuring localization systems},
	shorttitle = {Scalable coordination for wireless sensor networks},
	url = {http://gicl.cs.drexel.edu/people/regli/Classes/CS680/Papers/Sensor%20Nets/iscta-2001.pdf},
	urldate = {2013-02-15TZ},
	booktitle = {International {Symposium} on {Communication} {Theory} and {Applications} ({ISCTA} 2001), {Ambleside}, {UK}},
	author = {Bulusu, Nirupama and Estrin, Deborah and Girod, Lewis and Heidemann, John},
	year = {2001}
}

@book{newberry_paleozoic_1889,
	title = {The {Paleozoic} {Fishes} of {North} {America}},
	language = {en},
	publisher = {U.S. Government Printing Office},
	author = {Newberry, John Strong},
	year = {1889}
}

@article{daeschler_late_2011,
	title = {Late {Devonian} paleontology and paleoenvironments at {Red} {Hill} and other fossil sites in the {Catskill} {Formation} of north-central {Pennsylvania}},
	volume = {20},
	url = {http://books.google.com/books?hl=en&lr=&id=ELq09RwIiSsC&oi=fnd&pg=PA1&ots=mb2xch1K4o&sig=cUwIZc2qe_tgeFBcveC6sPSJrCg},
	urldate = {2013-02-11TZ},
	journal = {Field Guides},
	author = {Daeschler, E. B. and Cressler, W. L.},
	year = {2011},
	pages = {1--16}
}

@book{ruffolo_shield_2011,
	title = {From the {Shield} to the {Sea}: {Geological} {Field} {Trips} from the 2011 {Joint} {Meeting} of the {Gsa} {Northeastern} and {North}-{Central} {Sections}},
	isbn = {9780813700205},
	shorttitle = {From the {Shield} to the {Sea}},
	abstract = {Features field guides and descriptions of eight geological field trips of the area near Pittsburgh, Pennsylvania. The trips highlight the region's geology from eastern Ohio to the Central Appalachian Valley and Ridge.},
	language = {en},
	publisher = {Geological Society of America},
	author = {Ruffolo, Richard M.},
	month = apr,
	year = {2011},
	keywords = {Science / Earth Sciences / Geology, Science / Earth Sciences / Sedimentology \& Stratigraphy}
}

@article{ovono_effects_2009,
	title = {Effects of reducing sugar concentration on in vitro tuber formation and sprouting in yam ({Dioscorea} cayenensis–{D}. rotundata complex)},
	volume = {99},
	issn = {0167-6857, 1573-5044},
	url = {http://link.springer.com/article/10.1007/s11240-009-9575-1},
	doi = {10.1007/s11240-009-9575-1},
	abstract = {The effects of reducing sucrose level on tuber formation (\% of cultures with microtubers), development (length and fresh weight of microtubers) and sprouting in yam Dioscorea cayenensis–D. rotundata complex in vitro were investigated. Only 29\% of the explants showed tuber formation after 3 weeks in the presence of 1\% sucrose in contrast to 100\% with 3\%. After 120 days of culture, the length and the weight of the tubers obtained in the presence of 1\% sucrose were less than with 3\% sucrose. Addition of sorbitol to keep osmolarity at the same level did not restore normal rate of tuber formation. Similar results were obtained with the use of reduced fructose or glucose level. Microtuber sprouting was also affected by sucrose level incorporated into the tuberisation medium. Tubers obtained on reduced sucrose level sprouted later and the increase of osmolarity with sorbitol did not restore normal sprouting. The bigger tubers obtained on high sucrose media could contain more carbohydrate reserves that could partially explain a higher sprouting rate. These results can be used for optimising in vitro conditions for mass production of microtubers in yam and especially in Dioscorea cayenensis–D. rotundata complex, a very important species in West Africa. They specially showed the importance of tuberisation conditions on precocity of tuberisation, on tuber length and weight and on their further sprouting.},
	language = {en},
	number = {1},
	urldate = {2013-01-23TZ},
	journal = {Plant Cell, Tissue and Organ Culture (PCTOC)},
	author = {Ovono, Paul Ondo and Kevers, Claire and Dommes, Jacques},
	month = oct,
	year = {2009},
	keywords = {Dioscorea cayenensis–D. rotundata, Microtubers, Plant Genetics \& Genomics, Plant Pathology, Plant Physiology, Plant Sciences, Sucrose, Yam, sprouting},
	pages = {55--59}
}

@article{pak_importance_1995,
	title = {Importance of dormancy and sink strength in sprouting of onions ({Allium} cepa) during storage},
	volume = {94},
	issn = {1399-3054},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.1995.tb05312.x/abstract},
	doi = {10.1111/j.1399-3054.1995.tb05312.x},
	abstract = {In onion (Allium cepa L.) postponement of sprouting is necessary to achieve long term storage. We studied the factors determining sprouting during dry storage at 16°C. The period to visible sprouting depends on the length of the dormancy period, if present, and on the growth rate of the sprout. In the three cultivars tested, sprouts were initiated within 2 weeks after harvest indicating the absence of a real dormancy period. Sprout length increased linearly during storage. The mitotic activity of the apex decreased before harvest, was low at the transition from scale to leaf formation, and increased again when the sprout was initiated. From a few weeks before harvest, the initially high fructan content of the scales decreased, leading to a large increase in fructose. The sprout always contained enough carbohydrates for growth (between 50 and 60 mg g−1 dry weight, of which 30\% was fructan). The activity of sucrose synthase (EC 2.4.1.13) increased as the sprout grew, indicating an increase in sink strength. Invertase (EC 3.2.1.26) was absent in all bulb organs, during the various developmental stages. Although carbohydrates and enzymes were available for fast sprouting, sprout growth was still linear instead of exponential during dry storage at temperatures favorable for growth (16°C). The relative importance of factors determining sprouting are discussed.},
	language = {en},
	number = {2},
	urldate = {2013-01-23TZ},
	journal = {Physiologia Plantarum},
	author = {Pak, Caroline and van der Plas, Linus H. W. and de Boer, A. Douwe},
	year = {1995},
	keywords = {Allium cepa, carbohydrate metabolism, dormancy, fructan, mitotic index, onion, sink strength, sprouting, storage},
	pages = {277--283}
}
@article{bailey_reproductive_1994,
	title = {Reproductive biology and fertility of {Fallopia} japonica ({Japanese} knotweed) and its hybrids in the {British} {Isles}.},
	abstract = {The reproductive biology by F. japonica [Reynoutria japonica] is discussed, with particular reference to hybrids and hybridization, seed production, viability of seed and the establishment of seedlings. Since R. japonica cannot reproduce sexually in the UK because of the absence of male-female clones, spread was concluded to be by vegetative means.},
	language = {English},
	author = {Bailey, J. P.},
	year = {1994},
	pages = {141--158}
}

@article{bailey_asexual_2008,
	title = {Asexual spread versus sexual reproduction and evolution in {Japanese} {Knotweed} s.l. sets the stage for the “{Battle} of the {Clones}”},
	volume = {11},
	issn = {1387-3547, 1573-1464},
	url = {http://www2.le.ac.uk/departments/biology/people/bailey/publications},
	doi = {10.1007/s10530-008-9381-4},
	number = {5},
	urldate = {2013-01-23TZ},
	journal = {Biological Invasions},
	author = {Bailey, John P. and Bímová, Kateřina and Mandák, Bohumil},
	month = oct,
	year = {2008},
	pages = {1189--1203}
}

@article{skinner_planting_2012,
	title = {Planting {Native} {Species} to {Control} {Site} {Reinfestation} by {Japanese} {Knotweed} ({Fallopia} japonica)},
	volume = {30},
	url = {http://er.uwpress.org/content/30/3/192.short},
	number = {3},
	urldate = {2013-01-23TZ},
	journal = {Ecological Restoration},
	author = {Skinner, R. H. and van der Grinten, M. and Gover, A. E.},
	year = {2012},
	pages = {192--199}
}

@article{delbart_can_2012,
	title = {Can {Land} {Managers} {Control} {Japanese} {Knotweed}? {Lessons} from {Control} {Tests} in {Belgium}},
	volume = {50},
	issn = {0364-152X, 1432-1009},
	shorttitle = {Can {Land} {Managers} {Control} {Japanese} {Knotweed}?},
	url = {http://link.springer.com/article/10.1007/s00267-012-9945-z},
	doi = {10.1007/s00267-012-9945-z},
	abstract = {Japanese knotweed Fallopia japonica is an extremely abundant invasive plant in Belgium and surrounding countries. To date, no eradication method is available for land managers facing the invasion of this rhizomatous plant. We tested different chemical herbicides with two application methods (spraying and stem injection), as well as mechanical treatments, on knotweed clones throughout southern Belgium. The tested control methods were selected to be potentially usable by managers, e.g., using legally accepted rates for herbicides. Stem volume, height and density reduction were assessed after one or two years, depending on the control method. Labor estimations were made for each control method. No tested control method completely eradicated the clones. Stem injection with glyphosate-based herbicide (3.6 kg ha−1 of acid equivalent glyphosate) caused the most damage, i.e., no sprouting shoots were observed the year following the injection. The following year, though, stunted shoots appeared. Among the mechanical control methods, repeated cuts combined with native tree transplanting most appreciably reduced knotweed development. The most efficient methods we tested could curb knotweed invasion, but are not likely to be effective in eradicating the species. As such, they should be included in a more integrated restoration strategy, together with prevention and public awareness campaigns.},
	language = {en},
	number = {6},
	urldate = {2013-01-23TZ},
	journal = {Environmental Management},
	author = {Delbart, Emmanuel and Mahy, Grégory and Weickmans, Bernard and Henriet, François and Crémer, Sébastien and Pieret, Nora and Vanderhoeven, Sonia and Monty, Arnaud},
	month = dec,
	year = {2012},
	keywords = {Atmospheric Protection/Air Quality Control/Air Pollution, Control, Ecology, Environmental Management, Fallopia japonica, Forestry Management, Herbicide, Invasive plant management, Nature Conservation, Polygonum cuspidatum, Reynoutria japonica, Stem-injection, Waste Water Technology / Water Pollution Control / Water Management / Aquatic Pollution},
	pages = {1089--1097}
}

@article{seiger_mechanical_1997,
	title = {Mechanical control of {Japanese} knotweed ({Fallopia} japonica [{Houtt}.] {Ronse} {Decraene}): effects of cutting regime on rhizomatous reserves.},
	volume = {17},
	shorttitle = {Mechanical control of {Japanese} knotweed ({Fallopia} japonica [{Houtt}.] {Ronse} {Decraene})},
	abstract = {Fallopia japonica [Reynoutria japonica] is an invasive exotic species that spreads by an extensive rhizome system, but does not reproduce by seed outside of its native range. Greenhouse experiments explored the effectiveness of cutting as a control measure. Patterns of biomass allocation to above- and below-ground portions of uncut plants over a growing season were monitored, and cutting experiments were performed to determine the effects on below-ground biomass of cutting, timing of cutting, time interval between cuts, and multiple cuts. The allocation to below-ground biomass was continuous during the growing season, with the total below-ground biomass exceeding the above-ground biomass in the latter half of the growing season. Cut plants had significantly less below-ground biomass accumulation at the end of the growing season compared to uncut controls. Rhizome biomass at the end of the growing season was inversely related to the number of cuts. With 1, 2, and 3 cuts, below-ground biomass was 65, 31 and 13\%, respectively, of uncut controls. Regression analysis predicted that a minimum of 4 cuts are needed during a single growing season to cause a net depletion of below-ground biomass. The timing of cutting does not appear to be critical as long as it is done at least 7 weeks prior to senescence. Given its continuous allocation to rhizomes and its ability to sprout from as little as 7 g of rhizome, it is unlikely that F. japonica can be eradicated by cutting alone.},
	language = {English},
	number = {4},
	journal = {Natural Areas Journal},
	author = {Seiger, L. A. and Merchant, H. C.},
	year = {1997},
	pages = {341--345}
}

@article{melander_direct_2012,
	title = {Direct control of perennial weeds between crops – {Implications} for organic farming},
	volume = {40},
	issn = {0261-2194},
	url = {http://www.sciencedirect.com/science/article/pii/S0261219412001299},
	doi = {10.1016/j.cropro.2012.04.029},
	abstract = {Perennial weeds can be a major constraint to organic crop production and direct control actions applied between crops can then be necessary to reduce the problems. We conducted two experiments, one on a sandy loam and one on a sandy soil in Denmark, with the aim of studying the efficacy of different implement types and strategies. The treatments were employed against mixed stands of perennials after harvest of spring barley in two consecutive years. Time of treatment, cultivation depth and combinations of implements constituted the strategies. Treatment effects were evaluated in the growing season that followed the post-harvest treatments. In the one experiment, repeated tine cultivation caused an 80–90\% annual reduction of the population of mainly Cirsium arvense. With treatments conducted in two consecutive years, the accumulated effects reached 99\% control. In the second experiment, power take-off driven implements with rotating weeding devices demonstrated similar control efficacies against a mixed stand composing C. arvense, Tussilago farfara, Elytrigia repens and Artemisia vulgaris. One pass was conducted a week after barley harvest followed by another pass 3 weeks later and ending the strategy with mouldboard ploughing in the succeeding spring. Grain yields did not differ among the treatments in the two experiments as a result of the generally high effectiveness exerted by the control strategies. Especially post-harvest control strategies based on rotating weed devices and mouldboard ploughing appear to be effective solutions against mixed stands of perennials on sandy soils but they do not comply with optimal nutrient management in organic cropping. Therefore, intensive autumn cultivation is only relevant where a perennial weed problem is uncontrollable by other means.},
	urldate = {2013-01-22TZ},
	journal = {Crop Protection},
	author = {Melander, Bo and Holst, Niels and Rasmussen, Ilse Ankjær and Hansen, Preben Klarskov},
	month = oct,
	year = {2012},
	keywords = {Cirsium arvense, Elytrigia repens, Mechanical weed control, Sonchus arvensis, Tussilago farfara},
	pages = {36--42}
}

@article{spencer_soluble_2001,
	title = {Soluble sugar concentrations associated with tuber and winter bud sprouting},
	volume = {39},
	issn = {0146-6623},
	abstract = {Many aquatic weeds rely on vegetative structures for survival and propagation, rather than seeds. American pondweed (Potamogeton nodosus Poiret) winter buds, and hydrilla (Hydrib la verticillata (L.f.) Royle, monoecious and dioecious types) tubers were allowed to sprout in water in the dark. At two-to-three day intervals individual propagules and dependent shoots were analyzed for soluble sugars. There was a significant decline in propagule fresh weight over time indicating mobilization of stored materials. Sucrose was the most abundant in all the propagules, but found in higher soluble concentrations in American pondweed winter buds than in hydrilla propagules. Fructose, glucose, raffinose, and sucrose were present in American pondweed, and hydrilla. Stachyose was present in all except dioecious hydrilla and sorbitol was not detected. During sprouting, soluble sugar concentrations decreased within the original propagule and increased in shoots for hydrilla biotypes. Fructose and glucose concentrations were greater in newly formed shoots than in winter buds of American pondweed by day 14 and in hydrilla shoots versus propagules by day 22. The striking increases in concentrations of these soluble sugars in propagules and newly emergent leaf tissue suggest that starch hydrolysis is a key metabolic control point during sprouting.},
	language = {English},
	journal = {JOURNAL OF AQUATIC PLANT MANAGEMENT},
	author = {Spencer, DF and Ryan, FJ and Aung, L and Ksander, GG},
	month = jan,
	year = {2001},
	note = {40th Annual Meeting of the Aquatic-Plant-Management-Society, SAN DIEGO, CALIFORNIA, JUL 16-20, 2000},
	keywords = {aquatic weeds, hydrilla, physiological ecology, pondweeds},
	pages = {45--47}
}

@article{onoda_seasonal_2005,
	title = {Seasonal change in the balance between capacities of {RuBP} carboxylation and {RuBP} regeneration affects {CO}2 response of photosynthesis in {Polygonum} cuspidatum},
	volume = {56},
	issn = {0022-0957, 1460-2431},
	url = {http://jxb.oxfordjournals.org/content/56/412/755},
	doi = {10.1093/jxb/eri052},
	abstract = {The balance between the capacities of RuBP (ribulose-1,5-bisphosphate) carboxylation (Vcmax) and RuBP regeneration (expressed as the maximum electron transport rate, Jmax) determines the CO2 dependence of the photosynthetic rate. As it has been suggested that this balance changes depending on the growth temperature, the hypothesis that the seasonal change in air temperature affects the balance and modulates the CO2 response of photosynthesis was tested. Vcmax and Jmax were determined in summer and autumn for young and old leaves of Polygonum cuspidatum grown at two CO2 concentrations (370 and 700 μmol mol−1). Elevated CO2 concentration tended to reduce both Vcmax and Jmax without changing the Jmax:Vcmax ratio. The seasonal environment, on the other hand, altered the ratio such that the Jmax:Vcmax ratio was higher in autumn leaves than summer leaves. This alternation made the photosynthetic rate more dependent on CO2 concentration in autumn. Therefore, when photosynthetic rates were compared at growth CO2 concentration, the stimulation in photosynthetic rate was higher in young-autumn than in young-summer leaves. In old-autumn leaves, the stimulation of photosynthesis brought by a change in the Jmax:Vcmax ratio was partly offset by accelerated leaf senescence under elevated CO2. Across the two seasons and the two CO2 concentrations, Vcmax was strongly correlated with Rubisco and Jmax with cytochrome f content. These results suggest that seasonal change in climate affects the relative amounts of photosynthetic proteins, which in turn affect the CO2 response of photosynthesis.},
	language = {en},
	number = {412},
	urldate = {2013-01-22TZ},
	journal = {Journal of Experimental Botany},
	author = {Onoda, Yusuke and Hikosaka, Kouki and Hirose, Tadaki},
	month = feb,
	year = {2005},
	keywords = {Allocation of photosynthetic proteins, Jmax, Rubisco, Vcmax, cytochrome f, seasonality, stimulation of photosynthesis, temperature acclimation},
	pages = {755--763}
}

@article{emeneker_modeling_nodate,
	title = {On modeling contention for shared caches in multi-core processors with techniques from ecology},
	issn = {1567-7818, 1572-9796},
	url = {http://link.springer.com/article/10.1007/s11047-012-9348-3},
	doi = {10.1007/s11047-012-9348-3},
	abstract = {Multi-core x86\_64 processors introduced an important change in architecture, a shared last level cache. Historically, each processor has had access to a large private cache that seamlessly and transparently (to end users) interfaced with main memory. Previously, processes or threads only had to compete for memory bandwidth, but now they are competing for actual space. Competition for space and environmental resources is a problem studied in other scientific domains. This paper introduces methods from ecology to model multi-core cache usage with the competitive Lotka–Volterra equations. A model is presented and validated for characterizing the interaction of cores through shared caching, and for predicting the degree to which different workloads will interfere with each others’ execution from cache contention.},
	language = {en},
	urldate = {2013-01-03TZ},
	journal = {Natural Computing},
	author = {Emeneker, Wesley and Apon, Amy},
	keywords = {Artificial Intelligence (incl. Robotics), Evolutionary Biology, Lotka–Volterra, Multi-core cache, Performance modeling, Performance profiling, Processor Architectures, Shared cache, Statistical Physics, Dynamical Systems and Complexity, Theory of Computation},
	pages = {1--18}
}

@book{hardacre_marketing_1999,
	title = {Marketing the {Menacing} {Fetus} in {Japan}},
	isbn = {9780520216549},
	abstract = {Helen Hardacre provides new insights into the spiritual and cultural dimensions of abortion debates around the world in this careful examination of mizuko kuyo--a Japanese religious ritual for aborted fetuses. Popularized during the 1970s, when religious entrepreneurs published frightening accounts of fetal wrath and spirit attacks, mizuko kuyo offers ritual atonement for women who, sometimes decades previously, chose to have abortions. As she explores the complex issues that surround this practice, Hardacre takes into account the history of Japanese attitudes toward abortion, the development of abortion rituals, the marketing of religion, and the nature of power relations in intercourse, contraception, and abortion.Although abortion in Japan is accepted and legal and was commonly used as birth control in the early postwar period, entrepreneurs used images from fetal photography to mount a surprisingly successful tabloid campaign to promote mizuko kuyo. Enthusiastically adopted by some religionists as an economic strategy, it was soundly rejected by others on doctrinal, humanistic, and feminist grounds.In four field studies in different parts of the country, Helen Hardacre observed contemporary examples of mizuko kuyo as it is practiced in Buddhism, Shinto, and the new religions. She also analyzed historical texts and contemporary personal accounts of abortion by women and their male partners and conducted interviews with practitioners to explore how a commercialized ritual form like mizuko kuyo can be marketed through popular culture and manipulated by the same forces at work in the selling of any commodity. Her conclusions reflect upon the deep current of misogyny and sexism running through these rites and through feto-centric discourse in general.},
	language = {en},
	publisher = {University of California Press},
	author = {Hardacre, Helen},
	month = apr,
	year = {1999},
	keywords = {Business \& Economics / Marketing / General, Religion / Buddhism / Rituals \& Practice, Religion / Christian Rituals \& Practice / General, Religion / Comparative Religion, Religion / Eastern, Religion / General, Social Science / Abortion \& Birth Control, Social Science / Anthropology / Cultural, Social Science / Gender Studies}
}

@article{selby_comparative_nodate,
	title = {A {Comparative} {Examination} of {Coded} {Women}’s {Roles} in the {Tokugawa} and {Meiji} {Periods}},
	url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.122.849&rep=rep1&type=pdf#page=36},
	urldate = {2012-12-21TZ},
	journal = {By Neil Wilson, Editor in Chief},
	author = {Selby, E.},
	pages = {36}
}

@incollection{noriko_kawahashi_re-imagining_2012,
	title = {Re-imagining {Buddhist} women in contemporary {Japan}},
	isbn = {9789004234352},
	abstract = {Representing work by some of the leading scholars in the field, this volume presents important topics in the religious environment of contemporary Japan by surveying exciting trends, religious change and innovation, and the interactivity of religion with market and global forces.},
	language = {en},
	booktitle = {Handbook of {Contemporary} {Japanese} {Religions}},
	publisher = {BRILL},
	author = {{Noriko Kawahashi}},
	month = sep,
	year = {2012},
	keywords = {Religion / General},
	pages = {197--212}
}

@incollection{fujimura-fanselow_womens_1995,
	title = {Women's place and image in {Japanese} {Buddhism}},
	isbn = {9781558610941},
	abstract = {This volume presents, for the first time ever, a wide-ranging collection of essays on women in Japanese society written by Japanese women themselves. Drawing upon their day-to-day experiences as daughters, sisters, wives, mothers, students, and professionals living and working in Japanese society, Japanse scholars/writers describe and analyze the historical background, current status, and future prospects for Japanese women. Essays focus on the family, language, art, education, religion, the work place, and politics, and highlight the changes in attitudes and consciousness that are taking place in Japan today. This body of scholarship is unrivaled in scope; there is no comparable collection.  *Included in Japanese Women* -Historian Sachiko Kaneko describes the struggle for women's suffrage and changes in the family system from the Meiji period through the late twentieth century in "The Struggle for Legal Rights and Reform." -Orie Endo, in "Aspects of Sexism in the Japanese Language," analyzes unequal gender status and relationships in the language. -Midori Wakakuwa reveals how "Three Women Artists of the Meiji Period (1868-1912)" escaped the confines of the paternalistic family system. -In "Pornographic Culture and Sexual Violence," Kuniko Funabashi studies mass-produced visual media and discusses false notions of femininity and masculinity that have shaped behavior and promoted sexual violence in Japan. -Mioko Fujeida profiles key figures in the early feminist movement during the Meiji-Taisho period in "Japan's First Phase of Feminism."},
	language = {en},
	booktitle = {Japanese {Women}: {New} {Feminist} {Perspectives} on the {Past}, {Present}, and {Future}},
	publisher = {Feminist Press at CUNY},
	author = {Haruko, Okano},
	editor = {Fujimura-Fanselow, Kumiko and Kameda, Atsuko},
	year = {1995},
	keywords = {History / Asia / Japan, Literary Collections / Essays, Social Science / Feminism \& Feminist Theory, Social Science / General, Social Science / Women's Studies},
	pages = {15--27}
}

@incollection{kanami_sotoba_2000,
	title = {Sotoba {Komachi}},
	isbn = {9781891369193},
	abstract = {Preface Going out for a long walk, the nineteenth-century novelist and essayist Robert Louis Stevenson would bring with him the classic English walking essay, William Hazlitt's "On Going a Journey" (1821), about which he claimed, passionately if dogmatically, it is "so good that there should be a tax levied on all who have not read it." Imagine being so taken with an essay on walking! But history, at least of a past two hundred years, reveals that walkers have loved to read about their passion; and-given the perennial market for magazine essays and fictions, poems, and novels either describing a walk or set on a walk-that non-walking readers also like to imagine life occurring on the path or pavement. The three editors have in common a love of walking and love of the literature of walking. We are all university scholars who have written books on literature and walking, and through this last connection have come to know one another. The mutually infectious nature of the subject and our dedication to it led to the present volume. To this end we have walked the streets of Manhattan and around the Central Park Reservoir, huddled in a Chicago hotel room, and tramped the bluffs on the Northern California coast, culling from memory our favorite walking pieces from the great collective wellspring of human writing. We have composed our anthology for both pedestrian and non-pedestrian readers. Is there a person alive, except for the physically disabled, who is not a walker? Everyone walks, but we address those wholovewalking, either on the ground or in the imagination. When about 100 years ago he compiledThe Lore of the Wanderer: An Open-Air Anthology, a small plain blue-covered book one could put in a back pocket, George Goodchild-in perhaps the first of a substantial cluster of such collections-caught the spirit of our end-of-this-century volume: a book (a companion) to be taken with you; or, if you cannot get out for a walk, you can read one at home. There are, however, important differences between Goodchild's collection and ours. By "Open-Air" he meant the air of the country-side far from the polluting enclosures of the city. By insisting upon walking as a rural pleasure, Goodchild bl},
	language = {en},
	booktitle = {The {Walker}'s {Literary} {Companion}},
	publisher = {Breakaway Books},
	author = {Kanami, Kiyotsugu},
	editor = {{Roger Gilbert} and Robinson, Jeffrey Cane and Wallace, Anne D.},
	translator = {Brock, Sam},
	month = may,
	year = {2000},
	keywords = {Fiction / General, Health \& Fitness / Exercise, Literary Collections / Essays, Literary Collections / General, Literary Criticism / Reference, Sports \& Recreation / Walking},
	pages = {218--224}
}

@book{kanami_sotoba_nodate,
	title = {Sotoba {Komachi}},
	language = {en},
	author = {Kanami}
}

@article{norgren_abortion_1998,
	title = {Abortion before {Birth} {Control}: {The} {Interest} {Group} {Politics} {Behind} {Postwar} {Japanese} {Reproduction} {Policy}},
	volume = {24},
	copyright = {Copyright © 1998 The Society for Japanese Studies},
	issn = {0095-6848},
	shorttitle = {Abortion before {Birth} {Control}},
	url = {http://www.jstor.org/stable/132939},
	doi = {10.2307/132939},
	abstract = {Why is Japanese abortion policy liberal, whereas contraception policy is conservative? The government legalized late-term abortions in 1948 but has not yet approved oral contraception (the pill). This paper argues that the contradictory policies are products of very different interest group configurations and historical circumstances. Doctors and family planners used a small window of opportunity to legalize abortion; afterward, doctors and women battled religious groups to uphold the law. The pill first appeared at a historically inauspicious time, and the pharmaceutical industry was its lone champion: until recently, doctors, midwives, family planners, and women opposed the pill as a threat to their livelihoods, abortion rights, and women's health.},
	number = {1},
	urldate = {2012-12-21TZ},
	journal = {Journal of Japanese Studies},
	author = {Norgren, Tiana},
	month = jan,
	year = {1998},
	note = {ArticleType: research-article / Full publication date: Winter, 1998 / Copyright © 1998 The Society for Japanese Studies},
	pages = {59--94}
}

@book{yu_gendered_2009,
	title = {Gendered {Trajectories}: {Women}, {Work}, and {Social} {Change} in {Japan} and {Taiwan}},
	isbn = {9780804760096},
	shorttitle = {Gendered {Trajectories}},
	abstract = {Gendered Trajectories explores why industrial societies vary in the pace at which they reduce gender inequality and compares changes in women's employment opportunities in Japan and Taiwan over the last half-century. Japan has undergone much less improvement in women's economic status than Taiwan, despite its more advanced economy and greater welfare provisions. The difference is particularly puzzling because the two countries share many institutional practices and values.Drawing on historical trends, survey statistics, and personal interviews with people in both countries, Yu shows how country-specific organizational arrangements and industrial policies affect women's employment. In particular, the conditions faced by Japanese and Taiwanese women in the workplace have a profound effect on their labor force participation at critical points in their lives. Women's lifetime employment decisions in turn shape the divergent trajectories in gender equality.Few studies documenting the development of women's economic lives are based on non-Western societies and even fewer adopt a comparative perspective. This perceptive work demonstrates and underscores the importance of understanding gender inequality as a long-term, dynamic social process.},
	language = {en},
	publisher = {Stanford University Press},
	author = {Yu, Wei-Hsin},
	month = feb,
	year = {2009},
	keywords = {Business \& Economics / Women in Business, Political Science / Labor \& Industrial Relations, Social Science / Gender Studies, Social Science / General, Social Science / Sociology / General}
}

@book{mackie_creating_2002,
	title = {Creating {Socialist} {Women} in {Japan}: {Gender}, {Labour} and {Activism}, 1900-1937},
	isbn = {9780521523257},
	shorttitle = {Creating {Socialist} {Women} in {Japan}},
	abstract = {This book tells the inspiring story of a group of women who challenged the expectations of their society in their writings and in their actions. Vera Mackie surveys the development of socialist women's activism in Japan from the 1900s to the 1930s, in the broader context of the industrial and political development of modern Japan. She outlines the major socialist womens' organizations and their debates with their liberal and anarchist sisters. The book also offers close analyses of the political and creative writings of socialist women.},
	language = {en},
	publisher = {Cambridge University Press},
	author = {Mackie, Vera},
	month = aug,
	year = {2002},
	keywords = {History / Modern / 20th Century, Political Science / Political Ideologies / Communism, Post-Communism \& Socialism, Social Science / Women's Studies}
}

@book{norgren_abortion_2001,
	title = {Abortion {Before} {Birth} {Control}: {The} {Politics} of {Reproduction} in {Postwar} {Japan}},
	isbn = {9780691070056},
	shorttitle = {Abortion {Before} {Birth} {Control}},
	abstract = {Why has postwar Japanese abortion policy been relatively progressive, while contraception policy has been relatively conservative? The Japanese government legalized abortion in 1948 but did not approve the pill until 1999. In this carefully researched study, Tiana Norgren argues that these contradictory policies flowed from very different historical circumstances and interest group configurations. Doctors and family planners used a small window of opportunity during the Occupation to legalize abortion, and afterwards, doctors and women battled religious groups to uphold the law. The pill, on the other hand, first appeared at an inauspicious moment in history. Until circumstances began to change in the mid-1980s, the pharmaceutical industry was the pill's lone champion: doctors, midwives, family planners, and women all opposed the pill as a potential threat to their livelihoods, abortion rights, and women's health.Clearly written and interwoven with often surprising facts about Japanese history and politics, Norgren's book fills vital gaps in the cross-national literature on the politics of reproduction, a subject that has received more attention in the European and American contexts. Abortion Before Birth Control will be a valuable resource for those interested in abortion and contraception policies, gender studies, modern Japanese history, political science, and public policy. This is a major contribution to the literature on reproductive rights and the role of civil society in a country usually discussed in the context of its industrial might.},
	language = {en},
	publisher = {Princeton University Press},
	author = {Norgren, Tiana and Norgren, Christiana A. E.},
	year = {2001},
	keywords = {History / Asia / Japan, History / General, History / Social History, Medical / Reproductive Medicine \& Technology, Political Science / Public Policy / General, Social Science / Abortion \& Birth Control, Social Science / Sociology / General, Social Science / Sociology / Marriage \& Family, Social Science / Women's Studies}
}

@book{anderson_place_2010,
	title = {A {Place} in {Public}: {Women}'s {Rights} in {Meiji} {Japan}},
	isbn = {9780674056053},
	shorttitle = {A {Place} in {Public}},
	abstract = {This book addresses how gender became a defining category in the political and social modernization of Japan. During the early decades of the Meiji period (1868–1912), the Japanese encountered an idea with great currency in the West: that the social position of women reflected a country’s level of civilization. Although elites initiated dialogue out of concern for their country’s reputation internationally, the conversation soon moved to a new public sphere where individuals engaged in a wide-ranging debate about women’s roles and rights. By examining these debates throughout the 1870s and 1880s, Marnie S. Anderson argues that shifts in the gender system led to contradictory consequences for women. On the one hand, as gender displaced status as the primary system of social and legal classification, women gained access to the language of rights and the chance to represent themselves in public and play a limited political role; on the other, the modern Japanese state permitted women’s political participation only as an expression of their “citizenship through the household” and codified their formal exclusion from the political process through a series of laws enacted in 1890. This book shows how “a woman’s place” in late-nineteenth-century Japan was characterized by contradictions and unexpected consequences, by new opportunities and new constraints.},
	language = {en},
	publisher = {Harvard University Press},
	author = {Anderson, Marnie S.},
	year = {2010},
	keywords = {Political Science / Civil Rights, Political Science / Human Rights, Social Science / Gender Studies, Social Science / Regional Studies, Social Science / Sociology / General}
}

@article{uno_maternalism_1993,
	title = {Maternalism in {Modern} {Japan}},
	volume = {5},
	issn = {1527-2036},
	url = {http://muse.jhu.edu/journals/journal_of_womens_history/v005/5.2.article_sub06.html},
	doi = {10.1353/jowh.2010.0143},
	number = {2},
	urldate = {2012-12-21TZ},
	journal = {Journal of Women's History},
	author = {Uno, Kathleen S.},
	year = {1993},
	note = {{\textless}p{\textgreater}Volume 5, Number 2, Fall 1993{\textless}/p{\textgreater}},
	pages = {126--130}
}

@book{sievers_flowers_1983,
	title = {Flowers in {Salt}: {The} {Beginnigs} of {Feminist} {Consciousness} in {Modern} {Japan}},
	isbn = {9780804713825},
	shorttitle = {Flowers in {Salt}},
	language = {en},
	publisher = {Stanford University Press},
	author = {Sievers, Sharon L.},
	month = jun,
	year = {1983},
	keywords = {Social Science / Feminism \& Feminist Theory, Social Science / Women's Studies}
}

@article{meeks_buddhist_2010,
	title = {Buddhist {Renunciation} and the {Female} {Life} {Cycle}: {Understanding} {Nunhood} in {Heian} and {Kamakura} {Japan}},
	volume = {70},
	shorttitle = {Buddhist {Renunciation} and the {Female} {Life} {Cycle}},
	url = {http://muse.jhu.edu/journals/jas/summary/v070/70.1.meeks.html},
	number = {1},
	urldate = {2012-12-20TZ},
	journal = {Harvard Journal of Asiatic Studies},
	author = {Meeks, L.},
	year = {2010},
	pages = {1--59}
}

@book{musume_confessions_1973,
	title = {The {Confessions} of {Lady} {Nijō}},
	isbn = {9780804709309},
	language = {en},
	publisher = {Stanford University Press},
	author = {Musume, Nakanoin Masatada no and Brazell, Professor Karen},
	year = {1973},
	keywords = {Biography \& Autobiography / Historical, History / Asia / Japan, Literary Criticism / Asian / Japanese}
}

@book{meeks_hokkeji_2010,
	title = {Hokkeji and the {Reemergence} of {Female} {Monastic} {Orders} in {Premodern} {Japan}},
	isbn = {9780824833947},
	abstract = {Hokkeji, an ancient Nara temple that once stood at the apex of a state convent network established by Queen-Consort Kōmyō (701-760), possesses a history that in some ways is bigger than itself. Its development is emblematic of larger patterns in the history of female monasticism in Japan. In this volume, Lori Meeks explores the revival of Japan's most famous convent and the reestablishment of a nuns' ordination lineage in Japan. Meeks considers a broad range of issues surrounding women's engagement with Buddhism during a time when their status within the tradition was undergoing significant change. Hokkeji rejects the commonly accepted notion that women simply internalized orthodox Buddhist discourses meant to discourage female practice and offers new perspectives on the religious lives of women in premodern Japan. Its attention to the relationship between doctrine and socio-cultural practice produces a fuller view of Buddhism as it was practiced on the ground, outside the rarefied world of Buddhist scholasticism.},
	language = {en},
	publisher = {University of Hawaii Press},
	author = {Meeks, Lori R.},
	month = apr,
	year = {2010},
	keywords = {Religion / Buddhism / General, Religion / Buddhism / History, Religion / Buddhism / Rituals \& Practice, Religion / Christianity / Catholic, Religion / Eastern, Religion / Monasticism}
}

@article{tonomura_coercive_2006,
	title = {Coercive {Sex} in the {Medieval} {Japanese} {Court}: {Lady} {Nij}{\textbackslash}{AA}'s {Memoir}},
	volume = {61},
	shorttitle = {Coercive {Sex} in the {Medieval} {Japanese} {Court}},
	url = {http://muse.jhu.edu/journals/mni/summary/v061/61.3tonomura.html},
	number = {3},
	urldate = {2012-12-20TZ},
	journal = {Monumenta Nipponica},
	author = {Tonomura, H.},
	year = {2006},
	pages = {283--338}
}

@article{khor_organizing_1999,
	title = {Organizing for {Change}: {Women}'s {Grassroots} {Activism} in {Japan}},
	volume = {25},
	copyright = {Copyright © 1999 Feminist Studies, Inc.},
	issn = {0046-3663},
	shorttitle = {Organizing for {Change}},
	url = {http://www.jstor.org/stable/3178660},
	doi = {10.2307/3178660},
	number = {3},
	urldate = {2012-12-11TZ},
	journal = {Feminist Studies},
	author = {Khor, Diana},
	month = oct,
	year = {1999},
	note = {ArticleType: research-article / Full publication date: Autumn, 1999 / Copyright © 1999 Feminist Studies, Inc.},
	pages = {633--661}
}

@article{eto_womens_2005,
	title = {Women's movements in {Japan}: the intersection between everyday life and politics},
	volume = {17},
	issn = {0955-5803},
	shorttitle = {Women's movements in {Japan}},
	url = {http://www.tandfonline.com/doi/abs/10.1080/09555800500283810},
	doi = {10.1080/09555800500283810},
	number = {3},
	urldate = {2012-12-11TZ},
	journal = {Japan Forum},
	author = {Eto, Mikiko},
	year = {2005},
	pages = {311--333}
}

@article{kamiya_women_1986,
	title = {Women in {Japan}},
	volume = {20},
	url = {http://heinonline.org/HOL/Page?handle=hein.journals/ubclr20&id=453&div=&collection=journals},
	journal = {University of British Columbia Law Review},
	author = {Kamiya, Masako},
	year = {1986},
	pages = {447}
}

@article{molony_japans_1995,
	title = {Japan's 1986 {Equal} {Employment} {Opportunity} {Law} and the {Changing} {Discourse} on {Gender}},
	volume = {20},
	copyright = {Copyright © 1995 The University of Chicago Press},
	issn = {0097-9740},
	url = {http://www.jstor.org/stable/3174950},
	doi = {10.2307/3174950},
	number = {2},
	urldate = {2012-12-11TZ},
	journal = {Signs},
	author = {Molony, Barbara},
	month = jan,
	year = {1995},
	note = {ArticleType: research-article / Full publication date: Winter, 1995 / Copyright © 1995 The University of Chicago Press},
	pages = {268--302}
}

@book{tokuza_rise_2000,
	address = {Tokyo},
	title = {The rise of the feminist movement in {Japan}},
	isbn = {4766407318 9784766407310},
	language = {English},
	publisher = {Keio Univ. Press},
	author = {Tokuza, Akiko},
	year = {2000}
}

@article{gerteis_[untitled]_2007,
	title = {[untitled]},
	volume = {66},
	copyright = {Copyright © 2007 Association for Asian Studies},
	issn = {0021-9118},
	url = {http://www.jstor.org/stable/20203219},
	doi = {10.2307/20203219},
	number = {3},
	urldate = {2012-12-11TZ},
	journal = {The Journal of Asian Studies},
	author = {Gerteis, Christopher},
	month = aug,
	year = {2007},
	note = {ArticleType: book-review / Full publication date: Aug., 2007 / Copyright © 2007 Association for Asian Studies},
	pages = {848--849}
}

@book{murase_cooperation_2006,
	title = {Cooperation {Over} {Conflict}: {The} {Women}'s {Movement} {And} the {State} in {Postwar} {Japan}},
	isbn = {9780415976572},
	shorttitle = {Cooperation {Over} {Conflict}},
	abstract = {Japan's postwar transformation has been hailed as nothing short of a miracle. Yet, in the midst of massive social, economic, political, and cultural change, gender inequality persists at remarkably high levels. The paradox of Japan's progress against the persistence of gender inequality raises the question of why women remain a half-step behind men, more than a half century after women were granted equal rights under the postwar constitution. This question has been studied from a variety of perspectives. Anthropologists observe gender roles in Japanese culture, while economists study labor market conditions in Japan. This book offers a political perspective, and analyzes gender inequality in terms of power - specifically the power, or lack of power, that women themselves may exercise to create social change. Through the examination of women's groups, women's centers, and women's policy, this book documents state intervention in the women's movement in Japan. This intervention takes the form of regulations that limit the independence of women's organizations, as well as resources that aid and influence their activities. The result is a relationship between women and the state that is more cooperative than conflictual, leading to a slow and incremental process of social change for women in Japan.},
	language = {en},
	publisher = {Taylor \& Francis Group},
	author = {Murase, Miriam},
	year = {2006},
	keywords = {History / Asia / Japan, Political Science / Political Freedom, Social Science / Ethnic Studies / General, Social Science / Feminism \& Feminist Theory, Social Science / Gender Studies, Social Science / General, Social Science / Women's Studies}
}

@article{michele_marra_buddhist_1993,
	title = {The {Buddhist} {Mythmaking} of {Defilement}: {Sacred} {Courtesans} in {Medieval} {Japan}},
	volume = {52},
	number = {1},
	journal = {The Journal of Asian Studies},
	author = {{Michele Marra}},
	month = feb,
	year = {1993},
	pages = {49--65}
}

@incollection{sarah_m._strong_women_nodate,
	title = {Women and {Performance}},
	booktitle = {Performing the courtesan: {In} search of ghosts at {Zushin}-{In} letter mound},
	author = {{Sarah M. Strong}},
	pages = {80 -- 95}
}

@article{etsuko_terasaki_is_1992,
	title = {Is the {Courtesan} of {Eguchi} a {Buddhist} {Metaphorical} {Woman}? {A} {Feminist} {Reading} of a {No} {Play} in the {Japanese} {Medieval} {Theater}},
	volume = {21},
	number = {4},
	journal = {Women's Studies: An Interdisciplinary Journal},
	author = {{Etsuko Terasaki}},
	year = {1992},
	pages = {431--456}
}

@incollection{steels_fifty_2007,
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Fifty {Years} of {AI}: {From} {Symbols} to {Embodiment} - and {Back}},
	volume = {4850},
	isbn = {978-3-540-77295-8},
	url = {http://dx.doi.org/10.1007/978-3-540-77296-5_3},
	booktitle = {50 {Years} of {Artificial} {Intelligence}},
	publisher = {Springer Berlin / Heidelberg},
	author = {Steels, Luc},
	editor = {Lungarella, Max and Iida, Fumiya and Bongard, Josh and Pfeifer, Rolf},
	year = {2007},
	note = {10.1007/978-3-540-77296-5\_3},
	keywords = {Computer, Science},
	pages = {18--28}
}

@article{rouifed_contrasting_2011,
	title = {Contrasting {Response} to {Clipping} in the {Asian} {Knotweeds} {Fallopia} japonica and {Fallopia} × bohemica},
	volume = {18},
	issn = {1195-6860},
	url = {http://www.bioone.org/doi/abs/10.2980/18-2-3408},
	doi = {10.2980/18-2-3408},
	number = {2},
	urldate = {2012-10-31TZ},
	journal = {Ecoscience},
	author = {Rouifed, Soraya and Bornette, Gudrun and Mistler, Lubiana and Piola, Florence},
	month = jun,
	year = {2011},
	pages = {110--114}
}

@article{clune_selective_2010,
	title = {Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory},
	issn = {0962-8452, 1471-2954},
	shorttitle = {Selective pressures for accurate altruism targeting},
	url = {http://rspb.royalsocietypublishing.org/content/early/2010/09/15/rspb.2010.1557},
	doi = {10.1098/rspb.2010.1557},
	abstract = {Inclusive fitness theory predicts that natural selection will favour altruist genes that are more accurate in targeting altruism only to copies of themselves. In this paper, we provide evidence from digital evolution in support of this prediction by competing multiple altruist-targeting mechanisms that vary in their accuracy in determining whether a potential target for altruism carries a copy of the altruist gene. We compete altruism-targeting mechanisms based on (i) kinship (kin targeting), (ii) genetic similarity at a level greater than that expected of kin (similarity targeting), and (iii) perfect knowledge of the presence of an altruist gene (green beard targeting). Natural selection always favoured the most accurate targeting mechanism available. Our investigations also revealed that evolution did not increase the altruism level when all green beard altruists used the same phenotypic marker. The green beard altruism levels stably increased only when mutations that changed the altruism level also changed the marker (e.g. beard colour), such that beard colour reliably indicated the altruism level. For kin- and similarity-targeting mechanisms, we found that evolution was able to stably adjust altruism levels. Our results confirm that natural selection favours altruist genes that are increasingly accurate in targeting altruism to only their copies. Our work also emphasizes that the concept of targeting accuracy must include both the presence of an altruist gene and the level of altruism it produces.},
	language = {en},
	urldate = {2012-10-22TZ},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	author = {Clune, Jeff and Goldsby, Heather J. and Ofria, Charles and Pennock, Robert T.},
	month = sep,
	year = {2010},
	keywords = {Avida, altruism, digital evolution, green beard, inclusive fitness, kin selection}
}

@incollection{engel_concept_2010,
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Concept {Formation} {Using} {Incremental} {Gaussian} {Mixture} {Models}},
	volume = {6419},
	isbn = {978-3-642-16686-0},
	url = {http://www.springerlink.com/content/y43lr8662v646430/abstract/},
	abstract = {This paper presents a new algorithm for incremental concept formation based on a Bayesian framework. The algorithm, called IGMM (for Incremental Gaussian Mixture Model), uses a probabilistic approach for modeling the environment, and so, it can rely on solid arguments to handle this issue. IGMM creates and continually adjusts a probabilistic model consistent to all sequentially presented data without storing or revisiting previous training data. IGMM is particularly useful for incremental clustering of data streams, as encountered in the domain of moving object trajectories and mobile robotics. It creates an incremental knowledge model of the domain consisting of primitive concepts involving all observed variables. Experiments with simulated data streams of sonar readings of a mobile robot shows that IGMM can efficiently segment trajectories detecting higher order concepts like “wall at right” and “curve at left”.},
	urldate = {2012-10-22TZ},
	booktitle = {Progress in {Pattern} {Recognition}, {Image} {Analysis}, {Computer} {Vision}, and {Applications}},
	publisher = {Springer Berlin / Heidelberg},
	author = {Engel, Paulo and Heinen, Milton},
	editor = {Bloch, Isabelle and Cesar, Roberto},
	year = {2010},
	keywords = {Computer Science},
	pages = {128--135}
}

@article{tan_depth:_2011,
	title = {{DEPTH}: a web server to compute depth and predict small-molecule binding cavities in proteins},
	volume = {39},
	number = {2},
	journal = {Nucleic Acids Research},
	author = {Tan, Kuan Pern and Varadarajan, Raghavan and Madhusudhan, M. S.},
	month = may,
	year = {2011},
	pages = {242--248}
}

@article{jorgensen_pruning_2008,
	title = {Pruning artificial neural networks using neural complexity measures.},
	volume = {18},
	number = {5},
	journal = {International journal of neural systems},
	author = {Jorgensen, T.D. and Haynes, B.P. and Norlund, CC},
	year = {2008},
	pages = {389}
}

@misc{kaplinsky_nick_biol_2012,
	address = {Swarthmore College},
	title = {{BIOL} 25: {Plant} {Biology}},
	author = {{Kaplinsky, Nick}},
	month = apr,
	year = {2012}
}

@article{ellis_arabidopsis_2002,
	title = {The {Arabidopsis} mutant cev1 links cell wall signaling to jasmonate and ethylene responses},
	volume = {14},
	number = {7},
	journal = {The Plant Cell Online},
	author = {Ellis, C. and Karafyllidis, I. and Wasternack, C. and Turner, J.G.},
	year = {2002},
	pages = {1557--1566}
}

@article{avanci_jasmonates_2010,
	title = {Jasmonates are phytohormones with multiple functions, including plant defense and reproduction},
	volume = {9},
	number = {1},
	journal = {Genetics and Molecular Research},
	author = {Avanci, NC and Luche, DD and Goldman, GH and Goldman, MHS},
	year = {2010},
	pages = {484--505}
}

@article{turner_jasmonate_2002,
	title = {The {Jasmonate} {Signal} {Pathway}},
	volume = {14},
	url = {http://www.plantcell.org/content/14/suppl_1/S153.short},
	doi = {10.1105/tpc.000679},
	number = {suppl 1},
	journal = {The Plant Cell Online},
	author = {Turner, John G. and Ellis, Christine and Devoto, Alessandra},
	month = may,
	year = {2002},
	pages = {S153 --S164}
}

@article{thines_jaz_2007,
	title = {{JAZ} repressor proteins are targets of the {SCFCOI}1 complex during jasmonate signalling},
	volume = {448},
	issn = {0028-0836},
	url = {http://dx.doi.org/10.1038/nature05960},
	doi = {10.1038/nature05960},
	number = {7154},
	journal = {Nature},
	author = {Thines, Bryan and Katsir, Leron and Melotto, Maeli and Niu, Yajie and Mandaokar, Ajin and Liu, Guanghui and Nomura, Kinya and He, Sheng Yang and Howe, Gregg A. and Browse, John},
	year = {2007},
	pages = {661--665}
}

@article{chini_jaz_2007,
	title = {The {JAZ} family of repressors is the missing link in jasmonate signalling},
	volume = {448},
	issn = {0028-0836},
	url = {http://dx.doi.org/10.1038/nature06006},
	doi = {10.1038/nature06006},
	number = {7154},
	journal = {Nature},
	author = {Chini, A. and Fonseca, S. and Fernandez, G. and Adie, B. and Chico, J. M. and Lorenzo, O. and Garcia-Casado, G. and Lopez-Vidriero, I. and Lozano, F. M. and Ponce, M. R. and Micol, J. L. and Solano, R.},
	year = {2007},
	pages = {666--671}
}

@article{oraby_enhanced_2007,
	title = {Enhanced conversion of plant biomass into glucose using transgenic rice-produced endoglucanase for cellulosic ethanol},
	volume = {16},
	issn = {0962-8819},
	url = {http://dx.doi.org/10.1007/s11248-006-9064-9},
	number = {6},
	journal = {Transgenic Research},
	author = {Oraby, Hesham and Venkatesh, Balan and Dale, Bruce and Ahmad, Rashid and Ransom, Callista and Oehmke, James and Sticklen, Mariam},
	year = {2007},
	note = {10.1007/s11248-006-9064-9},
	pages = {739--749}
}

@inproceedings{james_comparative_2004,
	title = {A comparative analysis of simplification and complexification in the evolution of neural network topologies},
	booktitle = {Proc. of {Genetic} and {Evolutionary} {Computation} {Conference}},
	author = {James, D. and Tucker, P.},
	year = {2004}
}

@article{stanley_competitive_2004,
	title = {Competitive coevolution through evolutionary complexification},
	volume = {21},
	journal = {J. Artif. Intell. Res. (JAIR)},
	author = {Stanley, K.O. and Miikkulainen, R.},
	year = {2004},
	pages = {63--100}
}

@article{knox_effects_1991,
	title = {Effects of hyperthermia on microtubule organization and cytolytic activity of murine cytotoxic {T} lymphocytes},
	volume = {194},
	issn = {0014-4827},
	url = {http://www.sciencedirect.com/science/article/pii/0014482791903652},
	doi = {10.1016/0014-4827(91)90365-2},
	number = {2},
	journal = {Experimental Cell Research},
	author = {Knox, J.David and Mitchel, Ron E.J. and Brown, David L.},
	year = {1991},
	pages = {275 -- 283}
}

@article{voss_hsp70_2012,
	title = {Hsp70 {Alters} {Tau} {Function} and {Aggregation} in an {Isoform} {Specific} {Manner}},
	volume = {51},
	issn = {0006-2960},
	doi = {10.1021/bi2018078},
	abstract = {Tauopathies are characterized by abnormal aggregation of the microtubule associated protein tau. This aggregation is thought to occur when tau undergoes shifts from its native conformation to one that exposes hydrophobic areas on separate monomers, allowing contact and subsequent association into oligomers and filaments. Molecular chaperones normally function by binding to exposed hydrophobic stretches on proteins and assisting in their refolding. Chaperones of the heat shock protein 70 (Hsp70) family have been implicated in the prevention of abnormal tau aggregation in adult neurons. Tau exists as six alternatively spliced isoforms, and all six isoforms appear capable of forming the pathological aggregates seen in Alzheimer's disease. Because tau isoforms differ in primary sequence, we sought to determine whether Hsp70 would differentially affect the aggregation and microtubule assembly characteristics of the various tau isoforms. We found that Hsp70 inhibits tau aggregation directly and not through inducer-mediated effects. We also determined that Hsp70 inhibits the aggregation of each individual tau isoform and was more effective at inhibiting the three repeat isoforms. Finally, all tau isoforms robustly induced microtubule formation while in the presence of Hsp70. The results presented herein indicate that Hsp70 affects tau isoform dysfunction while having very little impact on the normal function of tau to mediate microtubule assembly. This indicates that targeting Hsp70 to tau may provide a therapeutic approach for the treatment of tauopathies that avoids disruption of normal tau function.},
	number = {4},
	journal = {BIOCHEMISTRY},
	author = {Voss, Kellen and Combs, Benjamin and Patterson, Kristina R. and Binder, Lester I. and Gamblin, T. Chris},
	month = jan,
	year = {2012},
	pages = {888--898}
}

@article{enquist_general_2007,
	title = {A general integrative model for scaling plant growth, carbon flux, and functional trait spectra},
	volume = {449},
	url = {http://www.nature.com/nature/journal/v449/n7159/full/nature06061.html},
	doi = {10.1038/nature06061},
	abstract = {Linking functional traits to plant growth is critical for scaling attributes of organisms to the dynamics of ecosystems1, 2 and for understanding how selection shapes integrated botanical phenotypes3. However, a general mechanistic theory showing how traits specifically influence carbon and biomass flux within and across plants is needed. Building on foundational work on relative growth rate4, 5, 6, recent work on functional trait spectra7, 8, 9, and metabolic scaling theory10, 11, here we derive a generalized trait-based model of plant growth. In agreement with a wide variety of empirical data, our model uniquely predicts how key functional traits interact to regulate variation in relative growth rate, the allometric growth normalizations for both angiosperms and gymnosperms, and the quantitative form of several functional trait spectra relationships. The model also provides a general quantitative framework to incorporate additional leaf-level trait scaling relationships7, 8 and hence to unite functional trait spectra with theories of relative growth rate, and metabolic scaling. We apply the model to calculate carbon use efficiency. This often ignored trait, which may influence variation in relative growth rate, appears to vary directionally across geographic gradients. Together, our results show how both quantitative plant traits and the geometry of vascular transport networks can be merged into a common scaling theory. Our model provides a framework for predicting not only how traits covary within an integrated allometric phenotype but also how trait variation mechanistically influences plant growth and carbon flux within and across diverse ecosystems.},
	number = {7159},
	journal = {Nature},
	author = {Enquist, Brian J. and Kerkhoff, Andrew J. and Stark, Scott C. and Swenson, Nathan G. and McCarthy, Megan C. and Price, Charles C.},
	month = sep,
	year = {2007},
	keywords = {growth, model},
	pages = {218--222}
}

@article{payne_end-permian_2012,
	title = {End-{Permian} {Mass} {Extinction} in the {Oceans}: {An} {Ancient} {Analog} for the {Twenty}-{First} {Century}?},
	volume = {40},
	url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-earth-042711-105329},
	doi = {10.1146/annurev-earth-042711-105329},
	number = {1},
	journal = {Annual Review of Earth and Planetary Sciences},
	author = {Payne, Jonathan L. and Clapham, Matthew E.},
	year = {2012},
	pages = {null}
}

@book{raup_extinction:_1992,
	edition = {1},
	title = {Extinction: {Bad} {Genes} or {Bad} {Luck}?},
	isbn = {0393309274},
	publisher = {W. W. Norton and Company},
	author = {Raup, David M.},
	month = nov,
	year = {1992}
}

@article{price_seasonal_2001,
	title = {Seasonal patterns of partitioning and remobilization of \<sup\>14\</sup\>{C} in the invasive rhizomatous perennial {Japanese} knotweed (\<i\>{Fallopia} japonica\</i\> ({Houtt}.) {Ronse} {Decraene})},
	volume = {15},
	issn = {0269-7653},
	url = {http://dx.doi.org/10.1023/A:1016036916017},
	number = {4},
	journal = {Evolutionary Ecology},
	author = {Price, Elizabeth A.C. and Gamble, Rebecca and Williams, Gareth G. and Marshall, Christopher},
	year = {2001},
	note = {10.1023/A:1016036916017},
	pages = {347--362}
}
@inproceedings{ewen-campen_characterization_2006,
	title = {Characterization of genotypic variation of the invasive plant
Fallopia japonica ({Japanese} {Knotweed}) in the {Crum} {Woods},
Swarthmore, {PA}},
	booktitle = {Spring 2006 {Biodiversity} and {Ecosystem} {Functioning} {Seminar} {Student} {Research} {Reports}},
	publisher = {Jose-Luis Machado},
	author = {Ewen-Campen, Ben and Glick, Alex and Strong, Aaron},
	month = may,
	year = {2006},
	pages = {5--20}
}

@article{maruta_growth_1983,
	title = {Growth and survival of current-year seedlings of {Polygonum} cuspidatum at the upper distribution limit on {Mt}. {Fuji}},
	volume = {60},
	issn = {0029-8549},
	url = {http://dx.doi.org/10.1007/BF00376845},
	number = {3},
	journal = {Oecologia},
	author = {Maruta, Emiko},
	year = {1983},
	note = {10.1007/BF00376845},
	pages = {316--320}
}

@article{francis_vegetative_2008,
	title = {Vegetative regeneration of {Fallopia} japonica ({Houtt}.) {Ronse} {Decraene} ({Japanese} knotweed) at varying burial depths},
	volume = {8},
	number = {1},
	journal = {Weed Biology and Management},
	author = {Francis, R. A and RILEY, K. A and HOGGART, S. P.G},
	year = {2008},
	keywords = {japonica, regeneration, rhizome},
	pages = {69--72}
}

@inproceedings{moore_spatial_2006,
	address = {Swarthmore College},
	title = {The {Spatial} {Distribution} of {Japanese} {Knotweed} ({F}. japonica) in
the {Crum} {Woods} of {Swarthmore} {College} in {Spring} 2006},
	booktitle = {Spring 2006 {Biodiversity} and {Ecosystem} {Functioning} {Student} {Research} {Project} {Reports}},
	publisher = {Jose-Luis Machado},
	author = {Moore, D and Hsu, H. and Cava, E.},
	month = may,
	year = {2006},
	pages = {38--61}
}

@misc{center_for_history_and_new_media_zotero_nodate,
	title = {Zotero {Quick} {Start} {Guide}},
	url = {http://zotero.org/support/quick_start_guide},
	author = {{Center for History and New Media}}
}

@misc{noauthor_carbohydrate_nodate,
	title = {Carbohydrate dynamics in roots and rhizomes of {Cirsium} arvense and {Tussilago} farfara - {NKURUNZIZA} - 2011 - {Weed} {Research} - {Wiley} {Online} {Library}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3180.2011.00866.x/full},
	urldate = {2011-06-16TZ}
}

@article{dassonville_niche_2011,
	title = {Niche construction by the invasive {Asian} knotweeds (species complex \textit{{Fallopia}}): impact on activity, abundance and community structure of denitrifiers and nitrifiers},
	volume = {13},
	issn = {1387-3547},
	url = {http://dx.doi.org/10.1007/s10530-011-9954-5},
	doi = {10.1007/s10530-011-9954-5},
	abstract = {Big Asian knotweeds (Fallopia spp.) are among the most invasive plant species in north-western Europe. We suggest that their success is partially explained by biological and chemical niche construction. In this paper, we explored the microbial mechanisms by which the plant modifies the nitrogen cycle. We found that Fallopia spp. decreased potential denitrification enzyme activity (DEA) by reducing soil moisture and reducing denitrifying bacteria density in the soil. The plant also reduced potential ammonia and nitrite oxydizing bacteria enzyme activities (respectively, AOEA and NOEA) in sites with high AOEA and NOEA in uninvaded situation. Modification of AOEA and NOEA were not correlated to modifications of the density of implicated bacteria. AOB and Nitrobacter-like NOB community genetic structures were significantly different in respectively two and three of the four tested sites while the genetic structure of denitrifying bacteria was not affected by invasion in none of the tested sites. Modification of nitrification and denitrification functioning in invaded soils could lead to reduced nitrogen loss from the ecosystem through nitrate leaching or volatilization of nitrous oxides and dinitrogen and could be considered as a niche construction mechanism of Fallopia.},
	number = {5},
	journal = {Biological Invasions},
	author = {Dassonville, Nicolas and Guillaumaud, Nadine and Piola, Florence and Meerts, Pierre and Poly, Franck},
	month = may,
	year = {2011},
	keywords = {Biomedical and Life Sciences, allelopathy, japonica, niche construction, nitrogen, nitrogen cycling, soil microbes},
	pages = {1115--1133}
}

@article{bram_seed_2004,
	title = {Seed {Germinability} and {Its} {Seasonal} {Onset} of {Japanese} {Knotweed} ({Polygonum} cuspidatum)},
	volume = {52},
	issn = {00431745},
	url = {http://www.jstor.org/stable/4046821},
	abstract = {Sexual reproduction is known to be an important means of propagation for native Japanese knotweed populations in Asia. For naturalized populations in the United States, however, its relative importance compared with propagation by rhizome and stem fragments has not been established. This article presents two related studies that address two basic questions regarding the potential for propagation by seed: (1) are seeds that are produced by Japanese knotweed in areas of Philadelphia, PA, capable of germinating in the field? If so, (2) when and how rapidly during the year do these seeds acquire germinability? Field germination experiments assessed germination of planted seeds at intervals during the growing season at two different study sites (one in 2000 and the other in 2002) and showed that germination was common at both sites. The 2002 experiment also demonstrated that germination occurred both within existing stands of Japanese knotweed and in areas well removed from existing stands, and that both planted and naturally occurring seeds germinated. Experiments on seasonal acquisition of seed germinability used batches of seeds collected weekly between early September and November 2000 from three different study sites. Results showed that at two of the study sites, a rapid increase in germinability from less than 10\% to greater than 90\% occurred between collection dates in mid-September and mid-October 2000. A smaller and more gradual change occurred at the third site, where maximum germinability was roughly 50\%. Regarding management of Japanese knotweed, the field germination experiments suggest that spread of this plant by seed is a realistic possibility in the United States. Because of the rapidity with which germinability is acquired, the high germinability attained, and the large number of seeds produced, we recommend that female (male-sterile) plants or their inflorescences be removed from seed-producing populations before the formation of fruits to minimize spread by seed.},
	number = {5},
	journal = {Weed Science},
	author = {Bram, Margot R. and McNair, James N.},
	year = {2004},
	note = {ArticleType: research-article / Full publication date: Sep. - Oct., 2004 / Copyright © 2004 Weed Science Society of America},
	keywords = {clonality, genetics, hybrids, japonica},
	pages = {759--767}
}

@article{braatne_leaf_2007,
	title = {Leaf {Decomposition} and {Stream} {Macroinvertebrate} {Colonisation} of {Japanese} {Knotweed}, an {Invasive} {Plant} {Species}},
	volume = {92},
	issn = {1522-2632},
	url = {http://dx.doi.org/10.1002/iroh.200611009},
	doi = {10.1002/iroh.200611009},
	number = {6},
	journal = {International Review of Hydrobiology},
	author = {Braatne, Jeffrey H. and Sullivan, S. Mažeika P. and Chamberlain, Erin},
	year = {2007},
	keywords = {Japanese knotweed, allochthonous inputs, decomposition rate, japonica, model parameters},
	pages = {656--665}
}

@article{allison_rapid_2004,
	title = {Rapid nutrient cycling in leaf litter from invasive plants in {Hawai}’i},
	volume = {141},
	issn = {0029-8549},
	url = {http://dx.doi.org/10.1007/s00442-004-1679-z},
	doi = {10.1007/s00442-004-1679-z},
	abstract = {Physiological traits that contribute to the establishment and spread of invasive plant species could also have impacts on ecosystem processes. The traits prevalent in many invasive plants, such as high specific leaf areas, rapid growth rates, and elevated leaf nutrient concentrations, improve litter quality and should increase rates of decomposition and nutrient cycling. To test for these ecosystem impacts, we measured initial leaf litter properties, decomposition rates, and nutrient dynamics in 11 understory plants from the Hawaiian islands in control and nitrogen + phosphorus fertilized plots. These included five common native species, four of which were ferns, and six aggressive invasive species, including five angiosperms and one fern. We found a 50-fold variation in leaf litter decay rates, with natives decaying at rates of 0.2–2.3 year −1 and invaders at 1.4–9.3 year −1. This difference was driven by very low decomposition rates in native fern litter. Fertilization significantly increased the decay rates of leaf litter from two native and two invasive species. Most invasive litter types lost nitrogen and phosphorus more rapidly and in larger quantities than comparable native litter types. All litter types except three native ferns lost nitrogen after 100 days of decomposition, and all litter types except the most recalcitrant native ferns lost \>50\% of initial phosphorus by the end of the experiment (204–735 days). If invasive understory plants displace native species, nutrient cycling rates could increase dramatically due to rapid decomposition and nutrient release from invasive litter. Such changes are likely to cause a positive feedback to invasion in Hawai’i because many invasive plants thrive on nutrient-rich soils.},
	number = {4},
	journal = {Oecologia},
	author = {Allison, Steven D. and Vitousek, Peter M.},
	month = dec,
	year = {2004},
	keywords = {Biomedical and Life Sciences, case study, litterfall, nitrogen cycling},
	pages = {612--619}
}

@article{murrell_invasive_2011,
	title = {Invasive knotweed affects native plants through allelopathy},
	volume = {98},
	url = {http://www.amjbot.org/content/98/1/38.abstract},
	abstract = {• Premise of study: There is increasing evidence that many plant invaders interfere with native plants through allelopathy. This allelopathic interference may be a key mechanism of plant invasiveness. One of the most aggressive current plant invaders is the clonal knotweed hybrid Fallopia × bohemica, which often forms monocultures in its introduced range. Preliminary results from laboratory studies suggest that allelopathy could play a role in this invasion.• Methods: We grew experimental communities of European plants together with F. × bohemica. We used activated carbon to test for allelopathic effects, and we combined this with single or repeated removal of Fallopia shoots to examine how mechanical control can reduce the species’ impact.• Key results: Addition of activated carbon to the soil significantly reduced the suppressive effect of undamaged F. × bohemica on native forbs. The magnitude of this effect was similar to that of regular cutting of Fallopia shoots. Regular cutting of Fallopia shoots efficiently inhibited the growth of rhizomes, together with their apparent allelopathic effects.• Conclusions: The ecological impact of F. × bohemica on native forbs is not just a result of competition for shared resources, but it also appears to have a large allelopathic component. Still, regular mechnical control successfully eliminated allelopathic effects. Therefore, allelopathy will create an additional challenge to knotweed management and ecological restoration only if the allelochemicals are found to persist in the soil. More research is needed to examine the mechanisms underlying Fallopia allelopathy, and the long-term effects of soil residues.},
	number = {1},
	journal = {American Journal of Botany},
	author = {Murrell, Craig and Gerber, Esther and Krebs, Christine and Parepa, Madalin and Schaffner, Urs and Bossdorf, Oliver},
	month = jan,
	year = {2011},
	keywords = {activated carbon, allelopathy, bohemica, cutting, greenhouse, rhizome},
	pages = {38 --43}
}

@article{siemens_evaluation_2007,
	title = {An evaluation of mechanisms preventing growth and survival of two native species in invasive {Bohemian} knotweed ({Fallopia} xbohemica, {Polygonaceae})},
	volume = {94},
	url = {http://www.amjbot.org/content/94/5/776.abstract},
	abstract = {Restoring native diversity to habitats dominated by invasive plants requires improved understanding of mechanisms that allow introduced plants to retain dominance. We used a factorial transplant experiment to assess whether light limitation, nutrient limitation, or allelopathic interference by Fallopia xbohemica reduces growth or survival of Eupatorium perfoliatum or Acer saccharinum. Increased light improved A. saccharinum performance but had no effect on E. perfoliatum growth. Increased light had no effect on A. saccharinum survival but improved E. perfoliatum survival. Activated carbon addition had short-term benefits allowing E. perfoliatum plants to grow for 4 wk and increased A. saccharinum leaf width but not biomass. Nutrient addition had no beneficial effect on transplants. These results in combination with the outcome of a cutting experiment suggest that F. xbohemica achieves competitive superiority primarily by limiting access to light. Species-specific effects and significant interaction effects particularly of light and activated carbon suggest additional mechanisms. Allelopathic interference or interaction with microbial soil organisms may contribute to the lack of native species in populations of F. xbohemica. Restoration efforts should combine selective F. xbohemica control with soil amendments (such as activated carbon) to assess their potential to facilitate return of native species to invaded habitats.},
	number = {5},
	journal = {American Journal of Botany},
	author = {Siemens, Tania J. and Blossey, Bernd},
	month = may,
	year = {2007},
	keywords = {activated carbon, allelopathy, bohemica, experimental, light limitation, nutrient addition, plot comparisons},
	pages = {776 --783}
}

@article{dassonville_invasion_2011,
	title = {Invasion by {Fallopia} japonica increases topsoil mineral nutrient concentrations},
	volume = {14},
	issn = {1195-6860},
	url = {http://dx.doi.org/10.2980/1195-6860(2007)14[230:IBFJIT]2.0.CO;2},
	doi = {doi: 10.2980/1195-6860(2007)14[230:IBFJIT]2.0.CO;2},
	number = {2},
	journal = {Ecoscience},
	author = {DASSONVILLE, Nicolas and VANDERHOEVEN, Sonia and GRUBER, Wolf and MEERTS, Pierre},
	month = jun,
	year = {2011},
	keywords = {homogenization, japonica, nitrogen, nutrient cycling, observational, plot comparisons},
	pages = {230--240}
}

@article{hirose_nitrogen_1986,
	title = {Nitrogen {Uptake} and {Plant} {Growth} {I}. {Effect} of {Nitrogen} {Removal} on {Growth} of {Polygonum} cuspidatum},
	volume = {58},
	url = {http://aob.oxfordjournals.org/content/58/4/479.abstract},
	doi = {10.1093/annbot/58.4.479},
	abstract = {Polygonum cuspidatum was grown hydroponically to examine the effect of nitrogen removal from the nutrient solution upon plant growth and the partitioning of dry matter and nitrogen among organs. Nitrogen removal reduced the growth rate mainly due to the reduced growth of leaf area. Accelerated root growth was observed only in plants which earlier had received high levels of nitrogen. Nitrogen removal caused almost exclusive allocation of available nitrogen to root growth. Nitrogen flux from the shoot to the root occurred in plants which had received low nitrogen. Not only was net assimilation rate (NAR) little affected by nitrogen removal, but it also was not correlated with the concentration of leaf nitrogen on an area basis. Light-saturated CO. exchange rate (CER) was highly correlated with the concentration of leaf nitrogen. Nitrogen use efficiency (NUE) in CER (CER divided by leaf nitrogen) remained constant against leaf nitrogen, indicating efficient use of nitrogen under light saturation, while NUE in terms of NAR decreased with higher concentration of leaf nitrogen.},
	number = {4},
	journal = {Annals of Botany},
	author = {Hirose, T. and Kitajima, K.},
	month = oct,
	year = {1986},
	keywords = {greenhouse, growth rate, hydroponic, japonica, nitrogen, nitrogen limitation},
	pages = {479 --486}
}

@article{beerling_fallopia_1994,
	title = {Fallopia {Japonica} ({Houtt}.) {Ronse} {Decraene}},
	volume = {82},
	issn = {00220477},
	url = {http://www.jstor.org/stable/2261459},
	number = {4},
	journal = {Journal of Ecology},
	author = {Beerling, David J. and Bailey, John P. and Conolly, Ann P.},
	month = dec,
	year = {1994},
	note = {ArticleType: research-article / Full publication date: Dec., 1994 / Copyright © 1994 British Ecological Society},
	keywords = {general, growth rate, review},
	pages = {959--979}
}

@article{eppinga_litter_2011,
	title = {Litter feedbacks, evolutionary change and exotic plant invasion},
	volume = {99},
	issn = {1365-2745},
	url = {http://dx.doi.org/10.1111/j.1365-2745.2010.01781.x},
	doi = {10.1111/j.1365-2745.2010.01781.x},
	number = {2},
	journal = {Journal of Ecology},
	author = {Eppinga, Maarten B. and Kaproth, Matthew A. and Collins, Alexandra R. and Molofsky, Jane},
	year = {2011},
	keywords = {C:N ratio, Carex hystericina, Phalaris arundinacea, critical transitions, decomposition, invasion ecology, litter:biomass ratio, modelling, plant competition, threshold effects},
	pages = {503--514}
}

@article{chiba_nitrogen_1993,
	title = {Nitrogen {Acquisition} and {Use} in {Three} {Perennials} in the {Early} {Stage} of {Primary} {Succession}},
	volume = {7},
	number = {3},
	journal = {Functional Ecology},
	author = {Chiba, N and Hirose, T},
	year = {1993},
	keywords = {greenhouse, growth rate, japonica, nitrogen, nitrogen allocation, nitrogen limitation},
	pages = {287--292}
}

@article{bashtanova_review:_2009,
	title = {Review: {Physiological} approaches to the improvement of chemical control of {Japanese} {Knotweed}},
	volume = {57},
	number = {6},
	journal = {Weed Science},
	author = {Bashtanova, Uliana B. and Beckett, K. Paul and Flowers, Timothy J.},
	year = {2009},
	keywords = {japonica, review, rhizome, seasonality, translocation},
	pages = {584--592}
}

@article{wolf_growth_1971,
	title = {The growth rate of {Polgonum} cuspidatum},
	volume = {46},
	number = {2},
	journal = {Journal of te Tennessee Academy of Science},
	author = {Wolf, Fredrick T.},
	year = {1971},
	keywords = {growth rate, japonica}
}

@inproceedings{brock_regeneration_1992,
	address = {Dijon},
	title = {Regeneration of {Japanese} {Knotweed} ({Fallopia} japonica) from rhizome and stems: {Observations} from greenhouse trials},
	author = {Brock, John and Wade, Max},
	year = {1992},
	keywords = {greenhouse, hydroponic, japonica, regeneration, rhizome},
	pages = {85--94}
}

@article{bimova_experimental_2003,
	title = {Experimental study of vegetative regeneration in four invasive {Reynoutria} taxa ({Polygonaceae})},
	volume = {166},
	number = {1},
	journal = {Plant Ecology},
	author = {Bímová, K. and Mandák, B. and Pyšek, P.},
	year = {2003},
	keywords = {bohemica, greenhouse, hydroponic, japonica, regeneration, rhizome},
	pages = {1--11}
}

@article{smith_simulation_2007,
	title = {A simulation model of rhizome networks for {Fallopia} japonica ({Japanese} knotweed) in the {United} {Kingdom}},
	volume = {200},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380006003863},
	doi = {doi: 10.1016/j.ecolmodel.2006.08.004},
	number = {3-4},
	journal = {Ecological Modelling},
	author = {Smith, J.M.D. and Ward, J.P. and Child, L.E. and Owen, M.R.},
	month = jan,
	year = {2007},
	keywords = {Clonal plant, Correlated random walk, Invasive alien weed, Japanese knotweed, Rhizome morphology, Simulation, japonica},
	pages = {421--432}
}

@misc{noauthor_sciencedirect_nodate,
	title = {{ScienceDirect} - {Ecological} {Modelling} : {A} simulation model of rhizome networks for {Fallopia} japonica ({Japanese} knotweed) in the {United} {Kingdom}},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380006003863},
	urldate = {2011-06-14TZ}
}