PT - JOURNAL ARTICLE
AU - Huelsenbeck, John P.
AU - Larget, Bret
AU - Swofford, David
TI - A Compound Poisson Process for Relaxing the Molecular Clock
DP - 2000 Apr 01
TA - Genetics
PG - 1879--1892
VI - 154
IP - 4
4099 - http://www.genetics.org/content/154/4/1879.short
4100 - http://www.genetics.org/content/154/4/1879.full
SO - Genetics2000 Apr 01; 154
AB - 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.