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Answer by kmm for The parts of the phylogenetic nomenclature that need to be "unique"

Many of the problems you are discovering are the basis for phylogenetic classification. Without necessarily answering each of your question specifically, I'll mention some of the basics of phylogenetic classification as compared to traditional Linnean classification:

  1. Species are the main "currency". We classify species and species alone.
  2. All taxonomic groups higher than the species level are arbitrary. The Linnean system of Kingdom - Phylum - Class, etc. has no biological meaning. For example, Reptilia and Aves can't both be classes, because birds are reptiles (a class within another class).

These two points alone address most of the questions. There are no general rules (and lots of arguments) for naming clades above the level of species. Clades are names following the main rule of "the most recent common ancestor of [taxon] and all of its descendants". This conveniently does away with all the business about "Supraclass" and "Infraorder" and such.

The implication of this scheme is that there are no (extant) species at the bifurcations, so there is no taxon that is not assignable to a "tip" on the tree. In other words, "we do not find direct ancestors in the fossil record", which basically answers your third question.


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