Global connections with some genomic differentiation occur between Indo‐Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish

AIM: Globally distributed pelagic fishes are typified by very low to negligible genetic differentiation at oceanic scales arising from high gene flow and (or) large population sizes. However, genomic approaches employing thousands of loci to characterise genetic variation can illuminate subtle patterns of genetic structure and facilitate demographic inference, such that effects arising from gene flow and population size can be partially decoupled. We used a population genomics approach to identify putative stocks in a circumtropical pelagic fish, wahoo, and to assess global connectivity in this species. LOCATION: Indo‐Pacific and Atlantic Oceans. TAXON: Wahoo, Acanthocybium solandri (Cuvier, 1832). METHODS: Globally distributed wahoo samples from 11 locations (representing a total of 296 individuals) were sequenced using a pool‐seq ezRAD approach to obtain 1289–9825 genome‐wide SNP loci per population pair for analyses of genetic structure at a minor allele frequency (MAF) >0.05. Demographic inference using a diffusion approximation method (∂a∂i) was performed using 11,495–12,812 SNPs per population pair at a MAF >0.02. RESULTS: Genetic structure, measured as FST, was overall low, suggesting very little heterogeneity amongst sample pairs (pairwise FST ≤ 0.021). However, there was a clear signal of regional genetic structuring between ocean basins. A principal coordinate analysis separated samples from the Indo‐Pacific with those from the Atlantic and an analysis of molecular variance suggested that ~77% of variation in genetic structure was amongst regions. Our demographic analyses found greater support for models including migration over simple models of isolation. MAIN CONCLUSIONS: Our study provides the most thorough genetic investigation of wahoo to date. We provide evidence for global connectivity of wahoo populations over their evolutionary history, but we also provide the first indication of subtle regional structure between the Indo‐Pacific and Atlantic Oceans, which occurs against a background of high gene flow. The identification of regional stocks will inform new management strategies and guide future investigations in wahoo, an increasingly important species in global fisheries.