http://lod.bco-dmo.org/id/dataset/1004745
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2026-08-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Genetic diversity metrics for oyster genetic clusters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2018-2020
2026-08-12
publication
2026-08-12
revision
BCO-DMO Linked Data URI
2026-08-12
creation
http://lod.bco-dmo.org/id/dataset/1004745
A. Randall Hughes
Northeastern University
principalInvestigator
Sarit Truskey
Northeastern University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Hughes, A. R., Truskey, S. (2026) Genetic diversity metrics for oyster genetic clusters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2018-2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/1004745 [access date]
Individual genetic assignments from hatchery samples and restored reefs Dataset Description: Methods and Sampling: <p>These data were published in Truskey et al. 2025 (Evolutionary Applications).&nbsp;</p>
<p>This dataset contains genetic cluster-level estimates of genetic diversity for eastern oysters (<em>Crassostrea virginica</em>, 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&nbsp;live oysters from each reef on scuba or snorkel.&nbsp;Oysters were put on ice and transported to the Northeastern University Marine Science Center where they were held at −80°C until DNA extraction.</p>
<p>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&nbsp;sequence metadata for all sampled oysters and individual genetic assignments source data.</p>
<p><strong>Estimating genetic diversity by oyster genetic cluster</strong></p>
<p>We used the primary SNP dataset (4679 SNPs; filtered for MAF &gt; 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<sub>o</sub>) and expected (H<sub>e</sub>) heterozygosity,&nbsp;F<sub>IS</sub>&nbsp;inbreeding coefficients, and allelic richness (A<sub>r</sub>). Bootstrapped confidence intervals for&nbsp;F<sub>IS</sub> were generated using the boot.ppfis function applying 1000 bootstrap replicates.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1652320 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1652320
onGoing
A. Randall Hughes
Northeastern University
781-581-7370
430 Nahant Rd.
Nahant
MA
01908
USA
ann.hughes@northeastern.edu
pointOfContact
Sarit Truskey
Northeastern University
240-205-3117
sbtruskey@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
yearcoll
block
reef
primary_genetic_assignment
n_inds
Ho
He
Ar
FIS
FIS_ll
FIS_hl
Illumina HiSeq 2500
Illumina NovaSeq 6000
scuba
theme
None, User defined
season
site
seq_descrip
count
ratio
mean
No BCO-DMO term
confidence_interval
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
Manual Biota Sampler
Self-Contained Underwater Breathing Apparatus
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
https://osprey.bco-dmo.org/project/709942
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
<p><em>NSF Award Abstract:</em><br />
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.</p>
<p>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.</p>
Seagrass and Oyster Ecosystems
largerWorkCitation
project
eng; USA
biota
oceans
-71.6929
-71.6929
41.3549
41.3549
2018-11-07
2020-10-07
Coastal New England
0
BCO-DMO catalogue of parameters from Genetic diversity metrics for oyster genetic clusters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2018-2020
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/1004767.rdf
Name: yearcoll
Units: unitless
Description: <p>Year and season of sample collection (e.g., F2018 = Fall 2018, F2020 = Fall 2020)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004768.rdf
Name: block
Units: unitless
Description: <p>Experimental block in which a restored reef was situated (A - D)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004769.rdf
Name: reef
Units: unitless
Description: <p>Restored reef from which an individual was collected. Letter refers to experimental block and number refers to the reef number within a block (e.g., D3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004770.rdf
Name: primary_genetic_assignment
Units: unitless
Description: <p>Assigned genetic cluster for an individual using the primary genetic assignment set applied to all main text analyses (DAPC approach, SNP set filtered for MAF > 0.01, LD pruning, and Fall 2020 missing data). Label names correspond to the state of origin of the hatchery source associated with a given genetic cluster (gME, gMA, gNY, gVA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004771.rdf
Name: n_inds
Units: count
Description: <p>Number of individuals sampled for this reef x genetic cluster combination</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004772.rdf
Name: Ho
Units: unitless (proportion)
Description: <p>Observed heterozygosity: mean proportion of heterozygous loci across individuals. Value: 0 to 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004773.rdf
Name: He
Units: unitless (proportion)
Description: <p>Expected heterozygosity under Hardy-Weinberg equilibrium. Value: 0 to 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004774.rdf
Name: Ar
Units: alleles per locus (standardized)
Description: <p>Allelic richness: rarefied mean number of alleles per locus, standardized to account for differences in sample size. Derived from rarefaction; Value: 1 to 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004775.rdf
Name: FIS
Units: unitless
Description: <p>Inbreeding coefficient (FIS) estimated using hierfstat. Value: -1 to 1; Negative = excess heterozygosity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004776.rdf
Name: FIS_ll
Units: unitless
Description: <p>Lower limit of 95% confidence interval for FIS via bootstrap</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004777.rdf
Name: FIS_hl
Units: unitless
Description: <p>Upper limit of 95% confidence interval for FIS via bootstrap</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/1004745/data/download
download
onLine
dataset
<p>These data were published in Truskey et al. 2025 (Evolutionary Applications).&nbsp;</p>
<p>This dataset contains genetic cluster-level estimates of genetic diversity for eastern oysters (<em>Crassostrea virginica</em>, 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&nbsp;live oysters from each reef on scuba or snorkel.&nbsp;Oysters were put on ice and transported to the Northeastern University Marine Science Center where they were held at −80°C until DNA extraction.</p>
<p>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&nbsp;sequence metadata for all sampled oysters and individual genetic assignments source data.</p>
<p><strong>Estimating genetic diversity by oyster genetic cluster</strong></p>
<p>We used the primary SNP dataset (4679 SNPs; filtered for MAF &gt; 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<sub>o</sub>) and expected (H<sub>e</sub>) heterozygosity,&nbsp;F<sub>IS</sub>&nbsp;inbreeding coefficients, and allelic richness (A<sub>r</sub>). Bootstrapped confidence intervals for&nbsp;F<sub>IS</sub> were generated using the boot.ppfis function applying 1000 bootstrap replicates.</p>
Specified by the Principal Investigator(s)
- Loaded table Truskey_EVA2025_gdmetrics_reefxcluster.csv
- Output file as 1004745_v1_gdmetrics_reefxcluster.csv
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 PI Supplied Instrument Description:See Related Datasets for individual genetic assignments from hatchery samples and restored reefs and sequence metadata for NCBI dataset.
The initial and fall 2020 batches were sequenced on a single lane of the Illumina HiSeq 2500 at Tufts University Core Facility Genomics; the fall 2018 batch was sequenced on two lanes of the Illumina NovaSeq 6000 at the University of Texas at Austin Genomic Sequencing and Analysis Facility. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Illumina NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 PI Supplied Instrument Description:See Related Datasets for individual genetic assignments from hatchery samples and restored reefs and sequence metadata for NCBI dataset.
The initial and fall 2020 batches were sequenced on a single lane of the Illumina HiSeq 2500 at Tufts University Core Facility Genomics; the fall 2018 batch was sequenced on two lanes of the Illumina NovaSeq 6000 at the University of Texas at Austin Genomic Sequencing and Analysis Facility. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: PI Supplied Instrument Description: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. Instrument Name: Manual Biota Sampler Instrument Short Name:Manual Biota Sampler Instrument Description: "Manual Biota Sampler" indicates that a sample was collected in situ by a person, possibly using a hand-held collection device such as a jar, a net, or their hands. This term could also refer to a simple tool like a hammer, saw, or other hand-held tool. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/90/
scuba
scuba
PI Supplied Instrument Name: scuba PI Supplied Instrument Description: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. Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.
Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html