Effect of the Central American Isthmus on gene flow and divergence of the American crocodile Crocodylus acutus

The final formation of the Central American Isthmus (CAI) about 3.5 Ma altered global ocean circulation, connected North and South America terrestrial biotas and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile Crocodylus acutus, to study the genomic variation of C. acutus on both sides of the CAI, infer its demographic history and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: 1) Caribbean and the Panama Canal, 2) Pacific coast, and 3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20 ka, which is two orders of magnitude younger than the formation of the CAI, but coincides with the Last Glacial Ma...