Congruence among Mammalian Mitochondrial Genes

Abstract

Mitochondrial protein coding genes were combined into a single matrix that included the 13 protein coding genes for 22 mammals, resulting in 11,448 characters each, or more than a quarter of a million base pairs of mitochondrial sequence. This matrix was examined for three separate a priori weighting strategies, including equal weighting, transversion weighting, and codon weighting. The incongruence length difference test obtained a significant value for equally weighted data and for one of our differentially weighted analyses. Thus, in one case, transversion only, weighting did effect previously incongruent data matrices, making them congruent. The tree produced for the various weighting strategies was identical in all of the treatments. These results support the conclusion that a priori weighting schemes should not be used to remove incongruence (presumably one does not want to introduce incongruence), but instead a simultaneous analysis strategy which includes treating all of the data equally weighted should be considered.