Genetic Diversity and Structure Analysis of Wild Oysters ( Crassostrea virginica ) Within and Between River Systems Reveals Spatial Genetic Structure and Salinity‐Adaptive Variation Across the Canadian M

ABSTRACT

In the Canadian Maritimes, the eastern oyster ( Crassostrea virginica ) industry has been shaped by population‐scale events, including ~90% reductions of natural beds from Malpeque disease. For many years, Maritime oyster populations were considered genetically homogenous due to large‐scale transplants to rehabilitate depleted beds; however, recent studies suggest that ancestral populations survived. We characterized genetic diversity and geographical genetic structure (using ddRAD‐seq) of wild oysters from 24 locations ( n =  1409) across New Brunswick (NB), Prince Edward Island (PEI), and Nova Scotia (NS), including multiple locations along estuarine gradients within the same river systems. While genetic differentiation was low  between Maritime locations ( F _st  = 0.012), ADMIXTURE analysis demonstrated spatial structure with cross‐validation (CV) error optimized at K = 4 ancestral populations. Oysters from the Bras d'Or Lakes in NS, and Miramichi and Richibucto in NB were characterized by distinct dominant ancestries, whereas populations from Bouctouche and Caraquet in NB, the Foxley, Grand, and Brudenell Rivers on PEI, and Pictou in NS shared a common dominant ancestry. Populations from coastal Cape Breton (Aspy River and Arichat) in NS exhibited mixed ancestry, primarily consisting of Bras d'Or Lake and ‘Gulf’ lineages. Within estuaries, genetic differentiation between upriver and downriver sites was minimal ( F _st  = 0.002–0.003), suggesting ongoing gene flow along estuarine gradients; however, each estuary contained a subset of SNP loci putatively under selection, indicating potential local adaptation despite high connectivity. Functional annotation of candidate loci identified genes associated with membrane transport, cellular stress response, protein turnover, and metabolic pathways, suggesting that environmental gradients may contribute to adaptive divergence. Ultimately, this reveals a complex genetic landscape and demonstrates that oyster beds in the Maritime provinces have retained genetic structure from both historical transfer activity in the region and local adaptation. The results provide important insights for the conservation, management, and restoration of eastern oyster populations throughout Atlantic Canada.