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 ).

Contents

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

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]

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]

NameRankTypePossible 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 ClassN/AClade originating with the most recent common ancestor of humans, Homo sapiens Linnaeus 1758, and platypuses, Ornithorhynchus anatinus Shaw 1799
Rodentia OrderN/AMost inclusive clade containing the house mouse, Mus musculus Linnaeus 1758, but not the eastern cottontail, Sylvilagus floridanus Allen 1890
Neornithes
(Modern birds)		SubclassN/AClade 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 SuperclassN/AClade originating with the earliest ancestor from which Homo sapiens Linnaeus 1758 inherited limbs with fingers or toes

Versions

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

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

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. [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

(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

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

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.

Related Research Articles

In biology, taxonomy is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum, class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.

<span class="mw-page-title-main">Rosidae</span> Subclass of plants

Under the International Code of Nomenclature for algae, fungi, and plants (ICN), Rosidae is a botanical name at the rank of subclass. Circumscription of the subclass will vary with the taxonomic system being used; the only requirement being that it includes the family Rosaceae.

<span class="mw-page-title-main">Taxon</span> Grouping of biological populations

In biology, a taxon is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and given a particular ranking, especially if and when it is accepted or becomes established. It is very common, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion, especially in the context of rank-based ("Linnaean") nomenclature. If a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping.

<span class="mw-page-title-main">Sauropsid</span> Taxonomic clade

Sauropsida is a clade of amniotes, broadly equivalent to the class Reptilia, though typically used in a broader sense to include both extinct stem-group relatives of modern reptiles, as well as birds. The most popular definition states that Sauropsida is the sibling taxon to Synapsida, the other clade of amniotes which includes mammals as its only modern representatives. Although early synapsids have historically been referred to as "mammal-like reptiles", all synapsids are more closely related to mammals than to any modern reptile. Sauropsids, on the other hand, include all amniotes more closely related to modern reptiles than to mammals. This includes Aves (birds), which are now recognized as a subgroup of archosaurian reptiles despite originally being named as a separate class in Linnaean taxonomy.

<span class="mw-page-title-main">Reptiliomorpha</span> Clade of reptile-like animals

Reptiliomorpha is a clade containing the amniotes and those tetrapods that share a more recent common ancestor with amniotes than with living amphibians (lissamphibians). It was defined by Michel Laurin (2001) and Vallin and Laurin (2004) as the largest clade that includes Homo sapiens, but not Ascaphus truei. Laurin and Reisz (2020) defined Pan-Amniota as the largest total clade containing Homo sapiens, but not Pipa pipa, Caecilia tentaculata, and Siren lacertina.

<span class="mw-page-title-main">Lepidosauromorpha</span> Clade of reptiles

Lepidosauromorpha is a group of reptiles comprising all diapsids closer to lizards than to archosaurs. The only living sub-group is the Lepidosauria, which contains two subdivisions, Squamata, which contains lizards and snakes, and Rhynchocephalia, the only extant species of which is the tuatara.

Nomenclature codes or codes of nomenclature are the various rulebooks that govern the naming of living organisms. Standardizing the scientific names of biological organisms allows researchers to discuss findings.

<span class="mw-page-title-main">Evolutionary grade</span> Non-monophyletic grouping of organisms united by morphological or physiological characteristics

A grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.

Jacques Armand Gauthier is an American vertebrate paleontologist, comparative morphologist, and systematist, and one of the founders of the use of cladistics in biology.

<span class="mw-page-title-main">Avemetatarsalia</span> Clade of archosaur reptiles

Avemetatarsalia is a clade of diapsid reptiles containing all archosaurs more closely related to birds than to crocodilians. The two most successful groups of avemetatarsalians were the dinosaurs and pterosaurs. Dinosaurs were the largest terrestrial animals for much of the Mesozoic Era, and one group of small feathered dinosaurs has survived up to the present day. Pterosaurs were the first flying vertebrates and persisted through the Mesozoic before dying out at the Cretaceous-Paleogene (K-Pg) extinction event. Both dinosaurs and pterosaurs appeared in the Triassic Period, shortly after avemetatarsalians as a whole. The name Avemetatarsalia was first established by British palaeontologist Michael Benton in 1999. An alternate name is Pan-Aves, or "all birds", in reference to its definition containing all animals, living or extinct, which are more closely related to birds than to crocodilians.

<span class="mw-page-title-main">Pterodactyloidea</span> Suborder of monofenestratan pterosaurs

Pterodactyloidea is one of the two traditional suborders of pterosaurs, and contains the most derived members of this group of flying reptiles. They appeared during the middle Jurassic Period, and differ from the basal rhamphorhynchoids by their short tails and long wing metacarpals. The most advanced forms also lack teeth, and by the late Cretaceous, all known pterodactyloids were toothless. Many species had well-developed crests on the skull, a form of display taken to extremes in giant-crested forms like Nyctosaurus and Tupandactylus. Pterodactyloids were the last surviving pterosaurs when the order became extinct at the end of the Cretaceous Period, together with the non-avian dinosaurs and most marine reptiles.

Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional method, by which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is regulated currently by the International Code of Phylogenetic Nomenclature (PhyloCode).

The International Society for Phylogenetic Nomenclature was established to encourage and facilitate the development and use of, and communication about, phylogenetic nomenclature. It organizes periodic scientific meetings and is overseeing the completion and implementation of the PhyloCode.

<span class="mw-page-title-main">Pygostylia</span> Clade of dinosaurs

Pygostylia is a group of avialans which includes the Confuciusornithidae and all of the more advanced species, the Ornithothoraces.

<span class="mw-page-title-main">Stegocephali</span> Clade of tetrapodomorphs

Stegocephali is a clade of vertebrate animals containing all fully limbed tetrapodomorphs. It is equivalent to a broad definition of the superclass Tetrapoda: under this broad definition, the term "tetrapod" applies to any animal descended from the first vertebrate with four limbs each with five digits in the extremity (pentadactyly), rather than fins of their sarcopterygian relatives.

<span class="mw-page-title-main">Mesangiospermae</span> One of two clades of flowering plants

Mesangiospermae is a clade of flowering plants (angiosperms), informally called "mesangiosperms". They are one of two main groups of angiosperms. It is a name created under the rules of the PhyloCode system of phylogenetic nomenclature. There are about 350,000 species of mesangiosperms. The mesangiosperms contain about 99.95% of the flowering plants, assuming that there are about 175 species not in this group and about 350,000 that are. While such a clade with a similar circumscription exists in the APG III system, it was not given a name.

<span class="mw-page-title-main">Arctoidea</span> Infraorder of mammals

Arctoidea is a clade of mostly carnivorous mammals which include the extinct Hemicyonidae (dog-bears), and the extant Musteloidea, Pinnipedia, and Ursidae (bears), found in all continents from the Eocene, 46 million years ago, to the present. The oldest group of the clade is the bears, as their CMAH gene is still intact. The gene became non-functional in the common ancestor of the Mustelida. Arctoids are caniforms, along with dogs (canids) and extinct bear dogs (Amphicyonidae). The earliest caniforms were superficially similar to martens, which are tree-dwelling mustelids. Together with feliforms, caniforms compose the order Carnivora; sometimes Arctoidea can be considered a separate suborder from Caniformia and a sister taxon to Feliformia.

The Sporolithaceae is the only known family of algae in the Sporolithales order.

Kevin de Queiroz is a vertebrate, evolutionary, and systematic biologist. He has worked in the phylogenetics and evolutionary biology of squamate reptiles, the development of a unified species concept and of a phylogenetic approach to biological nomenclature, and the philosophy of systematic biology.

<span class="mw-page-title-main">Hadrosauromorpha</span> Extinct clade of dinosaurs

Hadrosauromorpha is a clade of iguanodontian ornithopods, defined in 2014 by David B. Norman to divide Hadrosauroidea into the basal taxa with compressed manual bones and a pollex, and the derived taxa that lack them. The clade is defined as all the taxa closer to Edmontosaurus regalis than Probactrosaurus gobiensis. This results in different taxon inclusion depending on the analysis.

References

  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   12396594.
  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 . Retrieved 19 August 2021.
  32. ↑ Queiroz, Kevin De; Cantino, Philip D.; Gauthier, Jacques A. (27 May 2020). Phylonyms : a companion to the PhyloCode. ISBN   9781138332935.
  33. ↑ Laurin, Michel (3 August 2023). The Advent of PhyloCode: The Continuing Evolution of Biological Nomenclature. CRC Press. ISBN   978-1-003-09282-7.

Literature

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