http://lod.bco-dmo.org/id/dataset/1004478
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
2026-08-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Oyster morphometric, condition, and parasite infection data from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2018-2020
2026-08-11
publication
2026-08-11
revision
BCO-DMO Linked Data URI
2026-08-11
creation
http://lod.bco-dmo.org/id/dataset/1004478
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) Oyster morphometric, condition, and parasite infection data 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 2026-08-11 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/1004478 [access date]
Morphometric, condition, and parasite trait data for oysters on restored reefs Dataset Description: Methods and Sampling: <p>These data were published in Truskey et al. 2025 (Evolutionary Applications).&nbsp;</p>
<p>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.</p>
<p><strong>Measuring oyster traits</strong></p>
<p>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&nbsp;1985; Mann&nbsp;1978).</p>
<p>Additionally, for oysters sampled in fall 2018, we assessed infection by four common oyster parasites: the microparasites <em>Perkinsus marinus</em> (urn:lsid:marinespecies.org:taxname:562957)&nbsp;and <em>Haplosporidium costale&nbsp;</em>(urn:lsid:marinespecies.org:taxname:394948), the causative pathogens of Dermo disease and SSO disease, respectively, and the macroparasites, <em>Cliona</em> spp. boring sponges and <em>Polydora</em> 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&nbsp;2001) and a quantitative polymerase chain reaction (qPCR) assay for Dermo (De Faveri et&nbsp;al.&nbsp;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 (<em>P. marinus</em> and mud blister worm) as an additional axis of potential variation in the response (tolerance) of oysters to parasites. Standardized intensity values for <em>P. marinus</em> 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&nbsp;al.&nbsp;2004) following protocols from Hanley et&nbsp;al.&nbsp;(2023).</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
ind_id
reef
block
primary_genetic_assignment
library
total_tissue_dryweight
total_shell_dryweight
condition_index_eq
shell_height
shell_length
taggedoutlier_ci
taggedoutlier_height
mb_present
bs_present
sso_present
dermo_present
dermo_intensity
mb_intensity
scuba
theme
None, User defined
season
sample identification
site
No BCO-DMO term
seq_descrip
dry_wgt
height
length
flag
featureType
BCO-DMO Standard Parameters
Manual Biota Sampler
qPCR Thermal Cycler
scale or balance
Self-Contained Underwater Breathing Apparatus
Thermal Cycler
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 Oyster morphometric, condition, and parasite infection data 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/1004638.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/1004639.rdf
Name: ind_id
Units: unitless
Description: <p>Unique identifier for each individual oyster. This identifier corresponds to the associated FASTQ sequence file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004640.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/1004641.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/1004642.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/1004643.rdf
Name: library
Units: unitless
Description: <p>RADseq library batch in which an individual was processed and sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004644.rdf
Name: total_tissue_dryweight
Units: grams (g)
Description: <p>Total dry weight of soft tissue from an individual oyster</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004645.rdf
Name: total_shell_dryweight
Units: grams (g)
Description: <p>Total dry weight of shell from an individual oyster</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004646.rdf
Name: condition_index_eq
Units: unitless (ratio)
Description: <p>Condition index, calculated as (dry tissue weight / dry shell weight) * 100</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004647.rdf
Name: shell_height
Units: millimeter (mm)
Description: <p>Maximum shell height measured in mm from the hinge to the outer shell edge</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004648.rdf
Name: shell_length
Units: millimeter (mm)
Description: <p>Maximum shell length measured in mm from one lateral edge of shell to the other at the widest point perpendicular to height</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004649.rdf
Name: taggedoutlier_ci
Units: unitless
Description: <p>Flag indicating whether the individual was identified as an outlier for condition index (1) or not tagged (0)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004650.rdf
Name: taggedoutlier_height
Units: unitless
Description: <p>Flag indicating whether the individual was identified as an outlier for shell height (1) or not tagged (0)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004651.rdf
Name: mb_present
Units: unitless
Description: <p>Presence (1) or absence (0) of blisters on shell associated with mud blister worm <em>Polydora sp.</em> infection</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004652.rdf
Name: bs_present
Units: unitless
Description: <p>Presence (1) or absence (0) of holes in shell associated with boring sponge <em>Cliona spp.</em> infection</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004653.rdf
Name: sso_present
Units: unitless
Description: <p>Presence (1) or absence (0) of <em>Haplosporidium costale</em> infection based on PCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004654.rdf
Name: dermo_present
Units: unitless
Description: <p>Presence (1) or absence (0) of <em>Perkinsus marinus</em> infection based on qPCR assay</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004655.rdf
Name: dermo_intensity
Units: log10-transformed copy number Perkinsus marinus per mg of oyster tissue
Description: <p>Intensity of <em>Perkinsus marinus</em> infection reflected as the mean concentration (copy number based on gBlocks standard) per wet weight oyster tissue (in mg); calculated for infected oysters only</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004656.rdf
Name: mb_intensity
Units: percent
Description: <p>Mean percent of oyster shell (top and bottom valves) with blisters characteristic of mud blister worm <em>Polydora sp</em>. infection ((total infected area/total shell area)*100), calculated for infected oysters only</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/1004478/data/download
download
onLine
dataset
<p>These data were published in Truskey et al. 2025 (Evolutionary Applications).&nbsp;</p>
<p>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.</p>
<p><strong>Measuring oyster traits</strong></p>
<p>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&nbsp;1985; Mann&nbsp;1978).</p>
<p>Additionally, for oysters sampled in fall 2018, we assessed infection by four common oyster parasites: the microparasites <em>Perkinsus marinus</em> (urn:lsid:marinespecies.org:taxname:562957)&nbsp;and <em>Haplosporidium costale&nbsp;</em>(urn:lsid:marinespecies.org:taxname:394948), the causative pathogens of Dermo disease and SSO disease, respectively, and the macroparasites, <em>Cliona</em> spp. boring sponges and <em>Polydora</em> 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&nbsp;2001) and a quantitative polymerase chain reaction (qPCR) assay for Dermo (De Faveri et&nbsp;al.&nbsp;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 (<em>P. marinus</em> and mud blister worm) as an additional axis of potential variation in the response (tolerance) of oysters to parasites. Standardized intensity values for <em>P. marinus</em> 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&nbsp;al.&nbsp;2004) following protocols from Hanley et&nbsp;al.&nbsp;(2023).</p>
Specified by the Principal Investigator(s)
<p><strong>Individual-level trait data</strong></p>
<p>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.</p>
<p>Dermo intensity values represent the <em>log10-transformed</em> copy number of <em>Perkinsus marinus</em> generated from the standardized qPCR protocol.</p>
<p><strong>Reef-level parasite prevalence by genetic cluster</strong></p>
<p>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.</p>
Specified by the Principal Investigator(s)
- 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
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
PI Supplied Instrument Name: PI Supplied Instrument Description:In fall 2018, we haphazardly sampled live oysters from each reef on scuba or snorkel (N = 512 individuals total, 32 per reef). 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/
PI Supplied Instrument Name: PI Supplied Instrument Description:Standardized intensity values for P. marinus were generated through the above cited qPCR protocol. Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
PI Supplied Instrument Name: PI Supplied Instrument Description: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). Instrument Name: scale or balance Instrument Short Name: Instrument Description: Devices that determine the mass or weight of a sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/
scuba
scuba
PI Supplied Instrument Name: scuba PI Supplied Instrument Description:In fall 2018, we haphazardly sampled live oysters from each reef on scuba or snorkel (N = 512 individuals total, 32 per reef). 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
PI Supplied Instrument Name: PI Supplied Instrument Description: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). Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)