NDLI: Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

Content Provider	PubMed Central
Author	Li, Wai Lok Sibon Drummond, Alexei J.
Copyright Year	2012
Abstract	We describe a procedure for model averaging of relaxed molecular clock models in Bayesian phylogenetics. Our approach allows us to model the distribution of rates of substitution across branches, averaged over a set of models, rather than conditioned on a single model. We implement this procedure and test it on simulated data to show that our method can accurately recover the true underlying distribution of rates. We applied the method to a set of alignments taken from a data set of 12 mammalian species and uncovered evidence that lognormally distributed rates better describe this data set than do exponentially distributed rates. Additionally, our implementation of model averaging permits accurate calculation of the Bayes factor(s) between two or more relaxed molecular clock models. Finally, we introduce a new computational approach for sampling rates of substitution across branches that improves the convergence of our Markov chain Monte Carlo algorithms in this context. Our methods are implemented under the BEAST 1.6 software package, available at http://beast-mcmc.googlecode.com.
Related Links	http://dx.doi.org/10.1093/molbev/msr232
Ending Page	761
Page Count	11
Starting Page	751
File Format	PDF
ISSN	07374038
e-ISSN	15371719
Journal	Molecular Biology and Evolution
Issue Number	2
Volume Number	29
Language	English
Publisher	Oxford University Press
Publisher Date	2012-02-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Ecology, Evolution, Behavior and Systematics Molecular Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Molecular Biology Ecology, Evolution, Behavior and Systematics

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