Abstract
Aim Bats are the only group of mammals with extant native species present throughout the islands of the Antilles, Central America, and South America. Here, we test competing hypotheses of species diversification in mastiff bats and deepen our understanding of the dominant biogeographical processes involved in evolution and distribution in the Neotropics. We estimated the number of dispersals between the major geographic areas and whether vicariant events, such as the Andean uplift in the Miocene/Pliocene and Pleistocene glaciations, disrupted gene flow. Location South America, Central America, and Caribbean. Taxon Molossus , Neotropical mastiff bats. Methods We used the phylogeny derived from a Genotype by Sequencing approach to test different biogeographical models in the Neotropics. Bayesian inference with molecular and geological calibration points was also used to estimate the age of major lineage divergences within Molossus and to infer speciation events. Results Most diversification within Molossus occurred relatively recently and over a short period of time during the Pleistocene. The best‐fit model, dispersal‐extinction cladogenesis, showed that anagenetic dispersal, sympatric speciation, and vicariance all appear to have been involved in the evolutionary history of the Neotropics. Divergence times suggest that geological and paleo‐climatic events were important factors in Molossus diversification. Main conclusions Pleistocene refugia in South America and the formation of the Panama Isthmus are likely to have played an important role in speciation within Molossus , while the Caribbean species are the result of at least two independent dispersal events to the archipelago from South America and Central America, coinciding with low sea levels during the Pleistocene.