Biology:PhyloCode

Short description: Draft for a new code of nomenclature for clades

The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, 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, leaving the governance of species names up to the rank-based Nomenclature codes (ICN, ICZN, ICNB, ICTV).

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

The PhyloCode proposes to regulate phylogenetic nomenclature by providing rules for how to decide which associations of names and definitions will be considered established, which of those will be considered homonyms or synonyms, and which one of a set of synonyms or homonyms will be considered accepted (generally the one registered first; see below). The PhyloCode will only allow the naming of clades, not of paraphyletic or polyphyletic groups, and will only allow the use of specimens, species, and apomorphies as specifiers (anchors).

Phylogenetic nomenclature

Unlike rank-based nomenclatural codes (ICN, ICZN, ICNB), the PhyloCode does not require the use of ranks, although it does optionally allow their use. The rank-based codes define taxa using a rank (such as genus, family, etc.) and, in many cases, a type specimen or type subtaxon. The exact content of a taxon, other than the type, is not specified by the rank-based codes.

In contrast, under phylogenetic nomenclature, the content of taxa are delimited using a definition that is based on phylogeny (i.e., ancestry and descent) and uses specifiers (e.g., species, specimens, apomorphies) to indicate actual organisms. The formula of the definition indicates an ancestor. The defined taxon, then, is that ancestor and all of its descendants. Thus, the content of a phylogenetically defined taxon relies on a phylogenetic hypothesis.

The following are examples of types of phylogenetic definition (capital letters indicate specifiers):

• Node-based: "the clade originating with the most recent common ancestor of A and B" or "the least inclusive clade containing 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" or "the most inclusive clade containing A but not Z." Another term for definitions of this sort is stem-based.
• Apomorphy-based: "the clade originating with the first organism or species to possess apomorphy M inherited by A".

Other types of definition are possible as well, taking into account not only organisms' phylogenetic relations and apomorphies but also whether or not related organisms are extant.

The following table gives examples of phylogenetic definitions of clades that also have ranks in traditional nomenclature. When all the specifiers in a node-based definition are extant specimens or species, as in the following definition of Mammalia, a crown group is defined. (The traditional definition of Mammalia is less restrictive, including some fossil groups outside of the crown group.)

Name	Rank	Type	Possible phylogenetic definition
Tyrannosauridae	Family	Tyrannosaurus Osborn 1905	Least inclusive clade containing Tyrannosaurus rex Osborn 1905, Gorgosaurus libratus Lambe 1914, and Albertosaurus sarcophagus Osborn 1905
Mammalia	Class	N/A	Clade originating with the most recent common ancestor of humans, Homo sapiens Linnaeus 1758, and platypuses, Ornithorhynchus anatinus Shaw 1799
Rodentia	Order	N/A	Most inclusive clade containing the house mouse, Mus musculus Linnaeus 1758, but not the eastern cottontail, Sylvilagus floridanus Allen 1890
Neornithes (Modern birds)	Subclass	N/A	Clade originating with the most recent common ancestor of the extant members of the most inclusive clade containing the house sparrow Passer domesticus Linnaeus 1758 but not the dinosaur Stegosaurus armatus Marsh 1887
Tetrapoda	Superclass	N/A	Clade originating with the earliest ancestor from which Homo sapiens Linnaeus 1758 inherited limbs with fingers or toes

Versions

The draft of the PhyloCode has gone through several revisions. All older versions can be found on the website. As of July 2024, the current version is 4c.

Organization

As with other nomenclatural codes, the rules of the PhyloCode are organized as articles, which in turn are organized as chapters. Each article may also contain notes, examples, and recommendations.

Table of contents

• Preface (including Literature Cited)
• Preamble
• Division I. Principles
• Division II. Rules
  • Chapter I. Taxa (Arts. 1-3)
  • Chapter II. Publication (Arts. 4-5)
  • Chapter III. Names (Arts. 6-8)
  • Chapter IV. Clade Names (Arts. 9-11)
  • Chapter V. Selection of Established Names (Arts. 12-15)
  • Chapter VI. Provisions for Hybrids (Art. 16)
  • Chapter VII. Orthography (Arts. 17-18)
  • Chapter VIII. Authorship of Names (Art. 19)
  • Chapter IX. Citation of Authors and Registration Numbers (Art. 20)
  • Chapter X. Species Names (Art. 21)
  • Chapter XI. Governance (Art. 22)
• Glossary
• Tables
• Appendices
  • Appendix A. Registration Procedures and Data Requirements
  • Appendix B. Code of Ethics

Registration database

Once 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.

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.).

The Third International Phylogenetic Nomenclature Meeting took place from July 21, 2008 to July 22, 2008 at Dalhousie University (Halifax, Nova Scotia, Canada). (A published report is forthcoming.)

Influences

The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and Gauthier, which was foreshadowed by earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree.

Whenever possible, the writers of the PhyloCode used the draft BioCode, which attempted to unify the rank-based approach into a single code, as a model. Thus, the organization of the PhyloCode, some of its terminology, and the wording of certain rules are derived from the BioCode. Other rules are derived from one or more of the rank-based codes, particularly the botanical and zoological codes. However, many rules in the PhyloCode have no counterpart in any code based on taxonomic ranks because of fundamental differences in the definitional foundations of the alternative systems.

Future

The PhyloCode is controversial and has inspired considerable criticism from some taxonomists. While inaugurated more than a decade ago, the number of supporters for widespread adoption of the PhyloCode is still small. It remains unclear, as of 2024, when if ever 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.

Literature

• 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. PMID 12396594. 
• Baum, D. A.; W. S. Alverson; 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. doi:10.1111/j.1469-185X.2000.tb00055.x. ISSN 0006-3231. PMID 11117201. Archived from the original on 2011-06-05. https://web.archive.org/web/20110605090428/http://palaeo.gly.bris.ac.uk/Essays/phylocode/biolrev.html. 
• Cantino, Philip D. (2000). "Phylogenetic nomenclature: addressing some concerns". Taxon (International Association for Plant Taxonomy (IAPT)) 49 (1): 85–93. doi:10.2307/1223935. 
• Cantino, Philip D. (2004). "Classifying species versus naming clades". Taxon (International Association for Plant Taxonomy (IAPT)) 53 (3): 795–798. doi:10.2307/4135453. 
• Carpenter, J. M. (2003). "Critique of pure folly". The Botanical Review 69 (1): 79–92. doi:10.1663/0006-8101(2003)069[0079:COPF2.0.CO;2]. ISSN 0006-8101. 
• de Queiroz, K. (1992). "Phylogenetic definitions and taxonomic philosophy". Biol. Philos. 7 (3): 295–313. doi:10.1007/BF00129972. 
• de Queiroz, K. (2006). "The PhyloCode and the distinction between taxonomy and nomenclature". Syst. Biol. 55 (1): 160–162. doi:10.1080/10635150500431221. PMID 16507533. 
• de Queiroz, K.; P. D. Cantino (2001). "Phylogenetic nomenclature and the PhyloCode". Bull. Zool. Nomencl. 58: 254–271. ISSN 0007-5167. 
• de Queiroz, K.; J. Gauthier (1990). "Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names". Syst. Zool. (Society of Systematic Biologists) 39 (4): 307–322. doi:10.2307/2992353. 
• de Queiroz, K.; J. Gauthier. (1992). "Phylogenetic taxonomy". Annu. Rev. Ecol. Syst. 23: 449–480. doi:10.1146/annurev.es.23.110192.002313. ISSN 0066-4162. 
• de Queiroz, K.; 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. PMID 21236760. 
• Dominguez, E.; Q. D. Wheeler (1997). "Taxonomic stability is ignorance". Cladistics 13 (4): 367–372. doi:10.1006/clad.1997.0050. ISSN 0748-3007. 
• Donoghue, M. J.; J. A. Gauthier (2004). "Implementing the PhyloCode". Trends Ecol. Evol. 19 (6): 281–282. doi:10.1016/j.tree.2004.04.004. PMID 16701272. 
• Gauthier, J.; 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. pp. 7–41 pp. 
• Laurin, M. (2005). "Dites oui au PhyloCode!" (PDF fulltext). Bull. Soc. Fr. Syst. 34: 25–31. ISSN 1240-3253. Archived from the original on 2007-08-08. https://web.archive.org/web/20070808045610/http://sfs.snv.jussieu.fr/pdf/bulletin/bulletin_34.pdf. 
• Laurin, M.; Philip 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. 
• Laurin, M.; K. de Queiroz; Philip D. Cantino (2006). "Sense and stability of taxon names". Zool. Scr. 35 (1): 113–114. doi:10.1111/j.1463-6409.2006.00219.x. 
• Nordal, I.; B. Stedje (2005). "Letters to the Editor: Paraphyletic taxa should be accepted" (PDF fulltext). Taxon 54 (1): 5–6. doi:10.2307/25065296. ISSN 0040-0262. Archived from the original on 2006-02-28. https://web.archive.org/web/20060228095440/http://www.anbg.gov.au/asbs/newsletter/newsletter-pdf/04-sept-120.pdf.  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. doi:10.1111/j.1096-0031.2006.00097.x. http://www.blackwell-synergy.com/doi/abs/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. PMID 12066711. 
• Sereno, P. C. (2005). "The logical basis of phylogenetic taxonomy". Syst. Biol. 54 (4): 595–619. doi:10.1080/106351591007453. PMID 16109704. 

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)