Phylogenetic nomenclature



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 implemented.

The terms cladism and cladist were first introduced by Ernst W. Mayr in 1965. They sometimes refer to cladistics as a whole, but often in particular the former refers to phylogenetic nomenclature and those who advocate a taxonomy founded on cladistics, going beyond mere use of phylogenetic analyses as a tool of systematics. These terms are particularly frequently used by those who prefer a rank-based nomenclature, and are thus often used somewhat disparagingly.

Phylogenetic definitions
All forms of phylogenetic definitions are ways of specifying the ancestor in the definition of a clade name, some straightforward, some requiring several steps. Possible formats of phylogenetic definitions include, but are not limited to:


 * Ancestor-based: "A and all its descendants". This is the only definition type that only needs a single specifier/anchor (see below); all others require at least two. It has so far never been used because the fossil record is hardly ever good enough that we can expect to find a direct ancestor of any known organism, let alone to recognize it as such with reasonable confidence.
 * Node-based: "the most recent common ancestor (MRCA) of A and B (and C etc. as needed), and all its descendants" = "the smallest clade that includes A and B (and C etc.)". (Note: Trivially, A and B are descendants of the MRCA of A and B.)
 * Branch-based: "all organisms or species that share a more recent common ancestor with A (and B, C, etc. as needed) than with Z (and with Y, X, etc. as needed)" = "the largest clade that includes A (and B, C, etc.) but not Z (and also not Y, X, etc.)". (Note: Trivially, A shares a more recent common ancestor with itself than with Z.)
 * Apomorphy-based: "the first organism or species to possess apomorphies M (and N etc. as needed) as inherited by A (and B etc. as needed), and all its descendants" = "the clade diagnosed by the presence of M (and N etc.) as inherited by A (and B etc.)". (Notes: if M evolves more than once, only the one event from which A has inherited it counts: if M is "walking on two legs" and A is Homo sapiens, then birds are not members of the clade; when the apomorphy is lost, the organisms that have lost it stay members of the clade: if M is flight and A is a sparrow, ostriches and penguins are members of the clade.)
 * Branch-modified node-based: "the crown clade that includes all extant (or Recent) organisms or species which share a more recent common ancestor with A (and B etc. as needed) than with Z (and with Y etc. as needed), and all its descendants" = "the crown-clade of the clade consisting of all organisms or species that belong to the largest clade that includes A (and B etc.) but not Z (and Y etc.)". (Notes: The specifiers of the node-based clade are not explicitely mentioned; instead "all extant/Recent organisms/species that share a more recent common ancestor with A than with Z" – the extant/Recent members of a different, larger clade – are its specifiers. A and B etc. will in all likelihood be extant themselves and therefore be members of the clade to which the name applies. Both of these notes also apply to the following definition type.)
 * Apomorphy-modified node-based: "the crown clade that includes all extant (or Recent) organisms or species which are descended from the first organism to possess apomorphy M (and N etc. as needed) as inherited by A (and B etc. as needed)" = "the crown clade of the clade diagnosed by the presence of M (and N etc.) as inherited by A (and B etc.)".

Letters indicate "specifiers" (also called "anchors" ); specifically, A, B, C, X, Y, and Z indicate specimens, species, or larger taxa, and M and N indicate derived character states (apomorphies). To avoid ambiguity, the use of taxa larger than species as anchors is now widely discouraged (and will not be provided for under the PhyloCode).

So-called "taxon-based definitions" can be encountered in literature from the late 1980s and early 1990s. These are not definitions, but merely non-exhaustive lists of contents, and are therefore not unambiguously applicable to all phylogenetic hypotheses.

Universality
As long as all their anchors share any common ancestor at any time in the present or past, and provided they do not contain a qualifying clause (see below), node-based definitions (whether modified or not) always objectively refer to a clade, whether that clade has been correctly identified (by phylogenetics) or not. This also holds for branch- and apomorphy-based definitions that mention only one species or specimen that must belong to the clade they refer to.

Branch- and apomorphy-based definitions with more than one internal anchor (here A, B, and C etc.) cannot be applied to all imaginable phylogenetic hypotheses: for example, if B shares a more recent common ancestor with Z than with A, there are no "organisms that share a more recent common ancestor with A and B than with Z". Under phylogenetic hypotheses where such definitions cannot be applied, they "self-destruct" by not referring to any clade. They stay valid under other phylogenetic hypotheses.

It is also possible to deliberately restrict the applicability of phylogenetic definitions by qualifying clauses, as in this example: "the MRCA of A and B, and all its descendants, provided that B shares a more recent MRCA with A than with C". If B instead shares a more recent MRCA with C than with A, the definition "self-destructs".

Phylogenetic definitions that contain taxa as anchors that subsequently turn out to be para- or polyphyletic run the risk of "self-destructing" despite the author's intention. Therefore the use of taxa larger than species as anchors has greatly decreased and will not be provided for under the PhyloCode.

Extensions
The definition types listed above all define clade names. Indeed, all users of phylogenetic nomenclature have so far advocated the principle that only clades (and, usually, species) should be named, and this is also all the PhyloCode (which will leave species nomenclature to the rank-based codes) will allow. However, it is possible to create phylogenetic definitions for the names of paraphyletic taxa. Assuming Mammalia and Aves are defined, Reptilia could be defined as "the MRCA 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.