Systematic Zoology Advance Access published online on October 13, 2009
Systematic Zoology, doi:10.1093/sysbio/syp072
Relaxed Molecular Clocks, the Bias–Variance Trade-off, and the Quality of Phylogenetic Inference
1 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
* Correspondence to be sent to: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA; E-mail: wertheim{at}email.arizona.edu.
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Abstract |
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Because a constant rate of DNA sequence evolution cannot be assumed to be ubiquitous, relaxed molecular clock inference models have proven useful when estimating rates and divergence dates. Furthermore, it has been recently suggested that using relaxed molecular clocks may provide superior accuracy and precision in phylogenetic inference compared with traditional time-free methods that do not incorporate a molecular clock. We perform a simulation study to determine if assuming a relaxed molecular clock does indeed improve the quality of phylogenetic inference. We analyze sequence data simulated under various rate distributions using relaxed-clocks, strict-clocks, and time-free Bayesian phylogenetic inference models. Our results indicate that no difference exists in the quality of phylogenetic inference between assuming a relaxed molecular clock and making no assumption about the clock-likeness of sequence evolution. This pattern is likely due to the bias–variance trade-off inherent in this type of phylogenetic inference. We also compared the quality of inference between Bayesian and maximum likelihood time-free inference models and found them to be qualitatively similar.
Keywords: Bayesian; bias–variance trade-off; maximum likelihood; relaxed molecular clock; Robinson–Foulds tree-to-tree distance
Received September 22, 2008; Revised December 22, 2008; Accepted September 10, 2009