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 approach, in 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 currently regulated by the International Code of Phylogenetic Nomenclature (PhyloCode).
Definitions
Phylogenetic nomenclature ties names to clades, groups consisting of an ancestor and all its descendants. These groups can equivalently be called monophyletic. There are slightly different ways 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 named taxon. Listing all these organisms (i.e. providing a full circumscription) requires the full phylogenetic tree to be known. In practice, there are only one or more hypotheses as to the correct tree. Different hypotheses lead to different organisms being thought to be included in the named taxon, but do not affect what organisms the name actually applies to. In this sense the name is independent of theory revision.
Phylogenetic definitions of clade names
Phylogenetic nomenclature ties names to clades, groups consisting solely of an ancestor and all its descendants. All that is needed to specify a clade, therefore, is to designate the ancestor. There are a number of ways 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 called 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 ways 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.