Abstract
Demographics of co‐occurring species can often be diagnosed through population genomic analyses of single nucleotide polymorphisms (SNPs). These data can define population structure, gene flow, and candidate regions in the genome that potentially reflect local adaptations. They can also gauge whether populations are demographically “open” or “closed” (i.e., with global or local recruitment). We derived SNPs from double‐digest restriction‐site associated DNA (ddRAD) to test the demographics of commercially important bonefish Albula vulpes ( N = 117) and queen conch Lobatus gigas ( N = 60) from two northeast Caribbean Basin islands (Grand Bahama to the north and Eleuthera to the south). Specifically, we tested the hypothesis that the strong west‐to‐east current in the Great Bahama Canyon is a vicariant barrier separating the two islands. We conducted Bayesian assignment tests on putatively neutral ( A. vulpes = 36,206 SNPs; L. gigas = 64,863) and highly differentiated outlier datasets ( A. vulpes = 123 and 79 SNPs; L. gigas = 88 and 51, respectively). For bonefish, results diagnosed asymmetrical gene flow and north‐south differentiation, as potentially driven by adult mobility and easterly currents. However, both analyses indicated genetic structure in conch, substantiating the vicariant hypothesis. These results provide templates for future research endeavors with these impacted species. Outlier loci, for example, can potentially place populations of each within a demographic continuum, rather than within a dichotomous “open/closed” framework, as well as diagnose “source” and “sink” populations, as herein. These methodologies can then be applied to co‐distributed species with similar but less well‐understood ecologies so as to evaluate basin‐wide trends in connectivity and local adaptation.