Abstract
Four species of true crocodile (genus Crocodylus) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions—Crocodylus intermedius in South America, C. moreletii along the Caribbean coast of Mesoamerica, and C. rhombifer confined to Cuba. The fourth, C. acutus, is narrowly sympatric with each of the other three species. In this study, we sampled 113 crocodiles across Crocodylus 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 C. acutus. One lineage, found in the continental Americas, is the sister taxon to C. intermedius, while the Greater Antillean lineage is most closely related to C. rhombifer. In addition to the paraphyly of the two C. acutus 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 C. acutus populations are consistent with interspecific differentiation within the genus and suggest that the current taxon recognized as C. acutus 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 C. acutus. 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.
Highlights
The order Crocodylia is currently comprised of 27 recognized or proposed living species distributed among three families (Alligatoridae, Crocodylidae, and Gavialidae) and nine genera (Alligator, Caiman, Melanosuchus, Paleosuchus, Crocodylus, Mecistops, Osteolaemus, Tomistoma, and Gavialis) representing, along with birds, the unique surviving members of the Archosauria (Grigg & Kirshner, 2015)
Previous studies have indicated that the phylogenetic placement of C. acutus is sensitive to sampling location, with most studies relying solely on individuals sampled from continental populations in Central and/or South America (Meredith et al, 2011; Milián-García et al, 2011, 2015; Oaks, 2011)
Among the wild caught individuals, the most common haplotype was identical to the a haplotype (Weaver et al, 2008; Milián-García et al, 2015), which is shared by C. rhombifer (n = 30) and hybrids (n = 2) from Zapata Swamp, as well as for C. acutus from Cienfuegos (n = 1) and Zapata Swamp (n = 1) (Fig. 2)
Summary
The order Crocodylia is currently comprised of 27 recognized or proposed living species distributed among three families (Alligatoridae, Crocodylidae, and Gavialidae) and nine genera (Alligator, Caiman, Melanosuchus, Paleosuchus, Crocodylus, Mecistops, Osteolaemus, Tomistoma, and Gavialis) representing, along with birds, the unique surviving members of the Archosauria (Grigg & Kirshner, 2015). Previous studies have indicated that the phylogenetic placement of C. acutus is sensitive to sampling location, with most studies relying solely on individuals sampled from continental populations in Central and/or South America (Meredith et al, 2011; Milián-García et al, 2011, 2015; Oaks, 2011) In these cases, a sister taxon relationship between C. acutus and C. intermedius has been consistently recovered with high support (Brochu & McEachran, 2000; Meganathan et al, 2010; Meredith et al, 2011; Hekkala et al, 2011; Oaks, 2011). The observed inconsistency in phylogenetic placement of C. acutus is likely a consequence of excluding intraspecific genetic variation when trying to resolve higher order relationships
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