Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 18, Issue 3, Pages 352-361Publisher
SOC MOLECULAR BIOLOGY EVOLUTION
DOI: 10.1093/oxfordjournals.molbev.a003811
Keywords
molecular clock; phylogeny; Markov chain Monte Carlo; Metropolis-Hastings algorithm
Funding
- NIGMS NIH HHS [GM45344] Funding Source: Medline
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Rates of molecular evolution vary over time and, hence, among lineages. In contrast, widely used methods for estimating divergence times from molecular sequence data assume constancy of rates. Therefore, methods for estimation of divergence times that incorporate rate variation are attractive. Improvements on a previously proposed Bayesian technique for divergence time estimation are described. New parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Fossil information and other evidence can now be included in Bayesian analyses in the form of constraints on divergence times. Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included.
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