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Phylogenetic nomenclature
Phylogenetic nomenclature (PN) is an alternative to rank-based nomenclature. Its two defining features are the use of phylogenetic definitions of biological taxon names, and the lack of obligatory ranks. It is currently not regulated, but the PhyloCode (International Code of Phylogenetic Nomenclature) is intended to regulate it once implemented. Note that monophyly of taxa is considered desirable by most scientists accepting evolution as the prime force driving biological diversity;; The "-phyly" refers back to the 19th-century concept of "branches" of an evolutionary tree - a phylogeny - shift from creationist to evolutionary theories. Paraphyletic taxa are generally tolerated and occsionally endorsed by some under Linnean nomenclature, while they are not possible under PN. Additional recommended knowledge
Phylogenetic definitionsAll forms of phylogenetic definitions are ways of specifying the ancestor in the definition of "clade" (which is "an ancestor and all its descendants"). Possible formats of phylogenetic definitions include:
Letters indicate "specifiers" (also called "anchors"); specifically, A, B, C, X, Y, and Z indicate specimens, species, or larger taxa, and M and N indicate derived character states (apomorphies). To avoid ambiguity, the use of taxa larger than species as anchors is now widely discouraged (and will be forbidden under the PhyloCode). So-called "taxon-based definitions" can be encountered in literature from the late 1980s and early 1990s. These are not definitions, but merely non-exhaustive lists of contents, and are therefore not unambiguously applicable to all phylogenetic hypotheses. Accordingly, they are no longer used. UniversalityAs long as all their anchors share any common ancestor at any time in the present or past, node-based definitions (whether modified or not) always objectively refer to a clade, whether that clade has been correctly identified (by phylogenetics) or not. This also holds for branch- and apomorphy-based definitions that mention only one species or specimen that must belong to the clade they refer to. Branch- and apomorphy-based definitions with more than one internal anchor (here A, B, and C etc.) cannot be applied to all imaginable phylogenetic hypotheses: for example, if B shares a more recent common ancestor with Z than with A, there are no "organisms that share a more recent common ancestor with A and B than with Z". Under phylogenetic hypotheses where such definitions cannot be applied, they "self-destruct" by not referring to any clade. They stay valid under other phylogenetic hypotheses. It is also possible to deliberately restrict the applicability of phylogenetic definitions by qualifying clauses, as in this example: "the MRCA of A and B, and all its descendants, provided that B shares a more recent MRCA with A than with C". If B does share a more recent MRCA with C than with A, the definition "self-destructs". Phylogenetic definition that contain taxa as anchors that subsequently turn out to be para- or polyphyletic run the risk of "self-destructing" despite the author's intention. Therefore the use of taxa larger than species as anchors has greatly decreased and will be forbidden under the PhyloCode. ExtensionsThe definition types listed above all define clade names. Indeed, all users of phylogenetic nomenclature have so far advocated the principle that only clades (and, usually, species) should be named, and this is also all the PhyloCode will allow. However, it is possible to create phylogenetic definitions for the names of paraphyletic taxa. Assuming Mammalia and Aves are defined, Reptilia could be defined as "the MRCA of birds and mammals and all its descendants except birds and mammals" [1]. This includes taxa that are not currently named and even taxa that cannot be named under the existing codes without seriously disrupting existing classifications, such as "all organisms that share a more recent common ancestor with Homo sapiens than with birds and plesiomorphically keep laying eggs". Names of polyphyletic taxa could be defined by referring to the sum of two or more clades or paraphyletic taxa. Comparison to traditional nomenclatureDefinitionsUnder the currently existing codes of biological nomenclature, taxon names have (implicit) definitions that consist of a type and a rank. For example, Hominidae is the family that includes the genus Homo. The term "family" is not defined; therefore, the size of this taxon remains entirely at the discretion of the individual systematist, even if everyone agrees on the phylogeny of the potential members of Hominidae. Indeed, the use of Hominidae has over the last few decades changed from including only Homo and Australopithecus to including the chimpanzees and gorillas, then also the orangutans, and occasionally the gibbons as well. There is no way to say that any of these usages are "right" or "wrong", none of them correspond to testable scientific hypotheses – only aesthetic and utilitarian arguments can be made, and even the latter cannot be quantified or otherwise made objective. (See references for reviews: [2][3].) A growing number of biologists consider this situation unsatisfactory and feel that instability in nomenclature should only reflect instability of our knowledge of phylogeny, not instability in subjective opinions about which ranks should be given to which groups.[4][5][6] Phylogenetic nomenclature, on the other hand, uses phylogenetic definitions (as explained above) to tie a name to a clade in such a manner that the meaning of the name is objective under any phylogenetic hypothesis, thus preventing splitting and lumping (unless definitions are changed in the process, which will not be allowed under the PhyloCode). Lack of obligatory ranksThe current codes of biological nomenclature stipulate that taxa cannot be given a valid name without being given a rank; as mentioned above, the rank is part of the definition of every valid taxon name. However, the number of generally recognized ranks is limited; this means that many taxa must go unnamed because no ranks are available for them. Accordingly, the number of commonly used ranks has increased from the five to seven Linnaeus used (variety, species, genus, order, class; kingdom, arguably empire) to about twenty-one (by the addition of family, phylum/division, domain, and the prefixes super- and sub- and occasionally infra-; "empire" is not used, and "variety" is only used in botany). Given the million or more of known species, this is still not enough; for example, Gauthier et al. (1988)[2] showed that a classification which uses the common array of ranks, but includes Aves within Reptilia and keeps Reptilia at its traditional rank of class, is forced to demote Aves to the rank of genus, despite the ~ 12,000 known species of extant and extinct birds that would have to be incorporated into this one genus. To reduce this problem, Patterson and Rosen (1977)[7] suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell (1997)[8] introduced a large array of new ranks in order to cope with the diversity of Mammalia, to cite only the two most famous examples. None of these proposals has become widely applied, mostly because they contain too many ranks to remember easily, and because there are never enough ranks to name all clades on a sufficiently large phylogenetic tree. In practice, this means that some taxon names are used by biologists, but either not made official or not used in classifications because no rank is available for them. Examples include the "tricolpates" in botany (no rank available) and Amniota, Tetrapoda, and/or Gnathostomata in zoology (ranks for one or two are available, but not for the third; selections of which names are not acknowledged vary). Phylogenetic nomenclature does not require that names have ranks. The limited number of ranks also discourages researchers in another way from naming taxa when they discover them (see e.g. [9]). If a new name is introduced into a classification that already exhausts the available ranks, for example when two of three suborders of an order are recognized as a clade that might be interesting enough to be named, either rank shifts elsewhere in the classification (the order might be promoted to superorder, and the third suborder to order; or the two suborders might be demoted to superfamilies) or removing names from the classification because no rank is available for them any longer. By allowing unranked names, phylogenetic nomenclature circumvents this problem. Furthermore, the current codes each have rules saying that names must have certain endings if they are applied to taxa that have certain ranks. When a taxon changes rank from one classification to another, its name must change its suffix. To return to the example of Hominidae, Ereshefsky (1997:512)[10] stated: The Linnaean rule of assigning rank-specific suffices [sic] gives rise to even more confusing cases. Simpson (1963, 29–30) and Wiley (1981, 238) agree that the genus Homo belongs to a particular taxon. They disagree, however, on that taxon's rank. Acting in accord with the Linnaean system, they attach different suffixes to the root Homini [actually Homin-] and give the taxon in question different names: Wiley calls it 'Hominini' [tribe rank] and Simpson calls it 'Hominidae' [family rank]. Their disagreement does not stop there. Wiley believes that the taxon just cited is a part of a more inclusive taxon which is a family. Using the root Homini, and following the rules of the Linnaean system [more precisely, the zoological code], he names the more inclusive taxon 'Hominidae.' So for Wiley and Simpson, the name 'Hominidae' refers to two different taxa. In brief, the Linnaean system causes Wiley and Simpson to assign different names to what they agree is the same taxon, and it causes them to give the same name to what they agree are different taxa. In phylogenetic nomenclature, ranks have no bearing on the spelling of taxon names (see e.g. [11]; see also the PhyloCode). Perhaps most importantly, ranks encourage the misperception that taxa of the same rank are equivalent in a meaningful way (see e.g. [3] and [12], but also [13] who argue against phylogenetic nomenclature and for obligatory ranks). Many authors have treated genera, families, or orders as countable, using a count of such taxa as a measure (or proxy) of biodiversity. But because the ranks are not defined, taxa at the same rank are not equivalent in any objective way, so counting them does not tell us anything about nature – at most, it reveals the personal taxonomic preferences held by the authors of such studies. Alternative measures of biodiversity exist, such as the Phylogenetic Diversity Index[14][15][16], which has occasionally been used in recent literature (e.g. [17]). Ranks are, however, not altogether forbidden in phylogenetic nomenclature. They are merely decoupled from nomenclature: they do not influence which names can be used, which taxa are associated with which names, and which names can refer to nested taxa (e.g. [18][19][20]). HistoryUse of phylogenetic criteria was one of the logical consequences the emergence of evolutionary theory had on taxonomy. As early as 1866, controversial biologist Ernst Haeckel proposed a monophyletic tree of life for example. While his attempt is outdated in many aspects, the division between protists, animals and plants was already realized as necessary. The "Protoctista" had been proposed only 6 years ago by John Hogg as one of the first major effects the theory of evolution had on the proposed "tree of life". Most of the basic tenets of phylogenetic nomenclature (lack of obligatory ranks, and something close to phylogenetic definitions) can be traced to 1916, when Edwin Goodrich[21] interpreted the name Sauropsida, erected 40 years earlier by T. H. Huxley, to include the birds (Aves) as well as part of Reptilia, and coined the new name Theropsida to include the mammals as well as another part of Reptilia, but did not give them ranks, and treated them exactly as if they had what would today be termed branch-based definitions, using neither contents nor diagnostic characters to decide whether a given animal should belong to Theropsida, Sauropsida, or something else once its phylogenetic position was agreed upon. Goodrich also opined that the name Reptilia should be abandoned once the phylogeny of the reptiles would be better known. The lack of compatibility of his scheme with the existing rank-based classifications (despite agreement on the phylogeny in all but details), and the lack of a method of phylogenetics at this time, are the most likely reasons why Goodrich's suggestions were largely ignored. The principle that only clades (monophyletic taxa – an ancestor plus all its descendants) should be formally named became popular in the second half of the 20th century. It spread together with the methods for discovering clades (cladistics). At the same time, it became apparent that the obligatory ranks that are part of the traditional systems of nomenclature produced problems (see above under "Comparison to traditional nomenclature"). Some authors suggested abandoning them altogether, starting with Willi Hennig's abandonment[22] of his earlier proposal to define ranks as geological age classes[23][24]. The origin of phylogenetic nomenclature can be dated to 1986, when Jacques Gauthier used phylogenetic definitions for the first time in a published work. Theoretical papers outlining the principles of phylogenetic nomenclature, as well as further publications containing applications of phylogenetic nomenclature (mostly to vertebrates), soon followed (see Literature section). Since then, the number of publications using phylogenetic nomenclature has steadily increased. So has the number of parts of the tree of life to which phylogenetic nomenclature has been applied, although great disparities still remain, most notably a bias towards fossil vertebrates and extant flowering plants (for example, all workers on Mesozoic dinosaur phylogeny today use phylogenetic nomenclature, while no entomologists use it). Gauthier and de Queiroz appealed to the International Commission on Zoological Nomenclature to have phylogenetic definitions included in zoological nomenclature[citation needed]. When this proposal was rejected, they and the botanist Philip Cantino started drafting their own code of nomenclature, the PhyloCode, for regulating phylogenetic nomenclature.
Important literatureOnly a few seminal publications are cited here (in roughly chronological order from top to bottom) and in the references (below). An exhaustive list can be found on the website of the International Society for Phylogenetic Nomenclature.
References
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This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Phylogenetic_nomenclature". A list of authors is available in Wikipedia. |