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lpsn.qmd
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lpsn.qmd
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# LPSN: the List of Prokaryotic names with Standing in Nomenclature
Although we have referred to authoritative sources there is, in fact, no offical classification of prokaryotes (@Tindall1999-qe). Also, the terms _nomenclature_, _taxonomy_, and _phylogeny_ are not interchangeable.
::: { .callout-tip title="Understanding the difference"}
- **phylogeny**: A _phylogeny_ is the evolutionary history of a set of organisms, or a model (such as a phylogentic tree) representing that history
- **taxonomy**: A _taxonomy_ is a scheme for ordering objects into groups or classes, or the rules for doing so
- **nomenclature**: _Nomenclature_ is the set of names assigned to groups in a taxonomy, or the set of rules for doing so
:::
We do not know the "true" evolutionary histories of organisms, so the _phylogenies_ we reconstruct as scientists are estimates - sometimes very precise estimates! - of evolutionary history.
The _phylogenies_ we construct allow us to make decisions about how to organise organisms into a _taxonomy_: groups of organisms (taxa) that comprise species, genera, phyla, and so on.
The names we give to taxa are governed by the rules of _nomenclature_. Those names are regulated by the [International Code of Nomenclature of Prokaryotes (ICNP)](https://the-icsp.org/index.php/code-of-nomenclatur). This document is produced by the [International Committee on Systematics of Prokaryotes (ICSP)](https://the-icsp.org/index.php), a group of about 35 scientists who compose the rules by which bacteria are named.
::: { .callout-warning title="ICSP Do Not Have a Taxonomic Opinion"}
The ICSP do not decide which organisms go into any particular taxon (genus, species, etc.) - scientific opinion is ever-changing in this area. ICSP, through the ICNP, only decide what is a validly published name. The name of a taxon is validly published, and therefore _has standing in nomenclature_, only if certain criteria are met.
:::
::: { .callout-note title="The [LPSN](https://www.bacterio.net/) is the authoritative database of validly-published names for prokaryotes." }
:::
## Investigating your classification at LPSN
- Go to the [LPSN](https://www.bacterio.net/) server
- Enter the species classification you think should be assigned to your organism in the `Search taxonomy` field, and hit `Return`/`Enter`. The result should appear immediately.
::: { .callout-important title="Questions"}
1. What kind of taxonomic category does the name of your organism represent?
2. What does the name mean, and what does it imply about the organism?
3. Is the name you entered a validly published taxonomic name?
4. What is the parent taxon for this name?
:::
- Click on the link by `Parent taxon:` (the value here is also the answer to question 4. above).
::: { .callout-important title="Questions"}
1. What kind of taxonomic category does this name represent?
2. What does the name mean, and what does it imply about the bacteria?
3. Is the name you entered a validly published taxonomic name?
4. What is the `Taxonomic status` of this name?
5. Is this name the "correct name" for the organism?
:::
::: { .callout-warning collapse="true"}
## What does "correct name" mean in a taxonomic context?
The precise meaning of "correct name" in this context is provided in a [glossary at LPSN](https://lpsn.dsmz.de/text/glossary). The key points in that text are:
- Any taxon may have only one _correct_ name. This is usually the earliest validly published, legitimate name.
- The LPSN selects certain taxon names as _correct_ names. If more than one option is available, then the LPSN's choice reflects only _one_ of the taxonomic opinions expressed in the literature.
- The _correct_ name for an organism should be used in the literature.
- Other valid names are given _synonym_ status.
- Other scientists may express distinct taxonomic opinions and are permitted to do so, by using a _synonym_.
**The term _correct_ is therefore used in a technical sense, in a taxonomic context. The existence of a _correct_ name for a taxon does not imply that other names (_synonyms_) are invalid or cannot be used.**
:::
- Read the `Notes` section on the LPSN page for _Ochrobactrum_ (the genus).
::: { .callout-important title="Questions"}
1. How do the notes on this page reflect the controversy over naming of _Ochrobactrum_/_Brucella_ described in the [Introduction](intro.qmd)?
2. Does the LPSN page affect your opinion about how you have classified your isolate?
3. Finally, what is the taxonomic name you think is most appropriate for your isolate?
:::