Dataset: Genetic diversity metrics for oyster genetic clusters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2017-2020

These data were published in Truskey et al. 2025 (Evolutionary Applications). 

This dataset contains genetic cluster-level estimates of genetic diversity for eastern oysters (Crassostrea virginica, urn:lsid:marinespecies.org:taxname:140657) sampled from each of the 12 experimental restored reefs in Ninigret Pond, Rhode Island, USA in fall 2018 and fall 2020, as part of a multi-year oyster reef restoration experiment using oysters sourced from four commercial hatcheries along the U.S. Atlantic coast. We sampled live oysters from each reef on scuba or snorkel. Oysters were put on ice and transported to the Northeastern University Marine Science Center where they were held at −80°C until DNA extraction.

Raw sequence reads for this study are deposited in the NCBI SRA (BioProject ID PRJNA1280068) and linked in the Related Datasets section. Also see Related Datasets for sequence metadata for all sampled oysters and individual genetic assignments source data.

Estimating genetic diversity by oyster genetic cluster

We used the primary SNP dataset (4679 SNPs; filtered for MAF >  0.01 and fall 2020 batch missing data, and pruned for linkage disequilibrium) to estimate genetic diversity metrics within assigned genetic clusters separately for each reef in fall 2018 and 2020. Using the hierfstat R package (Goudet, J., & Jombart, T., 2004; version 0.5-11), we estimated observed (H_o) and expected (H_e) heterozygosity, F_IS inbreeding coefficients, and allelic richness (A_r). Bootstrapped confidence intervals for F_IS were generated using the boot.ppfis function applying 1000 bootstrap replicates.