Genomic evidence of divergence-with-gene-flow in the pink shrimp Farfantepenaeus brasiliensis.

Divergence in marine environments is complex, often occurring despite the absence of physical barriers. This study investigates the genomic structure and demographic history of the economically important pink shrimp Farfantepenaeus brasiliensis across its Western Atlantic distribution using genomic data (ddRAD) and mitochondrial sequences. We tested the hypothesis that oceanographic features in the region act as barriers, generating genetically divergent groups despite high connectivity potential. Samples from four regions (Florida-USA, Northeastern-Brazil, Eastern-Brazil, and Southeastern-Brazil) were analyzed, covering the full range of the species' distribution. Results revealed two distinct genetic clusters corresponding to northern and southern populations, with evidence of asymmetrical gene flow. Genetic diversity was higher in the northern population. Demographic analyses indicated population expansions following the Last Glacial Maximum and recent declines, particularly in the southern population. The most likely demographic scenario involved allopatric divergence followed by secondary contact, with an estimated split ~2 million years ago (Mya). Phylogenetic and species delimitation analyses supported the separation of northern and southern populations into distinct taxonomic units. Despite divergence, ongoing gene flow was detected, suggesting a divergence-with-gene-flow scenario and potentially different species. The Amazon-Orinoco Plume appears to act as the main semi-permeable barrier, allowing intermittent connectivity while facilitating divergence through genetic drift. This study provides insights into marine divergence processes, highlighting how ecological factors and oceanographic barriers shape genetic differentiation in high-dispersal marine species. The findings have implications for taxonomy, evolution, fishing and conservation of F. brasiliensis, emphasizing the need for integrated management approaches considering cryptic genetic diversity.