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

Crassostrea virginica, LSID (urn:lsid:marinespecies.org:taxname:140657)

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

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...

(n.d.). MVP-H2F-HatcheryField: MVP experimental data hatchery to field [Software repository]. 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

Acronyms:

Crassostrea virginica, LSID (urn:lsid:marinespecies.org:taxname:140657)

IsRelatedTo

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

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

Software

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

(n.d.). MVP-H2F-HatcheryField: MVP experimental data hatchery to field [Software repository]. GitHub. https://github.com/DrK-Lo/MVP-H2F-HatcheryField

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 common garden 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

9

0

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 common garden 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

9

0

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 common garden 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

9

0

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 common garden 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

9

0

Related Datasets

Related Publications