Western Fisheries Research Center

Publications

Below is a list of available WFRC peer reviewed and published science.

Filter Total Items: 2,354
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Year Published: 2020

Development of two quantitative PCR assays for detection of several Cottus species from environmental DNA in Pacific coast watersheds of North America

We developed two quantitative PCR assays for use with environmental DNA (eDNA) to detect numerous species in the genus Cottus that are indigenous to the Pacific coast watersheds of North America. We conducted in vitro assay validations on ten Cottus species and 32 potentially co-occurring non-Cottus species. We demonstrate...

Hoy, Marshal; Ostberg, Carl

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Year Published: 2019

Effect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon

Background Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising either from selective breeding (i.e. domestication) or genetic modification. Such distinct routes to accelerated growth may have...

Kim, Jin-Hyoung; Macqueen, Daniel J; Winton, James; Hansen, John D.; Park, Hyun; Devlin, Robert H

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Year Published: 2019

Characterization of immunoglobulin light chain utilization and variable family diversity in rainbow trout

This study characterizes immunoglobulin light chain (IgL) expression and variable family usage in rainbow trout. IgL transcripts were generated by 5’ RACE from both immune and TNP-KLH immunized fish. Phylogenetic analysis revealed that the IgL variable regions clustered into seven different families: three kappa families (two newly described in...

Rego, Katherine; Bengtén, Eva; Wilson, Melanie; Hansen, John D.; Bromage, Erin S

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Year Published: 2019

Generation of lamprey monoclonal antibodies (Lampribodies) using the phage display system

The variable lymphocyte receptors (VLRs) consist of leucine rich repeats (LRRs) and comprise the humoral antibodies produced by lampreys and hagfishes. The diversity of the molecules is generated by stepwise genomic rearrangements of LRR cassettes dispersed throughout the VLRB locus. Previously, target-specific monovalent VLRB antibodies were...

Hassan, Khan M A; Hansen, John; Herrin, Brantley R; Amemiya, Chris T

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Year Published: 2019

Seasonal use of a nonnatal marine basin by juvenile hatchery chinook salmon

Information on the movement patterns of fishes is essential for managers that are making critical resource decisions. We examined the frequency of a keystone species, Chinook Salmon Oncorhynchus tshawytscha that migrated from different marine basins to the Nisqually River estuary, which lies within the southernmost marine basin (hereafter, “South...

Hayes, Michael C.; Hodgson, Sayre; Ellings, Christopher S.; Duval, Walker D; Rubin, Steve

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Year Published: 2019

Using the STARS Model to evaluate the effects of two proposed projects for the long-term operation of State Water Project Incidental Take Permit Application and CEQA compliance

The California Department of Water Resources (DWR) requested analysis of juvenile Chinook salmon survival in the Sacramento-San Joaquin River Delta (henceforth identified as “the Delta”) as part of an effects analysis that will be included in an Incidental Take Permit (ITP) Application. This application is in compliance with the California...

Perry, Russell W.; Hansen, Amy C.; Evans, Scott D.; Kock, Tobias J.
Perry, R.W., Hansen, A.C., Evans, S.D., and Kock, T.J., 2019, Using the STARS Model to evaluate the effects of two proposed projects for the long-term operation of State Water Project Incidental Take Permit Application and CEQA compliance (ver. 2.0, February 2020): U.S. Geological Survey Open-File Report 2019-1127, 39 p. plus appendixes, https://doi.org/10.3133/ofr20191127.

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Year Published: 2019

Using the STARS model to evaluate the effects of the proposed action for the reinitiation of consultation on the coordinated long-term operation of the Central Valley and State Water Project

In 2016, the U.S. Bureau of Reclamation (USBR) and California Department of Water Resources requested a reinitiation of consultation under Section 7 of the Endangered Species Act on the coordinated long-term operations of the Central Valley and State Water Projects. This resulted in a Biological Assessment released by USBR in 2019. In its analysis...

Perry, Russell W.; Pope, Adam C.; Sridharan, Vamsi K.
Perry, R.W., Pope, A.C., and Sridharan, V.K., 2019, Using the STARS model to evaluate the effects of the proposed action for the reinitiation of consultation on the coordinated long-term operation of the Central Valley and State Water Project: U.S. Geological Survey Open-File Report 2019–1125, 31 p. plus appendixes, https://doi.org/10.3133/ofr20191125.

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Year Published: 2019

Standardized IMGT nomenclature of salmonidae IGH genes, the paradigm of Atlantic salmon and rainbow trout: From genomics to repertoires

In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune...

Magadan, Susana; Krasnov, Aleksei; Hadi-Saljoki, Saida; Afanasyev, Sergey; Mondot, Stanislas; Castro, Rosario; Salinas, Irene; Sunyer, Oriol; Hansen, John; Koop, Ben F; Lefranc, Marie-Paule; Boudinot, Pierre

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Year Published: 2019

Evolutionary dynamics of Ceratonova species (Cnidaria: Myxozoa) reveal different host adaptation strategies

The myxozoan parasite Ceratonova shasta is an important pathogen that infects multiple species of Pacific salmonids. Ongoing genetic surveillance has revealed stable host-parasite relationships throughout the parasite's endemic range. We applied Bayesian phylogenetics to test specific hypotheses about the evolution of these host-parasite...

Breyta, Rachel B.; Atkinson, Stephen D; Bartholomew, Jerri L

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Year Published: 2019

A geographic hot spot of Ichthyophonus infection in the southern Salish Sea, USA

The prevalence of Ichthyophonus infection in Pacific herring Clupea pallasii was spatially heterogeneous in the southern Salish Sea, Washington State, USA. Over the course of 13 mo, 2232 Pacific herring were sampled from 38 midwater trawls throughout the region. Fork length was positively correlated with Ichthyophonus infection at all sites. After...

Hershberger, Paul; Mackenzie, Ashley; Gregg, Jacob; Lindquist, A; Sandell, T; Groner, Maya L.; Lowry, D

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Year Published: 2019

Using the stream salmonid simulator (S3) to assess juvenile Chinook salmon (Oncorhynchus tshawytscha) production under historical and proposed action flows in the Klamath River, California

Executive SummaryThe production of Klamath River fall Chinook salmon (Oncorhynchus tshawytscha) in northern California and southern Oregon is thought to be limited by poor survival during freshwater juvenile life stages, in part a result of Ceratonova shasta—a highly infectious disease that can lead to high fish mortality. Higher flushing river...

Plumb, John M.; Perry, Russell W.; Som, Nicholas A.; Alexander, Julie; Hetrick, Nicholas J.
Plumb, J.M., Perry, R.W., Som, N.A., Alexander, J., and Hetrick, N.J., 2019, Using the stream salmonid simulator (S3) to assess juvenile Chinook salmon (Oncorhynchus tshawytscha) production under historical and proposed action flows in the Klamath River, California: U.S. Geological Survey Open-File Report 2019-1099, 43 p., https://doi.org/10.3133/ofr20191099.

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Year Published: 2019

Application of the Stream Salmonid Simulator (S3) to Klamath River fall Chinook salmon (Oncorhynchus tshawytscha), California—Parameterization and calibration

Executive SummaryIn this report, we describe application of the Stream Salmonid Simulator (S3) to Chinook salmon (Oncorhynchus tshawytscha) in the Klamath River between Keno Dam in southern Oregon and the ocean in northern California. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of...

Perry, Russell W.; Plumb, John M.; Jones, Edward C.; Som, Nicholas A.; Hardy, Thomas B.; Hetrick, Nicholas J.
Perry, R.W., Plumb, J.M., Jones, E.C., Som, N.A., Hardy, T.B., and Hetrick, N.J., 2019, Application of the Stream Salmonid Simulator (S3) to Klamath River fall Chinook salmon (Oncorhynchus tshawytscha), California—Parameterization and calibration: U.S. Geological Survey Open-File Report 2019–1107, 89 p., https://doi.org/10.3133/ofr20191107.