Data from: Influence of gene flow on divergence dating – implications for speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to but notoriously difficult in the study of the evolutionary history of organisms. The difficulty is largely rooted in variations in ancestral population size or in separation history across loci. In order to depict speciation processes and divergent histories of three monophyletic Takydromus species endemic to Taiwan, 20 nuclear and one mitochondrial loci were sequenced and analyzed by a multispecies coalescent approach under a Bayesian framework. Divergence dating based on the gene tree approach showed great variation among loci and the results were more ancient than when derived by the species tree approach. To test whether variations in ancestral population size account for the majority of the above observations, i.e., whether gene flow must be invoked during speciation, we conducted computer simulations under isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favored over the isolation model and initiation of the speciation process was far more ancient than gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographic isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, the current study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating.