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Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

Ho, Simon Y.W., Phillips, Matthew, Drummond, Alexei, & Cooper, Alan (2005) Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Molecular Biology and Evolution, 22(5), pp. 1355-1363.

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Abstract

In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of autocorrelated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.

Impact and interest:

77 citations in Scopus
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76 citations in Web of Science®

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ID Code: 50527
Item Type: Journal Article
Keywords: Molecular rates, Relaxed clock, Penalized likelihood, Bayesian inference, Cambrian explosion
DOI: 10.1093/molbev/msi125
ISSN: 1537-1719
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400)
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Deposited On: 23 May 2012 08:07
Last Modified: 23 May 2012 08:08

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