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

Content Provider	PubMed Central
Author	Tal, Pupko Galtier, Nicolas
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.
Related Links	http://dx.doi.org/10.1098/rspb.2002.2025
Starting Page	1313
File Format	PDF
ISSN	14712954
e-ISSN	14712954
Journal	Proceedings of the Royal Society B: Biological Sciences
Issue Number	1498
Volume Number	269
Language	English
Publisher Date	2002-07-07
Access Restriction	Open
Subject Keyword	Biological Sciences Research in Higher Education
Content Type	Text
Resource Type	Article

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