PhyloCode
Encyclopedia
The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a developing draft for a formal set of rules governing phylogenetic nomenclature
. Its current version is specifically designed to regulate the naming of clade
s, 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).
Additionally, the PhyloCode will only allow the naming of clade
s, not of paraphyletic or polyphyletic groups, and will only allow the use of specimen
s, species
, and apomorphies as specifiers (anchors).
(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
, specimen
s, 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.
The following table gives examples of the differences between rank-based and phylogenetic definitions.
, called RegNum
, which will store all clade
names and definitions that will be considered acceptable. 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 specimen
s 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.
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 evolution
ary biologist
s 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 took place from July 21, 2008 to July 22, 2008 at Dalhousie University
(Halifax, Nova Scotia
, Canada
). (A published report is forthcoming.)
, 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 the any code based on taxonomic ranks because of fundamental differences in the definitional foundations of the alternative systems.
The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2011, 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.
Phylogenetic nomenclature
Phylogenetic nomenclature or phylogenetic taxonomy is an alternative to rank-based nomenclature, applying definitions from cladistics . Its two defining features are the use of phylogenetic definitions of biological taxon names, and the lack of obligatory ranks...
. Its current version is specifically designed to regulate the naming of clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
s, leaving the governance of species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
names up to the rank-based codes
Nomenclature Codes
Nomenclature codes or codes of nomenclature are the various rulebooks that govern biological taxonomic nomenclature, each in their own broad field of organisms...
(ICBN, ICZN
International Code of Zoological Nomenclature
The International Code of Zoological Nomenclature is a widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals...
, ICNB).
The PhyloCode is associated with the International Society for Phylogenetic Nomenclature
International Society for Phylogenetic Nomenclature
The International Society for Phylogenetic Nomenclature was established to encourage and facilitate the development and use of, and communication about, phylogenetic nomenclature. It organizes periodic scientific meetings and is overseeing the completion and implementation of the PhyloCode....
(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 clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
s, not of paraphyletic or polyphyletic groups, and will only allow the use of specimen
Specimen
A specimen is a portion/quantity of material for use in testing, examination, or study.BiologyA laboratory specimen is an individual animal, part of an animal, a plant, part of a plant, or a microorganism, used as a representative to study the properties of the whole population of that species or...
s, species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
, and apomorphies as specifiers (anchors).
Phylogenetic nomenclature
Unlike previous, rank-based nomenclatural codesNomenclature Codes
Nomenclature codes or codes of nomenclature are the various rulebooks that govern biological taxonomic nomenclature, each in their own broad field of organisms...
(ICBN, ICZN
International Code of Zoological Nomenclature
The International Code of Zoological Nomenclature is a widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals...
, ICNB), the PhyloCode does not require the use of ranks
Taxonomic rank
In biological classification, rank is the level in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, and class. Each rank subsumes under it a number of less general categories...
, although it does optionally allow their use. The rank-based codes define taxa
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...
using a rank (such as genus
Genus
In biology, a genus is a low-level taxonomic rank used in the biological classification of living and fossil organisms, which is an example of definition by genus and differentia...
, family
Family
In human context, a family is a group of people affiliated by consanguinity, affinity, or co-residence. In most societies it is the principal institution for the socialization of children...
, etc.) and, in many cases, a type specimen or type subtaxon
Biological type
In biology, a type is one particular specimen of an organism to which the scientific name of that organism is formally attached...
. 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
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
, specimen
Specimen
A specimen is a portion/quantity of material for use in testing, examination, or study.BiologyA laboratory specimen is an individual animal, part of an animal, a plant, part of a plant, or a microorganism, used as a representative to study the properties of the whole population of that species or...
s, 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):
- Node-based: "the clade originating with the most recent common ancestorMost recent common ancestorIn genetics, the most recent common ancestor of any set of organisms is the most recent individual from which all organisms in the group are directly descended...
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.
| Name | Rank | Type | Possible Phylogenetic Definition |
|---|---|---|---|
| Tyrannosauridae Tyrannosauridae Tyrannosauridae is a family of coelurosaurian theropod dinosaurs which comprises two subfamilies containing up to six genera, including the eponymous Tyrannosaurus. The exact number of genera is controversial, with some experts recognizing as few as three... |
Family | Tyrannosaurus Tyrannosaurus Tyrannosaurus meaning "tyrant," and sauros meaning "lizard") is a genus of coelurosaurian theropod dinosaur. The species Tyrannosaurus rex , commonly abbreviated to T. rex, is a fixture in popular culture. It lived throughout what is now western North America, with a much wider range than other... Osborn 1905 |
the least inclusive clade containing Tyrannosaurus rex Osborn 1905, Gorgosaurus libratus Lambe 1914, and Albertosaurus sarcophagus Osborn 1905 |
| Mammalia | Class | N/A | the clade originating with the most recent common ancestor of Homo sapiens Linnaeus 1758 and Ornithorhynchus anatinus Blumenbach 1800 |
Versions
The draft of the PhyloCode has gone through several revisions. All older versions can be found on the website. As of January 12, 2010, the current version is 4c.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
Registration database
Once implemented, the PhyloCode will be associated with a registration databaseDatabase
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
, called RegNum
Regnum
Regnum may refer to:* The inheritable power to govern in Ancient Rome * Kingdom * Regnum news agency, a Russian news agency* Regnum Online, a computer game...
, which will store all clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
names and definitions that will be considered acceptable. It is hoped that this will provide a publicly-usable tool for associating clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
names with definitions, which could then be associated with sets of subtaxa
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...
or specimen
Specimen
A specimen is a portion/quantity of material for use in testing, examination, or study.BiologyA laboratory specimen is an individual animal, part of an animal, a plant, part of a plant, or a microorganism, used as a representative to study the properties of the whole population of that species or...
s 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 PhyloCodes Preface.)The PhyloCode grew out of a workshop at Harvard University
Harvard University
Harvard University is a private Ivy League university located in Cambridge, Massachusetts, United States, established in 1636 by the Massachusetts legislature. Harvard is the oldest institution of higher learning in the United States and the first corporation chartered in the country...
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
World Wide Web
The World Wide Web is a system of interlinked hypertext documents accessed via the Internet...
and comments were solicited from the scientific community.
A second workshop was held at Yale University
Yale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
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
Paris
Paris is the capital and largest city in France, situated on the river Seine, in northern France, at the heart of the Île-de-France region...
, France
France
The French Republic , The French Republic , The French Republic , (commonly known as France , is a unitary semi-presidential republic in Western Europe with several overseas territories and islands located on other continents and in the Indian, Pacific, and Atlantic oceans. Metropolitan France...
, was attended by about 70 systematic
Systematics
Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...
and evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
ary biologist
Biologist
A biologist is a scientist devoted to and producing results in biology through the study of life. Typically biologists study organisms and their relationship to their environment. Biologists involved in basic research attempt to discover underlying mechanisms that govern how organisms work...
s 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
International Society for Phylogenetic Nomenclature
The International Society for Phylogenetic Nomenclature was established to encourage and facilitate the development and use of, and communication about, phylogenetic nomenclature. It organizes periodic scientific meetings and is overseeing the completion and implementation of the PhyloCode....
(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
Yale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
(New Haven, Connecticut
Connecticut
Connecticut is a state in the New England region of the northeastern United States. It is bordered by Rhode Island to the east, Massachusetts to the north, and the state of New York to the west and the south .Connecticut is named for the Connecticut River, the major U.S. river that approximately...
, U.S.A.).
The Third International Phylogenetic Nomenclature Meeting took place from July 21, 2008 to July 22, 2008 at Dalhousie University
Dalhousie University
Dalhousie University is a public research university located in Halifax, Nova Scotia, Canada. The university comprises eleven faculties including Schulich School of Law and Dalhousie University Faculty of Medicine. It also includes the faculties of architecture, planning and engineering located at...
(Halifax, Nova Scotia
Nova Scotia
Nova Scotia is one of Canada's three Maritime provinces and is the most populous province in Atlantic Canada. The name of the province is Latin for "New Scotland," but "Nova Scotia" is the recognized, English-language name of the province. The provincial capital is Halifax. Nova Scotia is the...
, Canada
Canada
Canada is a North American country consisting of ten provinces and three territories. Located in the northern part of the continent, it extends from the Atlantic Ocean in the east to the Pacific Ocean in the west, and northward into the Arctic Ocean...
). (A published report is forthcoming.)
Influences
The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and GauthierJacques Gauthier
Jacques Armand Gauthier is a vertebrate paleontologist, comparative morphologist, and systematist, and one of the founders of the use of cladistics in biology....
, which was foreshadowed by earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
.
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 the any code based on taxonomic ranks because of fundamental differences in the definitional foundations of the alternative systems.
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 2011, 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
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
, RegNum
Regnum
Regnum may refer to:* The inheritable power to govern in Ancient Rome * Kingdom * Regnum news agency, a Russian news agency* Regnum Online, a computer game...
, and that acceptance by the scientific community may proceed from the popularization of RegNum as a utility for finding clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...
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.
External links
- The PhyloCode (current draft)
- International Society for Phylogenetic Nomenclature
- International Society for Phylogenetic Nomenclature Discussion Forum
- Literature on Phylogenetic Nomenclature
- Christine Soares, What's in a Name?, Scientific American, (November 2004).
- PhyloCode debate
- What if we decide to rename every living thing on Earth?, Discovery Magazine, (04.28.2005)