Dataset: Genetic relatedness estimates calculated from SNP genotype data of oysters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2018-2020

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

This dataset contains pairwise individual relatedness estimates for eastern oysters (Crassostrea virginica, urn:lsid:marinespecies.org:taxname:140657) sampled from 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 pairwise individual relatedness

Pairwise relatedness was estimated for all individuals within the same genetic cluster on each reef using the Wang estimator (Wang 2002) implemented in the R package related v0.8 (Pew et al. 2015), applied to the primary SNP dataset (4679 SNPs filtered for MAF > 0.01 and fall 2020 batch missingness, and pruned for linkage disequilibrium). The Wang estimator was selected for its reduced bias at small sample sizes and among highly related individuals (Wang 2017), as expected within hatchery-bred lineages.