Genetic Impacts of Sustained Stock Enhancement on Wild Populations: A Case Study of Penaeus penicillatus in the Beibu Gulf, China

In recent decades, fishery stock enhancement has been increasingly utilized as a restoration tool to mitigate population declines and enhance the resilience of marine fisheries. Nevertheless, persistent enhancement efforts risk eroding the evolutionary potential of wild populations via genetic homogenization and maladaptive gene flow. Using long-term monitoring data (2017–2023), we quantified the effects of large-scale Penaeus penicillatus stock enhancement (~108 juveniles/yr) on wild population dynamics and genetic integrity in the Beibu Gulf ecosystem. Temporal genetic changes were assessed using eight highly polymorphic microsatellite loci, comparing founder (2017) and enhanced (2024) populations to quantify stocking impacts. Insignificantly lower expected heterozygosity was observed in the stocked population (He = 0.60, 2024) relative to natural populations (He = 0.62–0.66; p > 0.1), indicating genetic dilution effects from enhancement activities. No significant erosion of genetic diversity was detected post-enhancement, suggesting current stocking practices maintain short-term population genetic integrity. Despite conserved heterozygosity, pairwise Fst analysis detected significant genetic shifts between temporal cohorts (pre-enhancement—2017 vs. post-enhancement—2024; Fst = 0.25, p < 0.05), demonstrating stocking-induced population restructuring. Genetic connectivity analysis revealed that while the enhanced Beihai population (A-BH) maintained predominant self-recruitment (>90%), it experienced substantial stocking-derived gene flow (17% SW → A-BH). The post-stocking period showed both reduced genetic exchange with adjacent populations and increased asymmetric dispersal from A-BH (e.g., 5% to YJ), indicating that hatchery releases simultaneously enhanced population isolation while altering regional genetic structure. Our findings revealed the paradoxical dual effects of stock enhancement and allelic diversity while disrupting natural genetic architecture. This underscores the need for evolutionary-impact assessments in marine resource management.