PhyloCode



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, which do not have set ranks, unlike conventional Linnaean taxonomy. Later revisions may also include new rules for the naming of species, although it is likely that this will be left, at least provisionally, to the traditional codes (ICBN, ICZN, etc.).

Registration database
When implemented, the PhyloCode will be associated with a registration database, called RegNum, which will store clade names and definitions. It is hoped that this will provide a publicly-useable 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).

Definition forms
In the PhyloCode, a clade name may be defined in one of the following manners (not exhaustive):
 * Node-Based: "the most recent common ancestor (MRCA) of A and B (and C etc. as needed), and all its descendants" (note: A and B are descendants of the MRCA of A and B)
 * Branch-Based: "all organisms or species that share a more recent common ancestor with A (and B, C, etc. as needed) than with Z (and with Y, X, etc. as needed)" (note: A shares a more recent common ancestor with itself than with Z)
 * Apomorphy-Based: "the first organism or species to possess apomorphies M (and N etc. as needed) as inherited by A (and B etc. as needed), and all its descendants" (notes: if M evolves more than once, only the one event from which A has inherited it counts: if M is "walking on two legs" and A is Homo sapiens, then birds are not members of the clade; when the apomorphy is lost, the organisms that have lost it stay members of the clade: if M is flight and A is a sparrow, ostriches and penguins are members of the clade)
 * Branch-Modified Node-Based (to name a crown clade): "the most recent common ancestor of A (and B etc. as needed) and all extant (or Recent) organisms or species that share a more recent common ancestor with A (and B etc. as needed) than with Z (and with Y etc. as needed), and all its descendants" (note: the specifiers of the node-based clade are not explicitely mentioned; instead "all extant/Recent organisms/species that share a more recent common ancestor with A than with Z" – the extant/Recent members of a different, larger clade – are its specifiers; this also applies to the following definition type)
 * Apomorphy-Modified Node-Based (to name a crown clade): "the most recent common ancestor of A (and B etc. as needed) and all extant (or Recent) organisms or species that possess apomorphy M (and N etc. as needed) as inherited by A (and B etc. as needed), and all its descendants"

Letters indicate "specifiers" (also called "anchors"); specifically A, B, C, X, Y, and Z indicate specimens or species, and M and N indicate derived character states (apomorphies). All specifiers used in PhyloCode definitions must be specimens, species, or apomorphies. With the rather hypothetical exception of ancestor-based definitions ("A and all its descendants"), all definitions must have at least two specifiers.

History
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 July 6 – 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 June 28 – July 2, 2006 at Yale University (New Haven, Connecticut, U.S.A.).

Future
The PhyloCode is controversial. The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2006, 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.