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).

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, which of those will be considered homonyms or synonyms , 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, not of paraphyletic or polyphyletic groups, and will only allow the use of specimens, species, and apomorphies as specifiers (anchors).

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. 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) : Other types of definition are possible as well.
 * 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"

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 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

 * Preface (including Literature Cited)
 * Preamble
 * Division I. Principles
 * Division II. Rules
 * Chapter I. Taxa (Arts. 1-3)
 * Chapter II. Publication (Arts. 4-5)
 * Chapter III. Names (Arts. 6-8)
 * Chapter IV. Clade Names (Arts. 9-11)
 * Chapter V. Selection of Established Names (Arts. 12-15)
 * Chapter VI. Provisions for Hybrids (Art. 16)
 * Chapter VII. Orthography (Arts. 17-18)
 * Chapter VIII. Authorship of Names (Art. 19)
 * Chapter IX. Citation of Authors and Registration Numbers (Art. 20)
 * Chapter X. Species Names (Art. 21)
 * Chapter XI. Governance (Art. 22)
 * Glossary
 * Tables
 * Appendices
 * Appendix A. Registration Procedures and Data Requirements
 * Appendix B. Code of Ethics

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 Rcs (New Haven, Connecticut, U.S.A.).

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.)

Future
The PhyloCode is controversial, and has inspired downright hostility from some taxonomists. The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2009, whether the code will be implemented and if so, 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 ISPN's website, as can a list of rebuttals.

Literature



































 * including proposal, but without the 150 supporting signatories