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Syst. Biol. 51(5):703714, 2002 DOI: 10.1080/10635150290102375

Summary: Syst. Biol. 51(5):703­714, 2002
DOI: 10.1080/10635150290102375
Effects of Models of Rate Evolution on Estimation of Divergence
Dates with Special Reference to the Metazoan 18S Ribosomal
RNA Phylogeny
Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
Abstract.--The molecular clock, i.e., constancy of the rate of evolution over time, is commonly as-
sumed in estimating divergence dates. However, this assumption is often violated and has drastic
effects on date estimation. Recently, a number of attempts have been made to relax the clock assump-
tion. One approach is to use maximum likelihood, which assigns rates to branches and allows the
estimation of both rates and times. An alternative is the Bayes approach, which models the change of
the rate over time. A number of models of rate change have been proposed. We have extended and
evaluated models of rate evolution, i.e., the lognormal and its recent variant, along with the gamma,
the exponential, and the Ornstein­Uhlenbeck processes. These models were rst applied to a small
hominoid data set, where an empirical Bayes approach was used to estimate the hyperparameters
that measure the amount of rate variation. Estimation of divergence times was sensitive to these hy-
perparameters, especially when the assumed model is close to the clock assumption. The rate and
date estimates varied little from model to model, although the posterior Bayes factor indicated the
Ornstein­Uhlenbeck process outperformed the other models. To demonstrate the importance of al-


Source: Aris-Brosou, Stéphane - Department of Biology, University of Ottawa
Yang, Ziheng - Department of Genetics, Evolution and Environment, University College London


Collections: Biology and Medicine; Environmental Sciences and Ecology