Genome scans reveal extensive population structure in three neritic tuna and tuna-like species in the Indian Ocean

Abstract Neritic tunas and tuna-like species are an important resource for many coastal nations1 worldwide supporting both commercial and artisanal fisheries, but little is known about their population structure at a spatial scale required for effective fisheries management. In this study, we use Next Generation Sequencing methods to investigate the genetic connectivity of three major neritic tuna and tuna-like species in the Indian Ocean: Longtail Tuna (Thunnus tonggol), Kawakawa (Euthynnus affinis), and narrow-barred Spanish mackerel (Scomberomorus commerson). We sampled 293 Longtail Tuna from three locations, 362 Kawakawa from seven locations, and 210 narrow-barred Spanish mackerel from six locations. Genetic data showed clear evidence of heterogeneity in all three species, and patterns of isolation-by-distance were detected in Kawakawa and narrow-barred Spanish mackerel. Pairwise FST estimates of population differentiation and model-based grouping (mixture models) revealed that (i) individuals of Longtail Tuna from each sampling location belonged to a distinct genetic group, (ii) at least two different groups of Kawakawa were identified, and (iii) at least four groups of narrow-barred Spanish mackerel were identified across the sampled range within the north and eastern Indian Ocean. These results demonstrate that neritic tunas exhibit genetic structuring at small to medium spatial scales that need to be considered in the design of monitoring and assessment systems for fisheries management purposes in the northern and eastern parts of their range in the Indian Ocean. Further sampling, at a finer spatial resolution within the range of the current study, and across the north-western and western parts of their range of the Indian Ocean that were not covered in the current study, is required to provide a comprehensive understanding of the number of populations present and the spatial extent of individual populations in the Indian Ocean and adjacent seas.