ERDDAP > info > bcodmo_dataset_770157

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	Performance traits (e.g., survival, growth, size) for hatchery-produced oyster cohorts		I   M	background			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 VA). 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 error. 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
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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/770157
attribute	NC_GLOBAL	param_mapping	String	{'770157': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/770157/parameters
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/
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.