PhyloCode

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.).

Contents

1 Registration Database
2 Definition Forms
3 History
4 Future
5 References
6 External links

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).

Definition Forms

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

Node-Based: "the most recent common ancestor 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.

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. Other revisions have been made 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

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.

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 of Phylogenetic Nomenclature]
Christine Soares, [What's in a Name?], Scientific American, (November 2004).
[Phylocode debate]

[ edit] Topics in phylogenetics
Relevant fields: phylogenetics \| computational phylogenetics \| molecular phylogeny \| cladistics
Basic concepts: synapomorphy \| phylogenetic tree \| phylogenetic network \| long branch attraction
Phylogeny inference methods: maximum parsimony \| maximum likelihood \| neighbour joining \| UPGMA
Current topics: PhyloCode \| DNA barcoding
List of evolutionary biology topics

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