Genetic diversity and population structure of Metapenaeus ensis in the South China Sea determined via genotyping-by-sequencing

Metapenaeus ensis is a commercially important penaeid shrimp widely distributed across the Indo-West Pacific. However, the population genetic characteristics of its wild stocks along the Chinese coast remain poorly understood. This study employed genotyping-by-sequencing (GBS) to assess genetic diversity, population structure, and historical gene flow in six wild M. ensis populations collected along the Chinese coast, including Beibu Gulf (BB), Lingao (LG), Raoping (RP), Shanwei (SW), Sanya (SY), and Zhuhai (ZH). A total of 285,266 high-quality biallelic SNPs were obtained. All populations exhibited low genetic diversity, with observed heterozygosity ( Ho ) ranging from 0.0963 to 0.0983 and expected heterozygosity ( He ) from 0.1202 to 0.1238, along with signals of heterozygote deficiency. Pairwise Fst values ranged from -0.00012 (ZH and SW) to 0.02049 (ZH and BB), indicating weak overall genetic differentiation, although the ZH and BB populations showed relatively greater divergence. ADMIXTURE analysis identified two major ancestral components at K = 2, whereas PCA and neighbor-joining phylogeny revealed extensive individual overlap and limited topological resolution. The SY population may display admixed ancestry and represent a potential genetic admixture hub. TreeMix analysis identified the four-migration model and inferred multiple ancestral admixture events between two major clades (BB-LG and SY-RP-SW-ZH). Overall, the observed pattern of low genetic diversity and weak population differentiation suggests that these wild stocks may be managed as a coordinated fishery unit. Furthermore, these genomic resources provide valuable SNP markers to support germplasm conservation and sustainable fishery management of M. ensis in China.