http://lod.bco-dmo.org/id/dataset/998738
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
2026-05-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Eastern oyster parent genotypes from the Model Validation Program project
2026-05-18
publication
2026-05-18
revision
BCO-DMO Linked Data URI
2026-05-18
creation
http://lod.bco-dmo.org/id/dataset/998738
Katie Lotterhos
Northeastern University
principalInvestigator
Jessica Small
Virginia Institute of Marine Science
principalInvestigator
Ryan Carnegie
Virginia Institute of Marine Science
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: Bajaj, K., Eppley, M., Rumberger, C., Mongillo, N., Lotterhos, K., Small, J., Carnegie, R., Katsuki, S., Segnitz, Z. (2026) Eastern oyster parent genotypes. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998738 [access date]
Dataset Description: <p>Acronyms:<br />
<br />
SNP = Single-nucleotide Polymorphism<br />
MLA = Machine Learning Algorithm<br />
LD = Linkage Disequilibrium<br />
NCBI = National Center for Biotechnology Information<br />
DNA = Deoxyribonucleic acid<br />
MVP = Model Validation Program<br />
ABC = Aquaculture Genetics and Breeding Technology Center<br />
VIMS = Virginia Institute of Marine Science&nbsp;<br />
GO = Gene Ontology</p> Methods and Sampling: <p>Source populations for monoculture treatments included six wild populations and two proprietary broodstock lines (DEBY and LOLA) from the Aquaculture Genetics and Breeding Technology Center (ABC), Virginia Institute of Marine Science (VIMS). Wild populations spanned the species’ native range, which is structured into distinct genetic clusters separated by the Florida peninsula (Reeb &amp; Avise, 1990, Puritz et al., 2022). Populations included oysters from: a variable salinity site in Texas (W1-TX), a low salinity site in Louisiana (W2-LA), a high salinity site on the east coast of Florida (W3-FL), a moderate salinity site in the James River, Virginia (W4-VA), a variable salinity site in New Hampshire (W5-NH), and a high salinity site in Maine (W6-ME). W4-VA was considered local to both common garden sites due to its geographic proximity and intermediate salinity.&nbsp;</p>
<p>&nbsp;</p>
<p>Gill tissue was collected from each parent (<em>n</em> = 160) after spawning and stored in 95% ethanol at -80°C. DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit and shipped to Neogen Genomics (Lincoln, NE) for genotyping on a 200K ThermoFisher Affymetrix Axiom SNP array derived from a 600K array (Gómez-Chiarri et al., 2015; Guo et al., 2023; Modak et al., 2021; Puritz et al., 2024) aligned to the haplotig-masked <em>Crassostrea virginica</em> reference genome (C_virginica-3.0, GCA_002022765.4).</p>
<p>&nbsp;</p>
<p>Raw genotypes were processed and filtered in R v4.4.2 (R Core Team 2025). Missing SNPs were imputed using LEA v3.6.0 (Frichot &amp; François, 2015) with K = 2 ancestral groups to produce a full SNP set. We thinned SNPs for linkage disequilibrium (LD) for population structure analysis and neutral parameterization of genome scans (Lotterhos, 2019) using bigsnpr v1.11.3 (Privé et al., 2018). The archived genotype matrix contains the processed, imputed genotype calls per individual encoded in 0/1/2 integer format (homozygous reference, heterozygous, and homozygous alternate, respectively). The accompanying SNP metadata file provides per-locus descriptions including genomic position, gene identifiers, functional descriptions, Gene Ontology terms, and population genetic statistics derived from OutFLANK (FST, expected heterozygosity, p-values, q-values, and outlier flags), as well as a flag indicating inclusion in the LD-thinned dataset, enabling straightforward filtering for only LD-thinned SNPs.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2043905 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2043905
completed
Katie Lotterhos
Northeastern University
781-581-7370 X304
Northeastern University Marine Sciences Center 430 Nahant Rd.
Nahant
MA
01908
USA
k.lotterhos@northeastern.edu
pointOfContact
Jessica Small
Virginia Institute of Marine Science
jamoss@vims.edu
pointOfContact
Ryan Carnegie
Virginia Institute of Marine Science
carnegie@vims.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Affx_ID
AX_ID
Chromosome
Position
FST
He
pvalues
pvaluesRightTail
qvalues
OutlierFlag
gene_id
gene_description
go_ids
go_terms
SNPType
Tile_Std
Tile_max
Tile_v3
Replicates
Rank
Group
organism
cust_id
on_oystercv
mutID
chrom_position
scaffold
Sequence
thinned_dataset
theme
None, User defined
sample description
brief description
p-value
No BCO-DMO term
flag
gene identification
accession number
replicate
taxon
sequence
featureType
BCO-DMO Standard Parameters
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: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP)
https://osprey.bco-dmo.org/project/876610
CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP)
<p><strong>NSF Award Abstract:</strong><br />
Environmental change can be rapid and involve multiple aspects of the environment changing at the same time, such as warming and increased disease pressure. Rapid environmental change threatens the productivity of aquaculture and crops on which humans depend. Predicting organisms' vulnerabilities to rapid and multifactor environmental change, however, is a major scientific challenge. A hurdle to addressing this challenge arises from the complex and non-intuitive ways that organisms adapt, through changes at the level of the DNA sequence, to many environmental stresses at the same time. Thus, there is a need for new approaches to understand and predict adaptation in multivariate environments. To address this need, this project integrates research and education with a Model Validation Program (MVP). The research is developing and evaluating Machine Learning Algorithms (MLAs) for understanding and predicting adaptation of organisms to multivariate environments from their DNA sequences. To evaluate MLAs, this research combines both data simulation and an empirical test in the field with the Eastern Oyster, which provide important ecosystem services and support a multi-million dollar industry. For oysters, this research is studying how temperature, disease pressure, and salinity interact with evolutionary history to determine fitness in the field. This research advances efforts toward addressing the major scientific challenge of predicting adaptation in complex environments by integrating concepts across the frontiers of marine, evolutionary, and statistical sciences in a new way. Machine learning and model validation are not traditionally taught in the marine and environmental sciences, but are becoming increasingly relevant to these fields. As part of a broader education program, this research is developing MVP Learning Modules for high school students and undergraduates, which help students build the foundational knowledge they need to critically evaluate and apply models. Modules are being disseminated to hundreds of students in the greater Boston area and are being made available online for widespread use. The MVP mentoring program is training graduate students, undergraduates, and high school students in marine evolutionary ecology, statistical genomics, and machine learning. This research addresses a pressing societal need to more informatively match genotypes to environments for restoration, farming, and assisted gene flow efforts. Results are being disseminated to stakeholders in the oyster industry.</p>
<p>The goal of this research is to evaluate if MLAs, which can model non-linearities, can be used to understand and predict adaptation to multivariate environments under a wide range of scenarios. In Objective 1, the Principal Investigator (PI) is creating simulated datasets with different aspects of realism, and using them to evaluate and refine the MLAs. This novel set of simulations is studying genome evolution under high gene flow in complex, multivariate environments. In Objective 2, the PI is building on their expertise with the Eastern oyster to evaluate the MLAs in a field setting. The PI is first developing a comprehensive seascape genomic dataset and using it to train MLAs to predict an individual's multivariate environment based on a single nucleotide polymorphism genotype. Then, the PI is testing if the MLA prediction can predict the fitness of different genotypes from across the species range when raised in common garden field conditions. In Objective 3, the PI is integrating research and education by using the data obtained from Objs. 1 and 2 to develop a series of original "MVP Learning Modules" with interactive web apps for persons at different levels of understanding, using the relatable example of an oyster restoration project. This research lays the foundation for future studies by producing datasets that could become classical examples for developing and benchmarking innovative modeling approaches.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Model Validation Program
largerWorkCitation
project
eng; USA
oceans
-97.201
-69.55
28.084
43.986
2023-05-01
2025-05-01
East coast of North America
0
BCO-DMO catalogue of parameters from Eastern oyster parent genotypes from the Model Validation Program 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
http://lod.bco-dmo.org/id/dataset-parameter/998837.rdf
Name: Affx_ID
Units: unitless
Description: <p>Thermofisher SNP identifiers that refer to the specific probe or probe set as it was designed for the array</p>
http://lod.bco-dmo.org/id/dataset-parameter/998838.rdf
Name: AX_ID
Units: unitless
Description: <p>Thermofisher analysis-ready SNP identifiers that are assigned after the array is finalized</p>
http://lod.bco-dmo.org/id/dataset-parameter/998839.rdf
Name: Chromosome
Units: unitless
Description: <p>Chromosome where SNP occurs on assembly GCF_002022765.2_C_virginica-3.0_genomic</p>
http://lod.bco-dmo.org/id/dataset-parameter/998840.rdf
Name: Position
Units: unitless
Description: <p>Chromosomal position where SNP occurs on assembly GCF_002022765.2_C_virginica-3.0_genomic</p>
http://lod.bco-dmo.org/id/dataset-parameter/998841.rdf
Name: FST
Units: unitless
Description: <p>Fixation index for the locus calculated by OutFLANK (Whitlock and Lotterhos 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998842.rdf
Name: He
Units: unitless
Description: <p>Expected heterozygosity for the locus calculated by OutFLANK (Whitlock and Lotterhos 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998843.rdf
Name: pvalues
Units: unitless
Description: <p>Two-tailed p-value for the test of neutrality for the locus calculated by OutFLANK (Whitlock and Lotterhos 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998844.rdf
Name: pvaluesRightTail
Units: unitless
Description: <p>Right-tailed p-value for the test of neutrality for the locus calculated by OutFLANK (Whitlock and Lotterhos 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998845.rdf
Name: qvalues
Units: unitless
Description: <p>q-value for the test of neutrality for the locus based on the right-tailed p-value calculated by OutFLANK (Whitlock and Lotterhos 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998846.rdf
Name: OutlierFlag
Units: unitless
Description: <p>True (T) or False (F) if the SNP was detected as an outlier by OutFLANK (Whitlock and Lotterhos 2015)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998847.rdf
Name: gene_id
Units: unitless
Description: <p>Generic locus IDs (NCBI) for gene(s) where SNP occurs</p>
http://lod.bco-dmo.org/id/dataset-parameter/998848.rdf
Name: gene_description
Units: unitless
Description: <p>Functional description(s) of gene(s) where SNP occurs</p>
http://lod.bco-dmo.org/id/dataset-parameter/998849.rdf
Name: go_ids
Units: unitless
Description: <p>Unique seven-digit identifier for a gene ontology term</p>
http://lod.bco-dmo.org/id/dataset-parameter/998850.rdf
Name: go_terms
Units: unitless
Description: <p>Description for a gene ontology term</p>
http://lod.bco-dmo.org/id/dataset-parameter/998851.rdf
Name: SNPType
Units: unitless
Description: <p>K - G/T M - A/C R - A/G (most common) S - C/G (rarest) W - A/T Y - C/T (most common)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998852.rdf
Name: Tile_Std
Units: unitless
Description: <p>Affymetrix parameter for SNP chip design</p>
http://lod.bco-dmo.org/id/dataset-parameter/998853.rdf
Name: Tile_max
Units: unitless
Description: <p>Affymetrix parameter for SNP chip design</p>
http://lod.bco-dmo.org/id/dataset-parameter/998854.rdf
Name: Tile_v3
Units: unitless
Description: <p>SNPs tiled on the 200K chip</p>
http://lod.bco-dmo.org/id/dataset-parameter/998855.rdf
Name: Replicates
Units: unitless
Description: <p>Affymetrix parameter for SNP chip design</p>
http://lod.bco-dmo.org/id/dataset-parameter/998856.rdf
Name: Rank
Units: unitless
Description: <p>Affymetrix parameter for SNP chip design</p>
http://lod.bco-dmo.org/id/dataset-parameter/998857.rdf
Name: Group
Units: unitless
Description: <p>pathogen detection CN probesets, content of Axiom_OysterCV, additional well-performing markers from screen</p>
http://lod.bco-dmo.org/id/dataset-parameter/998858.rdf
Name: organism
Units: unitless
Description: <p>Genus species</p>
http://lod.bco-dmo.org/id/dataset-parameter/998859.rdf
Name: cust_id
Units: unitless
Description: <p>Annotation</p>
http://lod.bco-dmo.org/id/dataset-parameter/998860.rdf
Name: on_oystercv
Units: unitless
Description: <p>on Axiom_OysterCV developed be Breeding Consortium</p>
http://lod.bco-dmo.org/id/dataset-parameter/998861.rdf
Name: mutID
Units: unitless
Description: <p>Mutation ID Affymetrix parameter for SNP chip design</p>
http://lod.bco-dmo.org/id/dataset-parameter/998862.rdf
Name: chrom_position
Units: unitless
Description: <p>Chromosome location and position of SNP on the 200K array; separated by a '.'</p>
http://lod.bco-dmo.org/id/dataset-parameter/998863.rdf
Name: scaffold
Units: unitless
Description: <p>Scaffold on assembly GCF_002022765.2_C_virginica-3.0_genomic</p>
http://lod.bco-dmo.org/id/dataset-parameter/998864.rdf
Name: Sequence
Units: unitless
Description: <p>71mer sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/998865.rdf
Name: thinned_dataset
Units: unitless
Description: <p>True or False if the SNP occurs in the linkage-disequilibrium thinned SNP dataset</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/998738/data/download
download
onLine
dataset
<p>Source populations for monoculture treatments included six wild populations and two proprietary broodstock lines (DEBY and LOLA) from the Aquaculture Genetics and Breeding Technology Center (ABC), Virginia Institute of Marine Science (VIMS). Wild populations spanned the species’ native range, which is structured into distinct genetic clusters separated by the Florida peninsula (Reeb &amp; Avise, 1990, Puritz et al., 2022). Populations included oysters from: a variable salinity site in Texas (W1-TX), a low salinity site in Louisiana (W2-LA), a high salinity site on the east coast of Florida (W3-FL), a moderate salinity site in the James River, Virginia (W4-VA), a variable salinity site in New Hampshire (W5-NH), and a high salinity site in Maine (W6-ME). W4-VA was considered local to both common garden sites due to its geographic proximity and intermediate salinity.&nbsp;</p>
<p>&nbsp;</p>
<p>Gill tissue was collected from each parent (<em>n</em> = 160) after spawning and stored in 95% ethanol at -80°C. DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit and shipped to Neogen Genomics (Lincoln, NE) for genotyping on a 200K ThermoFisher Affymetrix Axiom SNP array derived from a 600K array (Gómez-Chiarri et al., 2015; Guo et al., 2023; Modak et al., 2021; Puritz et al., 2024) aligned to the haplotig-masked <em>Crassostrea virginica</em> reference genome (C_virginica-3.0, GCA_002022765.4).</p>
<p>&nbsp;</p>
<p>Raw genotypes were processed and filtered in R v4.4.2 (R Core Team 2025). Missing SNPs were imputed using LEA v3.6.0 (Frichot &amp; François, 2015) with K = 2 ancestral groups to produce a full SNP set. We thinned SNPs for linkage disequilibrium (LD) for population structure analysis and neutral parameterization of genome scans (Lotterhos, 2019) using bigsnpr v1.11.3 (Privé et al., 2018). The archived genotype matrix contains the processed, imputed genotype calls per individual encoded in 0/1/2 integer format (homozygous reference, heterozygous, and homozygous alternate, respectively). The accompanying SNP metadata file provides per-locus descriptions including genomic position, gene identifiers, functional descriptions, Gene Ontology terms, and population genetic statistics derived from OutFLANK (FST, expected heterozygosity, p-values, q-values, and outlier flags), as well as a flag indicating inclusion in the LD-thinned dataset, enabling straightforward filtering for only LD-thinned SNPs.</p>
Specified by the Principal Investigator(s)
<p>Raw genotypes were processed and filtered in R v4.4.2 (R Core Team 2025; Supp. Methods: genotype filtering). Missing SNPs were imputed using LEA v3.6.0 (Frichot &amp; François, 2015) with K = 2 ancestral groups to produce a <em>full SNP set</em>. We thinned SNPs for linkage disequilibrium (LD) for population structure analysis and neutral parameterization of genome scans (Lotterhos, 2019) using bigsnpr v1.11.3 (Privé et al., 2018).</p>
<p>https://github.com/DrK-Lo/MVP-H2F-HatcheryField</p>
Specified by the Principal Investigator(s)
- Loaded data from "Exp_parents_SNP_metadata.csv" into table "998738_v1_oyster-genotype-annotations" using CSV format with row 1 as header; treated empty strings and "nd" as missing values
- Renamed column "AX-ID" to "AX_ID"
- Set data types for all 29 columns: AX_ID, Affx_ID, Group, SNPType, Sequence, cust_id, gene_description, gene_id, go_ids, go_terms, mutID, on_oystercv, organism, scaffold, OutlierFlag, thinned_dataset as string; Chromosome, Position, Rank, Replicates, Tile_Std, Tile_max, Tile_v3 as integer; FST, He, chrom_position, pvalues, pvaluesRightTail, qvalues as number
- Output final table as "998738_v1_oyster-genotype-annotations.csv"
- Provided matrix file Exp_parents_full_SNP_matrix.rds attached as a data file directly. [not imported as a table]
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