Draft genome assembly of Ostrea edulis from Limfjord, Denmark. The ghost of oysters past: museomics reveals isolation, low diversity and adaptive signatures of an extinct oyster population

Understanding the factors that predispose species and populations to decline and extinction is a major challenge of biodiversity research. In the present study, we investigated the historical population genomics of an extinct oyster population from the Wadden Sea collected between 1868 and 1888, and compared it to French and British populations sampled at the same time. To map our museomic reads, we generated a draft genome assembly of a contemporary oyster collected in the Danish Limfjord. The Wadden Sea is a unique habitat on the northern edge of the European oyster distribution. Our museomic results indicate that the now-extinct population was genetically isolated and had a lower nuclear genomic diversity than the examined French and British populations. Furthermore, genome scans revealed signatures of local adaptation, and population-specific divergence in several loci linked to fitness-relevant traits. The Wadden Sea oysters may have been predisposed for extinction because they were not naturally replenished from other populations, and the small population size did not allow them to adapt to anthropogenically-driven environmental change. In addition, anthropogenic translocations could not successfully replenish or replace this population because these foreign oysters may have been unable to reproduce in the unique Wadden Sea habitat. In summary, the Wadden Sea oysters exhibited all intrinsic drivers expected in a population predisposed for extinction.