Unit Leader - Oregon Cooperative Fish and Wildlife Research Unit
Research Interests
Jim's research focuses on multiple aspects of aquatic ecology- with an emphasis on stream fish communities. Most of his work has been in identifying and quantifying the effects of physical and biotic factors on stream fishes at multiple scales. This includes studies of population dynamics, community production, and fish-habitat/landscape relationships. Other aspects of his research include evaluating the efficiency of fish collection and population-estimation techniques and computer software development. He believes that the status of natural resources is dependent upon the ability to predict the impacts of environmental perturbations or differing management schemes. Thus, the principal goal of his research is to develop the tools and understanding necessary for effective and efficient fisheries management and conservation.
Professional Experience
Assistant Unit Leader, Oregon Cooperative Fish and Wildlife Research Unit, 2011-2019
Assistant Unit Leader, Georgia Cooperative Fish and Wildlife Research Unit, 1999-2011
Education and Certifications
Ph D University of Missouri 1996
MS University of Illinois 1989
BS University of Illinois 1986
Science and Products
SERAP: The Effects of Climate Change on Aquatic Species and Habitat in the Southeast
Oregon spotted frog (Rana pretiosa) monitoring data for metademographic analysis 2010-2018, Oregon
Long-term amphibian monitoring data from the Willamette Valley, Oregon (2004-2015)
Fish misidentification and potential implications to monitoring within the San Francisco Estuary, California
Assessment of habitat availability for juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in the Willamette River, Oregon
Integrated tools for identifying optimal flow regimes and evaluating alternative minimum flows for recovering at-risk salmonids in a highly managed system
Laboratory infection rates and associated mortality of juvenile Chinook Salmon (Oncorhynchus tshawytscha) from parasitic copepod (Salmincola californiensis)
Rapid phenotypic stock identification of Chinook Salmon in recreational fishery management
Application of genetic stock identification and parentage-based tagging in a mixed-stock recreational chinook salmon fishery
Concealment of juvenile bull trout in response to temperature, light, and substrate: Implications for detection
Decision analysis for greater insights into the development and evaluation of Chinook salmon restoration strategies in California’s Central Valley
Using a bayesian multistate occupancy model to assess seabird and shorebird status in Glacier Bay, Alaska
Estimation of metademographic rates and landscape connectivity for a conservation-reliant anuran
Comparing environmental flow implementation options with structured decision making: Case study from the Willamette River, Oregon
Odds ratios and hurdle models: a long-term analysis of parasite infection patterns in endangered young-of-the-year suckers from Upper Klamath Lake, Oregon, USA
Science and Products
- Science
SERAP: The Effects of Climate Change on Aquatic Species and Habitat in the Southeast
USGS researchers assessed how climate change can affect land cover and flow in river systems, examining a variety of resolutions for detecting and projecting the conditions of aquatic habitats and species. - Data
Oregon spotted frog (Rana pretiosa) monitoring data for metademographic analysis 2010-2018, Oregon
This dataset contains information from surveys conducted 2010-2018 by USGS as part of a long-term Oregon spotted frog monitoring effort in the central Oregon range. Data consist of site, survey, habitat, and species detection covariates, as well as inter-site distance measurements.Long-term amphibian monitoring data from the Willamette Valley, Oregon (2004-2015)
This dataset contains information from surveys conducted 2004-2015 by USGS as part of a long-term amphibian monitoring effort in the Willamette Valley, Oregon. Data consist of site, survey, habitat, and species detection covariates. - Publications
Filter Total Items: 54
Fish misidentification and potential implications to monitoring within the San Francisco Estuary, California
Fish monitoring programs often rely on the collection, species identification, and counting of individual fish over time to inform natural resource management decisions. Thus, the utility of the data used to inform these decisions can be negatively affected by species misidentification. Fish species misidentification bias can be minimized by confirming identification using genetic techniques, traiAuthorsJ. E. Kirsch, J. L. Day, James Peterson, D. K. FullertonAssessment of habitat availability for juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in the Willamette River, Oregon
The Willamette River, Oregon, is home to two salmonid species listed as threatened under the Endangered Species Act, Upper WIllamette River spring Chinook salmon (Oncorhynchus tshawytscha) and Upper Willamette River winter steelhead (O. mykiss). Streamflow in the Willamette River is regulated by upstream dams, 13 of which are operated by the U.S. Army Corps of Engineers (USACE) as part of the WillAuthorsJames S. White, James T. Peterson, Laurel E. Stratton Garvin, Tobias J. Kock, J. Rose WallickIntegrated tools for identifying optimal flow regimes and evaluating alternative minimum flows for recovering at-risk salmonids in a highly managed system
Water resource managers are faced with difficult decisions on how to satisfy human water needs while maintaining or restoring riverine ecosystems. Decision sciences have developed approaches and tools that can be used to break down difficult water management decisions into their component parts. An essential aspect of these approaches is the use of quantitative models to evaluate alternative managAuthorsJames Peterson, Jessica E. Pease, Luke Whitman, James White, Laurel E. Stratton Garvin, Stewart A. Rounds, J. Rose WallickLaboratory infection rates and associated mortality of juvenile Chinook Salmon (Oncorhynchus tshawytscha) from parasitic copepod (Salmincola californiensis)
Pacific salmon (Oncorhynchus spp.) rearing in lakes and reservoirs above dams have been known to become heavily infected with an ectoparasitic copepod (Salmincola californiensis). Little is known about the factors that affect the parasite infection prevalence and intensity. However, previous research suggests that the parasite may negatively affect the fitness and survival of the host fish. The efAuthorsTravis Neal, Michael L. Kent, Justin Sanders, Carl B. Schreck, James PetersonRapid phenotypic stock identification of Chinook Salmon in recreational fishery management
Rapid phenotypic stock identification in mixed-stock fisheries can provide a useful alternative to more time-intensive methods (e.g., coded wire tags, genetics) in assessing harvest and informing management decisions. We leveraged local ecological knowledge, existing stock identification methods, and understanding of life history differences to develop rapid stock identification tools for fall-runAuthorsAlexander J. Jensen, Carl B. Schreck, James PetersonApplication of genetic stock identification and parentage-based tagging in a mixed-stock recreational chinook salmon fishery
Genetic methods can guide and improve the management of recreational mixed-stock fisheries by informing stock-specific estimates of harvest. We applied genetic stock identification and parentage-based tagging to a recreational Chinook Salmon Oncorhynchus tshawytscha fishery in the Columbia River to illustrate the value of genetic analysis in management. We sampled landed catch in 2017 and 2018, asAuthorsAlexander J. Jensen, Carl B. Schreck, Jon E. Hess, Sandra Bohn, Kathleen G. O’Malley, James PetersonConcealment of juvenile bull trout in response to temperature, light, and substrate: Implications for detection
Bull trout (Salvelinus confluentus) are challenging to detect as a result of the species cryptic behavior and coloration, relatively low densities in complex habitats, and affinity for cold, high clarity, low conductivity waters. Bull trout are also closely associated with the stream bed, frequently conceal in substrate, and this concealment behavior is poorly understood. Consequently, populationAuthorsRussell F. Thurow, James Peterson, Gwynne L. Chandler, Christine M. Moffitt, Theodore C. BjornnDecision analysis for greater insights into the development and evaluation of Chinook salmon restoration strategies in California’s Central Valley
Considerable amounts of resources have been invested in ecological restoration projects across the globe to restore ecosystem integrity. Restoration strategies are often diverse and have been met with mixed success. In this paper, we describe the Chinook salmon (Oncorhynchus tshawytscha) decision-support models developed by the Central Valley Project Improvement Act Science Integration Team as parAuthorsJames Peterson, Adam DuarteUsing a bayesian multistate occupancy model to assess seabird and shorebird status in Glacier Bay, Alaska
The U.S. Department of Interior National Park Service is charged with both monitoring avian communities and evaluating the influence of visitors to National Parks on sensitive species; however, this task is challenging considering that sampling programs often involve multiple species, each with differing behavior, habitat requirements, and detectability. Our objectives were to build a model to desAuthorsSteven L. Whitlock, Tania Lewis, James PetersonEstimation of metademographic rates and landscape connectivity for a conservation-reliant anuran
ContextAmphibian conservation efforts commonly assume populations are tied to waterbodies that collectively function as a metapopulation. This assumption is rarely evaluated, and there is a need to understand the degree of connectivity among patches to appropriately define, manage, and conserve biological populations.ObjectivesOur objectives were to quantify local persistence, colonization, and reAuthorsAdam Duarte, James Peterson, Christopher Pearl, Jennifer Christine Rowe, Brome McCreary, Stephanie Galvan, Michael AdamsComparing environmental flow implementation options with structured decision making: Case study from the Willamette River, Oregon
Many frameworks have been used to identify environmental flows for sustaining river ecosystems or specific taxa in the face of widespread flow alteration for human use. However, these methods mostly focus on identifying suitable flows and largely ignore the important links between management actions, resulting flows, flow variability, and ecosystem or social responses. Structured decision making (AuthorsJ. Tyrell DeWeber, James PetersonOdds ratios and hurdle models: a long-term analysis of parasite infection patterns in endangered young-of-the-year suckers from Upper Klamath Lake, Oregon, USA
We used odds ratios and a hurdle model to analyze parasite co-infections over 25 years on >20,000 young-of-the year of endangered Shortnose and Lost River Suckers. Host ecologies differed as did parasite infections. Shortnose Suckers were more likely to be caught inshore and 3–5 times more likely to have Bolbophorus spp. and Contracaecum sp. infections, and Lost River Suckers were more likely to bAuthorsDouglas F. Markle, Andrew Janik, James Peterson, Anindo Choudhury, David C. Simon, Vasyl V. Tkach, Mark R. Terwilliger, Justin L. Sanders, Michael L. Kent