Bayesian inference under the multispecies coalescent with ancient DNA sequences

Ancient DNA (aDNA) is increasingly being used to investigate questions
such as the phylogenetic relationships and divergence times of extant and
extinct species. If aDNA samples are sufficiently old, expected branch
lengths (in units of DNA substitutions) are reduced relative to
contemporary samples. This can be accounted for by incorporating sample
ages into phylogenetic analyses. Existing methods that use tip (sample)
dates infer gene trees rather than species trees, which can lead to
incorrect or biased inferences of the species tree. Methods using a
multispecies coalescent (MSC) model overcome these issues. We developed an
MSC model with tip dates and implemented it in the program bpp. The method
performed well for a range of biologically realistic scenarios, estimating
calibrated divergence times and mutation rates precisely. Simulations
suggest that estimation precision can be best improved by prioritizing
sampling of many loci and more ancient samples. Incorrectly treating
ancient samples as contemporary in analyzing simulated data, mimicking a
common practice of empirical analyses, led to large systematic biases in
model parameters, including divergence times. Two genomic datasets of
mammoths and elephants were analyzed, demonstrating the method's
empirical utility.