Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences
is essential in many biological investigations,
including phylogeography, phylodynamics, and species delimitation studies.
In these investigations, multiple sequence alignments consist of
both intra- and inter-species samples (mixed samples). As a
result, the phylogenetic trees contain inter-species, inter-population,
and within-population divergences. Bayesian relaxed clock methods are
often employed in these analyses, but they assume the same tree prior for
both inter- and intra-species branching processes and require
specification of a clock model for branch rates (independent vs.
autocorrelated rates models). We evaluated the impact of a single tree
prior onBayesian divergence time estimates by
analyzing computer-simulated datasets. We also examined
the effectof the assumption of independence of evolutionary rate
variation among branches when the branch rates are autocorrelated.
Bayesian approach with coalescent tree priors generally
produced excellent molecular dates and highest posterior
densities with high coverage probabilities. We also evaluated the
performance of a non-Bayesian method, RelTime, which does not require the
specification of a tree prior or a clock model. RelTime's performance
was similar to that of the Bayesian approach, suggesting that it is also
suitable to analyze datasets containing both populations and species
variation when its computational-efficiency is needed.