Genome-wide genetic-marker variation uncovers potential stock structuring of oceanic tuna (skipjack) and coastal tuna (kawakawa) within the western Indian Ocean

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Tuna and tuna-like species are highly mobile and migratory, and therefore assumed to have single highly connected populations over large ocean regions. However, empirical data on the genetic population structure of such species in the western Indian Ocean (WIO) remain limited. Understanding these structures is crucial for managing stocks across territorial and transnational waters. This study tested the hypothesis of single genetic stocks of skipjack tuna Katsuwonus pelamis and kawakawa Euthynnus affinis within the WIO region, specifically off Kenya, Tanzania, Mozambique, South Africa and the Seychelles. Samples were collected from commercial fishers, between September 2019 and July 2020. Genome-wide single-nucleotide polymorphism (SNP) data for skipjack (7 005 loci, average H O = 0.206) revealed low overall genetic differentiation (global F ST = 0.003; between-sample F ST = 0–0.013, where F ST is the genetic-distance value), but significant genetic differences between skipjack taken from a northern sampling region (i.e. central Tanzania, Kenya and Sri Lanka) and from a southern region (i.e. southern Tanzania, Mozambique and South Africa), with samples from the Seychelles falling closer to the southern grouping. SNP data for kawakawa (14 806 loci, average H O = 0.2585) indicate a patchy distribution of low but significant genetic differentiation among these WIO sites (global F ST = 0.018; between-sample F ST = 0.003–0.036), yet with no obvious geographically-based pattern. In comparison with data from previous studies, we conclude that there is evidence of subpopulations of skipjack and kawakawa within the WIO, and that a precautionary approach should be adopted for future fishery management.