Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number

The release of captive-bred plants and animals has increased worldwide to
augment declining species. However, insufficient attention has been given
to understanding how neutral and adaptive genetic variation are
partitioned within and among proximal natural populations, and the
patterns and drivers of gene flow over small spatial scales, which can be
important for restoration success. A seascape genomics approach was used
to investigate population structure, local adaptation, and the extent to
which environmental gradients influence genetic variation among natural
and restored populations of Chesapeake Bay eastern
oysters Crassostrea virginica. We also investigated the impact of
hatchery practices on neutral genetic diversity of restored reefs and
quantified the broader genetic impacts of large-scale hatchery-based
bivalve restoration. Restored reefs showed similar levels of diversity as
natural reefs, and striking relationships were found between planting
frequency and broodstock numbers and genetic diversity metrics (effective
population size and relatedness), suggesting that hatchery practices can
have a major impact on diversity. Despite long-term restoration
activities, haphazard historical translocations, and high dispersal
potential of larvae that could homogenize allele frequencies among
populations, moderate neutral population genetic structure was uncovered.
Moreover, environmental factors, namely salinity, pH, and temperature,
play a major role in the distribution of neutral and adaptive genetic
variation. For marine invertebrates in heterogeneous seascapes, collecting
broodstock from large populations experiencing similar environments to
candidate sites may provide the most appropriate sources for restoration
and ensure population resilience in the face of rapid environmental
change. This is one of a few studies to demonstrate empirically that
hatchery practices have a major impact on the retention of genetic
diversity. Overall, these results contribute to the growing body of
evidence for fine-scale genetic structure and local adaptation in
broadcast-spawning marine species and provide novel information for the
management of an important fisheries resource.