Bayesian phylogenetic estimation of fossil ages
Alexei J. Drummond, Tanja Stadler

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular the fossilized birth-death tree prior and the Lewis-MK model of evolution of discrete morphological change allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by estimating the phylogenetic age of each fossil in turn, within two rich and well-characterized data sets of fossil and extant species. We find that we can accurately estimate the age of individual fossils based only on phylogenetic evidence. In fact in the two data sets we analyze the phylogenetic age of a fossil species is on average <2My from the midpoint age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses provides strong evidence that the Bayesian statistical model employed is a good fit for both the geological and morphological data, and provides striking evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing the “morphological clock”, and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.