A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes |
| |
Authors: | Pupko Tal Galtier Nicolas |
| |
Affiliation: | The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu Minato-ku, Tokyo 106-8569, Japan. |
| |
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. |
| |
Keywords: | |
本文献已被 PubMed 等数据库收录! |
|