Whole Genome Resequencing Reveals High Genetic Homogeneity and Localized Candidate Differentiation Signals in Saxidomus purpuratus Along the Yellow and Bohai Sea

Saxidomus purpuratus (S. purpuratus) is an economically important bivalve along the northern coast of China, where intensifying fishing pressure threatens its wild stocks. Its genome-wide population genetic variation remains poorly characterized. We resequenced 75 wild individuals from five populations spanning the northern Yellow Sea (Donggang, DDDG; Ganjingzi, DLGJ; Huancui, WHHC) and the Bohai Sea (Changdao, YTCD; Laizhou, YTLZ). The sampled populations exhibited relatively low genetic diversity (He = 0.1301–0.1324), weak among-population differentiation (Fst = 0.0035–0.0040), and heterozygosity deficiency (Fis = 0.0480–0.0831). PCA, NJ, and ADMIXTURE detected no geographic structure. PSMC revealed concordant demographic histories, with a sustained decline following a Middle Pleistocene expansion, consistent with historical allele exchange. Selection scans (DDDG as the target population; WHHC and YTCD as references) identified 1268 candidate genes, of which 197 were shared across the two comparisons. After masking a tandem histone gene cluster, the remaining 155 non-histone genes fell into five functional categories: receptor and signal transduction, membrane transport and ion channels, innate immunity and defense, extracellular matrix and adhesion, and detoxification and metabolism. These signals recurred in both comparisons, identifying DDDG as a candidate population for genotype–environment association testing. Together, these results provide the first genome-wide assessment of S. purpuratus and indicate that the five populations constitute a single genetically connected unit, while pinpointing a small set of candidate loci that may underpin local adaptation and warrant monitoring in stock-enhancement programmes.