Genomic differentiation and interoceanic population structure of two large pelagic scombrid species

Abstract

Tunas of the family Scombridae are of paramount importance for fisheries and the international seafood trade. In order to ensure a sustainable use of these valuable resources, it is crucial that stock delineation and management plans are in accordance. Here, we examined the population genetic structure of the two data-poor scombrid species wahoo (Acanthocybium solandri) and bigeye tuna (Thunnus obesus), both of growing significance in tuna fisheries. Our study employed whole-genome sequencing methods to conduct the most extensive genomic analysis of wahoo and bigeye tuna samples to date, collected from the Atlantic, Indian and Pacific Oceans. For both species, we observe genome-wide differentiation between samples from the Atlantic and the Indo-Pacific regions with little or no genetic structure within each of the ocean basins, indicative of high gene flow. However, by applying a set of extreme outlier tests, genomic differentiation between locations was identified within the Pacific Ocean for both species, as well as for wahoo within the Atlantic Ocean. Additionally, for bigeye tuna, we uncovered a putative chromosomal inversion with patterns of highly linked loci and strong population divergence, that may be involved in adaptive divergence across the distributional range of the species. Taken together, despite considerable gene flow, the detected substructures – most likely driven by local adaptation – challenge previously held assumptions of panmixia in both species. Our findings show that future stock assessment should consider genetic differences at both neutral and divergent loci to develop sustainable conservation and management actions for these valuable marine resources.

Keywords

• Biodiversity
• Stock structure
• Adaptive variation
• Outlier test
• Scombridae