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Abstract
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.