Genomic data reveals cryptic diversity and suggests five putative species in the broad-snouted caiman in South America.

The inclusion of molecular data in evolutionary studies revealed a vast underestimation of species richness and allowed for assessing the relative importance of landscape features on the evolutionary history of species with different ecological requirements. Here, we used genomic-scale data to assess the genetic diversity of the crocodylian Caiman latirostris, exploring drivers of diversification. Using phylogenomic analysis, we identified five deeply diverged populations that are putative new species under C. latirostris. Genetic structure is coherent with South American watersheds, with evolutionary significant units/unconfirmed candidate species occurring mainly in the Atlantic Eastern Northeast Coast, São Francisco, Atlantic Southeastern, Atlantic South, and Paraná watersheds. Populations also show congruence with freshwater ecoregions, suggesting that not only watersheds, but also other landscape features, may act on species diversification. This is reinforced by a low migration rate between populations separated by mountain ranges. We highlight the need for separate management plans for each population of this historically threatened species due to their unique evolutionary history and genetic diversity. Future studies focusing on possible morphological and ecological differences, as well as demographic history, may reinforce the existence of putative species.