Slowly-evolving protein loci and higher-level snake phylogeny: A reanalysis

Abstract

We reanalyzed data from a recently published study of higher-level snake relationships based on four slowly-evolving protein loci. The original study used phenetic clustering of genetic similarities and presented a single, highly resolved tree. Our reanalyses of these data reveal that the single published phenogram is only one of at least 10,000 equivalent UPGMA phenograms, the consensus of which is largely unresolved. Additive distance analysis and character-based parsimony analysis of the data also yield little resolution, indicating that these data are highly ambiguous regarding higher-level snake phylogeny. The high degree of resolution in the published phenogram is an analytical artifact resulting from the failure to consider alternative trees implied by tied distance values, which are numerous in the distance matrix derived from this particular data set. Although the published phenogram exhibits general agreement with traditional hypotheses about snake relationships, the same appears to be true for the thousands of equivalent phenograms, discrepancies among which sum to a substantial loss of resolution. Although the four loci sampled are evolving slowly relative to other commonly surveyed protein loci, they are nevertheless evolving too rapidly to be informative about the higher level phylogeny of snakes.