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DownloadedBy:[Yang,Ziheng]At:16:0313June2007 Syst. Biol. 56(3):453466, 2007

Summary: DownloadedBy:[Yang,Ziheng]At:16:0313June2007
Syst. Biol. 56(3):453­466, 2007
Copyright c Society of Systematic Biologists
ISSN: 1063-5157 print / 1076-836X online
DOI: 10.1080/10635150701420643
Inferring Speciation Times under an Episodic Molecular Clock
Genome Center and Section of Evolution and Ecology, University of California, Davis, California, USA
Department of Biology, University College London, London, UK; E-mail: z.yang@ucl.ac.uk
Abstract.-- We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species diver-
gence times to allow variable evolutionary rates among lineages. The method can use heterogeneous data from multiple gene
loci and accommodate multiple fossil calibrations. Uncertainties in fossil calibrations are described using flexible statistical
distributions. The prior for divergence times for nodes lacking fossil calibrations is specified by use of a birth-death process
with species sampling. The prior for lineage-specific substitution rates is specified using either a model with autocorrelated
rates among adjacent lineages (based on a geometric Brownian motion model of rate drift) or a model with independent
rates among lineages specified by a log-normal probability distribution. We develop an infinite-sites theory, which predicts
that when the amount of sequence data approaches infinity, the width of the posterior credibility interval and the posterior


Source: Anisimova, Maria - Institute of Scientific Computing, Eidgenössische Technische Hochschule Zürich (ETHZ)
Yang, Ziheng - Department of Genetics, Evolution and Environment, University College London


Collections: Biology and Medicine; Environmental Sciences and Ecology