PhyloCode

Types of clade (Note: "stem-based" is now "branch-based".)

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.).

Registration Database

When implemented, 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).

Definition Forms

In PhyloCode, a clade name may be defined in one of the following manners (not exhaustive):

• Node-Based: "the clade stemming from the most recent common ancestor of 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"
• Apomorphy-Based: "the clade stemming from the first organism or species to possess apomorphy M as inherited by A"
• Branch-Modified Crown Clade: "the clade stemming from the most recent common ancestor of A and all extant (or Recent) organisms or species that share a more recent common ancestor with A than with Z"
• Apomorphy-Modified Crown Clade: "the clade stemming from the most recent common ancestor of A and all extant (or Recent) organisms or species that possess apomorphy M as inherited by A"

Letters indicate "specifiers"; specifically A, B, and Z indicate specimens or species, and M indicates a derived character trait, or apomorphy. All specifiers used in PhyloCode definitions must be specimens, species, or apomorphies.

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. Minor revisions have been posted from time to time as well.

The First International Phylogenetic Nomenclature Meeting, which took place July 6 - 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 June 28 - July 2, 2006 at Yale University (New Haven, Connecticut, U.S.A.).

Future

PhyloCode is still a contentious issue. The number of supporters for official adoption of 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 even believe that it should only be implemented, at least at first, as rules accompanying the associated registration database, RegNum, and that authority may proceed from the popularization of RegNum as a utility for finding clade names and definitions.

References

• Andersion, 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 rules
• International Society of Phylogenetic Nomenclature
• Christine Soares, What's in a Name?, Scientific American, (November 2004).
• Phylocode debate