Applied population genomics in the native European flat oyster (Ostrea edulis)

The native European flat oyster (Ostrea edulis) has been facing challenges since ancient times. Originally found in Europe, we have evidence of important fisheries for the species since the Mesolithic. Cultivation was practiced by the Romans as early as the 2nd century AD. And O. edulis wild stocks continued to be commercially exploited during the Renaissance, leading to overfishing and causing local extinction. Anthropogenic activities have also played a significant role in the spread of lethal disease that further depleted natural populations. Today, multiple projects are underway to restore the O. edulis habitat and overcome its decline.

This Phd thesis participates in advancing our understanding of the restoration success for the native European flat oyster, by examining the genetic diversity of the species wild and cultured populations, and offering recommendations for genetic monitoring and hatchery production protocols.

Initial findings, grounded in the assembly of a high-quality O. edulis genome, elucidates the population structure of wild remnants O. edulis populations and sheds light on the structural variation in their genomes, including the discovery of previously unidentified genetic clusters of natural population in Scandinavia. We also probed into the potential effects of local adaptation and analyzed geographical heterogeneity in genomic regions linked to resistance to Bonamia ostrea, a parasite significantly affecting local populations and restoration programmes.

Then, investigations into the best protocols for maintaining genetic diversity reveal that active management, combined with genetic monitoring of spat production methods, is critical in preventing the loss of genetic diversity in hatchery strains. The findings underscore the Ryman-Laikre effects as a substantial challenge in flat oyster restoration. In response, we propose a method to estimate parentage, relatedness, and genetic variation in both wild and hatchery scenarios as an effective tool to control and implement new hatchery protocols.

Lastly, the implications of hatchery-reared oyster supplementation for population genetic diversity were investigated. We observe profound genomic changes even after a few generations, emphasizing the necessity for genetic diversity monitoring in hatcheries. Consequently, we propose the implementation of production protocols that aim to limit genomic change away from origin source populations and suggest a focus on natural recruitment processes for local biodiversity. The outcomes of this research contribute to the knowledge base required for effective restoration programmes of O. edulis, ultimately enhancing ecosystem function and supporting sustainable, low-carbon emission food resources.