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

Extant species in the order Crocodylia are remnants of an ancient lineage
of large-bodied archosaur reptiles. Despite decades of systematic studies,
phylogenetic relationships among members of the genus Crocodylus (true
crocodiles) in the Neotropics are poorly understood. Here we estimated
phylogenomic relationships among the four extant Crocodylus species in the
Americas. 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.