Out with the old, introgression with the new: Signals of ancient and recent admixture in hybridizing Mesoamerican crocodiles

In this study, we investigated hybridization dynamics and genetic diversity of Crocodylus acutus and Crocodylus moreletii from Belize to ascertain whether genetic exchange through admixture displayed signs of evolutionary significance. We used genomic reduced representation (3RAD) datasets from 242 wild crocodile samples and found evidence of population structure among C. acutus, as well as ancient bidirectional gene flow that had occurred between C. acutus and C. moreletii. Notably, we also found evidence of high levels of recent admixture along the coastal populations of Crocodylus spp. in areas with extensive habitat modification due to human impact. These findings as well as a discovered disconnect between morphological and genetic species assignments used to identify populations have implications for conservation management practices and suggest a range of additional genetic investigations to understand the natural and anthropogenic role of hybridization in large long-lived tropical predators that span marine and terrestrial ecosystems.