Inferring Species Trees Using Integrative Models of Species Evolution

Bayesian methods can be used to accurately estimate species tree topologies, times and other parameters, but only when the models of evolution which are available and utilized sufficiently account for the underlying evolutionary processes. Multispecies coalescent (MSC) models have been shown to accurately account for the evolution of genes within species in the absence of strong gene flow between lineages, and fossilized birth-death (FBD) models have been shown to estimate divergence times from fossil data in good agreement with expert opinion. Until now dating analyses using the MSC have been based on a fixed clock or informally derived node priors instead of the FBD. On the other hand, dating analyses using an FBD process have concatenated all gene sequences and ignored coalescence processes. To address these mirror-image deficiencies in evolutionary models, we have developed an integrative model of evolution which combines both the FBD and MSC models. By applying concatenation and the MSC (without employing the FBD process) to an exemplar data set consisting of molecular sequence data and morphological characters from the dog and fox subfamily Caninae, we show that concatenation causes predictable biases in estimated branch lengths. We then applied concatenation using the FBD process and the combined FBD-MSC model to show that the same biases are still observed when the FBD process is employed. These biases can be avoided by using the FBD-MSC model, which coherently models fossilization and gene evolution, and does not require an a priori substitution rate estimate to calibrate the molecular clock. We have implemented the FBD-MSC in a new version of StarBEAST2, a package developed for the BEAST2 phylogenetic software.