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MBE Advance Access originally published online on December 29, 2004
Molecular Biology and Evolution 2005 22(4):914-924; doi:10.1093/molbev/msi076
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Molecular Biology and Evolution vol. 22 no. 4 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

Covarion Structure in Plastid Genome Evolution: A New Statistical Test

Cécile Ané1, J. Gordon Burleigh, Michelle M. McMahon and Michael J. Sanderson

Section of Evolution and Ecology, University of California, Davis

E-mail: ane{at}stat.wisc.edu.

Covarion models of molecular evolution allow the rate of evolution of a site to vary through time. There are few simple and effective tests for covarion evolution, and consequently, little is known about the presence of covarion processes in molecular evolution. We describe two new tests for covarion evolution and demonstrate with simulations that they perform well under a wide range of conditions. A survey of covarion evolution in sequenced plastid genomes found evidence of covarion drift in at least 26 out of 57 genes. Covarion evolution is most evident in first and second codon positions of the plastid genes, and there is no evidence of covarion evolution in third codon positions. Therefore, the significant covarion tests are likely due to changes in the selective constraints of amino acids. The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes.

Key Words: covarion • model testing • parametric bootstrap • plastid genome evolution


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