This Month at WFRC

Release Date:

This page contains WFRC "Highlights" reported November, 2019


USGS at Environmental DNA Technical Exchange Workshop: On November19-21, 2019 USGS Western Fisheries Research Center scientists Carl Ostberg and Jeff Duda attended the 3rd Environment DNA Technical Exchange Workshop in St. Petersburg, Florida. The first two days were workshops featuring talks about the latest research in targeted methodologies, data integration, and management, as well as a focus on the use of eDNA metabarcoding and other novel molecular techniques. The last day is a USGS-NOAA bilateral meeting with the goal of formulating opportunities to work together to advance eDNA science and accelerate the transfer of technology into operational use across the two agencies.

Contact Carl Ostberg, or Jeff Duda,

USGS scientist provides imaging sonar technical assistance to U.S. Army Corps of Engineers scientists on the Sacramento River: From November 4 -6, 2019 USGS scientist Collin Smith, with the Western Fisheries Research Center's Columbia River Research Laboratory, provided imaging sonar technical assistance to U.S. Army Corps of Engineers scientists at a dredging site on the Sacramento River, CA. The assistance was provided to explore the deployment and use of imaging sonar to evaluate fish behavior and abundance near active dredging operations. Annual dredging occurs on the Sacramento River to permit inland ship navigation, with little knowledge of how fish either interact with or are impacted by these operations.

Contact Collin Smith,

New Publications

New publication utilizes current genomic resources and immunoinformatics to comprehensively describe salmon antibody repertoires: The availability of the updated Atlantic salmon and rainbow trout genome assemblies coupled with high throughput RNA sequencing has led to a need for standardized antibody nomenclature for describing B-cell responses to infection or immunization. Antibodies represent a key line of host defense against microbial pathogens, therefore variations between germline repertoires of immunoglobulin genes across commercial and wild stocks have implications for aquaculture and conservation of these species. Using rules established by the international ImMunoGeneTics (IMGT®, a  consortium of scientists from the US, Spain, Norway, France, Russia and Canada have developed reference antibody gene databases for Atlantic salmon and rainbow trout. In a new publication in Frontiers in Immunology, scientists provides annotation of adaptive immune receptor repertoire datasets to facilitate direct comparisons of high-throughput sequencing (AIRRseq) between studies and species on a global scale.

Magadan S., A. Krasnov, S. Hadi-Saljoqi, S. Afanasyev, S. Mondot, D. Lallias, R. Castro, I. Salinas, O. Sunyer, J. Hansen, B. Koop, M-P Lefranc, and P. Boudinot. 2019. Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires. Frontiers in Immunology 2541, 16 p.

Contact John Hansen at

New publication explores statistical methods for temporal variation in mark-recapture analysis of migratory animals: Understanding drivers of temporal variation in demographic parameters is a central goal of mark‐recapture analysis. To estimate survival of migrating animal populations in migration corridors, space‐for‐time mark‐recapture models employ discrete sampling locations in space to monitor marked populations as they move past monitoring sites, rather than the standard practice of using fixed sampling points in time. For example, these types of models are regularly used in the Columbia River to estimate fish survival through the FCRPS. However, these models focus on estimating survival over discrete spatial segments, model parameters are implicitly integrated over the temporal dimension, and modeling the effect of time‐varying covariates on model parameters is complicated by unknown passage times for individuals that are not detected at monitoring sites. Thus, it is difficult under existing methods to test the effect of environmental and operational metrics (e.g. discharge and spill) on fish survival if these metrics vary over time. In a new publication of Biometrics, scientists at USGS Western Fisheries Research Center extended the Cormack‐Jolly‐Seber (CJS) framework to estimate temporally‐stratified survival and capture probabilities by including a discretized arrival time process in a Bayesian framework. The publication demonstrates the framework by fitting three competing models to estimate daily survival, capture and arrival probabilities at four hydroelectric dams for over 200,000 individually tagged migratory juvenile salmon released into the Snake River. This new method has many possible uses such as assessing effects of daily dam operations on the survival of migrating juvenile salmon.

Hance, D.J., R.W. Perry, J.M. Plumb, and A.C. Pope. 2019. A temporally-stratified extension of space-for-time Cormack-Jolly-Seber for migratory animals. Biometrics

Contact Dalton Hance at

New publication describes the development of environmental DNA (eDNA) assays for detection of several sculpin species in Pacific coast watersheds. Freshwater sculpins are an ecologically important, diverse group of small benthic fish that inhabit streams, rivers and lakes and knowledge of their distribution across landscapes can inform on their role in aquatic communities. Aquatic environmental DNA (eDNA) offers an economical and highly sensitive alternative method for detecting species and could be used for identifying sculpin distributions. In a recent publication, scientists from USGS Western Fisheries Research Center developed eDNA assays for detection of numerous freshwater sculpin species commonly occurring in Pacific coast watersheds. The assays will be useful for detecting sculpin in habitats where one (or more) of several sculpin species could be present.

Hoy, M. S. and C. O. Ostberg. 2019. Development of two quantitative PCR assays for detection of several Cottus species from environmental DNA in Pacific coast watersheds of North America. Conservation Genetics Resources.

Contact: Marshal Hoy, or Carl Ostberg,

In the News

On November 9, 2019 USGS scientists Dave Beauchamp and Tessa Code were contacted by Rob Lyon, a freelance writing for Northwest Fly Fishing Magazine, about competition for food between shiners and juvenile trout in Ross Lake, WA. Both fish species target insects and zooplankton populations and there is concern of what will happen to native fish populations if there are limited food resources.

Contact Dave Beauchamp,

On November 1, 2019 USGS Western Fisheries Research Center senior scientist emeritus Jim Winton was mentioned in an article of The Seattle Times about an aquaculture company seeking to farm steelhead trout in the Puget Sound, WA. Winton commented on the risks related to aquaculture and disease. 

Contact Jim Winton,