Western Fisheries Research Center

Publications

Filter Total Items: 2,279
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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

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 the efficacy of these...

Hoy, Marshal; Ostberg, Carl

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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.

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Year Published: 2019

Movement and apparent survival of acoustically tagged juvenile late-fall run chinook salmon released upstream of Shasta Reservoir, California

Stakeholder interests have spurred the reintroduction of the critically endangered populations of Chinook Salmon to tributaries upstream of Shasta Dam, in northern California. We released two groups of acoustically tagged, juvenile hatchery, late-fall Chinook Salmon to determine how juvenile salmon would distribute and survive. We measured travel...

Plumb, John; Hansen, Amy; Adams, Noah S.; Evans, Scott D.; John Hannon

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Year Published: 2019

Evaluating the potential for sea lice to evolve freshwater tolerance as a consequence of freshwater treatments in salmon aquaculture

Increasing usage of non-medicinal methods (NMMs) to control sea louse infestations on salmon farms has raised questions about whether sea lice may be able to evolve tolerance of NMMs. Of particular concern is the potential for sea lice to evolve freshwater tolerance as a result of freshwater treatments. Wild trout and some juvenile salmonids swim...

Groner, Maya; Laurin, Emilie; Stormoen, Marit; Sanchez, Javier; Fast, Mark D; Revie, Crawford W.

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Year Published: 2019

Estimating annual Ceratonova shasta mortality rates in juvenile Scott and Shasta River coho salmon that enter the Klamath River mainstem

The impacts of Ceratonova shasta on Klamath River salmonids have been the focus of tremendous research and monitoring over the past decade. Knowledge gained from the various studies has resulted in a growing suite of decision support tools that can be used to predict the prevalence of infection and mortality that can be expected from varying...

Som, Nicholas A.; Hetrick, Nicholas J.; Perry, Russell; Alexander, Julie D

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Year Published: 2019

The nucleoprotein and phosphoprotein are major determinants of the virulence of viral hemorrhagic septicemia virus in rainbow trout

Viral hemorrhagic septicemia virus (VHSV), a fish rhabdovirus, infects several marine and freshwater fish species. There are many strains of VHSV that affect different fish, but some strains of one genetic subgroup have gained high virulence in rainbow trout (Oncorhynchus mykiss). To define the genetic basis of high virulence in trout, we used...

Vakharia, Vikram N; Liu, Jie; Mckenney, Douglas; Kurath, Gael

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Year Published: 2019

Juvenile Chinook salmon (Oncorhynchus tshawytscha) survival in Lookout Point Reservoir, Oregon, 2018

A field study was conducted to estimate survival of juvenile Chinook salmon (Oncorhynchus tshawytscha) in Lookout Point Reservoir, Oregon, during 2018. The study consisted of releasing three groups of genetically-marked fish into the reservoir, and sampling them monthly. Juveniles were released during April 10–13 (116,708 fish), May 15–18 (31,911...

Kock, Tobias J.; Perry, Russell W.; Hansen, Gabriel S.; Haner, Philip V.; Pope, Adam C.; Plumb, John M.; Cogliati, Karen M.; Hansen, Amy C.
Kock, T.J., Perry, R.W., Hansen, G.S., Haner, P.V., Pope, A.C., Plumb, J.M., Cogliati, K.M., and Hansen, A.C., 2019, Juvenile Chinook salmon (Oncorhynchus tshawytscha) survival in Lookout Point Reservoir, Oregon, 2018: U.S. Geological Survey Open-File Report 2019–1097, 41 p., https://doi.org/10.3133/ofr20191097.