Table of Contents

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

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

In fall 2018, we haphazardly collected live oysters from each reef by scuba or snorkel. We repeated sampling in fall 2020, when lower live oyster densities resulted in variable sample sizes among reefs. Following collection, oysters were placed on ice, transported to the Northeastern University Marine Science Center, and stored at −80°C until subsequent processing and analysis.

Measuring oyster traits

To assess variation in oyster traits associated with genetic cluster identity, we recorded the following size-related measurements for all oysters sampled in fall 2018 and 2020: shell height (mm) from the hinge to the outer shell edge; shell length (mm) from one lateral shell edge to the other at the widest point perpendicular to height; total mass (g); dry tissue and shell mass (g; tissue and shells dehydrated in drying oven for ≥ 48 h). We calculated oyster condition index as dry tissue mass × 100 divided by dry shell mass (i.e., dry tissue weight: dry shell weight ratio; Lucas and Beninger 1985; Mann 1978).

Additionally, for oysters sampled in fall 2018, we assessed infection by four common oyster parasites: the microparasites Perkinsus marinus (urn:lsid:marinespecies.org:taxname:562957) and Haplosporidium costale (urn:lsid:marinespecies.org:taxname:394948), the causative pathogens of Dermo disease and SSO disease, respectively, and the macroparasites, Cliona spp. boring sponges and Polydora sp. mud blister worms. To assess infection by the microparasites, we used DNA extracted from the 32 oysters sampled per reef in 2018 and performed a polymerase chain reaction (PCR) assay protocol developed for SSO (Stokes and Burreson 2001) and a quantitative polymerase chain reaction (qPCR) assay for Dermo (De Faveri et al. 2009). For macroparasite presence, we surveyed the shells of individual oysters for physical signatures of macroparasites (i.e., holes characteristic of boring sponge; interior blisters indicating burrowing by mud blister worms). In addition to infection presence, we also report infection intensities (parasite load or concentration, per infected host) for the two most prevalent oyster parasites (P. marinus and mud blister worm) as an additional axis of potential variation in the response (tolerance) of oysters to parasites. Standardized intensity values for P. marinus were generated through the above cited qPCR protocol. For mud blister worm intensity, we quantified the overall proportion of parasite-affected shell area using ImageJ (Abràmoff et al. 2004) following protocols from Hanley et al. (2023).

Individual-level trait data

Outlier flags are provided for individuals identified as statistical outliers for condition index and shell height in collections from 2018 and from 2020 based on the Rosner Test.

Dermo intensity values represent the log10-transformed copy number of Perkinsus marinus generated from the standardized qPCR protocol.

Reef-level parasite prevalence by genetic cluster

To evaluate patterns of parasite infection by genetic cluster, we calculated the prevalence of each parasite as the proportion of individuals infected (the number infected/the total number of individuals sampled for an observed parasite) for each genetic cluster on each reef.

- Loaded file Truskey_EVA2025_ind_traits_parasites_combined_bcodmo.csv
- Stripped trailing unit suffixes (_g, _mm) from column names total_tissue_dryweight_g, total_shell_dryweight_g, shell_height_mm, shell_length_mm, renaming them to total_tissue_dryweight, total_shell_dryweight, shell_height, shell_length in compliance with BCO-DMO parameter guidelines
- Replaced value "x" with "1" in columns taggedoutlier_ci and taggedoutlier_height
- Set remaining null/missing values in taggedoutlier_ci to 0, keeping already-converted 1 values, cast to integer
- Set remaining null/missing values in taggedoutlier_height to 0, keeping already-converted 1 values, cast to integer
- Output file as 1004478_v1_ind_traits_parasites.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.