Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • BCO-DMO Processing Description
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

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, 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.

- Loaded table Truskey_EVA2025_gdmetrics_reefxcluster.csv
- Output file as 1004745_v1_gdmetrics_reefxcluster.csv

NSF Award Abstract:
Disease outbreaks in the ocean are increasing, causing losses of ecologically important marine species, but the factors contributing to these outbreaks are not well understood. This 5-year CAREER project will study disease prevalence and intensity in two marine foundation species - the seagrass Zostera marina and the Eastern oyster Crassostrea virginica. More specifically, host-disease relationships will be explored to understand how genetic diversity and population density of the host species impacts disease transmission and risk. This work will pair large-scale experimental restorations and smaller-scale field experiments to examine disease-host relationships across multiple spatial scales. Comparisons of patterns and mechanisms across the two coastal systems will provide an important first step towards identifying generalities in the diversity-density-disease relationship. To enhance the broader impacts and utility of this work, the experiments will be conducted in collaboration with restoration practitioners and guided by knowledge ascertained from key stakeholder groups. The project will support the development of an early career female researcher and multiple graduate and undergraduate students. Students will be trained in state-of-the-art molecular techniques to quantify oyster and seagrass parasites. Key findings from the surveys and experimental work will be incorporated into undergraduate courses focused on Conservation Biology, Marine Biology, and Disease Ecology. Finally, students in these courses will help develop social-ecological surveys and mutual learning games to stimulate knowledge transfer with stakeholders through a series of workshops.

The relationship between host genetic diversity and disease dynamics is complex. In some cases, known as a dilution effect, diversity reduces disease transmission and risk. However, the opposite relationship, known as the amplification effect, can also occur when diversity increases the risk of infection. Even if diversity directly reduces disease risk, simultaneous positive effects of diversity on host density could lead to amplification by increasing disease transmission between infected and uninfected individuals. Large-scale field restorations of seagrasses (Zostera marina) and oysters (Crassostrea virginica) will be utilized to test the effects of host genetic diversity on host population density and disease prevalence/intensity. Additional field experiments independently manipulating host genetic diversity and density will examine the mechanisms leading to dilution or amplification. Conducting similar manipulations in two marine foundation species - one a clonal plant and the other a non-clonal animal - will help identify commonalities in the diversity-density-disease relationship. Further, collaborations among project scientists, students, and stakeholders will enhance interdisciplinary training and help facilitate the exchange of information to improve management and restoration efforts. As part of these efforts, targeted surveys will be used to document the perceptions and attitudes of managers and restoration practitioners regarding genetic diversity and its role in ecological resilience and restoration.