Nucleotide transitions are frequently down-weighted relative to transversions in 
phylogenetic analysis. This is based on the assumption that transitions, by 
virtue of their greater evolutionary rate, exhibit relatively more homoplasy and 
are therefore less reliable phylogenetic characters. Relative amounts of 
homoplastic and consistent transition and transversion changes in mitochondrial 
protein coding genes were determined from character-state reconstructions on a 
highly corroborated phylogeny of mammals. We found that although homoplasy was 
related to evolutionary rates and was greater for transitions, the absolute 
number of consistent transitions greatly exceeded the number of consistent 
transversions. Consequently, transitions provided substantially more useful 
phylogenetic information than transversions. These results suggest that 
down-weighting transitions may be unwarranted in many cases. This conclusion was 
supported by the fact that a range of transition: transversion weighting schemes 
applied to various mitochondrial genes and 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.