Phylogenetic nomenclature (PN) or phylogenetic taxonomy is an alternative to rank-based nomenclature, applying definitions from cladistics (or phylogenetic systematics). 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 it is ratified.
The terms cladism and cladist were first introduced by Ernst W. Mayr in 1965. They sometimes refer to cladistics as a whole.
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Under the rank-based codes of biological nomenclature, names themselves do not have definitions, but are instead usually linked to a type. Some biologists have claimed that this is unsatisfactory and 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.[1][2][3] Phylogenetic nomenclature, on the other hand, uses phylogenetic definitions to tie a name to a clade, a group consisting solely of a species and all its descendants, in such a manner that the meaning of the name is objective under any phylogenetic hypothesis. This prevents splitting and lumping (unless definitions are changed in the process, which will be allowed under the PhyloCode only under carefully restricted circumstances).
Traditionally, groups named in phylogenetic nomenclature are usually monophyletic-that is, they define a natural group made up of all descendants of a single common ancestor. However, it is also possible to create phylogenetic definitions for the names of paraphyletic taxa .[4] Assuming Mammalia and Aves are defined, Reptilia could be defined as "the most recent common ancestor of birds and mammals and all its descendants except birds and mammals". This includes taxa that are not currently named and even taxa that cannot be named under the rank-based 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 .[4]
Rank-based and phylogenetic nomenclature differ in philosophical outlook. This manifests itself, particularly, in different approaches to the definitions of taxonomic terms. In providing the definition of "mammal," for example, users of rank-based nomenclature will start with the extension of the term that they want to define, perhaps the collection consisting of all animals with hair and mammary glands, and then formulate a definition satisfied by exactly these animals; users of phylogenetic nomenclature, rather, will formulate a definition, perhaps "the least inclusive clade containing brown bears and short-beaked echidnas," and stipulate that it defines the word "mammal."[5]
Put another way, users of a rank-based system name species and classify them into higher taxa, only some of which are clades, while proponents of phylogenetic nomenclature focus on clades and name them as entities that are of interest in their own right.[6]
Proponents of phylogenetic nomenclature claim that, as rank-based nomenclature does not delimit taxa precisely, its definitions will need to change as the science of biology advances. They see their approach as preferable in that their definitions are not susceptible to this kind of instability.[7] It is a disputed matter whether such changes are characteristic of sciences outside of biology and whether, if so, biology should follow the example of such sciences. Chemistry has been used as an example.
Michel Laurin, one of the foremost advocates of phylogenetic nomenclature, considers that the concept of a chemical element has been stable ever since Dmitri Mendeleev put forth the periodic table in 1869.[7] Biology should, on Laurin’s view, follow the example of chemistry and define its terms as precisely as possible.
The historian and philosopher Thomas Kuhn argued that changing the meaning of established concepts is central to significant advances in science.[8] Prior to John Dalton’s work, he pointed out, the criteria for something’s being a chemical compound were such as to include salt water; by new criteria adopted afterwards, this fluid was excluded.[9]
Michael Benton, a prominent defender of rank-based nomenclature, regards biology as an endeavor very different from chemistry. Chemical classification, as he sees it, circumscribes entities in terms of properties that enter into knowable laws; biology, lacking such laws, must look to the usefulness of classifications. From this perspective, he argues, it is less important that the definition of a term classifying organisms remain constant than it is that the term continue to apply to most of the same organisms. As he views phylogenetic nomenclature as seeking the former kind of stability and rank-based nomenclature as seeking the latter, he considers rank-based nomenclature to be preferable.[10]
The current codes of biological nomenclature stipulate that taxa cannot be given a valid name without being given a rank. However, the number of generally recognized ranks is limited. Gauthier et al. (1988)[11] claimed that a classification which uses the common array of ranks, while including Aves within Reptilia and keeping Reptilia at its traditional rank of class, is forced to demote Aves substantially, perhaps to the rank of genus. This despite the ~ 12,000 known species of extant and extinct birds that would have to be incorporated into such a genus. To reduce this problem, Patterson and Rosen (1977)[12] suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell (1997)[13] introduced a large array of new ranks in order to cope with the diversity of Mammalia.
The current codes also 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. Ereshefsky (1997:512)[14] 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.;[15] see also the PhyloCode). 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.[16][17][18]).
Ultimately, phylogenetic nomenclature is a result of Darwin's discovery that the diversity and history of life is best represented in tree-shaped diagrams. This discovery immediately led to changes in the existing classifications. For example, John Hogg proposed the term Protoctista in 1860 for organisms that did not seem closely related to either animals or plants. In 1866, the controversial biologist Ernst Haeckel for the first time reconstructed a single tree of all life (see figure) and immediately proceeded to translate it into a classification. This classification was rank-based, in accordance with the only code of biological nomenclature that existed at the time, but did not contain taxa that Haeckel considered polyphyletic; in it, Haeckel introduced the rank of phylum which carries a connotation of monophyly in its name.
Ever since it has been debated in which ways and to what extent the phylogeny of life should be used as a basis for its classification, with views ranging from "numerical taxonomy" (phenetics) over "evolutionary taxonomy" (gradistics) to "phylogenetic systematics" (cladistics – today, the term "cladistics" is only used for the method of phylogeny reconstruction, but its inventor, Willi Hennig,[19] regarded this method as a mere tool for the purpose of classification). From the 1960s onwards, rankless classifications were occasionally proposed, but in general the principles of rank-based nomenclature were used by all three schools of thought.
Most of the basic tenets of phylogenetic nomenclature (lack of obligatory ranks, and something close to phylogenetic definitions) can, however, be traced to 1916, when Edwin Goodrich[20] interpreted the name Sauropsida, erected 40 years earlier by 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 phylogenetic 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) and is an integral part of phylogenetic systematics (see above). At the same time, it became apparent that the obligatory ranks that are part of the traditional systems of nomenclature produced problems. Some authors suggested abandoning them altogether, starting with Willi Hennig's abandonment[21] of his earlier proposal to define ranks as geological age classes.[19][22]
The origin of phylogenetic nomenclature can be dated to 1986, when Jacques Gauthier used phylogenetic definitions for the first time in a published work.[23] 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).
In an attempt to avoid a schism in the biologist community, "Gauthier suggested to two members of the ICZN to apply formal taxonomic names ruled by the zoological code only to clades (at least for supraspecific taxa) and to abandon Linnean ranks, but these two members promptly rejected these ideas" (Laurin, 2008: 224).[7] This led him, Kevin de Queiroz, and the botanist Philip Cantino to start drafting their own code of nomenclature, the PhyloCode, for regulating phylogenetic nomenclature in 2000. The number of supporters for widespread adoption of the PhyloCode is however still small, and it is uncertain (as of 2011) whether the code will be implemented and if so, how widely it will be followed.
A few seminal publications not cited in the references are cited here. An exhaustive list of publications about phylogenetic nomenclature can be found on the website of the International Society for Phylogenetic Nomenclature.