TY - JOUR
T1 - A covarion-based method for detecting molecular adaptation
T2 - Application to the evolution of primate mitochondrial genomes
AU - Pupko, Tal
AU - Galtier, Nicolas
PY - 2002/7/7
Y1 - 2002/7/7
N2 - 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.
AB - 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.
KW - Covarion
KW - Maximum likelihood
KW - Mitochondrial genome
KW - Positive Darwinian selection
KW - Primates
UR - http://www.scopus.com/inward/record.url?scp=0037036501&partnerID=8YFLogxK
U2 - 10.1098/rspb.2002.2025
DO - 10.1098/rspb.2002.2025
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AN - SCOPUS:0037036501
SN - 0962-8452
VL - 269
SP - 1313
EP - 1316
JO - Proceedings of the Royal Society B: Biological Sciences
JF - Proceedings of the Royal Society B: Biological Sciences
IS - 1498
ER -