PhyloCode

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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).

Contents

[edit] Overview

The PhyloCode will regulate phylogenetic nomenclature by providing rules for how to decide which combinations of names and definitions will be considered validly published (Ch. II), which of those will be considered homonyms (Art. 13) or synonyms (Art. 14), and which one of a set of synonyms or homonyms will be considered valid (generally the one registered first, see below).

Additionally, the PhyloCode will only allow the naming of clades (Art. 1.1), not of paraphyletic or polyphyletic groups, and will only allow the use of specimens, species, and apomorphies as specifiers (anchors) (Art. 11).

However the degree to which this can be done is questionable, as an article from Discovery Magazine notes: "The traditional Linnaean system for classifying organisms and the upstart PhyloCode look very similar at first glance. Species are organized in a branching hierarchy, and their names bear more than a passing resemblance. But a closer look reveals some fundamental differences. In the Linnaean system, groups of organisms are nested within each other based on their physical similarity. The hierarchy is organized in neat rows so that every species belongs to a family, every family to an order, and so on. The PhyloCode does away with these strict rankings. Instead, it classifies species in a true family tree, with each organism connected to others by common ancestry. Biologists now know, for instance, that crocodiles and birds are descended from the same early reptiles. The PhyloCode reflects this by grouping Crocodilia and Aves on adjacent branches that lead back to the group Reptilia. Taxonomists have tried to reshuffle the Linnaean system in recent years to take common ancestry into account, but vestiges of the old thinking remain. For example, in the Linnaean scheme above (one of several configurations), Reptilia and Aves are both major classes of equal rank in the hierarchy."

[edit] Registration database

If and when it is implemented, the PhyloCode will be associated with a registration database, called RegNum, which will store all clade names and definitions that will be considered potentially valid. 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 valid: the one with the lowest registration number, except in cases of conservation. (Preventing homonyms and some types of synonyms of valid names from being registered is, of course, easy in a computerized database.)

[edit] History

(Condensed from the PhyloCode's 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. 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.).

The Third International Phylogenetic Nomenclature Meeting will take place from July 21, 2008 to July 23, 2008 at Dalhousie University (Halifax, Nova Scotia, Canada).

[edit] Future

The PhyloCode is controversial. The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2007, 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 literature critiquing the PhyloCode can be found on the ISPN's website, as can a list of rebuttals.

[edit] References

[edit] External links

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Topics in phylogenetics
Relevant fields
Basic concepts
Inference methods
Current topics
PhyloCode · DNA barcoding
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