Research Project: Improving the Sustainability and Productivity of Shellfish Culture in Pacific Estuaries

Location: Pacific Shellfish Research Unit

Publications (Clicking on the reprint icon will take you to the publication reprint.)

A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon - (Peer Reviewed Journal)
Anderson, E.C., Clemento, A.J., Campbell, M.A., Pearse, D., Beulke, A.K., Columbus, C., Campbell, E., Thompson, N., Garza, J.C. 2025. A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon. Evolutionary Applications. 18(5). Article e70110. https://doi.org/10.1111/eva.70110.

Investigating gene expression plasticity in pacific oyster (Magallana gigas) larvae subjected to ocean acidification conditions - (Abstract Only)

“Gender reveal” for oysters? An investigation of early sex determination mechanisms in pacific oysters, Magallana gigas - (Abstract Only)

Investigating the physiological effects of harmful algal bloom (HABs) toxins on juvenile pacific oysters Magallana gigas - (Abstract Only)

Evaluation of genetic diversity in Pacific oysters from the US west coast using whole-genome re-sequencing - (Abstract Only)

Weak genetic divergence and signals of adaptation obscured by high gene flow in an economically important aquaculture species - (Peer Reviewed Journal)
Calla, B., Song, J., Thompson, N. 2025. Weak genetic divergence and signals of adaptation obscured by high gene flow in an economically important aquaculture species. BMC Genomics. 26. Article 112. https://doi.org/10.1186/s12864-025-11259-9.

Advancing genetic improvement in the omics era: Status and priorities for United States aquaculture - (Peer Reviewed Journal)
Andersen, L.K., Thompson, N., Abernathy, J.W., Ahmed, R.O., Ali, A., Al-Tobasei, R., Beck, B.H., Calla, B., Delomas, T.A., Dunham, R.A., Elsik, C.G., Fuller, S.A., Garcia, J.C., Gavery, M.R., Hollenbeck, C.M., Johnson, K.M., Kunselman, E., Legacki, E.L., Liu, S., Liu, Z., Martin, B., Matt, J.L., May, S.A., Older, C.E., Overturf, K.E., Palti, Y., Peatman, E.J., Peterson, B.C., Phelps, M.P., Plough, L.V., Polinski, M.P., Proestou, D.A., Purcell, C.M., Quiniou, S., Raymo, G., Rexroad III, C.E., Riley, K.L., Roberts, S.B., Roy, L.A., Salem, M., Simpson, K., Waldbieser, G.C., Wang, H., Waters, C.D., Reading, B.J. 2025. Advancing genetic improvement in the omics era: Status and priorities for United States aquaculture. BMC Genomics. 26. Article 155. https://doi.org/10.1186/s12864-025-11247-z.

Evaluating a new population of Kumamoto oysters (Crassostrea sikamea) for breeding on the U.S. Pacific Coast - (Peer Reviewed Journal)
Langdon, C., de Melo, C.M., Divilov, K., Schoolfield, B., Merz, N., Thompson, N. 2024. Evaluating a new population of Kumamoto oysters (Crassostrea sikamea) for breeding on the U.S. Pacific Coast. Aquaculture. 598. Article 742031. https://doi.org/10.1016/j.aquaculture.2024.742031.

A free lunch: Microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster - (Peer Reviewed Journal)
Thompson, N., Sutherland, B.J., Green, T.J., Delomas, T.A. 2024. A free lunch: Microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster. G3: Genes, Genomes, Genetics. 15(2). Article jkae280. https://doi.org/10.1093/g3journal/jkae280.

Efficacy, non-target impacts, and costs of mechanical control options against a bioturbator in bivalve aquaculture - (Peer Reviewed Journal)
Ruesink, J.L., Mawson, C., Allen, B., Barrett, J., Beugli, D., Booth, S., Butler, L., Dewey, B., Donoghue, C.R., Dumbauld, B.R., Feldman, K., Forster, Z., Garcia, S., Gross, J.A., Hudson, B., Hull, W., Iyer, V., Katla, A., Kraft, L., Paul, B., Pruitt, C., Vashisth, A., Patten, K. 2025. Efficacy, non-target impacts, and costs of mechanical control options against a bioturbator in bivalve aquaculture. Aquaculture. 596(1). Article 741788. https://doi.org/10.1016/j.aquaculture.2024.741788.

Intraspecific variation in resilience traits of eelgrass across intertidal stress gradients and oyster aquaculture methods - (Peer Reviewed Journal)
Ruesink, J., Houle, K., Kroeker, K., Dumbauld, B.R., Boardman, F., Lewis, N., Mc Intyre, B.A., Suhrbier, A., Hudson, B. 2024. Intraspecific variation in resilience traits of eelgrass across intertidal stress gradients and oyster aquaculture methods. Frontiers in Marine Science. 11. Article 1427595. https://doi.org/10.3389/fmars.2024.1427595.

Improving hatchery efficiency: New insights into sex determination in Pacific oysters - (Abstract Only)

An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster - (Peer Reviewed Journal)
Sutherland, B.J., Thompson, N., Surry, L.B., Gujjula, K., Carrasco, C.D., Chadaram, S., Lunda, S.L., Langdon, C.J., Chan, A.M., Suttle, C.A., Green, T.J. 2024. An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. G3, Genes/Genomes/Genetics. Article jkae125. https://doi.org/10.1093/g3journal/jkae125.

Assessing selection potential for Pacific oyster (Crassostrea gigas) to a North American OsHV-1 µvar: Comparing two experimental assay methods - (Peer Reviewed Journal)
Thompson, N., Agnew, M.V., Calla, B., Burge, C.A. 2024. Assessing selection potential for Pacific oyster (Crassostrea gigas) to a North American OsHV-1 µvar: Comparing two experimental assay methods. Aquaculture. 590. Article 741076. https://doi.org/10.1016/j.aquaculture.2024.741076.

Microhaplotpes boost power for relatedness analysis from SNP-based amplicon sequence panels in Pacific oyster - (Abstract Only)
Thompson, N., Sutherland, B., Green, T., Delomas, T.A. 2024. Microhaplotpes boost power for relatedness analysis from SNP-based amplicon sequence panels in Pacific oyster. Plant and Animal Genome Conference.

Distinct patterns of inheritance shape life-history traits in steelhead trout - (Peer Reviewed Journal)
Beulke, A.K., Abadia-Cardoso, A., Pearse, D.E., Goetz, L., Thompson, N., Anderson, E.C., Garza, J. 2023. Distinct patterns of inheritance shape life-history traits in steelhead trout. Molecular Ecology. 32(24):6896-6912. https://doi.org/10.1111/mec.17182.

Relationship between a parasite, their ghost shrimp host, and sturgeon in US west coast estuaries - (Abstract Only)

Landscape-scale assessment of nekton production in channel-fringing habitats provided by eelgrass and oyster aquaculture - (Abstract Only)

Evaluating recent shifts in long-term trajectories of burrowing shrimp in two US west coast estuaries - (Abstract Only)

Monitoring recent shifts in burrowing shrimp populations in coastal estuaries: are they new phenomena and should a shellfish grower be concerned? - (Abstract Only)

Influence of seagrass on juvenile Pacific oyster growth in two US west coast estuaries with different environmental gradients - (Peer Reviewed Journal)
Dumbauld, B.R., Mc Intyre, B.A. 2023. Influence of seagrass on juvenile Pacific oyster growth in two US west coast estuaries with different environmental gradients. Aquaculture Environment Interactions. 15:287-306. https://doi.org/10.3354/aei00466.

Multi-decade changes in the condition index of adult Pacific oysters (Crassostrea gigas) in response to climate in a US west coast estuary - (Peer Reviewed Journal)
Dumbauld, B.R., Du, X., Hunsicker, M., Forster, Z. 2023. Multi-decade changes in the condition index of adult Pacific oysters (Crassostrea gigas) in response to climate in a US west coast estuary. Journal of Sea Research. 193. Article 102383. https://doi.org/10.1016/j.seares.2023.102383.

Genetics of tolerance in honeybees to the neonicotinoid clothianidin - (Peer Reviewed Journal)
Tsvetkov, N., Bahia, S., Calla, B., Berenbaum, M.R., Zayed, A. 2023. Genetics of tolerance in honeybees to the neonicotinoid clothianidin. iScience. 26(3). Article 106084. https://doi.org/10.1016/j.isci.2023.106084.

Flooding and herbivory: The effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties - (Peer Reviewed Journal)
Ngumbi, E., Dady, E., Calla, B. 2022. Flooding and herbivory: The effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties. BMC Plant Biology. 22. Article 536. https://doi.org/10.1186/s12870-022-03911-3.

Predicted changes in seagrass cover and distribution in the face of sea level rise: Implications for bivalve aquaculture in a US West Coast estuary - (Peer Reviewed Journal)
Dumbauld, B.R., Graham, E.R., McCoy, L.M., Lewis, N. 2022. Predicted changes in seagrass cover and distribution in the face of sea level rise: Implications for bivalve aquaculture in a US West Coast estuary. Estuaries and Coasts - Journal of the Estuarine Research Federation. https://doi.org/10.1007/s12237-022-01060-2 .

Genetic improvement of survival in Pacific oysters to the Tomales Bay strain of OsHV-1 over two cycles of selection - (Peer Reviewed Journal)
Divilov, K., Schoolfield, B., Cortez, D.M., Wang, X., Fleener, G.B., Jin, L., Dumbauld, B.R., Langdon, C. 2021. Genetic improvement of survival in Pacific oysters to the Tomales Bay strain of OsHV-1 over two cycles of selection. Aquaculture. 543. Article 737020. https://doi.org/10.1016/j.aquaculture.2021.737020.

A comparison of juvenile dungeness crab (Metacarcinus magister) habitat provided by contemporary oyster aquaculture versus historical native oyster habitat in a U.S. West Coast estuary - (Peer Reviewed Journal)
Dumbauld, B.R., Murphy, J., McCoy, L., Lewis, N. 2021. A comparison of juvenile Dungeness crab (Metacarcinus magister) produced in current oyster aquaculture versus historical native oyster habitat in a U.S. West Coast estuary. Journal of Shellfish Research. 40(1):161-175. https://doi.org/10.2983/035.040.0116.

Differential mortality and high viral load in naive Pacific oyster families exposed to OsHV-1 suggests tolerance rather than resistance to infection - (Peer Reviewed Journal)
Agnew, M., Friedman, C.S., Langdon, C., Konstantin, D., Schoofield, B., Morga, B., Degremont, L., Dhar, A.K., Kirkland, P., Dumbauld, B.R., Burge, C.A. 2020. Differential mortality and high viral load in naive Pacific oyster families exposed to OsHV-1 suggests tolerance rather than resistance to infection. Journal of Pathogens. 9(12):1057. https://doi.org/10.3390/pathogens9121057.