Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)

Species-tree reconstructions using genotypic data from 17,538 SNPs collected for 33 individuals spanning six Crocodylus species (four ingroup and two outgroup) revealed novel relationships for all Neotropical species. For the first time, C. acutus, the American crocodile, was recovered as monophyletic when individuals from Antillean and continental populations were analyzed together. Our results also contradict previous inferences based on mitochondrial DNA data and a limited number of nuclear markers by robustly grouping Morelet's crocodile (C. moreletii) as the sister species to C. acutus., suggesting a novel phylogeographic hypothesis for the group.

The present study punctuates the importance of using nuclear genome-wide information and representative sampling for resolving phylogenetic relationships, especially in broadly distributed species and those with complex evolutionary histories. Methods nextRAD genotyping-by-sequencing libraries were constructed by SNPsaurus, LLC following Russello et al. (2015) PeerJ (doi.org/10.7717/peerj.1106)