Taxic Revisions

Parsimony analysis provides a straightforward way of assessing homology on a tree: a state shared by two terminals comprises homologous similarity if optimization attributes that state to all the stem species lying between those terminals. Three-taxon statements (3ts), although seemingly "exact" in that each either fits a tree or does not, do not provide a satisfactory assessment of homology, because that assessment can be internally contradictory and because 3ts systematically exclude homologous resemblance in reversed states. Modified 3ts analysis (m3ta), a method in which both plesiomorphic and apomorphic states of "paired homologue" (PH) characters (those other than presence/absence data) are regarded as "informative" (able to distinguish groups), can (obviously) group by symplesiomorphy and so form paraphyletic groups unless data are clocklike enough. Patterson's pattern analysis (ppa) has the same shortcoming, to which it adds the drawback that only characters fitting the tree perfectly are used, a restriction that can easily lead to discarding most of the structure in the data. Revised m3ta (rm3ta), a method in which plesiomorphic states are not taken as informative, can also form paraphyletic groups, because it cannot apply reversals as apomorphies. The idea that knowledge of phylogeny has been derived from classifications does not imply that nonevolutionary methods should be employed for classification, but instead means that systematic methods must be logically capable of phylogenetic interpretation. Neither m3ta nor rm3ta satisfies that requirement because of their contradictory assessments of homology.