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 Maximum. We hypothesize the glacial/interglacial cycles
facilitated gene flow between the Caribbean and Pacific crocodile
populations after the formation of the CAI, masking any genomic divergence
the CAI may have caused. There is no evidence of gene flow associated with
the opening of the Panama Canal.