TAXONOMIC CONGRUENCE VERSUS TOTAL EVIDENCE, AND AMNIOTE PHYLOGENY INFERRED FROM FOSSILS, MOLECULES, AND MORPHOLOGY

Taxonomic congruence and total evidence are competing paradigms in phy logenetic inference. Taxonomic congruence focuses on deriving a consen sus from the results obtained from separately analyzed data sets, wher eas total evidence uses character congruence in the search for the bes t-fitting hypothesis for all of the available character evidence. Expl icit or implicit use of taxonomic congruence is usually employed when an investigator either has both molecular and morphological data sets or has different gene-, rRNA-, or protein-sequence data sets available . Indeed, a taxonomic congruence rationale is frequently used as the b asis for exploring classes of data, thus allowing comparison between t he phylogenetic signal emerging from a particular data set and those o f other such classes. Problematic aspects of employing the taxonomic c ongruence approach include the potentially misleading and arbitrary ch oices of both a consensus method and the division of characters into s ubsets. If the goal of an analysis is to provide the best estimate of genealogy afforded by the available character evidence, then taxonomic congruence is substantially more arbitrary than a total evidence appr oach. The theoretical advantages of phylogenetic estimates based on to tal evidence are argued in the present study and are illustrated with an example of amniote relationships. We report conflicting results fro m total evidence and taxonomic congruence approaches, with analyses of previously reported data from both fossil and living amniotes and fro m bath morphology and molecules, the latter including available 18S rR NA, 28S rRNA, and protein sequences. We conclude that a more highly re solved and robust phylogenetic hypothesis of amniotes, the traditional one, emerges when a total evidence approach is employed.