Abstract
Advances in aquaculture have significantly enhanced food production and contributed to global food security. However, the selective pressures for aquaculture are strong and divergent compared to those occurring in natural systems, and displacement of standing genetic backgrounds by aquaculture backgrounds is a conservation concern across various species. The Asian sea bass or barramundi ( Lates calcarifer ) is a widely propagated species that has undergone intensive selective breeding and extensive translocations. There are uncertain impacts, if any, on wild stocks throughout the tropical Indo-West Pacific region as a result. Using whole-genome sequencing data, we characterize the genetic background of wild-caught fish from two previously unrepresented regions – Taiwan and Sri Lanka. In Taiwan, Asian sea bass aquaculture has been ongoing for decades, largely relying on broodstock from Thailand. Aquaculture of this taxon in Sri Lanka is more recent and less understood. We also sequenced two aquaculture strains from Australia and Sri Lanka, for a total of four aquaculture strains to better characterize aquaculture strains of Asian sea bass. Our results show that Taiwanese wild-caught fish exhibit admixture with aquaculture origin, alongside introgression of Indian Ocean mitochondrial haplotypes. Conversely, Sri Lankan wild-caught fish are not admixed with the local aquaculture strain and are similar to other Indian Ocean fish. Our findings indicate that mixture of distinctive genetic backgrounds of Asian sea bass is widespread in both culture and naturally recruiting populations. This underscores the urgent need for improved hatchery management and conservation measures to safeguard the long-term sustainability and genetic integrity of wild stocks.