DOI: 10.5061/dryad.47d7wm3fm
title: Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number

description: 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.
description: VCF file of 6,654 single nucleotide polymorphisms (SNPs) derived
 from double digest restriction-site associated DNA (ddRAD) sequencing of
 478 eastern oysters (Crassostrea virginica) sampled across natural and
 restored sites in the Chesapeake Bay, filtered for a minor allele
 frequency of  5%,  no more than 50% missing data.
 Genepop file of unlinked neutral SNPs of eastern oysters (4641
 SNPs, all populations) Genepop file unliked neutral
 SNPs of eastern oysters (4922 SNPs, inner Bay populations)
 List of SNPs detected as potentially under selection using
 pcadapt, Bayescan, OutFLANK, and RDA (all populations)
 List of SNPs detected as potentially under selection using
 pcadapt, Bayescan, OutFLANK, and RDA (inner Bay populations)
 Environmental data for the PCNM+RDA analysis
 Individual information (Individual, sampling site abbreviation,
 location, site, type, latitude, longitude)