PhyloCode


PhyloCode

The "International Code of Phylogenetic Nomenclature", known for short as the "PhyloCode", is a developing draft for a formal set of rules governing phylogenetic nomenclature. Its current version is specifically designed to regulate the naming of clades, leaving the governance of species names up to the rank-based codes ("ICBN", "ICZN", "ICNB").

The "PhyloCode" is associated with the International Society for Phylogenetic Nomenclature (ISPN). [ [http://phylonames.org/ International Society for Phylogenetic Nomenclature (website)] ]

Overview

The "PhyloCode" proposes to regulate phylogenetic nomenclature by providing rules for how to decide which associations of names and definitions will be considered established [ [http://www.ohiou.edu/phylocode/art4-5.html International Code of Phylogenetic Nomenclature, Version 4b - Chapter II. Publication] ] , which of those will be considered homonyms [ [http://www.ohiou.edu/phylocode/art13.html International Code of Phylogenetic Nomenclature, Version 4b - Article 13: Homonymy] ] or synonyms [ [http://www.ohiou.edu/phylocode/art14.html International Code of Phylogenetic Nomenclature Version 4b, Article 14: Synonymy] ] , and which one of a set of synonyms or homonyms will be considered accepted (generally the one registered first; see below).

Additionally, the "PhyloCode" will only allow the naming of clades [ [http://www.ohiou.edu/phylocode/art1-3.html#art1.1 International Code of Phylogenetic Nomenclature, Version 4b - Rule 1.1] ] , not of paraphyletic or polyphyletic groups, and will only allow the use of specimens, species, and apomorphies as specifiers (anchors) [ [http://www.ohiou.edu/phylocode/art11.html International Code of Phylogenetic Nomenclature, Version 4b - Article 11. Specifiers and Qualifying Clauses] ] .

Phylogenetic nomenclature

Unlike previous, rank-based nomenclatural codes ("ICBN", "ICZN", "ICNB"), the "PhyloCode" does not require the use of ranks, although it does optionally allow their use [ [http://www.ohiou.edu/phylocode/art1-3.html#art3 International Code of Phylogenetic Nomenclature, Version 4b - Article 3. Hierarchy and Rank] ] [Although note that the "PhyloCode" does not permit a taxon's name to change when its rank changes, while the rank-based codes require this for at least some names.] . The rank-based codes define taxa using a rank (such as genus, family, etc.) and, in many cases, a type specimen or type subtaxon. The exact content of a taxon, other than the type, is not specified by the rank-based codes.

In contrast, under phylogenetic nomenclature, the content of taxa are delimited using a definition that is based on phylogeny (i.e., ancestry and descent) and uses specifiers (e.g., species, specimens, apomorphies) to indicate actual organisms. The formula of the definition indicates an ancestor. The defined taxon, then, is that ancestor and all of its descendants. Thus, the content of a phylogenetically-defined taxon relies on a phylogenetic hypothesis.

The following are examples of types of phylogenetic definition (capital letters indicate specifiers) [ [http://www.ohiou.edu/phylocode/art9.html International Code of Phylogenetic Nomenclature, Version 4b - Article 9. General Requirements for Establishment of Clade Names] ] :
* Node-based: "the clade originating with the most recent common ancestor of A and B" or "the least inclusive clade containing A and B"
* Branch-based: "the clade consisting of A and all organisms or species that share a more recent common ancestor with A than with Z" or "the most inclusive clade containing A but not Z"
* Apomorphy-based: "the clade originating with the first organism or species to possess apomorphy M as inherited by A" or "the most inclusive clade exhibiting character state M synapomorphic with that in A"Other types of definition are possible as well.

The following table gives examples of the differences between rank-based and phylogenetic definitions.

Versions

The draft of the "PhyloCode" has gone through several revisions. All older versions can be found [http://www.ohiou.edu/phylocode/documents.html on the website] . As of September 12, 2007, the current version is 4b.

Organization

As with other nomenclatural codes, the rules of the "PhyloCode" are organized as articles, which in turn are organized as chapters. Each article may also contain notes, examples, and recommendations.

Table of contents

* [http://www.ohiou.edu/phylocode/preface.html Preface] (including [http://www.ohiou.edu/phylocode/citations.html Literature Cited] )
* [http://www.ohiou.edu/phylocode/preamble.html Preamble]
* [http://www.ohiou.edu/phylocode/principles.html Division I. Principles]
* [http://www.ohiou.edu/phylocode/art1-3.html Division II. Rules]
** [http://www.ohiou.edu/phylocode/art1-3.html#chapter1 Chapter I. Taxa] (Arts. 1-3)
** [http://www.ohiou.edu/phylocode/art4-5.html#chapter2 Chapter II. Publication] (Arts. 4-5)
** [http://www.ohiou.edu/phylocode/art6.html#chapter3 Chapter III. Names] (Arts. 6-8)
** [http://www.ohiou.edu/phylocode/art9.html#chaper4 Chapter IV. Clade Names] (Arts. 9-11)
** [http://www.ohiou.edu/phylocode/art12.html#chapter5 Chapter V. Selection of Established Names] (Arts. 12-15)
** [http://www.ohiou.edu/phylocode/art16.html#chapter6 Chapter VI. Provisions for Hybrids] (Art. 16)
** [http://www.ohiou.edu/phylocode/art17.html#chapter7 Chapter VII. Orthography] (Arts. 17-18)
** [http://www.ohiou.edu/phylocode/art19.html#chapter8 Chapter VIII. Authorship of Names] (Art. 19)
** [http://www.ohiou.edu/phylocode/art20.html#chapter9 Chapter IX. Citation of Authors and Registration Numbers] (Art. 20)
** [http://www.ohiou.edu/phylocode/art21.html#chapter10 Chapter X. Species Names] (Art. 21)
** [http://www.ohiou.edu/phylocode/art22.html#chapter11 Chapter XI. Governance] (Art. 22)
* [http://www.ohiou.edu/phylocode/glossary.html Glossary]
* [http://www.ohiou.edu/phylocode/table1.html Tables]
* [http://www.ohiou.edu/phylocode/appendixA.html Appendices]
** [http://www.ohiou.edu/phylocode/appendixA.html#appendix-a Appendix A. Registration Procedures and Data Requirements]
** [http://www.ohiou.edu/phylocode/appendixB.html#appendix-b Appendix B. Code of Ethics]

Registration database

Once implemented, the "PhyloCode" will be associated with a registration database, called RegNum, which will store all clade names and definitions that will be considered acceptable. [ [http://www.ohiou.edu/phylocode/art8.html International Code of Phylogenetic Nomenclature, Version 4b - Article 8. Registration] ] It is hoped that this will provide a publicly-usable tool for associating clade names with definitions, which could then be associated with sets of subtaxa or specimens through phylogenetic tree databases (such as TreeBASE).

As currently planned, however, the most important use of RegNum will be the decision of which one of a number of synonyms or homonyms will be considered accepted: the one with the lowest registration number, except in cases of conservation.

History

(Condensed from the "PhyloCode"'s Preface [ [http://www.ohiou.edu/phylocode/preface.html#preface-history International Code of Phylogenetic Nomenclature, Version 4b - Preface] ] .)

The "PhyloCode" grew out of a workshop at Harvard University in August 1998, where decisions were made about its scope and content. Many of the workshop participants, together with several other people who subsequently joined the project, served as an advisory group. In April 2000, a draft was made public on the web and comments were solicited from the scientific community.

A second workshop was held at Yale University in July 2002, at which some modifications were made in the rules and recommendations of the "PhyloCode". Other revisions have been made from time to time as well.

The First International Phylogenetic Nomenclature Meeting, which took place from July 6, 2004 to July 9, 2004 in Paris, France, was attended by about 70 systematic and evolutionary biologists from 11 nations [cite journal|last=Laurin|first=M.|coauthors=and P. D. Cantino|year=2004|title=First international phylogenetic nomenclature meeting: a report|url=|journal=Zool. Scr.|issn=0300-3256|volume=33|issue=5|pages=475–479|doi=10.1111/j.0300-3256.2004.00176.x] . This was the first open, multi-day conference that focused entirely on phylogenetic nomenclature, and it provided the venue for the inauguration of a new association, the International Society for Phylogenetic Nomenclature (ISPN). The ISPN membership elects the Committee on Phylogenetic Nomenclature (CPN), which has taken over the role of the advisory group that oversaw the earlier stages of development of the PhyloCode.

The Second International Phylogenetic Nomenclature Meeting took place from June 28, 2006 to July 2, 2006 at Yale University (New Haven, Connecticut, U.S.A.). [cite journal|last=Laurin|first=M.|coauthors=and P. D. Cantino|year=2007|title=Second meeting of the International Society for Phylogenetic Nomenclature: a report|journal=Zool. Scr.|volume=36|pages=109-117|doi=10.1111/j.1463-6409.2006.00268.x]

The Third International Phylogenetic Nomenclature Meeting took place from July 21, 2008 to July 22, 2008 at Dalhousie University (Halifax, Nova Scotia, Canada). (A published report is forthcoming.)

Influences

The theoretical foundation of the "PhyloCode" was developed in a series of papers by de Queiroz and Gauthier [cite journal|last=de Queiroz|first=K.|coauthors=and J. Gauthier|year=1990|title=Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names|journal=Syst. Zool|volume=39|pages=307–322] [cite journal|last=de Queiroz|first=K.|coauthors=and J. Gauthier|year=1992|title=Phylogenetic taxonomy|journal=Annu. Rev. Ecol. Syst.|volume=23|pages=449–480] [cite journal|last=de Queiroz|first=K.|coauthors=and J. Gauthier|year=1994|title=Toward a phylogenetic system of biological nomenclature|journal=Trends Ecol. Evol.|volume=9|pages=27–31] , which was foreshadowed by earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree [cite journal|last=Ghiselin|first=M. T.|year=1984|title="Definition," "character," and other equivocal terms|journal=Syst. Zool|volume=33|pages=104–110] .

Whenever possible, the writers of the "PhyloCode" used the draft "BioCode" [cite journal|last=Greuter|first=W.|coauthors=D. L. Hawksworth, J. McNeill, A. Mayo, A. Minelli, P. H. A. Sneath, B. J. Tindall, P. Trehane, and P. Tubbs|year=1998|title=Draft BioCode (1997): the prospective international rules for the scientific names of organisms|journal=Taxon|volume=47|pages=127–150] , which attempted to unify the rank-based approach into a single code, as a model. Thus, the organization of the "PhyloCode", some of its terminology, and the wording of certain rules are derived from the "BioCode". Other rules are derived from one or more of the rank-based codes, particularly the botanical [cite book|last=Greuter|first=W.|coauthors=F. R. Barrie, H. M. Burdet, W. G. Chaloner, V. Demoulin, D. L. Hawksworth, P. M. Jørgensen, J. McNeill, D. H. Nicolson, P. C. Silva, and P. Trehane|year=1994|title=International Code of Botanical Nomenclature (Tokyo Code)|publisher=Koeltz Scientific Books, Königstein, Germany] [cite book|last=Greuter|first=W.|coauthors=F. R. Barrie, H. M. Burdet, V. Demoulin, T. S. Filgueiras, D. L. Hawksworth, J. McNeill, D. H. Nicolson, P. C. Silva, J. E. Skog, P. Trehane, and N. J. Turland|year=2000|title=International Code of Botanical Nomenclature (Saint Louis Code)|publisher=Koeltz Scientific Books, Königstein, Germany] [cite book|last=McNeill|first=J.|coauthors=F. R. Barrie, H. M. Burdet, V. Demoulin, D. L. Hawksworth, K. Marhold, D. H. Nicolson, J. Prado, P. C. Silva, J. E. Skog, J. H. Wiersema, and N. J. Turland|year=2006|title=International Code of Botanical Nomenclature (Vienna Code)|publisher=Gantner, Ruggell, Liechtenstein] and zoological [cite book|last=International Commission on Zoological Nomenclature|year=1985|title=International Code of Zoological Nomenclature|edition=3rd ed.|publisher=International Trust for Zoological Nomenclature] [cite book|last=International Commission on Zoological Nomenclature|year=1999|title=International Code of Zoological Nomenclature|edition=4th ed.|publisher=International Trust for Zoological Nomenclature] codes. However, many rules in the "PhyloCode" have no counterpart in the any code based on taxonomic ranks because of fundamental differences in the definitional foundations of the alternative systems.

Future

The "PhyloCode" is controversial. The number of supporters for official adoption of the "PhyloCode" is still small, and it is uncertain, as of 2008, when the code will be implemented and how widely it will be followed. Some supporters believe that it should only be implemented, at least at first, as a set of rules accompanying the associated registration database, RegNum, and that acceptance by the scientific community may proceed from the popularization of RegNum as a utility for finding clade names and definitions.

A list of published critiques of the "PhyloCode" can be found on the [http://phylonames.org/literature.php?part=6 ISPN's website] , as can [http://phylonames.org/literature.php?part=7 a list of rebuttals] .

References

Literature

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* including proposal, but without the 150 supporting signatories
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External links

* [http://www.ohiou.edu/phylocode/index.html The PhyloCode (current draft)]
* [http://phylonames.org/ International Society for Phylogenetic Nomenclature]
* [http://www.phylonames.org/forum/ International Society for Phylogenetic Nomenclature Discussion Forum]
* [http://phylonames.org/literature.php Literature on Phylogenetic Nomenclature]
* Christine Soares, [http://www.sciam.com/article.cfm?articleID=000D7477-4199-1179-819983414B7FFE9F What's in a Name?] , "Scientific American", (November 2004).
* [http://www.systass.org/events_archive/phylocode-debate.html PhyloCode debate]
* [http://discovermagazine.com/2005/apr/pushing-phylocode What if we decide to rename every living thing on Earth?] , "Discovery Magazine", (04.28.2005)


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