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Bayesian methods are increasingly being used to estimate divergence times without the restrictive assumption of a global clock.
Little is known about their reliability for shallow phylogenies where DNA sequence divergence is low.
Our study demonstrates the impact of the prior on divergence times in shallow phylogenies and shows that 1) prior intervals on nodes should be assessed as a prerequisite to a dating analysis, 2) ≥ 1 kbp of quite rapidly evolving sequence may be required to obtain accurate posterior means and usefully narrow posterior intervals.
Over the past decade, there has been considerable progress in the development of phylogenetic methods for estimation of lineage divergence times.
Divergence time estimation may be less accurate and/or precise as a result. In this article, we focus on 2 different methods for specifying the prior on divergence times. Generation of internode times is repeated on different paths within the tree until all nodes have been assigned ages.Different divergence times priors within MCMCTREE, MULTIDIVTIME, and BEAST were used to analyze mitochondrial DNA data sets from a Bovid subfamily (the Caprinae) from Asian lizards.Posterior divergence times were quite sensitive to different BDS priors but less sensitive to different Dirichlet priors.This is implemented in the program MCMCTREE (Rannala and Yang 2007; Yang and Rannala 2006; Yang 2007).The BDS prior is specified by 3 parameters: per-lineage birth (λ) and death (μ) rates and the sampling proportion (ρ).