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PhyloCode

PhyloCode is a formal set of rules governing phylogenetic nomenclature. It is a cladistic scheme of taxonomy, designed to name the parts of the tree of life by explicit reference to phylogeny. Each named taxon must be a clade (a monophyletic group, that is, it must include all the descendents of some ancestor, and only the descendents of that ancestor).

Unlike conventional scientific nomenclature, PhyloCode does not use set taxon ranks. A taxon name may be defined in one of the following manners (not exhaustive):

1. Node-based: "the least inclusive clade containing A, B, ..."
2. Stem-based: "the clade consisting of A and all organisms or species that share a more recent common ancestor with A than with Z"
3. Linnaean classification of amniotes divides them into three classes, Reptilia, Aves (birds) and Mammalia. But in cladistics this scheme is no good because Reptilia is paraphyletic: any monophyletic group including all the reptiles must include the birds. A cladistic classification scheme for these groups must look like this:

• Amniota
  • Synapsida
    • Mammalia
  • Sauropsida
    •  Anapsida
      • Testudines (turtles)
    •  Diapsida
      • Lepidosauria
        • Squamata (lizards and snakes)
        • Sphenodontida (tuatara)
      • Archosauria
        • Crocodilia (crocodiles and alligators)
        • Aves (birds)

A particular clade may be identified by specifying a path through this tree from the root.

PhyloCode is controversial: many biologists believe that the conventional system has many advantages: it is standard, many more biologists and organizations work on it, it has 250 years of history, it preserves continuity with the past, it is capable of taking phylogenetic relationships into account (in particular, the class Reptilia is no longer widely used, and current scientific classification follows the cladistic classification scheme indicated above). They argue that phylogenetic relationships are subject to too much uncertainty to base a classification system on.