PhyloCode

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Overview

The PhyloCode will regulate phylogenetic nomenclature by providing rules for how to decide which combinations of names and definitions will be considered validly published (Ch. II), which of those will be considered homonyms (Art. 13) or synonyms (Art. 14), and which one of a set of synonyms or homonyms will be considered valid (generally the one registered first, see below).

Additionally, the PhyloCode will only allow the naming of clades (Art. 1.1), not of paraphyletic or polyphyletic groups, and will only allow the use of specimens, species, and apomorphies as specifiers/anchors (Art. 11).

Contrary to a common misconception, however, the use of ranks (genus, family, order etc.) will remain permitted (Art. 3); ranks will only be prevented from having any influence on the spelling or application of names. In other words, ranks can be added after nomenclature has been done.

Registration database

When implemented, the PhyloCode will be associated with a registration database, called RegNum, which will store all clade names and definitions that will be considered potentially valid. 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 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 valid: the one with the lowest registration number, except in cases of conservation. (Preventing homonyms and some types of synonyms of valid names from being registered is of course easy in a computerized database.)

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 Yale University (New Haven, Connecticut, U.S.A.).

Future

The PhyloCode is controversial. The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2007, 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.

References

• Anderson, J. S. (2002). "Use of well-known names in phylogenetic nomenclature: a reply to Laurin". Syst. Biol 51 (5): 822-827. doi:10.1080/10635150290102447. ISSN 1063-5157.
• Baum, D. A.; W. S. Alverson, and R. Nyffeler (1998). "A durian by any other name: taxonomy and nomenclature of the core Malvales". Harvard papers in botany 3: 315-330. ISSN 1043-4534.
• Benton, M. J. (2000). "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?". Biological Reviews 75 (4): 633-648. ISSN 0006-3231.
• Cantino, P. D. (2000). "Phylogenetic nomenclature: addressing some concerns". Taxon 49: 85-93. ISSN 0040-0262.
• Cantino, P. D. (2004). "Classifying species versus naming clades". Taxon 53: 795-798. ISSN 0040-0262.
• Carpenter, J. M. (2003). "Critique of pure folly". The Botanical Review 69 (1): 79-92. ISSN 0006-8101.
• de Queiroz, K. (1992). "Phylogenetic definitions and taxonomic philosophy". Biol. Philos. 7 (3): 295-313. doi:10.1007/BF00129972. ISSN 0169-3867.
• de Queiroz, K. (2006). "The PhyloCode and the distinction between taxonomy and nomenclature". Syst. Biol. 55 (1): 160-162. doi:10.1080/10635150500431221. ISSN 1063-5157.
• de Queiroz, K.; and P. D. Cantino (2001). "Phylogenetic nomenclature and the PhyloCode". Bull. Zool. Nomencl. 58: 254-271. ISSN 0007-5167.
• de Queiroz, K.; and J. Gauthier (1990). "Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names". Syst. Zool. 39: 307-322. ISSN 0039-7989.
• de Queiroz, K.; and J. Gauthier. (1992). "Phylogenetic taxonomy". Annu. Rev. Ecol. Syst. 23: 449-480. ISSN 0066-4162.
• de Queiroz, K.; and J. Gauthier (1994). "Toward a phylogenetic system of biological nomenclature". Trends Ecol. Evol. 9 (1): 27-31. doi:10.1016/0169-5347(94)90231-3. ISSN 0169-5347.
• Dominguez, E.; and Q. D. Wheeler (1997). "Taxonomic stability is ignorance". Cladistics 13 (4): 367-372. ISSN 748-3007.
• Donoghue, M. J.; and J. A. Gauthier (2004). "Implementing the PhyloCode". Trends Ecol. Evol. 19: 281-282. doi:10.1016/j.tree.2004.04.004. ISSN 0169-5347.
• Gauthier, J.; and K. de Queiroz (2001). "Feathered dinosaurs, flying dinosaurs, crown dinosaurs, and the name "Aves"", in J. A. Gauthier and L. F. Gall (eds.): New perspectives on the origin and early evolution of birds: proceedings of the International Symposium in Honor of John H. Ostrom. New Haven, Connecticut, U.S.A.: Peabody Museum of Natural History, Yale University, 7-41 pp. 
• Laurin, M. (2005). "Dites oui au PhyloCode!" (PDF fulltext). Bull. Soc. Fr. Syst. 34: 25-31. ISSN 1240-3253.
• Laurin, M.; and P. D. Cantino (2004). "First International Phylogenetic Nomenclature Meeting: a report". Zool. Scr. 33 (5): 475-479. doi:10.1111/j.0300-3256.2004.00176.x. ISSN 0300-3256.
• Laurin, M.; K. de Queiroz, and P. D. Cantino (2006). "Sense and stability of taxon names". Zool. Scr. 35 (1): 113-114. doi:10.1111/j.1463-6409.2006.00219.x. ISSN 0300-3256.
• Nordal, I.; and B. Stedje (Coordinators) (2005). "Letters to the Editor: Paraphyletic taxa should be accepted" (PDF fulltext). Taxon 54 (1): 5-6. ISSN 0040-0262. including proposal, but without the 150 supporting signatories
• Rieppel, O. (2006). "The PhyloCode: a critical discussion of its theoretical foundation" (HTML abstract). Cladistics 22 (2): 186-197. doi:10.1111/j.1096-0031.2006.00097.x.
• Sereno, P. C. (1999). "Definitions in phylogenetic taxonomy: critique and rationale". Syst. Biol. 48 (2): 329-351. doi:10.1080/106351599260328. ISSN 1063-5157.
• Sereno, P. C. (2005). "The logical basis of phylogenetic taxonomy". Syst. Biol. 54: 595-619. doi:10.1080/106351591007453. ISSN 1063-5157.