PhyloCode
The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a formal set of rules governing phylogenetic nomenclature. It is specifically designed to regulate the naming of clades, leaving the governance of species names up to the rank-based nomenclature codes.
The PhyloCode is associated with the International Society for Phylogenetic Nomenclature. The companion volume, Phylonyms, was published in 2020, establishing the first 300 clade names under the PhyloCode. RegNum is an associated online database for registered clade names.
The PhyloCode regulates phylogenetic nomenclature by providing rules for deciding which associations of names and definitions are 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. The PhyloCode only governs the naming of clades, not of paraphyletic or polyphyletic groups, and only allows the use of specimens, species, and apomorphies as specifiers.
Phylogenetic nomenclature
Unlike rank-based nomenclatural codes, 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 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 and uses specifiers 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 :
- Minimum-clade definition : "the clade originating with the most recent common ancestor of A and B" or "he smallest clade containing A and B"
- Maximum-clade definition : "the clade consisting of A and all organisms or species that share a more recent common ancestor with A than with Z" or "the clade originating in the earliest ancestor of A that is not an ancestor of Z" or "the largest clade containing A but not Z".
- Apomorphy-based definition: "the clade originating in the ancestor in which apomorphy M, as inherited by A, originated" or "the clade for which M, as inherited by A, is an apomorphy" or "the clade characterized by apomorphy M as inherited by A".
The following table gives examples of phylogenetic definitions of clades that also have ranks in traditional nomenclature. When all the specifiers in a node-based definition are extant specimens or species, as in the following definition of Mammalia, a crown group is defined.
| Name | Rank | Type | Phylogenetic definition |
| Hadrosauridae | Family | Hadrosaurus Leidy 1858 | The smallest clade containing Hadrosaurus foulkii Leidy 1858, Lambeosaurus lambei Parks 1923, and Saurolophus osborni Brown 1912. |
| Mammalia | Class | N/A | The smallest crown clade containing Homo sapiens Linnaeus 1758, Didelphis marsupialis Linnaeus 1758, and Tachyglossus aculeatus . |
Versions
PhyloCode has gone through several revisions., the current version is 6, released on the website on June 8, 2020.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
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Registration database
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 from July 6 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. The ISPN membership elects the Committee on Phylogenetic Nomenclature, 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.
The Third International Phylogenetic Nomenclature Meeting took place from July 21, 2008, to July 22, 2008, at Dalhousie University.
The PhyloCode went into effect with the publication of the companion volume, Phylonyms, in 2020.
Influences
The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and Gauthier, which was foreshadowed by earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree.Whenever possible, the writers of the PhyloCode used the draft BioCode, 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 and zoological codes. However, many rules in the PhyloCode have no counterpart in any code based on taxonomic ranks because of fundamental differences in the definitional foundations of the alternative systems. Note that the PhyloCode does not govern the names of species, whose rules of availability, typification, etc., remain regulated by the requisite traditional Code of Nomenclature.
Future
The PhyloCode is controversial and has inspired considerable criticism from some taxonomists. While inaugurated decades ago, the number of supporters for widespread adoption of the PhyloCode is still small, and the publication of PhyloCode literature stagnated in the mid-2010s, before accelerating after publication of Phylonyms in 2020 and of the launch of the , which is a journal dedicated to the publication of nomenclatural acts valid under the PhyloCode. To be valid under the PhyloCode, taxon names and associated definitions should be registered in the database.A list of published critiques of the PhyloCode can be found on the , as can a list of rebuttals.
Literature
- including proposal, but without the 150 supporting signatories