Phylogenetic nomenclature

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). 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 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.

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Crown group

In phylogenetics, the crown group or crown assemblage is a collection of species composed of the living representatives of the collection, the most recent common ancestor of the collection, and all descendants of the most recent common ancestor. It is thus a way of defining a clade, a group consisting of a species and all its extant or extinct descendants. For example, Neornithes (birds) can be defined as a crown group, which includes the most recent common ancestor of all modern birds, and all of its extant or extinct descendants.

Taxonomic rank

In biology, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system of biological classification (taxonomy) consists of species, genus, family, order, class, phylum, kingdom, and domain. While older approaches to taxonomic classification were phenomenological, forming groups on the basis of similarities in appearance, organic structure and behaviour, methods based on genetic analysis have opened the road to cladistics.

PhyloCode

The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a formal set of rules governing phylogenetic nomenclature. Its current version is specifically designed to regulate the naming of clades, leaving the governance of species names up to the rank-based nomenclature codes (ICN, ICNCP, ICNP, ICZN, ICVCN). The PhyloCode is associated with the International Society for Phylogenetic Nomenclature (ISPN). The companion volume, Phylonyms, establishes 300 taxon names under PhyloCode, serving as examples for those unfamiliar with the code.

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