Among-site rate variation and its impact on phylogenetic analyses.
Although several decades of study have revealed the ubiquity of variation of evolutionary rates among sites, reliable methods for studying rate variation were not developed until very recently. Early methods fit theoretical distributions to the numbers of changes at sites inferred by parsimony and substantially underestimate the rate variation. Recent analyses show that failure to account for rate variation can have drastic effects, leading to biased dating of speciation events, biased estimation of the transition:transversion rate ratio, and incorrect reconstruction of phylogenies.
Ziheng Yang is at the Dept of Integrative Biology, University of California, Berkeley, CA 94720, USA; College of Animal Science and Technology, Beijing Agricultural University, Beijing 100094, China.
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