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

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 phylogene

SUBMITTER: Wertheim JO 

PROVIDER: S-EPMC2909785 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature