Population genomics of eastern oysters, Crassostrea virginica, in a well-mixed estuarine system: advancement and implications for restoration strategies

Eastern oysters, Crassostrea virginica, are historically a keystone species in many of the estuaries in which they reside, providing critical ecosystem services. Because oyster populations have been on the decline for the past century, restoration initiatives currently are underway in many estuarine systems, including Great Bay Estuary (GBE), New Hampshire. Results of prior studies of eastern oyster population genomics cannot be applied directly to GBE, as it is a well-mixed estuarine system that is relatively contained, and the sources of recruits are split among cultivated and native. This study aimed to identify the population genomic structure of eastern oysters in GBE to facilitate determination of effective population size and estimation of genetic differentiation among subpopulations. Results showed moderate genomic differentiation among native, cultivated, and restoration C. virginica subpopulations in the Bay. A small number of breeders (N_e=163-276) was found in all subpopulations except the Lamprey River site (N_e=995). This research provides a contemporary snapshot of eastern oyster subpopulation structure at the genomic level in GBE that will facilitate restoration and enhanced management.