Abstract

The blood clam Anadara granosa is a commercially valuable bivalve widely distributed in China. However, intensive aquaculture has increasingly impacted wild population structure and genetic diversity, yet genomic data elucidating these anthropogenic impacts remain scarce. Here, we performed whole-genome resequencing of five geographically distinct populations along the Chinese coast to investigate their genomic landscape. The results showed that the blood clams could be divided into northern (N) and southern (S) populations based on genomic population structure. Fst, demographic history, gene flow, and diversity analyses suggest that extensive aquaculture may have contributed to the observed population structure. Selective sweep analyses further suggest stronger local adaptation in the N population. These signals, together with evidence of aquaculture-mediated introgression, are consistent with a role for both anthropogenic processes and natural selection in population divergence. Subsequently, we identified positively selected genes (PSGs) in both N and S populations. Analysis of missense variants in PSGs such as Npr1l , Manea , and Helz2l in the N population further suggests a potential role in local adaptation of metabolic and immune-related pathways. These findings provide novel insights into the interplay between anthropogenic pressure and natural selection, providing a theoretical basis for conservation and breeding programs.