title: A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes.
abstract: 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.
authors.affiliation: The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu Minato-ku, Tokyo 106-8569, Japan.
authors.forename: Tal
authors.initials: T
authors.lastname: Pupko
authors.forename: Nicolas
authors.initials: N
authors.lastname: Galtier
mesh_terms: D000818:Animals; D001188:Artiodactyla / Q000235:genetics; D002335:Carnivora / Q000235:genetics; D002591:Cetacea / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D004606:Elephants / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome; D007793:Lagomorpha / Q000235:genetics; D024101:Mitochondrial Proteins / Q000235:genetics; D009007:Monotremata / Q000235:genetics; D010527:Perissodactyla / Q000235:genetics; D010802:Phylogeny; D011323:Primates / Q000235:genetics*; D012377:Rodentia / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D024101:Mitochondrial Proteins