Types of Clade (Note: "Stem-based" is now "branch-based", to avoid confusion with the term "stem group" which means "total clade minus crown clade".)

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.). Types of biological clade, as used in PhyloCode Diagram by User:Gdr File links The following pages link to this file: Cladistics PhyloCode User:Gdr/Gallery Categories: GFDL images ... Total group is a term used in systematics to refer to a crown group and its stem group together. ... A crown group is a living monophyletic group or clade, consisting of the last common ancestor of all living examples, plus all of its descendants. ... In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e. ... A clade is a term belonging to the discipline of cladistics. ... Linnaean taxonomy classifies living things into a hierarchy, originally starting with kingdoms. ... In biology, a species is one of the basic units of biodiversity. ... The International Code of Botanical Nomenclature is the set of rules according to which plants are given their formal botanical names (scientific names). ... The International Code of Zoological Nomenclature (ICZN) is a set of rules in zoology that have one fundamental aim: to provide the maximum universality and continuity in classifying all animals according to taxonomic judgment. ...

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). The term or expression database originated within the computer industry. ... A clade is a term belonging to the discipline of cladistics. ... A clade is a term belonging to the discipline of cladistics. ... A taxon (plural taxa), or taxonomic unit, is a grouping of organisms (named or unnamed). ... In biology, specimen is an individual animal or a plant or a microorganism that is used as a representative to study the properties of the whole population of that species. ... In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e. ... A database is an information set with a regular structure. ...

Definition forms

In the PhyloCode, a clade name may be defined in one of the following manners (not exhaustive): A clade is a term belonging to the discipline of cladistics. ...

• 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. The most recent common ancestor (MRCA) of any set of organisms is the most recent individual from which all organisms in the group are directly descended. ... In biology and ecology, an organism (in Greek organon = instrument) is a living being. ... In biology, a species is one of the basic units of biodiversity. ... It has been suggested that Clade be merged into this article or section. ... This article or section does not cite its references or sources. ... In biology, a species is one of the basic units of biodiversity. ... It has been suggested that Clade be merged into this article or section. ... A crown group is a living monophyletic group or clade, consisting of the last common ancestor of all living examples, plus all of its descendants. ... The most recent common ancestor (MRCA) of any set of organisms is the most recent individual from which all organisms in the group are directly descended. ... Extant means still existing. It is the opposite of extinct, and can be applied to species, cultures and works of culture (e. ... The Holocene epoch is a geological period that extends from the present day back to about 10,000 radiocarbon years, approximately 11,430 ± 130 calendar years BP (between 9560 and 9300 BC). ... In biology and ecology, an organism (in Greek organon = instrument) is a living being. ... In biology, a species is one of the basic units of biodiversity. ... It has been suggested that Clade be merged into this article or section. ... A crown group is a living monophyletic group or clade, consisting of the last common ancestor of all living examples, plus all of its descendants. ... The most recent common ancestor (MRCA) of any set of organisms is the most recent individual from which all organisms in the group are directly descended. ... Extant means still existing. It is the opposite of extinct, and can be applied to species, cultures and works of culture (e. ... The Holocene epoch is a geological period that extends from the present day back to about 10,000 radiocarbon years, approximately 11,430 ± 130 calendar years BP (between 9560 and 9300 BC). ... In biology and ecology, an organism (in Greek organon = instrument) is a living being. ... In biology, a species is one of the basic units of biodiversity. ... It has been suggested that Clade be merged into this article or section. ... In biology, specimen is an individual animal or a plant or a microorganism that is used as a representative to study the properties of the whole population of that species. ... In biology, a species is one of the basic units of biodiversity. ... It has been suggested that Clade be merged into this article or section. ...

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. Harvard University (incorporated as The President and Fellows of Harvard College) , is a private university in Cambridge, Massachusetts, USA. Founded in 1636,[1] Harvard is the oldest institution of higher learning still operating in the United States. ... 1998 (MCMXCVIII) was a common year starting on Thursday of the Gregorian calendar, and was designated the International Year of the Ocean [1]. // Coated in ice, power and telephone lines sag and often break, resulting in power outages. ... This article is about the year 2000. ... WWWs historical logo designed by Robert Cailliau The World Wide Web (WWW or simply the Web) is a system of interlinked, hypertext documents that runs over the Internet. ...

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. Yale redirects here. ... For album titles with the same name, see 2002 (album). ...

The First International Phylogenetic Nomenclature Meeting, which took place July 6 Р9, 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. City flag City coat of arms Motto: Fluctuat nec mergitur (Latin: Tossed by the waves, she does not sink) Paris Eiffel tower as seen from the esplanade du Trocad̩ro. ... Biological systematics is the study of the diversity of life on the planet earth, both past and present, and the relationships among living things through time. ... This article is about evolution in biology. ... A biologist is a scientist devoted to and producing results in biology through the study of organisms. ... In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e. ...

The Second International Phylogenetic Nomenclature Meeting took place June 28 – July 2, 2006 at Yale University (New Haven, Connecticut, U.S.A.). Yale redirects here. ... This article is about the city in Connecticut. ... It has been suggested that this article be split into multiple articles. ... For other uses, see United States (disambiguation) and US (disambiguation). ...

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. For the Manfred Mann album, see 2006 (album). ... The term or expression database originated within the computer industry. ... A clade is a term belonging to the discipline of cladistics. ...

References

• Anderson, J. S. 2002. Use of well-known names in phylogenetic nomenclature: a reply to Laurin. Syst. Biol. 51:822-827
• Baum, D. A., W. S. Alverson, and R. Nyffeler. 1998. A durian by any other name: taxonomy and nomenclature of the core Malvales. Harv. Pap. Bot. 3:315-330
• Benton, M. 2000. Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead? Biological Reviews 75:633-648 HTML fulltext
• Cantino, P. D. 2000. Phylogenetic nomenclature: addressing some concerns. Taxon 49:85-93
• Cantino, P. D. 2004. Classifying species versus naming clades. Taxon 53:795-798
• Carpenter, J. M. 2003. Critique of pure folly. Bot. Rev. 69:79-92
• de Queiroz, K. 1992. Phylogenetic definitions and taxonomic philosophy. Biol. Philos. 7:295-313
• de Queiroz, K. 2006. The PhyloCode and the distinction between taxonomy and nomenclature. Syst. Biol. 55:160-162
• de Queiroz, K., and P. D. Cantino. 2001a. Phylogenetic nomenclature and the PhyloCode. Bull. Zool. Nomencl. 58:254-271
• de Queiroz, K., and J. Gauthier. 1990. Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39:307-322
• de Queiroz, K., and J. Gauthier. 1992. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23:449-480
• de Queiroz, K., and J. Gauthier. 1994. Toward a phylogenetic system of biological nomenclature. Trends Ecol. Evol. 9:27-31
• Dominguez, E., and Q. D. Wheeler. 1997. Taxonomic stability is ignorance. Cladistics 13:367-372
• Donoghue, M. J., and J. A. Gauthier. 2004. Implementing the PhyloCode. Trends Ecol. Evol. 19:281-282
• Gauthier, J., and K. de Queiroz. 2001. Feathered dinosaurs, flying dinosaurs, crown dinosaurs, and the name "Aves". Pages 7-41 in New perspectives on the origin and early evolution of birds: proceedings of the International Symposium in Honor of John H. Ostrom (J. A. Gauthier and L. F. Gall, eds.). Peabody Museum of Natural History, Yale University, New Haven, Connecticut, U.S.A.
• Laurin, M. 2005. Dites oui au PhyloCode! Bull. Soc. Fr. Syst. 34:25-31
• Laurin, M., and P. D. Cantino. 2004. First International Phylogenetic Nomenclature Meeting: a report. Zool. Scr. 33:475-479
• Laurin, M., K. de Queiroz, and P. D. Cantino. 2006. Sense and stability of taxon names. Zool. Scr. 35:113-114
• Nordal, I. and B. Stedje. (Coordinators) (2005): Letters to the Editor: Paraphyletic taxa should be accepted. Taxon 54(1):5-6 PDF fulltext including proposal, but without the 150 supporting signatories
• Rieppel, O. 2006. The PhyloCode: a critical discussion of its theoretical foundation. Cladistics 22(2):186-197 HTML abstract
• Sereno, P. C. 1999. Definitions in phylogenetic taxonomy: critique and rationale. Syst. Biol. 48:329-351
• Sereno, P. C. 2005. The logical basis of phylogenetic taxonomy. Syst. Biol. 54:595-619.

External links

• PhyloCode (current draft)
• International Society for Phylogenetic Nomenclature
• International Society for Phylogenetic Nomenclature Discussion Forum
• Christine Soares, What's in a Name?, Scientific American, (November 2004).
• Phylocode debate