Data File(s)	Type	Description	Action
998738_v1_oyster-genotype-annotations.csv (76.10 MB)	Comma Separated Values (.csv)	Data table for dataset ID 998738, version 1. This table contains per-SNP metadata and annotations corresponding to the loci in the SNP genotype matrix. Each row represents one SNP, identified by its Affymetrix probe ID (Affx_ID), which can be used to link this file to the columns of the genotype matrix. The metadata includes genomic location (chromosome, position, and scaffold on assembly GCF_0020...	998738_v1_oyster-genotype-annotations.csv View Table
Exp_parents_SNP_metadata.csv (76.08 MB)	Comma Separated Values (.csv)	This file contains per-SNP metadata and annotations corresponding to the loci in the SNP genotype matrix. Each row represents one SNP, identified by its Affymetrix probe ID (Affx_ID values of 0, 1, or 2), which can be used to link this file to the columns of the genotype matrix. The metadata includes genomic location (chromosome, position, and scaffold on assembly GCF_002022765.2), gene-level func...	Exp_parents_SNP_metadata.csv View Table

Supplemental File(s)	Type	Description	Action
Exp_parents_full_SNP_matrix.rds (6.65 MB)	Octet Stream	This file contains a numeric genotype matrix for Eastern oyster (Crassostrea virginica) SNPs genotyped on a 200K ThermoFisher Affymetrix Axiom SNP array. Rows represent individual samples (160 individuals total) and columns represent SNP loci (154102 SNPs total). Genotypes are encoded as integer values: 0 (homozygous reference), 1 (heterozygous), or 2 (homozygous alternate). Raw genotypes were pro...	Exp_parents_full_SNP_matrix.rds

Files

Filename: 998738_v1_oyster-genotype-annotations.csv (76.10 MB)
Type: Comma Separated Values (.csv)

Description:

Data table for dataset ID 998738, version 1. This table contains per-SNP metadata and annotations corresponding to the loci in the SNP genotype matrix. Each row represents one SNP, identified by its Affymetrix probe ID (Affx_ID), which can be used to...

998738_v1_oyster-genotype-annotations.csv View Table

Filename: Exp_parents_SNP_metadata.csv (76.08 MB)
Type: Comma Separated Values (.csv)

Description:

This file contains per-SNP metadata and annotations corresponding to the loci in the SNP genotype matrix. Each row represents one SNP, identified by its Affymetrix probe ID (Affx_ID values of 0, 1, or 2), which can be used to link this file to the co...

Exp_parents_SNP_metadata.csv View Table

Supplemental Files

Filename: Exp_parents_full_SNP_matrix.rds (6.65 MB)
Type: Octet Stream

Description:

This file contains a numeric genotype matrix for Eastern oyster (Crassostrea virginica) SNPs genotyped on a 200K ThermoFisher Affymetrix Axiom SNP array. Rows represent individual samples (160 individuals total) and columns represent SNP loci (154102...

Exp_parents_full_SNP_matrix.rds

Acronyms:

SNP = Single-nucleotide Polymorphism
MLA = Machine Learning Algorithm
LD = Linkage Disequilibrium
NCBI = National Center for Biotechnology Information
DNA = Deoxyribonucleic acid
MVP = Model Validation Program
ABC = Aquaculture Genetics and Breeding Technology Center
VIMS = Virginia Institute of Marine Science
GO = Gene Ontology

Organism identifiers:
Eastern oyster, Crassostrea virginica, urn:lsid:marinespecies.org:taxname:140657

IsRelatedTo

Dataset: CviMVP Experiment - Parents
Relationship Description:

The experimental results dataset (1007522) includes fitness data and metadata from a common garden experiment run as part of the CviMVP project from 2023-2025. In the experiment juvenile oysters were transplanted to two sites to assess fitness acros...

K. Eaton, A., Lotterhos, K., Rumberger, C., Eppley, M., Bajaj, K., Mongillo, N., Small, J., Carnegie, R., Segnitz, Z., Armstrong, M. (2026) Parent eastern oysters (Crassostrea virginica) from wild and hatchery populations along U.S. Atlantic and Gulf coasts (collected 2022), used as broodstock in a field experiment (2023–2025). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-30 http://lod.bco-dmo.org/id/dataset/1008652

IsRelatedTo

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA376014
Relationship Description:

NCBI BioProject with the related sequences and sample information in BioSample SAMN06349363.

McDonnell Genome Institute - Washington University School of Medicine (2017). Crassostrea virginica Genome sequencing and assembly. 2017/03. NCBI:BioProject: PRJNA376014 [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA376014

IsRelatedTo

Dataset: CviMVP Experiment - mortality, growth, and tissue sample metadata
Relationship Description:

Rumberger, C., Lotterhos, K., Eppley, M., Small, J., Katsuki, S., Mongillo, N., Bajaj, K., Carnegie, R., Segnitz, Z. (2026) Eastern oyster (Crassostrea virginica) mortality, growth, and tissue sample metadata from the common garden experiments run as part of CviMVP project from 2023-2025 in the Chesapeake Bay. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-10-06 http://lod.bco-dmo.org/id/dataset/1007522

IsRelatedTo

Dataset: CviMVP Experiment - Environmental Data
Relationship Description:

Rumberger, C., Lotterhos, K., Small, J., Eppley, M., Carnegie, R., Mongillo, N., Bajaj, K., Segnitz, Z. (2026) Environmental data from sites (source populations, and experimental sites) from common garden experiments with Eastern oyster (Crassostrea virginica) run as part of CviMVP project from 2023-2025 in the Chesapeake Bay. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-10-06 http://lod.bco-dmo.org/id/dataset/1007572

Software

Dataset: https://github.com/DrK-Lo/MVP-H2F-HatcheryField
Relationship Description:

This repository contains data and code for a hatchery-to-field (H2F) experiment evaluating survival, growth, and genetic predictors of performance in Eastern oysters (Crassostrea virginica), part of the project "CAREER: Evaluation of machine learning...

Bajaj, K., Eppley, M., Rumberger, C., Mongillo, N., Lotterhos, K., & Segnitz, Z. (n.d.). MVP-H2F-HatcheryField: MVP experimental data hatchery to field [Source code]. GitHub. https://github.com/DrK-Lo/MVP-H2F-HatcheryField

Results

Bajaj, K. E., Mongillo, N., Eppley, M. G., Rumberger, C. A., Segnitz, Z., Katsuki, S., Carnegie, R., Small, J., & Lotterhos, K. E. (2026). Contrasting effects of geographic distance, environmental distance, and intraspecific diversity on the performance of a marine invertebrate in common gardens. https://doi.org/10.64898/2026.04.02.716183

Relationship Description:

Pre-print of a pending peer-reviewed publication.

Methods

Frichot, E., & François, O. (2015). LEA: An R package for landscape and ecological association studies. Methods in Ecology and Evolution, 6(8), 925–929. Portico. https://doi.org/10.1111/2041-210x.12382

Methods

Guo, X., Puritz, J. B., Wang, Z., Proestou, D., Allen, S., Small, J., Verbyla, K., Zhao, H., Haggard, J., Chriss, N., Zeng, D., Lundgren, K., Allam, B., Bushek, D., Gomez-Chiarri, M., Hare, M., Hollenbeck, C., La Peyre, J., Liu, M., et al. (2023). Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica. Marine Biotechnology, 25(1), 174–191. https://doi.org/10.1007/s10126-022-10191-3

Methods

Gómez-Chiarri, M., Warren, W. C., Guo, X., & Proestou, D. (2015). Developing tools for the study of molluscan immunity: The sequencing of the genome of the eastern oyster, Crassostrea virginica. Fish &Amp; Shellfish Immunology, 46(1), 2–4. https://doi.org/10.1016/j.fsi.2015.05.004

Methods

Lotterhos, K. E. (2019). The Effect of Neutral Recombination Variation on Genome Scans for Selection. G3 Genes|Genomes|Genetics, 9(6), 1851–1867. https://doi.org/10.1534/g3.119.400088

Data File(s)	Type	Description	Action
998738_v1_oyster-genotype-annotations.csv (76.10 MB)	Comma Separated Values (.csv)	Data table for dataset ID 998738, version 1. This table contains per-SNP metadata and annotations corresponding to the loci in the SNP genotype matrix. Each row represents one SNP, identified by its Affymetrix probe ID (Affx_ID), which can be used to link this file to the columns of the genotype matrix. The metadata includes genomic location (chromosome, position, and scaffold on assembly GCF_0020...	998738_v1_oyster-genotype-annotations.csv View Table
Exp_parents_SNP_metadata.csv (76.08 MB)	Comma Separated Values (.csv)	This file contains per-SNP metadata and annotations corresponding to the loci in the SNP genotype matrix. Each row represents one SNP, identified by its Affymetrix probe ID (Affx_ID values of 0, 1, or 2), which can be used to link this file to the columns of the genotype matrix. The metadata includes genomic location (chromosome, position, and scaffold on assembly GCF_002022765.2), gene-level func...	Exp_parents_SNP_metadata.csv View Table

Supplemental File(s)	Type	Description	Action
Exp_parents_full_SNP_matrix.rds (6.65 MB)	Octet Stream	This file contains a numeric genotype matrix for Eastern oyster (Crassostrea virginica) SNPs genotyped on a 200K ThermoFisher Affymetrix Axiom SNP array. Rows represent individual samples (160 individuals total) and columns represent SNP loci (154102 SNPs total). Genotypes are encoded as integer values: 0 (homozygous reference), 1 (heterozygous), or 2 (homozygous alternate). Raw genotypes were pro...	Exp_parents_full_SNP_matrix.rds

Files

Filename: 998738_v1_oyster-genotype-annotations.csv (76.10 MB)
Type: Comma Separated Values (.csv)

Description:

998738_v1_oyster-genotype-annotations.csv View Table

Filename: Exp_parents_SNP_metadata.csv (76.08 MB)
Type: Comma Separated Values (.csv)

Description:

Exp_parents_SNP_metadata.csv View Table

Supplemental Files

Filename: Exp_parents_full_SNP_matrix.rds (6.65 MB)
Type: Octet Stream

Description:

Exp_parents_full_SNP_matrix.rds

Acronyms:

Organism identifiers:
Eastern oyster, Crassostrea virginica, urn:lsid:marinespecies.org:taxname:140657

IsRelatedTo

Dataset: CviMVP Experiment - Parents
Relationship Description:

IsRelatedTo

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA376014
Relationship Description:

NCBI BioProject with the related sequences and sample information in BioSample SAMN06349363.

IsRelatedTo

Dataset: CviMVP Experiment - mortality, growth, and tissue sample metadata
Relationship Description:

IsRelatedTo

Dataset: CviMVP Experiment - Environmental Data
Relationship Description:

Software

Dataset: https://github.com/DrK-Lo/MVP-H2F-HatcheryField
Relationship Description:

Results

Relationship Description:

Pre-print of a pending peer-reviewed publication.

Methods

Lotterhos, K. E. (2019). The Effect of Neutral Recombination Variation on Genome Scans for Selection. G3 Genes|Genomes|Genetics, 9(6), 1851–1867. https://doi.org/10.1534/g3.119.400088

Dataset: SNP genotypes of Eastern oysters (Crassostrea virginica) from wild and hatchery populations along U.S. Atlantic and Gulf coasts (collected 2022), used as broodstock in a field experiment (2023–2025)

Principal Investigator: Katie Lotterhos (Northeastern University)

Co-Principal Investigator: Jessica Small (Virginia Institute of Marine Science)

Scientist: Ryan Carnegie (Virginia Institute of Marine Science)

Student: Kiran Bajaj (Northeastern University)

Student: Madeline Eppley (Northeastern University)

Student: Shelley Katsuki (Virginia Institute of Marine Science)

Student: Nicole Mongillo (Northeastern University)

Student: Camille Rumberger (Northeastern University)

Student: Zea Segnitz (Northeastern University)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Project: CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP) (Model Validation Program)

Abstract

72

25

Files

Supplemental Files

Related Datasets

Related Publications

Dataset: SNP genotypes of Eastern oysters (Crassostrea virginica) from wild and hatchery populations along U.S. Atlantic and Gulf coasts (collected 2022), used as broodstock in a field experiment (2023–2025)

Principal Investigator: Katie Lotterhos (Northeastern University)

Co-Principal Investigator: Jessica Small (Virginia Institute of Marine Science)

Scientist: Ryan Carnegie (Virginia Institute of Marine Science)

Student: Kiran Bajaj (Northeastern University)

Student: Madeline Eppley (Northeastern University)

Student: Shelley Katsuki (Virginia Institute of Marine Science)

Student: Nicole Mongillo (Northeastern University)

Student: Camille Rumberger (Northeastern University)

Student: Zea Segnitz (Northeastern University)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Project: CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP) (Model Validation Program)

Abstract

72

25

Files

Supplemental Files

Related Datasets

Related Publications

Dataset: SNP genotypes of Eastern oysters (Crassostrea virginica) from wild and hatchery populations along U.S. Atlantic and Gulf coasts (collected 2022), used as broodstock in a field experiment (2023–2025)

Principal Investigator: Katie Lotterhos (Northeastern University)

Co-Principal Investigator: Jessica Small (Virginia Institute of Marine Science)

Scientist: Ryan Carnegie (Virginia Institute of Marine Science)

Student: Kiran Bajaj (Northeastern University)

Student: Madeline Eppley (Northeastern University)

Student: Shelley Katsuki (Virginia Institute of Marine Science)

Student: Nicole Mongillo (Northeastern University)

Student: Camille Rumberger (Northeastern University)

Student: Zea Segnitz (Northeastern University)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Project: CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP) (Model Validation Program)

Abstract

Metadata

72

25

Files

Supplemental Files

Related Datasets

Related Publications

Dataset: SNP genotypes of Eastern oysters (Crassostrea virginica) from wild and hatchery populations along U.S. Atlantic and Gulf coasts (collected 2022), used as broodstock in a field experiment (2023–2025)

Principal Investigator: Katie Lotterhos (Northeastern University)

Co-Principal Investigator: Jessica Small (Virginia Institute of Marine Science)

Scientist: Ryan Carnegie (Virginia Institute of Marine Science)

Student: Kiran Bajaj (Northeastern University)

Student: Madeline Eppley (Northeastern University)

Student: Shelley Katsuki (Virginia Institute of Marine Science)

Student: Nicole Mongillo (Northeastern University)

Student: Camille Rumberger (Northeastern University)

Student: Zea Segnitz (Northeastern University)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Project: CAREER: Evaluation of machine learning algorithms for understanding and predicting adaptation to multivariate environments with a Model Validation Program (MVP) (Model Validation Program)

Abstract

Metadata

72

25

Files

Supplemental Files

Related Datasets

Related Publications