Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference

Joel O. Wertheim, Michael J. Sanderson, Michael Worobey, Adam Bjork

Research output: Contribution to journalArticle

46 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1-8
Number of pages8
JournalSystematic biology
Volume59
Issue number1
DOIs
StatePublished - Jan 1 2010

Keywords

  • Bayesian
  • Bias-variance trade-off
  • Maximum likelihood
  • Relaxed molecular clock
  • Robinson-Foulds tree-to-tree distance

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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