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The ''International Code of Phylogenetic Nomenclature'', known as the ''PhyloCode'' for short, is a formal set of rules governing
phylogenetic nomenclature Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a '' type'', whi ...
. Its current version is specifically designed to regulate the naming of
clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyly, monophyletic – that is, composed of a common ancestor and all its lineage (evolution), lineal descendants – on a phylogenetic tree. ...
s, leaving the governance of
species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
names up to the rank-based nomenclature codes ('' ICN'', '' ICNCP'', '' ICNP'', '' ICZN'', '' ICVCN''). The ''PhyloCode'' is associated with the International Society for Phylogenetic Nomenclature (ISPN). The companion volume, ''Phylonyms'', establishes 300 taxon names under ''PhyloCode'', serving as examples for those unfamiliar with the code. 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 (generally the one registered first; see below). The ''PhyloCode'' only governs the naming of
clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyly, monophyletic – that is, composed of a common ancestor and all its lineage (evolution), lineal descendants – on a phylogenetic tree. ...
s, not of
paraphyletic In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and most of its descendants, excluding a few monophyletic subgroups. The group is said to be paraphyletic ''with respect to'' the excluded subgroups. In ...
or
polyphyletic A polyphyletic group is an assemblage of organisms or other evolving elements that is of mixed evolutionary origin. The term is often applied to groups that share similar features known as Homoplasy, homoplasies, which are explained as a result ...
groups, and only allows the use of specimens,
species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
, and apomorphies as specifiers (anchors).


Phylogenetic nomenclature

Unlike rank-based nomenclatural codes (''ICN'', ''ICZN'', ''ICNB''), the ''PhyloCode'' does not require the use of ranks, although it does optionally allow their use. The rank-based codes define
taxa In biology, a taxon (back-formation from ''Taxonomy (biology), taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known ...
using a rank (such as
genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...
,
family Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its ...
, 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 A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree (graph theory), tree showing the evolutionary relationships among va ...
(i.e., ancestry and descent) and uses specifiers (e.g., species, specimens, apomorphies) to indicate actual
organisms In biology, an organism () is any life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), taxonomy into groups such as Multicellular o ...
. 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 ancestor In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA) or concestor, of a set of organisms is the most recent individual from which all the organisms of the set are Common descent, ...
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." Another term for definitions of this sort is stem-based. * Apomorphy-based: "the clade originating with the first organism or species to possess apomorphy M inherited by A". Other types of definition are possible as well, taking into account not only organisms' phylogenetic relations and apomorphies but also whether or not related organisms are
extant Extant is the opposite of the word extinct. It may refer to: * Extant hereditary titles * Extant literature, surviving literature, such as ''Beowulf'', the oldest extant manuscript written in English * Extant taxon, a taxon which is not extinct, ...
. 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 In phylogenetics, the crown group or crown assemblage is a collection of species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A speci ...
is defined. (The traditional definition of Mammalia is less restrictive, including some fossil groups outside of the crown group.)


Versions

The draft of the ''PhyloCode'' has gone through several revisions. All older versions can be foun
on the website
, the current version is 5, finalized January 2014 and released 21 January 2019.


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



(includin







*

(Arts. 1–3) *

(Arts. 4–5) *

(Arts. 6–8) *

(Arts. 9–11) *

(Arts. 12–15) *

(Art. 16) *

(Arts. 17–18) *

(Art. 19) *

(Art. 20) *

(Art. 21) *

(Art. 22)





*

** ttp://www.ohio.edu/phylocode/appendixB.html#appendix-b Appendix B. Code of Ethics


Registration database

Once implemented, the ''PhyloCode'' will be associated with a registration
database In computing, a database is an organized collection of Data (computing), data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The Databas ...
, 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 specimens through
phylogenetic In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...
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 is a Private university, private Ivy League research university in Cambridge, Massachusetts. Founded in 1636 as Harvard College and named for its first benefactor, the History of the Puritans in North America, Puritan cler ...
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 Yale University is a Private university, private research university in New Haven, Connecticut. Established in 1701 as the Collegiate School, it is the List of Colonial Colleges, third-oldest institution of higher education in the United Sta ...
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 () is the Capital city, capital and List of communes in France with over 20,000 inhabitants, most populous city of France, with an estimated population of 2,165,423 residents in 2019 in an area of more than 105 km² (41 sq mi), ma ...
,
France France (), officially the French Republic ( ), is a country primarily located in Western Europe. It also comprises of Overseas France, overseas regions and territories in the Americas and the Atlantic Ocean, Atlantic, Pacific Ocean, Pac ...
, was attended by about 70 systematic and
evolution Evolution is change in the heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to ...
ary
biologist A biologist is a scientist who conducts research in biology. Biologists are interested in studying life on Earth, whether it is an individual Cell (biology), cell, a multicellular organism, or a Community (ecology), community of Biological inter ...
s from 11 nations. This was the first open, multi-day conference that focused entirely on
phylogenetic In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...
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 Yale University is a Private university, private research university in New Haven, Connecticut. Established in 1701 as the Collegiate School, it is the List of Colonial Colleges, third-oldest institution of higher education in the United Sta ...
(
New Haven New Haven is a city in the U.S. state of Connecticut. It is located on New Haven Harbor on the northern shore of Long Island Sound in New Haven County, Connecticut and is part of the New York City metropolitan area. With a population of 134,023 ...
,
Connecticut Connecticut () is the southernmost state in the New England region of the Northeastern United States. It is bordered by Rhode Island to the east, Massachusetts to the north, New York (state), New York to the west, and Long Island Sound to the ...
, U.S.). The Third International Phylogenetic Nomenclature Meeting took place from July 21, 2008, to July 22, 2008, at
Dalhousie University Dalhousie University (commonly known as Dal) is a large public university, public research university in Nova Scotia, Canada, with three campuses in Halifax, Nova Scotia, Halifax, a fourth in Bible Hill, Nova Scotia, Bible Hill, and a second med ...
( Halifax,
Nova Scotia Nova Scotia ( ; ; ) is one of the thirteen Provinces and territories of Canada, provinces and territories of Canada. It is one of the three Maritime Canada, Maritime provinces and one of the four Atlantic Canada, Atlantic provinces. Nova Scoti ...
, Canada). 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 A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree (graph theory), tree showing the evolutionary relationships among va ...
. 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 dos 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. While Phylonyms were published in spring 2020, it remains unclear how 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 published critiques of the ''PhyloCode'' can be found on th
ISPN's website
as can a list of rebuttals.


References


Literature

* * * * * * * * * * * * * * * * * * * including proposal, but without the 150 supporting signatories * * *


External links




International Society for Phylogenetic Nomenclature

International Society for Phylogenetic Nomenclature Discussion Forum

Literature on Phylogenetic NomenclatureRegNum
the official repository of phylogenetic clade names generated according to the rules of the PhyloCode * Christine Soares
What's in a Name?
''Scientific American'', (November 2004).
PhyloCode debateWhat if we decide to rename every living thing on Earth?
''Discovery Magazine'', (04.28.2005) {{Phylogenetics Nomenclature codes