A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes

A new method for detecting site–specific variation of evolutionary rate (the so–called covarion process) from protein sequence data is proposed. It involves comparing the maximum–likelihood estimates of the replacement rate of an amino acid site in distinct subtrees of a large tree. This approach allows detection of covarion at the gene or the amino acid levels. The method is applied to mammalian–mitochondrial–protein sequences. Significant covarion–like evolution is found in the (simian) primate lineage: some amino acid positions are fast–evolving (i.e. unconstrained) in non–primate mammals but slow–evolving (i.e. highly constrained) in primates, and some show the opposite pattern. Our results indicate that the mitochondrial genome of primates reached a new peak of the adaptive landscape through positive selection.