Manatee genomics supports a special conservation area in the Guianas coastline under the influence of the Amazon River plume

The West Indian manatee (Trichechus manatus) occurs along the Atlantic coastline and the adjacent freshwater systems of South, Central and North America, from Alagoas (Brazil) to Florida (USA) and the Greater Antilles. The Amazonian manatee (Trichechus inunguis) is the only sirenian adapted exclusively to freshwater and is endemic to the Amazon River basin. Previous studies have reported hybrids between T. inunguis and T. manatus close to the Amazon River mouth, likely composing an extensive hybrid zone under the influence of the Amazon River plume along the Guianas coast in South America. We have generated ddRAD SNP data, and sequences of nuclear and mtDNA loci to characterize the manatees’ genomic composition along the French Guiana coastline. Using analyses and simulations to examine the process of hybridization, we found this population to be formed by introgressed or later generation interspecific hybrids. We also describe the first pure T. inunguis found outside the Amazon River basin. Our results indicate that T. inunguis can survive in the Amazon River plume and have colonized independent water streams of the Guianas coastline where they likely hybridize with T. manatus. This hypothesis offers a plausible explanation for the known extension of the hybrid zone between the two species along the Guianas coastline. It also reinforces the importance of the Amazon plume, which flows westwards to the Guianas coastline and favors the dispersion of the freshwater species. The Amazon plume functions as a large estuary-like system that provides an ecological continuum from the Amazon River mouth to the disconnected waterflows of the Guianas, which deserves status as a special conservation area.