Phylogenetic nomenclature
Phylogenetic 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.
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 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 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 taxa.
- 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 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 taxa.
- 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.
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, for example, is:
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
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 is indicated by the suffix -idae. 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 ; 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 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, and two groups with the same name had different circumscriptions.
Especially in recent decades, taxonomists have named many "nested" 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. 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 suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell 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. 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. 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.For any individual, there has to be something that associates its temporal stages with each other by virtue of which it remains the same entity. For a person, the spatiotemporal continuity of the body provides the relevant conceptual continuity; from infancy to old age, the body traces a continuous path through the world and it is this continuity, rather than any characteristics of the individual, that associates the baby with the octogenarian. This is similar to the well-known philosophical problem of the Ship of Theseus. For a taxon, IF characteristics are not relevant, THEN it can only be ancestral relations that associate the Devonian Rhyniognatha hirsti with the modern monarch butterfly as representatives, separated by 400 million years, of the taxon Insecta. The opposing opinion questions the premise of that syllogism, and argues, from an epistemological perspective, that members of taxa are only recognizable empirically on the basis of their observable characteristics, and hypotheses of common ancestry are results of theoretical systematics, not a priori premises. If there are no characteristics that allow scientists to recognize a fossil as belonging to a taxonomic group, then it is just an unclassifiable piece of rock.
If ancestry is sufficient for the continuity of a taxon, then all descendants of a taxon member will also be included in the taxon, so all bona fide taxa are monophyletic; the names of paraphyletic groups do not merit formal recognition. As "Pelycosauria" refers to a paraphyletic group that includes some Permian tetrapods but not their extant descendants, it cannot be admitted as a valid taxon name. Again, while not disagreeing with the notion that only monophyletic groups should be named, empiricist systematists counter this ancestry essentialism by pointing out that pelycosaurs are recognized as paraphyletic precisely because they exhibit a combination of synapomorphies and symplesiomorphies indicating that some of them are more closely related to mammals than they are to other pelycosaurs. The material existence of an assemblage of fossils and its status as a clade are not the same issue. Monophyletic groups are worthy of attention and naming because they share properties of interest -- synapomorphies -- that are the evidence that allows inference of common ancestry.