Data from: The impact of the tree prior on molecular dating of data sets containing a mixture of inter- and intraspecies sampling

In Bayesian phylogenetic analyses of genetic data, prior probability
distributions need to be specified for the model parameters, including the
tree. When Bayesian methods are used for molecular dating, available tree
priors include those designed for species-level data, such as the
pure-birth and birth-death priors, and coalescent-based priors designed
for population-level data. However, molecular dating methods are
frequently applied to data sets that include multiple individuals across
multiple species. Such data sets violate the assumptions of both the
speciation and coalescent-based tree priors, making it unclear which
should be chosen and whether this choice can affect the estimation of node
times. To investigate this problem, we used a simulation approach to
produce data sets with different proportions of within- and
between-species sampling under the multispecies coalescent model. These
data sets were then analysed under pure-birth, birth-death, constant-size
coalescent, and skyline coalescent tree priors. We also explored the
ability of Bayesian model testing to select the best-performing priors. We
confirmed the applicability of our results to empirical data sets from
cetaceans, phocids, and coregonid whitefish. Estimates of node times were
generally robust to the choice of tree prior, but some combinations of
tree priors and sampling schemes led to large differences in the age
estimates. In particular, the pure-birth tree prior frequently led to
inaccurate estimates for data sets containing a mixture of inter- and
intraspecific sampling, whereas the birth-death and skyline coalescent
priors produced stable results across all scenarios. Model testing
provided an adequate means of rejecting inappropriate tree priors. Our
results suggest that tree priors do not strongly affect Bayesian molecular
dating results in most cases, even when severely misspecified. However,
the choice of tree prior can be significant for the accuracy of dating
results in the case of data sets with mixed inter- and intraspecies
sampling.