Molecular Biology and Evolution, Vol 10, 1170-1195, Copyright © 1993 by Society for Molecular Biology and Evolution
DJ Eernisse and AG Kluge
Taxonomic congruence and total evidence are competing paradigms in
phylogenetic inference. Taxonomic congruence focuses on deriving a
consensus from the results obtained from separately analyzed data sets,
whereas total evidence uses character congruence in the search for the
best-fitting hypothesis for all of the available character evidence.
Explicit 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 basis
for exploring classes of data, thus allowing comparison between the
phylogenetic signal emerging from a particular data set and those of other
such classes. Problematic aspects of employing the taxonomic congruence
approach include the potentially misleading and arbitrary choices of both a
consensus method and the division of characters into subsets. 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 approach. The theoretical advantages
of phylogenetic estimates based on total evidence are argued in the present
study and are illustrated with an example of amniote relationships. We
report conflicting results from total evidence and taxonomic congruence
approaches, with analyses of previously reported data from both fossil and
living amniotes and from both morphology and molecules, the latter
including available 18S rRNA, 28S rRNA, and protein sequences. We conclude
that a more highly resolved and robust phylogenetic hypothesis of amniotes,
the traditional one, emerges when a total evidence approach is employed.
ORIGINAL ARTICLE
Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology
Museum of Zoology, University of Michigan, Ann Arbor 48109-1079.
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