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PhyloCode

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The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is 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, ICNCP, ICNP, ICZN, ICVCN).

The PhyloCode is associated with the International Society for Phylogenetic Nomenclature (ISPN).[1] The companion volume, Phylonyms, establishes 300 taxon names under PhyloCode, serving as examples for those unfamiliar with the code.[2] RegNum is an associated online database for registered clade names.[3]

The PhyloCode regulates phylogenetic nomenclature by providing rules for deciding which associations of names and definitions are considered established,[4] which of those will be considered homonyms[5] or synonyms,[6] and which one of a set of synonyms or homonyms will be considered accepted (generally the one registered first; see below). The PhyloCode only governs the naming of clades,[7] not of paraphyletic or polyphyletic groups, and only allows the use of specimens, species, and apomorphies as specifiers (anchors).[8]

Phylogenetic nomenclature

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Main article: 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.[9][10] 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):[11]

  • 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.)[12]

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

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PhyloCode has gone through several revisions. As of November 2023, the current version is 6, released on the website on June 8, 2020.

Organization

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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

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Registration database

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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.[13] 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

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(Condensed from the PhyloCode's Preface.[14])

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.[15] 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.).[16]

The Third International Phylogenetic Nomenclature Meeting took place from July 21, 2008, to July 22, 2008, at Dalhousie University (Halifax, Nova Scotia, Canada).[17]

The PhyloCode went into effect with the publication of the companion volume, Phylonyms, in 2020.[18]

Influences

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The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and Gauthier,[19][20][21] which was foreshadowed by earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree.[22][23]

Whenever possible, the writers of the PhyloCode used the draft BioCode,[24] 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[25][26][27] and zoological[28][29] 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. Note that the PhyloCode does not govern the names of species, whose rules of availability, typification, etc., remain regulated by the requisite traditional Code of Nomenclature.

Future

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The PhyloCode is controversial and has inspired considerable criticism from some taxonomists.[30] While inaugurated decades ago, the number of supporters for widespread adoption of the PhyloCode is still small, and the publication of PhyloCode literature stagnated in the mid-2010s,[31] before accelerating after publication of Phylonyms in 2020 and of the launch of the Bulletin of Phylogenetic Nomenclature, which is a journal dedicated to the publication of nomenclatural acts (especially definition of taxon names) valid under the PhyloCode.[32][33] To be valid under the PhyloCode, taxon names and associated definitions should be registered in the RegNum database.

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

References

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  1. ^ "International Society for Phylogenetic Nomenclature (website)". Phylonames.org. Retrieved 2010-07-07.
  2. ^ Laurin, M.; Bryant, H. N. (2009). "Third Meeting of the International Society for Phylogenetic Nomenclature: a Report". Zoologica Scripta. 38 (3): 333–337. doi:10.1111/j.1463-6409.2008.00379.x. S2CID 221171579.
  3. ^ "RegNum". Florida Museum. Retrieved 4 April 2019.
  4. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Chapter II. Publication". Ohiou.edu. Retrieved 2010-07-07.
  5. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 13: Homonymy". ohiou.edu. Retrieved 2010-07-07.
  6. ^ "International Code of Phylogenetic Nomenclature Version 4b, Article 14: Synonymy". Ohiou.edu. Retrieved 2010-07-07.
  7. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Rule 1.1". Ohiou.edu. Retrieved 2010-07-07.
  8. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 11. Specifiers and Qualifying Clauses". Ohiou.edu. Retrieved 2010-07-07.
  9. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 3. Hierarchy and Rank". Ohiou.edu. Retrieved 2010-07-07.
  10. ^ Although note that the PhyloCode does not permit a taxon's name to change when its rank changes, while the rank-based codes require this for at least some names.
  11. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 9. General Requirements for Establishment of Clade Names". Ohiou.edu. Retrieved 2010-07-07.
  12. ^ Anderson, Jason S. (2002). "Use of Well-Known Names in Phylogenetic Nomenclature: A Reply to Laurin". Systematic Biology. 51 (5): 822–827. doi:10.1080/10635150290102447. PMID 12396863.
  13. ^ "The PhyloCode: Article 8".
  14. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Preface". Ohiou.edu. Retrieved 2010-07-07.
  15. ^ Laurin, M.; P. 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. S2CID 86552807.
  16. ^ Laurin, M.; P. D. Cantino (2007). "Second meeting of the International Society for Phylogenetic Nomenclature: a report". Zool. Scr. 36: 109–117. doi:10.1111/j.1463-6409.2006.00268.x. S2CID 222198538.
  17. ^ Laurin, M.; Bryant, H.N. (May 2009). "Third meeting of the International Society for Phylogenetic Nomenclature: a report". Zoologica Scripta. 38 (3): 333–337. doi:10.1111/j.1463-6409.2008.00379.x. S2CID 221171579.
  18. ^ de Queiroz. K., Cantino. P. D., Gauthier. J. A. eds. (2020). Phylonyms: A Companion to the PhyloCode. CRC Press Boca Raton, FL
  19. ^ de Queiroz, K.; J. Gauthier (1990). "Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names". Syst. Zool. 39 (4). Society of Systematic Biologists: 307–322. doi:10.2307/2992353. JSTOR 2992353.
  20. ^ de Queiroz, K.; J. Gauthier (1992). "Phylogenetic taxonomy". Annu. Rev. Ecol. Syst. 23: 449–480. doi:10.1146/annurev.es.23.110192.002313.
  21. ^ 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.
  22. ^ Griffiths, Graham CD. "On the foundations of biological systematics." Acta biotheoretica 23, no. 3-4 (1974): 85-131.
  23. ^ Ghiselin, M. T. (1984). ""Definition," "character," and other equivocal terms". Syst. Zool. 33 (1). Society of Systematic Biologists: 104–110. doi:10.2307/2413135. JSTOR 2413135.
  24. ^ Greuter, W.; D. L. Hawksworth; J. McNeill; A. Mayo; A. Minelli; P. H. A. Sneath; B. J. Tindall; P. Trehane; P. Tubbs (1998). "Draft BioCode (1997): the prospective international rules for the scientific names of organisms". Taxon. 47 (1). International Association for Plant Taxonomy (IAPT): 127–150. doi:10.2307/1224030. JSTOR 1224030.
  25. ^ Greuter, W.; F. R. Barrie; H. M. Burdet; W. G. Chaloner; V. Demoulin; D. L. Hawksworth; P. M. Jørgensen; J. McNeill; D. H. Nicolson; P. C. Silva; P. Trehane (1994). International Code of Botanical Nomenclature (Tokyo Code). Koeltz Scientific Books, Königstein, Germany. ISBN 1-878762-66-4.
  26. ^ Greuter, W.; F. R. Barrie; H. M. Burdet; V. Demoulin; T. S. Filgueiras; D. L. Hawksworth; J. McNeill; D. H. Nicolson; P. C. Silva; J. E. Skog; P. Trehane; N. J. Turland (2000). International Code of Botanical Nomenclature (Saint Louis Code). Koeltz Scientific Books, Königstein, Germany.
  27. ^ McNeill, J.; F. R. Barrie; H. M. Burdet; V. Demoulin; D. L. Hawksworth; K. Marhold; D. H. Nicolson; J. Prado; P. C. Silva; J. E. Skog; J. H. Wiersema; N. J. Turland (2006). International Code of Botanical Nomenclature (Vienna Code). Gantner, Ruggell, Liechtenstein. ISBN 3-906166-48-1.
  28. ^ International Commission on Zoological Nomenclature (1985). International Code of Zoological Nomenclature (3rd ed.). International Trust for Zoological Nomenclature. ISBN 0-85301-006-4.
  29. ^ International Commission on Zoological Nomenclature (1999). International Code of Zoological Nomenclature (4th ed.). International Trust for Zoological Nomenclature. ISBN 0-85301-006-4.
  30. ^ Nixon, Kevin C.; Carpenter, James M.; Stevenson, Dennis W. (2003). "The PhyloCode is fatally flawed, and the "Linnaean" System can easily be fixed". The Botanical Review. 69 (1): 111–120. doi:10.1663/0006-8101(2003)069[0111:TPIFFA]2.0.CO;2. Retrieved 12 February 2024.
  31. ^ Brower, Andrew V. Z. (2020). "Dead on arrival: a postmortem assessment of "phylogenetic nomenclature", 20 years on". Cladistics. 36 (6): 627–637. doi:10.1111/cla.12432. S2CID 224927279.
  32. ^ Queiroz, Kevin De; Cantino, Philip D.; Gauthier, Jacques A. (27 May 2020). Phylonyms : a companion to the PhyloCode. CRC Press. ISBN 9781138332935.
  33. ^ Laurin, Michel (3 August 2023). The Advent of PhyloCode: The Continuing Evolution of Biological Nomenclature. CRC Press. doi:10.1201/9781003092827. ISBN 978-1-003-09282-7.

Literature

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