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

Tal Pupko, Nicolas Galtier

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)1313-1316
Number of pages4
JournalProceedings of the Royal Society B: Biological Sciences
Volume269
Issue number1498
DOIs
StatePublished - 7 Jul 2002
Externally publishedYes

Keywords

  • Covarion
  • Maximum likelihood
  • Mitochondrial genome
  • Positive Darwinian selection
  • Primates

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