A Compound Poisson Process for Relaxing the Molecular Clock

A Compound Poisson Process for Relaxing the Molecular Clock John P. Huelsenbeck a , Bret Larget b , and David Swofford c a Department of Biology, University of Rochester, Rochester, New York 14627, b Department of Mathematics and Computer Science, Duquesne University, Pittsburgh, Pennsylvania 15282 c Laboratory of Molecular Systematics, Smithsonian Museum Support Center, Suitland, Maryland 20746 Corresponding author: John P. Huelsenbeck, Department of Biology, University of Rochester, Rochester, NY 14627., johnh@brahms.biology.rochester.edu (E-mail) Communicating editor: S. T AVAR É The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Genetics Genetics Society of America

A Compound Poisson Process for Relaxing the Molecular Clock

Genetics, Volume 154 (4): 1879 – Apr 1, 2000

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Publisher
Genetics Society of America
Copyright
Copyright © 2000 by the Genetics Society of America
ISSN
0016-6731
eISSN
1943-2631
Publisher site
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Abstract

John P. Huelsenbeck a , Bret Larget b , and David Swofford c a Department of Biology, University of Rochester, Rochester, New York 14627, b Department of Mathematics and Computer Science, Duquesne University, Pittsburgh, Pennsylvania 15282 c Laboratory of Molecular Systematics, Smithsonian Museum Support Center, Suitland, Maryland 20746 Corresponding author: John P. Huelsenbeck, Department of Biology, University of Rochester, Rochester, NY 14627., johnh@brahms.biology.rochester.edu (E-mail) Communicating editor: S. T AVAR É The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.

Journal

GeneticsGenetics Society of America

Published: Apr 1, 2000

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