Genome-Wide Population Structure in a Marine Keystone Species, the European Flat Oyster (Ostrea edulis)

Abstract

Ostrea edulis, the European flat oyster, was once a widespread economically and ecologically important marine species, but hassuffered dramatic declines over the past two centuries. Consequently, there has been a surge in European restoration efforts,many of which focus on restocking as a conservation measure. In this study, we used whole-genome sequencing (WGS) data toinvestigate the population structure, demographic history, and patterns of local adaptation of O. edulis across its natural distri-bution with increased sampling densities at Scandinavian localities. Results revealed seven distinct genetic clusters, includingpreviously undescribed complex population structure in Norway, and evidence for introgression between genetic clusters inScandinavia. We detected large structural variants (SVs) on three pseudo-chromosomes. These megabase long regions werecharacterised by strong linkage disequilibrium and clear geographical differentiation, suggestive of chromosomal inversions po-tentially associated with local adaptation. The results indicated that genomic traces of past translocations of non-native O. eduliswere still present in some individuals, but overall, we found limited evidence of major impacts of translocations on the scale ofcontemporary population structure. Our findings highlight the importance of considering population structure and signaturesof selection in the design of effective conservation strategies to preserve and restore wild native European flat oyster populations,and we provide direct knowledge safeguarding sustainable mitigation actions in this important species.