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      Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

      Molecular Biology and Evolution

      Oxford University Press (OUP)

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          The general stochastic model of nucleotide substitution.

          DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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            Estimating the rate of evolution of the rate of molecular evolution.

            A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.
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              Among-site rate variation and its impact on phylogenetic analyses.

               Ziheng Yang (1996)
              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.
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                Author and article information

                Journal
                Molecular Biology and Evolution
                Molecular Biology and Evolution
                Oxford University Press (OUP)
                0737-4038
                1537-1719
                January 01 2002
                January 01 2002
                : 19
                : 1
                : 101-109
                Article
                10.1093/oxfordjournals.molbev.a003974
                © 2002

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