Genetic evidence supports a distinct lineage of American crocodile (<i>Crocodylus acutus</i>) in the Greater Antilles

Abstract

Four species of true crocodile (genus <i>Crocodylus</i>) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions-<i>Crocodylus intermedius</i> in South America, <i>C. moreletii</i> along the Caribbean coast of Mesoamerica, and <i>C. rhombifer</i> confined to Cuba. The fourth, <i>C. acutus</i>, is narrowly sympatric with each of the other three species. In this study, we sampled 113 crocodiles across <i>Crocodylus</i> populations in Cuba, as well as exemplar populations in Belize and Florida (USA), and sequenced three regions of the mitochondrial genome (D-loop, cytochrome b, cytochrome oxidase I; 3,626 base pair long dataset) that overlapped with published data previously collected from Colombia, Jamaica, and the Cayman Islands. Phylogenetic analyses of these data revealed two, paraphyletic lineages of <i>C. acutus</i>. One lineage, found in the continental Americas, is the sister taxon to <i>C. intermedius</i>, while the Greater Antillean lineage is most closely related to <i>C. rhombifer</i>. In addition to the paraphyly of the two <i>C. acutus</i> lineages, we recovered a 5.4% estimate of Tamura-Nei genetic divergence between the Antillean and continental clades. The reconstructed paraphyly, distinct phylogenetic affinities and high genetic divergence between Antillean and continental <i>C. acutus</i> populations are consistent with interspecific differentiation within the genus and suggest that the current taxon recognized as <i>C. acutus</i> is more likely a complex of cryptic species warranting a reassessment of current taxonomy. Moreover, the inclusion, for the first time, of samples from the western population of the American crocodile in Cuba revealed evidence for continental mtDNA haplotypes in the Antilles, suggesting this area may constitute a transition zone between distinct lineages of <i>C. acutus</i>. Further study using nuclear character data is warranted to more fully characterize this cryptic diversity, resolve taxonomic uncertainty, and inform conservation planning in this system.