A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians

The mitochondrial genome encodes core subunits of the oxidative phosphorylation machinery, and it is expected that these mitochondria-encoded polypeptides would be shaped by bioenergetic needs corresponding to diverse diets and environments. Here, we have developed a robust and effective method for highlighting phylogenetic tree edges with unexpectedly rapid, and likely efficacious, mitochondrial protein evolution. Further, our approach allows detection of those discrete protein substitutions likely to alter enzyme performance. A survey of mammalian taxonomic groups performed using our method supports the idea that widely conserved residues in mitochondria-encoded proteins are more likely to rapidly mutate within specific clades. Intriguingly, primates share a substitution profile with a number of mammals characterized by low mass-specific rates of metabolism. Our data suggest low metabolic performance and activity of ancestral simians, as well as reduced cellular metabolism across many extant primates.