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Description

<b>Abstract</b><br/>

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 <i>Crocodylus</i> (true crocodiles) in the Neotropics are poorly understood. Here we estimated phylogenomic relationships among the four extant <i>Crocodylus </i>species in the Americas. Species-tree reconstructions using genotypic data from 17,538 SNPs collected for 33 individuals spanning six <i>Crocodylus </i>species (four ingroup and two outgroup) revealed novel relationships for all Neotropical species. For the first time, <i>C. acutus</i>, 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 (<i>C. moreletii</i>) as the sister species to <i>C. acutus</i>., 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.</p>; <b>Methods</b><br />

nextRAD genotyping-by-sequencing libraries were constructed by SNPsaurus, LLC following Russello et al. (2015) <em>PeerJ </em>(https://doi.org/10.7717/peerj.1106)</p>