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     data   graph     files  public Performance traits (e.g., survival, growth, size) for hatchery-produced oyster cohorts    ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_770157

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String In April 2012, we collected 100 adult oysters (80-100 mm shell length) from
3-5 separate reefs at each of 6 sites: St. Augustine, FL (FL-1; 30.0224,
-81.3287), Jacksonville, FL (FL-2; 30.4446, -81.4199), Sapelo Island, GA
(GA/SC-1; 31.4777, -81.2726), Ace Basin, SC (GA/SC-2; 32.4846, -80.6001),
Masonboro, NC (NC-1; 34.1510, -77.8551), and Middle Marsh, NC (NC-2; 34.6951,
-76.6183). They were held in flowing seawater tanks or suspended in cages from
docks in their home region for 2-3 weeks until 30 oysters from each site could
be tested and certified as disease free. The remaining 70 oysters were then
shipped on ice to a single hatchery facility in Florida (Research Aquaculture
Inc., Tequesta, FL; 26.9607, -80.0931) at the end of April.

The adult oysters from each site were used as the broodstock to produce 6
separate site-specific \"cohorts\" (one cohort per site). From their arrival
at the hatchery, the adult oysters were held for 2 weeks until they were ready
to spawn under the same conditions in separate flow-through seawater systems
to prevent cross-contamination. All families were manually spawned (i.e.,
strip spawned) on May 7 (see details below). Because the original FL-1 family
did not produce many offspring, the remaining broodstock oysters from this
site were spawned on June 1 using the same process. Due to variation in
ripeness and sex, the number of oysters spawned and the ratio of males to
females varied across broodstock (Table 1 of Hughes et al., 2019), though our
broodstock numbers for each cohort are comparable to those commonly used in
hatchery settings (30-60 individuals; Morvezen et al. 2016).

The broodstock oysters from each source site were strip spawned, sexed, and
fertilized on the same day by a team of 7 people, who each had a specific job
to perform: shucking the animals, sampling and preparing tissue for
microscopic analysis of sex, identifying the sex, stripping the male sperm,
stripping the female eggs, mixing the sperm and eggs after all of the animals
from a particular source were stripped, overseeing the process and keeping
track of broodstock source. We sanitized equipment between individuals and
again between broodstock sources. Stripping was done by broodstock source
independently and quickly so that the sperm and eggs would remain viable, and
all viable sperm and eggs were used. During the gamete mixing process, the
eggs from all females and the sperm from all males were first pre-mixed and
then combined to ensure equal access of gametes to one another. We allowed
30-60 minutes for fertilization; once 75-90% of the eggs were fertilized, they
were moved to larval tanks. All larvae were retained except for minimal
numbers of individuals in each cohort that did not grow or had improper
development. Larval culture occurred in 60-gallon conical tanks utilizing a
flow-through seawater system with Banjo screens that is commercially used in
multiple bivalve hatcheries (e.g., Taylor Shellfish in WA; Cherrystones in

Over a period of 3 days the week of May 28, oysters were sieved on a
250-micron sieve and settled on crushed oyster cultch in a recirculating flow-
through system. The week of June 11, once they reached 800 microns in size,
they were moved into a nursery facility compliant with state regulations,
again under flow-through seawater conditions (salinity = 32 ppt, temperature =
30\u00baC). In the hatchery and nursery stages, the oysters were fed a mixed
diet of T. isochrysis, Chaetocerous gracilis, and Tetraselmis via a constantly
running peristaltic pump. Although growth was similar during the larval
culture phase, some cohorts produced more juvenile oysters (\"spat\") than
others during settlement, despite following the same procedures for all. To
maintain consistency in their growing conditions, we selected a random sample
of each cohort to yield similar total abundances across cohorts on June 18. At
the end of June (June 27) at approximately 4mm in size, the 6 cohorts were
transferred to a common flow-through facility at the Whitney Marine Biological
Laboratory in St. Augustine, FL. To assess genetic diversity within and
between oyster cohorts produced in the hatchery, 50 individuals were
haphazardly collected from each juvenile cohort prior to the start of the
field experiments and preserved at -80\u1d52C for genetic analysis. This
sample size is sufficient to estimate allele frequencies accurately (Hale et
al. 2012).

To extract DNA, we ground each tissue sample with a pestle, and used the
tissue centrifugation protocol from the Omega Bio-Tek E-Z 96 Tissue DNA Kit.
We determined genetic diversity and population structure using 12 highly
variable microsatellite loci developed for C. virginica: Cvi9, Cvi11, and
Cvi13 from Brown et al. (2000); Cvi1i24b, Cvi2i23, Cvi2j24, and Cvi2k14 from
Reece et al. (2004); Cvi4313E-VIMS from Carlsson and Reece (2007); and RUCV1,
RUCV66, RUCV73, and RUCV74 from Wang and Guo (2007). We amplified four loci in
each multiplexed polymerase chain reaction (PCR) using the Qiagen Type-It
Microsatellite PCR Kit. Each 10 l reaction consisted of 1 l DNA template, 5 l
2X type-it multiplex master mix (Qiagen), 2.4 l water, and 0.2 l each 10 M
primer. Using a T100 thermal cycler (Bio-Rad), PCR cycling conditions included
initial activation/denaturation at 95\u1d52C for 5 min, followed by 28 cycles
of 95\u1d52C for 30 sec, 60\u1d52C for 90 sec, and 72\u1d52C for 30 sec, and
final extension at 60\u1d52C for 30 min. PCR products were separated on a
3730xl Genetic Analyzer (Applied Biosystems) with the internal size standard
GeneScan 500 LIZ (Applied Biosystems), and fragment analysis was performed
using GeneMarker version 2.6 (SoftGenetics).

We created panels for each multiplexed reaction in GeneMarker, which included
bins that were assigned manually for all alleles; the same panels were used to
score all samples, and the alignment of the panels was checked prior to each
analysis to account for any run-to-run variation and to identify any new
alleles. We used these panels to do a preliminary first assignment of alleles
based on peak position and bin position, but every sample was then scored
manually for all loci to examine signal intensity, to confirm the
presence/absence of alleles, and to identify any reruns. A subset of samples
was then rerun (at least 15% per multiplex PCR reaction) and manually scored
again to confirm any uncertain allele calls and account for any genotyping

We experimentally evaluated the performance (size, growth, survivorship) of
each 2012 juvenile oyster cohort in the field as a function of within-cohort
effective allelic diversity. These same oysters were analyzed for different
response variables as part of two other studies (Hanley et al. 2016, Hughes et
al 2017; see Appendix S1 of Hughes et al., 2019 for additional information).
These studies used the same experimental design. Namely, in each experiment,
12 spat from a single cohort were affixed to 10*10 cm experimental tiles using
the marine adhesive Z-spar. Tiles were held in flow-through seawater tables
for less than 48 hours until being deployed to the field. Prior to deployment,
we measured shell height of each spat and photographed all tiles. At the end
of each experiment, live oysters were counted and measured.

Oysters at three of the five sites included here have previously been analyzed
in a test of genetic by environmental variation across oyster cohorts (Hughes
et al. 2017): spat from each cohort were deployed on July 12-14, 2012 across 3
field sites in the South Atlantic Bight that spanned the geographic range of
the source populations: FL-EXP (29.6714, -81.2162); GA-EXP (31.9213,
-80.9880), or NC-EXP (34.7069, -76.7631). At each field site, we deployed 18
tiles (6 cohorts * 3 tiles per cohort) to each of 9 natural intertidal oyster
reefs. Low spat abundance in the FL-1 cohort limited replication of this
cohort to 4 reefs per experimental site (N=147 tiles total). The 3 tiles from
each cohort were haphazardly assigned to one of three predation treatments
(full cage, with mesh with 6mm*6mm openings; partial cage to control for
caging artifacts; no cage) and deployed on the reef in a completely randomized
design; only the full cage and no cage treatments are addressed further here.
This experiment lasted 6 weeks.

Data collected on oysters deployed at the other two field sites used in the
present study come from a concurrent longer-term experiment focused on the
effects of oyster cohort diversity that included additional treatments not
analyzed here (Hanley et al. 2016). In this study, 36 tiles were deployed (6
cohorts * 6 tiles per cohort) at each of two sites in the Matanzas River
estuary, FL (FL-North: 29.75177, -81.25578; FL-South: 29.65838, -81.22193) on
July 24-25, 2012. The 6 tiles from each cohort were split across the same
three predation treatments as above and deployed in a completely randomized
design. This experiment lasted 6 months.
attribute NC_GLOBAL awards_0_award_nid String 709941
attribute NC_GLOBAL awards_0_award_number String OCE-1652320
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1652320 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Oyster Cohort Traits
PI: Randall Hughes
Version date: 06-June-2019
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2019-06-07T15:52:30Z
attribute NC_GLOBAL date_modified String 2019-06-11T18:39:16Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.770157.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/770157 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 770186
attribute NC_GLOBAL instruments_0_description String General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String 3730xl Genetic Analyzer (Applied Biosystems)
attribute NC_GLOBAL instruments_1_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 770185
attribute NC_GLOBAL instruments_1_description String General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). 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.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute NC_GLOBAL instruments_1_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_1_instrument_nid String 471582
attribute NC_GLOBAL instruments_1_supplied_name String T100 thermal cycler (Bio-Rad)
attribute NC_GLOBAL keywords String alive, allelic, Allelic_richness, average, bco, bco-dmo, biological, cage, Cage_alive, Cage_dead, chemical, cohort, data, dataset, dead, diversity, dmo, eff, Eff_allelic_diversity, erddap, exp, final, Final_avg_size, genetic, Genetic_relatedness, growth, initial, Initial_avg_size, management, oceanography, office, open, Open_tile_alive, Open_tile_dead, preliminary, relatedness, richness, site, size, tile
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/770157/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/770157 (external link)
attribute NC_GLOBAL param_mapping String {'770157': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/770157/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Northeastern University
attribute NC_GLOBAL people_0_affiliation_acronym String NEU
attribute NC_GLOBAL people_0_person_name String A. Randall Hughes
attribute NC_GLOBAL people_0_person_nid String 522929
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Shannon Rauch
attribute NC_GLOBAL people_1_person_nid String 51498
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Seagrass and Oyster Ecosystems
attribute NC_GLOBAL projects_0_acronym String Seagrass and Oyster Ecosystems
attribute NC_GLOBAL projects_0_description String 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.
attribute NC_GLOBAL projects_0_end_date String 2022-01
attribute NC_GLOBAL projects_0_geolocation String Coastal New England
attribute NC_GLOBAL projects_0_name String CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
attribute NC_GLOBAL projects_0_project_nid String 709942
attribute NC_GLOBAL projects_0_start_date String 2017-02
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Performance traits (e.g., survival, growth, size) for hatchery-produced oyster cohorts.
attribute NC_GLOBAL title String Performance traits (e.g., survival, growth, size) for hatchery-produced oyster cohorts
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Exp   String  
attribute Exp bcodmo_name String exp_id
attribute Exp description String Unique identifier for the 2 experiments included in this dataset
attribute Exp long_name String Exp
attribute Exp units String unitless
variable Site   String  
attribute Site bcodmo_name String site
attribute Site description String Unique identifier for the site location within each experiment
attribute Site long_name String Site
attribute Site units String unitless
variable Eff_allelic_diversity   float  
attribute Eff_allelic_diversity _FillValue float NaN
attribute Eff_allelic_diversity actual_range float 3.781, 6.025
attribute Eff_allelic_diversity bcodmo_name String sample_descrip
attribute Eff_allelic_diversity description String Effective allelic diversity for that oyster cohort
attribute Eff_allelic_diversity long_name String Eff Allelic Diversity
attribute Eff_allelic_diversity units String unitless
variable Allelic_richness   float  
attribute Allelic_richness _FillValue float NaN
attribute Allelic_richness actual_range float 8.333, 12.917
attribute Allelic_richness bcodmo_name String sample_descrip
attribute Allelic_richness description String Number of alleles for that oyster cohort
attribute Allelic_richness long_name String Allelic Richness
attribute Allelic_richness units String Number of alleles
variable Genetic_relatedness   float  
attribute Genetic_relatedness _FillValue float NaN
attribute Genetic_relatedness actual_range float 0.02, 0.21
attribute Genetic_relatedness bcodmo_name String sample_descrip
attribute Genetic_relatedness description String Metric of genetic relatedness within that oyster cohort calculated using STORM (Frasier 2008)
attribute Genetic_relatedness long_name String Genetic Relatedness
attribute Genetic_relatedness units String unitless
variable Cohort   String  
attribute Cohort bcodmo_name String sample
attribute Cohort description String Unique identifier for one of 6 oyster cohorts used in the experiments
attribute Cohort long_name String Cohort
attribute Cohort nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Cohort units String unitless
variable Final_avg_size   double  
attribute Final_avg_size _FillValue double NaN
attribute Final_avg_size actual_range double 9.5, 30.45363636
attribute Final_avg_size bcodmo_name String height
attribute Final_avg_size description String Average shell height of the oysters remaining on that experimental replicate at the end of the experiment
attribute Final_avg_size long_name String Final Avg Size
attribute Final_avg_size units String millimeters (mm)
variable Initial_avg_size   double  
attribute Initial_avg_size _FillValue double NaN
attribute Initial_avg_size actual_range double 4.833333333, 13.83333333
attribute Initial_avg_size bcodmo_name String height
attribute Initial_avg_size description String Average shell height of the oysters on that experimental replicate at the start of the experiment
attribute Initial_avg_size long_name String Initial Avg Size
attribute Initial_avg_size units String millimeters (mm)
variable Cage_alive   double  
attribute Cage_alive _FillValue double NaN
attribute Cage_alive actual_range double 2.0, 12.0
attribute Cage_alive bcodmo_name String number
attribute Cage_alive description String Number of oysters alive at the end of the experiment in the cage (no predator) treatment
attribute Cage_alive long_name String Cage Alive
attribute Cage_alive units String Number of oysters
variable Cage_dead   double  
attribute Cage_dead _FillValue double NaN
attribute Cage_dead actual_range double 0.0, 10.0
attribute Cage_dead bcodmo_name String number
attribute Cage_dead description String Number of oysters that were dead at the end of the experiment in the cage (no predator) treatment
attribute Cage_dead long_name String Cage Dead
attribute Cage_dead units String Number of oysters
variable Open_tile_alive   double  
attribute Open_tile_alive _FillValue double NaN
attribute Open_tile_alive actual_range double 0.0, 11.0
attribute Open_tile_alive bcodmo_name String number
attribute Open_tile_alive description String Number of oysters alive at the end of the experiment in the open tile (control) treatment
attribute Open_tile_alive long_name String Open Tile Alive
attribute Open_tile_alive units String Number of oysters
variable Open_tile_dead   double  
attribute Open_tile_dead _FillValue double NaN
attribute Open_tile_dead actual_range double 1.0, 12.0
attribute Open_tile_dead bcodmo_name String number
attribute Open_tile_dead description String Number of oysters that were dead at the end of the experiment in the open tile (control) treatment
attribute Open_tile_dead long_name String Open Tile Dead
attribute Open_tile_dead units String Number of oysters
variable Growth   double  
attribute Growth _FillValue double NaN
attribute Growth actual_range double 1.24, 20.80545455
attribute Growth bcodmo_name String growth
attribute Growth description String Average difference in final shell height and initial shell height standardized by initial shell height for each oyster per experimental replicate
attribute Growth long_name String Growth
attribute Growth units String millimeters (mm)

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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