Heterotachy occurs when the relative evolutionary rates among sites are not the 
same across lineages. Sequence alignments are likely to exhibit heterotachy with 
varying severity because the intensity of purifying selection and adaptive 
forces at a given amino acid or DNA sequence position is unlikely to be the same 
in different species. In a recent study, the influence of heterotachy on the 
performance of different phylogenetic methods was examined using computer 
simulation for a four-species phylogeny. Maximum parsimony (MP) was reported to 
generally outperform maximum likelihood (ML). However, our comparisons of MP and 
ML methods using the methods and evaluation criteria employed in that study, but 
considering the possible range of proportions of sites involved in heterotachy, 
contradict their findings and indicate that, in fact, ML is significantly 
superior to MP even under heterotachy.