The PhyloCode is associated with the International Society for Phylogenetic Nomenclature (ISPN).

Overview

The PhyloCode proposes to regulate phylogenetic nomenclature by providing rules for how to decide which combinations of names and definitions will be considered established (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 accepted (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).

However the degree to which this can be done is questionable, as an article from Discovery Magazine notes:

The traditional Linnaean system for classifying organisms and the upstart PhyloCode look very similar at first glance. Species are organized in a branching hierarchy, and their names bear more than a passing resemblance. But a closer look reveals some fundamental differences. In the Linnaean system, groups of organisms are nested within each other based on their physical similarity. The hierarchy is organized in neat rows so that every species belongs to a family, every family to an order, and so on. The PhyloCode does away with these strict rankings. Instead, it classifies species in a true family tree, with each organism connected to others by common ancestry. Biologists now know, for instance, that crocodiles and birds are descended from the same early reptiles. The PhyloCode reflects this by grouping Crocodilia and Aves on adjacent branches that lead back to the group Reptilia. Taxonomists have tried to reshuffle the Linnaean system in recent years to take common ancestry into account, but vestiges of the old thinking remain. For example, in the Linnaean scheme above (one of several configurations), Reptilia and Aves are both major classes of equal rank in the hierarchy.

Registration database

If and when it is implemented, the PhyloCode will be associated with a registration database, called RegNum, which will store all clade names and definitions that will be considered acceptable. 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 accepted: 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.).

The Third International Phylogenetic Nomenclature Meeting will take place from July 21, 2008 to July 23, 2008 at Dalhousie University (Halifax, Nova Scotia, Canada).

The actual origins are a bit more complicated and revolutionary than such however, stemming from the inadequacy of the Linnean system with respect to practical application. The two scientists involved, after a period of intense frustration with the increasingly dysfunctional system decided to start from scratch. Again from Discovery Magazine:

They met in graduate school, first at San Diego State University, where they both received master’s degrees, and then in the Ph.D. program at the University of California at Berkeley in the early 1980s. They shared the same adviser there, Richard Estes, and wrote papers together on the phylogeny of lizards. As part of their work, they created a lizard family tree, but when they began to assign names to the important branching points on the tree, they realized there were more groups to name than there were ranks in the traditional system. “I started using these exotic ranks like parvorder, cohort, and microorder, and all that kind of crap,” Gauthier says. “Then we’d learn more about the tree, and all the names would have to change. I thought, ‘That sucks. All these ranks, they’re a problem.’”

Beginning in 1983, Gauthier and de Queiroz worked every Friday—“from whenever Jacques woke up until midnight”, de Queiroz says—trying to figure out a better scheme. Finally, in 1992, they published a rabble-rousing paper in Annual Review of Ecology and Systematics. The paper condemned the Linnaean system as “a body of conventions based on a pre-Darwinian worldview” and broadly outlined an alternate phylogenetic system of taxonomy. “My idea was that we’d let the traditional codes take up these ideas”, de Queiroz says. “But a lot of us figured we’d be waiting for decades.” He was reluctant to draft a new code on his own, knowing it would be a legalistic and intensely pedantic exercise. But eventually Philip Cantino, a botanist at Ohio University and an early adopter of the PhyloCode, agreed to help.

In 1998 a group of 27 scientists from five countries gathered for a workshop at Harvard University to discuss the new system. Two years later, a draft version of the PhyloCode—a preamble, 21 articles, and two appendixes—was posted on the Internet. That’s when things started to get ugly.

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.

A list of published critiques of the PhyloCode can be found on the ISPN's website, as can a list of rebuttals

References

• Anderson, J. S. (2002). "Use of well-known names in phylogenetic nomenclature: a reply to Laurin". Syst. Biol 51 (5): 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". Harvard papers in botany 3 315–330.
• Benton, M. J. (2000). "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?". Biological Reviews 75 (4): 633–648.
• 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". The Botanical Review 69 (1): 79–92.
• de Queiroz, K. (1992). "Phylogenetic definitions and taxonomic philosophy". Biol. Philos. 7 (3): 295–313.
• de Queiroz, K. (2006). "The PhyloCode and the distinction between taxonomy and nomenclature". Syst. Biol. 55 (1): 160–162.
• de Queiroz, K.; and P. D. Cantino (2001). "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 (1): 27–31.
• Dominguez, E.; and Q. D. Wheeler (1997). "Taxonomic stability is ignorance". Cladistics 13 (4): 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). 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.
• 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 (5): 475–479.
• Laurin, M.; K. de Queiroz, and P. D. Cantino (2006). "Sense and stability of taxon names". Zool. Scr. 35 (1): 113–114.
• Nordal, I.; and B. Stedje (Coordinators) (2005). "Letters to the Editor: Paraphyletic taxa should be accepted". Taxon 54 (1): 5–6. 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.
• Sereno, P. C. (1999). "Definitions in phylogenetic taxonomy: critique and rationale". Syst. Biol. 48 (2): 329–351.
• Sereno, P. C. (2005). "The logical basis of phylogenetic taxonomy". Syst. Biol. 54 595–619.

External links

• The PhyloCode (current draft)
• International Society for Phylogenetic Nomenclature
• International Society for Phylogenetic Nomenclature Discussion Forum
• Literature on Phylogenetic Nomenclature
• Christine Soares, What's in a Name?, Scientific American, (November 2004).
• PhyloCode debate
• What if we decide to rename every living thing on Earth?, Discovery Magazine, (04.28.2005)