Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis

Nucleotide transitions are frequently down-weighted relative to transversio ns in phylogenetic analysis. This is based on the assumption that transitio ns, by Virtue of their greater evolutionary rate, exhibit relatively more h omoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplastic and consistent transition and transversion changes i n mitochondrial protein coding genes were determined from character-state r econstructions on a highly corroborated phylogeny of mammals. We found that although homoplasy was related to evolutionary rates and was greater for t ransitions, the absolute number of consistent transitions greatly exceeded the number of consistent transversions. Consequently, transitions provided substantially more useful phylogenetic information than transversions. Thes e results suggest that down-weighting transitions may be unwarranted in man y cases. This conclusion was supported by the fact that a range of transiti on: transversion weighting schemes applied to various mitochondrial genes a nd genomic partitions rarely provided improvement in phylogenetic estimates relative to equal weighting, and in some cases weighting transitions more heavily than transversions was most effective.