Impact of model violations on the inference of species boundaries under the multispecies coalescent

The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence, and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown. This is concerning given the large amount of empirical data and theory that highlight the complexity of the speciation process. Here, we seek to fill this gap by using simulation to characterize the sensitivity of inference under the multispecies coalescent to several violations of model assumptions thought to be common in empirical data. We also assess the fit of the multispecies coalescent model to empirical data in the context of species delimitation. Our results show substantial variation in model fit across d...