Phylogenetic nomenclature (sometimes called cladistic nomenclature) is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names. Phylogenetic nomenclature assigns names to clades, groups consisting solely of an ancestor and all its descendants. 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).
Definitions Phylogenetic nomenclature associates names with clades, groups consisting of an ancestor and all its descendants. Such groups are said to be monophyletic. There are slightly different methods of specifying the ancestor, which are discussed below. Once the ancestor is specified, the meaning of the name is fixed: the ancestor and all organisms which are its descendants are included in the taxon named. Listing all these organisms (i.e. providing a full circumscription) requires the complete phylogenetic tree to be known. In practice, there are almost always one or more hypotheses as to the correct relationship. Different hypotheses result in different organisms being thought to be included in the named taxon, but application to the name in the context of various phylogenies generally remains unambiguous. Possible exceptions occur for apomorphy-based definitions, when optimization of the defining apomorphy is ambiguous.
Phylogenetic definitions of clade names All that is needed to specify a clade, is to designate the ancestor. There are a number of methods of doing this. Commonly, the ancestor is indicated by its relation to two or more specifiers (species, specimens, or traits) that are mentioned explicitly. The diagram shows three common ways of doing this. For previously defined clades A, B, and C, the clade X can be defined as:
A node-based definition could read: "the last common ancestor of A and B, and all descendants of that ancestor". Thus, the entire line below the junction of A and B does not belong to the clade to which the name with this definition refers. A crown group is a type of node-based group where A and B are extant (living) taxa. Example: The sauropod dinosaurs consist of the last common ancestor of Vulcanodon (A) and Apatosaurus (B) and all of that ancestor's descendants. This ancestor was the first sauropod. C could include other dinosaurs like Stegosaurus. A branch-based definition, often termed a stem-based definition, could read: "the first ancestor of A which is not also an ancestor of C, and all descendants of that ancestor". Thus, the entire line below the junction of A and B (other than the bottommost point) does belong to the clade to which the name with this definition refers. A pan-group or total group is a type of branch-based group where A and C are extant (living) taxa. Example (also a total group): The rodents consist of the first ancestor of the house mouse (A) that is not also an ancestor of the eastern cottontail rabbit (C) together with all descendants of that ancestor. Here, the ancestor of A (but not C) is the very first rodent. B is some other descendant of that first rodent, perhaps the red squirrel. An apomorphy-based definition could read: "the first ancestor of A to possess trait M that is inherited by A, and all descendants of that ancestor". In the diagram, M evolves at the intersection of the horizontal line with the tree. Thus, the clade to which the name with this definition refers contains that part of the line below the last common ancestor of A and B which corresponds to ancestors possessing the apomorphy M. The lower part of the line is excluded. It is not required that B have trait M; it may have disappeared in the lineage leading to B. Example: the tetrapods consist of the first ancestor of humans (A) from which humans inherited limbs with fingers or toes (M) and all descendants of that ancestor. These descendants include snakes (B), which do not have limbs.
Several other alternatives are provided in the PhyloCode,. (see below) though there is no attempt to be exhaustive.
Phylogenetic nomenclature allows the use, not only of ancestral relations, but also of the property of being extant. One of the many methods of specifying the Neornithes (modern birds), for example, is: The Neornithes consist of the last common ancestor of the extant members of the most inclusive clade containing the cockatoo Cacatua galerita but not the dinosaur Stegosaurus armatus, as well as all descendants of that ancestor. Neornithes is a crown clade, a clade for which the last common ancestor of its extant members is also the last common ancestor of all its members.
Node names Crown node: Most recent common ancestor of the sampled species of the clade of interest. Stem node: Most recent common ancestor of the clade of interest and its sibling clade.
Ancestry-based definitions of the names of paraphyletic and polyphyletic taxa For the PhyloCode, only a clade can receive a "phylogenetic definition", and this restriction is observed in the present article. However, it is also possible to create definitions for the names of other groups that are phylogenetic in the sense that they use only ancestral relations based on species or specimens. For example, assuming Mammalia and Aves (birds) are defined in this manner, Amniotes could be defined as "the most recent common ancestor of Mammalia and Aves and all its descendants except Mammalia and Aves". This is an example of a paraphyletic group, a clade minus one or more subordinate clades. Names of polyphyletic groups, characterized by a trait that evolved convergently in two or more subgroups, can be defined similarly as the sum of multiple clades.
Ranks Using the traditional nomenclature codes, such as the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants, taxa that are not associated explicitly with a rank cannot be named formally, because the application of a name to a taxon is based on both a type and a rank. Thus for example the "family" Hominidae uses the genus Homo as its type; its rank (family) is indicated by the suffix -idae (see discussion below). The requirement for a rank is a major difference between traditional and phylogenetic nomenclature. It has several consequences: it limits the number of nested levels at which names can be applied; it causes the endings of names to change if a group has its rank changed, even if it has precisely the same members (i.e. the same circumscription); and it is logically inconsistent with all taxa being monophyletic.
The current codes have rules stating that names must have certain endings depending on the rank of the taxa to which they are applied. When a group has a different rank in different classifications, its name must have a different suffix. Ereshefsky (1997:512) gave an example. He noted that Simpson in 1963 and Wiley in 1981 agreed that the same group of genera, which included the genus Homo, should be placed together in a taxon. Simpson treated this taxon as a family, and so gave it the name "Hominidae": "Homin-" from "Homo" and "-idae" as the suffix for family using the zoological code. Wiley considered it to be at the rank of "tribe", and so gave it the name "Hominini", "-ini" being the suffix for tribe. Wiley's tribe Hominini formed only part of a family which he termed "Hominidae". Thus, using the zoological code, two groups with precisely the same circumscription were given different names (Simpson's Hominidae and Wiley's Hominini), and two groups with the same name had different circumscriptions (Simpson's Hominidae and Wiley's Hominidae).
Especially in recent decades (due to advances in phylogenetics), taxonomists have named many "nested" taxa (i.e. taxa which are contained inside other taxa). No system of nomenclature attempts to name every clade; this would be particularly difficult with traditional nomenclature since every named taxon must be given a lower rank than any named taxon in which it is nested, so the number of names that can be assigned in a nested set of taxa can be no greater than the number of generally recognized ranks. Gauthier et al. (1988)Gauthier, J., Estes, R. & de Queiroz, K. 1988. A Phylogenetic Analysis of Lepidosauromorpha. Pp. 15–98 in R. Estes & G. Pregill (eds): Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford University Press. suggested that, if Reptilia is assigned its traditional rank of "class", then a phylogenetic classification has to assign the rank of genus to Aves. In such a classification, all ~12,000 known species of extant and extinct birds would then have to be incorporated into this genus.
Various solutions have been proposed while keeping the rank-based nomenclature codes. Patterson and Rosen (1977)Patterson, C. & Rosen, D. 1977 Review of ichthyodectiform and other Mesozoic teleost fishes and the theory and practice of classifying fossils. Bulletin of the American Museum of Natural History 158: 81–172. suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell (1997)McKenna, M. C. & Bell, S. K. 1997. Classification of Mammals Above the Species Level. Columbia University Press. introduced a large array of new ranks in order to cope with the diversity of Mammalia; these have not been adopted widely. For botany, the Angiosperm Phylogeny Group, responsible for the currently most widely used classification of flowering plants, chose a different method. They retained the traditional ranks of family and order, considering them to be of value for teaching and studying relationships between taxa, but also introduced named clades without formal ranks.
For phylogenetic nomenclature, ranks have no bearing on the spelling of taxon names (see e.g. Gauthier (1994) and the PhyloCode). Ranks are, however, not altogether forbidden for 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.
The principles of traditional rank-based nomenclature are incompatible logically with all taxa being strictly monophyletic. Every organism must belong to a genus, for example, so there would have to be a genus for every common ancestor of the mammals and the birds. For such a genus to be monophyletic, it would have to include both the class Mammalia and the class Aves. For rank-based nomenclature, however, classes must include genera, not the other way around.
Philosophy The conflict between phylogenetic and traditional nomenclature represents differing opinions of the metaphysics and epistemology of taxa. For the advocates of phylogenetic nomenclature, a taxon is an individual entity, an entity that may gain and lose attributes as time passes. This treatment of taxa as historical rather than extensionally defined is shared by homeostatic property cluster theory, on which changes over time in a kind's property cluster may preserve the identity of the kind. Just as a person does not become somebody else when his or her properties change through maturation, senility, or more radical changes like amnesia, the loss of a limb, or a change of sex, so a taxon remains the same entity whatever characteristics are gained or lost. Given the metaphysical claims regarding unobservable entities made by advocates of phylogenetic nomenclature, critics have referred to their method as origin essentialism.