PhyloCode

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CLADISTICS
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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".)
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

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 (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.

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.

Many think it would not be unreasonable for a Phylocode-based phylogenetic tree to exist in tandem with, and add an evolutionary perspective to, a traditional classification system. The major problem of a strictly phylogenetic taxonomy is that due to the inevitable incompleteness of the fossil record, definite assignment of transitional taxa to clades is often impossible because the MRCA can usually only be conjectured and even if likely candidates are found it is impossible to tell whether they are indeed the MRCA and not closely related species; only in Late Pleistocene and more recent species is it generally possible at all to assign them firmly to a place in the evolutionary sequence. In the most extreme case, if fossil forms close to the point of divergence of one lineage happen to be found in a sequence running backwards in time, and are one after another used to define clades, this may lead to an inordinate number of closely nested mini-clades (because new discoveries which are demonstrably part of the clade would still be excluded from it as per the previous definition), or a constant redefinition of clades, which would both be unacceptable. To put it bluntly, phylogenetic taxonomy would like full knowledge which taxa consititute nodes, but in reality such knowledge is generally unavailable.

A recent trend seems to be to combine the strong points of both systems: the Linnean hierarchy which is somewhat arbitrary is precisely for this reason able to include new, transitional forms without major reshuffling, while phylogenetic nomenclature can provide a better account of evolutionary relationships. Essentially, the result is a taxonomy utilizing the familiar Linnean levels, but also redefinition of these according to synapomorphic traits (the infrequent use of the latter has been long recognized as a major weakness of the Linnean system). Such an approach makes frequent use of intermediate Linnean levels such as subfamilies or tribes. This is possible because the Linnean hierarchy at least in categories lower than orders quite well corresponds to major radiation events (although these were not contemporaneous in different phyla; while most living bird families evolved during the Oligo-/Eocene, this is not correct for insects, for example). Should such an approach prove satisfying and find widespread use before PhyloCode is adapted by a significant number of scientists, the latter approach will probably be dropped as it would not provide an actual improvement while running danger of obfuscationd systematics by creating a large number of uninformative mini-clades or confusing junior synonyms.

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



Credits

Credits: This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "PhyloCode"; copied to Palaeos org MAK061004

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