Joseph R Benjamin
I am a Research Biologist at the USGS Forest and Rangeland Ecosystem Science Center in Boise, Idaho. My research provides natural resource managers with tools to make more informed decisions regarding the conservation of species and ecosystems.
My team works closely with cooperators to develop ecological models and decision-support tools that meet the needs of decision makers. We develop ecological models that integrate population dynamics, trophic interactions, and environmental variation at multiple scales to improve our understanding of ecosystem dynamics, including impacts of disturbances. Our decision-support models are used to explore management options for aquatic and terrestrial species and landscapes.
Professional Experience
2024 - Present: USGS Forest and Rangeland Ecosystem Science Center, Research Biologist, Boise, ID
2014 - 2024: USGS Forest and Rangeland Ecosystem Science Center, Ecologist/Biologist, Boise, ID
2013 - 2014: Quantitative Consultants, Inc., Staff Scientist, Boise, ID
2010 - 2013: USGS Columbia River Research Laboratory, Fish Biologist, Cook, WA
2006 - 2010: Department of Biology, Idaho State University, Research Assistant, Pocatello, ID
2002 - 2006: USDA Forest Service, Rocky Mountain Research Station, Fisheries Biologist, Boise, ID
Education and Certifications
Ph.D., Biology, Idaho State University, Pocatello, ID (2010)
M.S., Biology, Boise State University, Boise, ID (2006)
B.S., Biology, Boise State University, Boise, ID (1996)
Affiliations and Memberships*
American Fisheries Society
Ecological Society of America
Society for Freshwater Science
Science and Products
Aquatic & Landscape Ecology Research Team (FRESC)
Fresh waters are one of the most valuable and threatened resources worldwide. They supply critical services to society and harbor many of the world’s most imperiled species. We conduct research and provide technical assistance to address challenges to fresh waters. Our research focuses on ecological processes in freshwater and terrestrial systems and the effects of those processes on landscape...
Population viability assessment of native fish species in the Pacific Northwest accounting for instream conditions of water temperature and streamflow permanence
This data release contains geospatial representations of population viability analysis (PVA) of 23 species of Pacific Northwest non-salmonid fishes. The analysis evaluated long term species persistence (~100 years) based on species distribution models that combined 1) modeled climate, 2) instream conditions, and 3) presence/absence fish data based on species needs and current climate...
Species distribution models and model performance evaluations of twenty-four fishes native to Pacific Northwest US
This data release provides spatial data for species distribution models developed for 24 stream fishes native to the Pacific Northwest, USA and associated model evaluation metrics used to determine the best supported model. These models support a larger analysis for understanding native stream fish vulnerability in the region, specifically population viability analyses built to determine...
Occurrence, Rarity and Climate Sensitivity Index, and Components of 29 Fishes Native to the Pacific Northwest, USA
These datasets include the components of and results from the Rarity and Climate Sensitivity Index (RCS) and occurrence records used to calculate the index for 29 stream fishes native to the Pacific Northwest (Washington, Idaho, Oregon) of the United States. The RCS is an index that ranks species’ intrinsic sensitivity to climate change based on their area of occurrence and climate niche...
Simulated growth potential of redband trout in the Donner und Blitzen River Basin, southeastern Oregon, using a bioenergetics model
Growth potential of redband trout (Oncorhynchus mykiss newberri) was simulated across 175 river segments in the Donner und Blitzen River basin for water years 1980 through 2021 using a bioenergetics model. A previously published framework for assessing climate vulnerability of redband trout was used to simulate the growth potential of redband trout in relation to constraints on body size...
If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Filter Total Items: 27
Linking fire, food webs, and fish in stream ecosystems
As wildfire regimes shift, resource managers are concerned about potential threats to aquatic ecosystems and the species they support, especially fishes. However, predicting fish responses can be challenging because wildfires affect aquatic ecosystems via multiple pathways. Application of whole-ecosystem approaches, such as food web modeling, can act as heuristic tools that offer...
Authors
David A. Roon, J. Ryan Bellmore, Joseph R. Benjamin, François-Nicolas Robinne, Rebecca L. Flitcroft, Jana Compton, Joseph L. Ebersole, Jason B. Dunham, Kevin D. Bladon
Food-web dynamics of a floodplain mosaic overshadow the effects of engineered logjams for Pacific salmon and steelhead
Food webs vary in space and time. The structure and spatial arrangement of food webs are theorized to mediate temporal dynamics of energy flow, but empirical corroboration in intermediate-scale landscapes is scarce. River-floodplain landscapes encompass a mosaic of aquatic habitat patches and food webs, supporting a variety of aquatic consumers of conservation concern. How the structure...
Authors
James C. Paris, Colden Vance Baxter, James Bellmore, Joseph R. Benjamin
New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application
Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and...
Authors
Dylan Gerald-Everett Gomes, Joseph R. Benjamin, Benjamin J. Clemens, Ralph Lampman, Jason B. Dunham
Assisted migration of coho salmon: Influences of passage and habitat availability on population dynamics
Assisted migration is a means of introducing a species into a previously unoccupied area. Although this idea is relatively new for many species, there are many extant examples involving fish that can be instructive. We studied a case of assisted migration where upstream access of migrating adult coho salmon Oncorhynchus kisutch over a naturally impassible barrier was established through...
Authors
Joseph R. Benjamin, Jason B. Dunham, Nicholas Scheidt, Carla Rothenbuecher, Cory Sipher
Working with people to create and apply science in bull trout conservation
No abstract available.
Authors
Jason B. Dunham, Joseph R. Benjamin
Co-production of models to evaluate conservation alternatives for a threatened fish in a rapidly changing landscape
Reintroductions are one means of managing species distributions, but the feasibility of such efforts is uncertain. Here we consider reintroduction for threatened bull trout (Salvelinus confluentus) that currently occupy a small fraction of historically occupied habitats in the upper Klamath River basin owing to climate warming and human modifications of ecosystems. We engaged...
Authors
Joseph R. Benjamin, Jason B. Dunham, Nolan P. Banish, David K Hering, Zachary Tiemann
Climate vulnerability for a desert fish: Integrating hydrologic exposures, adaptive capacity, and growth potential
Climate vulnerability can be evaluated by multiple organismal responses. We developed a climate vulnerability framework focused on growth potential of redband trout (Oncorhynchus mykiss newberri). We employed a bioenergetics model to evaluate spatial variability in growth potential in relation to constraints on body size imposed by stream flow, physiological responses linked to variable...
Authors
Joseph R. Benjamin, Jason B. Dunham, Kara Anlauf-Dunn, Erika J. Eliason
Resist, accept, and direct responses to biological invasions: A social–ecological perspective
Biological invasions represent an important and unique case of ecological transformation that can strongly influence species and entire ecosystems. Challenges in managing invasions arise on multiple fronts, ranging from diverse and often divergent values associated with native and introduced species, logistical constraints, and transformation via other change agents (e.g., climate and...
Authors
Jason B. Dunham, Joseph R. Benjamin, David J. Lawrence, Katherine R. Clifford
Pathways of productivity and influences on top consumers in forested streams
Forested stream ecosystems involve complex physical and biotic pathways that can influence fish in numerous ways. Consequently, the responses of fish communities to disturbance can be difficult to understand. In this study, we employed a food web model that links biotic (e.g., physiology, predator–prey interactions) and abiotic (e.g., temperature, sunlight) attributes to address fish...
Authors
Joseph R. Benjamin, Jason B. Dunham, Sherri L Johnson, Linda Ashkenas, Brooke E. Penaluna, Richard E. Bilby, Douglas S. Bateman, David W. Leer, James Bellmore
Beyond sticks and stones: Integrating physical and ecological conditions into watershed restoration assessments using a food web modeling approach
Watershed assessments have become common for prioritizing restoration in river networks. These assessments primarily focus on geomorphic conditions of rivers but less frequently incorporate non-geomorphic abiotic factors such as water chemistry and temperature, and biotic factors such as the structure of food webs. Using a dynamic food web model that integrates physical and ecological...
Authors
Emily J Whitney, James Bellmore, Joseph R. Benjamin, Chris E. Jordan, Jason B. Dunham, Michael A. Newsom, Matt Nahorniak
Can nutrient additions facilitate recovery of Pacific salmon?
Multiple restoration actions have been implemented in response to declining salmon populations. Among these is the addition of salmon carcasses or artificial nutrients to mimic marine-derived nutrients historically provided by large spawning runs of salmon. A key assumption in this approach is that increased nutrients will catalyze salmon population growth. Although effects on aquatic...
Authors
Joseph R. Benjamin, James Bellmore, Emily J Whitney, Jason B. Dunham
Magnitude and direction of stream–forest community interactions change with timescale
Networks of direct and indirect biotic interactions underpin the complex dynamics and stability of ecological systems, yet experimental and theoretical studies often yield conflicting evidence regarding the direction (positive or negative) or magnitude of these interactions. We revisited pioneering data sets collected at the deciduous forested Horonai Stream and conducted ecosystem‐level...
Authors
Amy M Marcarelli, Colden Vance Baxter, Joseph R. Benjamin, Yo Miyake, Masashi Murakami, K.D. Fausch, Shigeru Nakano
Non-USGS Publications**
Malison, R.L., Benjamin, J.R., Baxter, C.V., 2010, Measuring adult insect emergence from streams- the influence of trap placement and a comparison with benthic sampling: Journal of the North American Benthological Society, v. 29, no. 2, p. 647-656, https://doi.org/10.1899/09-086.1.
Benjamin, J.R., Baxter, C.V., 2010, Do nonnative salmonines exhibit greater density and production than the natives they replace? A comparison of nonnative brook trout with native cutthroat trout: Transactions of the American Fisheries Society, v. 139, p. 641-651, https://doi.org/10.1577/T09-102.1.
Benjamin, J.R., Fausch, K.D., Baxter, C.V., 2011, Species replacement by a nonnative salmonid alters ecosystem function by reducing prey subsidies that support riparian spiders: Oecologia, v. 167, p. 503-512, https://doi.org/10.1007/s00442-011-2000-6. Catalog No: 50050
Benjamin, J.R., Baxter, C.V., 2012, Is a trout a trout? A range-wide comparison shows nonnative brook trout exhibit greater density, biomass, and production than native inland cutthroat trout: Biological Invasions, v. 14, p. 1865-1879, https://doi.org/10.1007/s10530-012-0198-9.
Lepori, F., Benjamin, J.R., Fausch, K.D., Baxter, C.V., 2012, Are invasive and native trout functionally equivalent predators? Results and lessons from a field experiment: Aquatic Conservation: Marine and Freshwater Ecosystems, v. 22, p. 787-798, https://doi.org/10.1002/aqc.2259.
Benjamin, J.R., Connolly, P.J., Romine, J.G., Perry, R.W., 2013, Potential effects of changes in temperature and food resources on life history trajectories of juvenile Oncorhynchus mykiss: Transactions of the American Fisheries Society, v. 142, p. 208-220, https://doi.org/10.1080/00028487.2012.728162.
Benjamin, J.R., Lepori, F., Baxter, C.V., Fausch, K.D., 2013, Can replacement of native by non-native trout alter stream-riparian food webs?: Freshwater Biology, v. 58, p. 1694-1709, https://doi.org/10.1111/fwb.12160.
Benjamin, J.R., Wetzel, L.A., Martens, K., Larsen, K., Connolly, P.J., 2014, Spatio-temporal variability in movement, age, and growth of mountain whitefish (Prosopium williamsoni) in a river network based upon PIT tagging and otolith chemistry: Canadian Journal Fisheries and Aquatic Sciences, v. 71, p. 131-140, https://doi.org/10.1139/cjfas-2013-0279.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Science and Products
Aquatic & Landscape Ecology Research Team (FRESC)
Fresh waters are one of the most valuable and threatened resources worldwide. They supply critical services to society and harbor many of the world’s most imperiled species. We conduct research and provide technical assistance to address challenges to fresh waters. Our research focuses on ecological processes in freshwater and terrestrial systems and the effects of those processes on landscape...
Population viability assessment of native fish species in the Pacific Northwest accounting for instream conditions of water temperature and streamflow permanence
This data release contains geospatial representations of population viability analysis (PVA) of 23 species of Pacific Northwest non-salmonid fishes. The analysis evaluated long term species persistence (~100 years) based on species distribution models that combined 1) modeled climate, 2) instream conditions, and 3) presence/absence fish data based on species needs and current climate...
Species distribution models and model performance evaluations of twenty-four fishes native to Pacific Northwest US
This data release provides spatial data for species distribution models developed for 24 stream fishes native to the Pacific Northwest, USA and associated model evaluation metrics used to determine the best supported model. These models support a larger analysis for understanding native stream fish vulnerability in the region, specifically population viability analyses built to determine...
Occurrence, Rarity and Climate Sensitivity Index, and Components of 29 Fishes Native to the Pacific Northwest, USA
These datasets include the components of and results from the Rarity and Climate Sensitivity Index (RCS) and occurrence records used to calculate the index for 29 stream fishes native to the Pacific Northwest (Washington, Idaho, Oregon) of the United States. The RCS is an index that ranks species’ intrinsic sensitivity to climate change based on their area of occurrence and climate niche...
Simulated growth potential of redband trout in the Donner und Blitzen River Basin, southeastern Oregon, using a bioenergetics model
Growth potential of redband trout (Oncorhynchus mykiss newberri) was simulated across 175 river segments in the Donner und Blitzen River basin for water years 1980 through 2021 using a bioenergetics model. A previously published framework for assessing climate vulnerability of redband trout was used to simulate the growth potential of redband trout in relation to constraints on body size...
If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Filter Total Items: 27
Linking fire, food webs, and fish in stream ecosystems
As wildfire regimes shift, resource managers are concerned about potential threats to aquatic ecosystems and the species they support, especially fishes. However, predicting fish responses can be challenging because wildfires affect aquatic ecosystems via multiple pathways. Application of whole-ecosystem approaches, such as food web modeling, can act as heuristic tools that offer...
Authors
David A. Roon, J. Ryan Bellmore, Joseph R. Benjamin, François-Nicolas Robinne, Rebecca L. Flitcroft, Jana Compton, Joseph L. Ebersole, Jason B. Dunham, Kevin D. Bladon
Food-web dynamics of a floodplain mosaic overshadow the effects of engineered logjams for Pacific salmon and steelhead
Food webs vary in space and time. The structure and spatial arrangement of food webs are theorized to mediate temporal dynamics of energy flow, but empirical corroboration in intermediate-scale landscapes is scarce. River-floodplain landscapes encompass a mosaic of aquatic habitat patches and food webs, supporting a variety of aquatic consumers of conservation concern. How the structure...
Authors
James C. Paris, Colden Vance Baxter, James Bellmore, Joseph R. Benjamin
New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application
Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and...
Authors
Dylan Gerald-Everett Gomes, Joseph R. Benjamin, Benjamin J. Clemens, Ralph Lampman, Jason B. Dunham
Assisted migration of coho salmon: Influences of passage and habitat availability on population dynamics
Assisted migration is a means of introducing a species into a previously unoccupied area. Although this idea is relatively new for many species, there are many extant examples involving fish that can be instructive. We studied a case of assisted migration where upstream access of migrating adult coho salmon Oncorhynchus kisutch over a naturally impassible barrier was established through...
Authors
Joseph R. Benjamin, Jason B. Dunham, Nicholas Scheidt, Carla Rothenbuecher, Cory Sipher
Working with people to create and apply science in bull trout conservation
No abstract available.
Authors
Jason B. Dunham, Joseph R. Benjamin
Co-production of models to evaluate conservation alternatives for a threatened fish in a rapidly changing landscape
Reintroductions are one means of managing species distributions, but the feasibility of such efforts is uncertain. Here we consider reintroduction for threatened bull trout (Salvelinus confluentus) that currently occupy a small fraction of historically occupied habitats in the upper Klamath River basin owing to climate warming and human modifications of ecosystems. We engaged...
Authors
Joseph R. Benjamin, Jason B. Dunham, Nolan P. Banish, David K Hering, Zachary Tiemann
Climate vulnerability for a desert fish: Integrating hydrologic exposures, adaptive capacity, and growth potential
Climate vulnerability can be evaluated by multiple organismal responses. We developed a climate vulnerability framework focused on growth potential of redband trout (Oncorhynchus mykiss newberri). We employed a bioenergetics model to evaluate spatial variability in growth potential in relation to constraints on body size imposed by stream flow, physiological responses linked to variable...
Authors
Joseph R. Benjamin, Jason B. Dunham, Kara Anlauf-Dunn, Erika J. Eliason
Resist, accept, and direct responses to biological invasions: A social–ecological perspective
Biological invasions represent an important and unique case of ecological transformation that can strongly influence species and entire ecosystems. Challenges in managing invasions arise on multiple fronts, ranging from diverse and often divergent values associated with native and introduced species, logistical constraints, and transformation via other change agents (e.g., climate and...
Authors
Jason B. Dunham, Joseph R. Benjamin, David J. Lawrence, Katherine R. Clifford
Pathways of productivity and influences on top consumers in forested streams
Forested stream ecosystems involve complex physical and biotic pathways that can influence fish in numerous ways. Consequently, the responses of fish communities to disturbance can be difficult to understand. In this study, we employed a food web model that links biotic (e.g., physiology, predator–prey interactions) and abiotic (e.g., temperature, sunlight) attributes to address fish...
Authors
Joseph R. Benjamin, Jason B. Dunham, Sherri L Johnson, Linda Ashkenas, Brooke E. Penaluna, Richard E. Bilby, Douglas S. Bateman, David W. Leer, James Bellmore
Beyond sticks and stones: Integrating physical and ecological conditions into watershed restoration assessments using a food web modeling approach
Watershed assessments have become common for prioritizing restoration in river networks. These assessments primarily focus on geomorphic conditions of rivers but less frequently incorporate non-geomorphic abiotic factors such as water chemistry and temperature, and biotic factors such as the structure of food webs. Using a dynamic food web model that integrates physical and ecological...
Authors
Emily J Whitney, James Bellmore, Joseph R. Benjamin, Chris E. Jordan, Jason B. Dunham, Michael A. Newsom, Matt Nahorniak
Can nutrient additions facilitate recovery of Pacific salmon?
Multiple restoration actions have been implemented in response to declining salmon populations. Among these is the addition of salmon carcasses or artificial nutrients to mimic marine-derived nutrients historically provided by large spawning runs of salmon. A key assumption in this approach is that increased nutrients will catalyze salmon population growth. Although effects on aquatic...
Authors
Joseph R. Benjamin, James Bellmore, Emily J Whitney, Jason B. Dunham
Magnitude and direction of stream–forest community interactions change with timescale
Networks of direct and indirect biotic interactions underpin the complex dynamics and stability of ecological systems, yet experimental and theoretical studies often yield conflicting evidence regarding the direction (positive or negative) or magnitude of these interactions. We revisited pioneering data sets collected at the deciduous forested Horonai Stream and conducted ecosystem‐level...
Authors
Amy M Marcarelli, Colden Vance Baxter, Joseph R. Benjamin, Yo Miyake, Masashi Murakami, K.D. Fausch, Shigeru Nakano
Non-USGS Publications**
Malison, R.L., Benjamin, J.R., Baxter, C.V., 2010, Measuring adult insect emergence from streams- the influence of trap placement and a comparison with benthic sampling: Journal of the North American Benthological Society, v. 29, no. 2, p. 647-656, https://doi.org/10.1899/09-086.1.
Benjamin, J.R., Baxter, C.V., 2010, Do nonnative salmonines exhibit greater density and production than the natives they replace? A comparison of nonnative brook trout with native cutthroat trout: Transactions of the American Fisheries Society, v. 139, p. 641-651, https://doi.org/10.1577/T09-102.1.
Benjamin, J.R., Fausch, K.D., Baxter, C.V., 2011, Species replacement by a nonnative salmonid alters ecosystem function by reducing prey subsidies that support riparian spiders: Oecologia, v. 167, p. 503-512, https://doi.org/10.1007/s00442-011-2000-6. Catalog No: 50050
Benjamin, J.R., Baxter, C.V., 2012, Is a trout a trout? A range-wide comparison shows nonnative brook trout exhibit greater density, biomass, and production than native inland cutthroat trout: Biological Invasions, v. 14, p. 1865-1879, https://doi.org/10.1007/s10530-012-0198-9.
Lepori, F., Benjamin, J.R., Fausch, K.D., Baxter, C.V., 2012, Are invasive and native trout functionally equivalent predators? Results and lessons from a field experiment: Aquatic Conservation: Marine and Freshwater Ecosystems, v. 22, p. 787-798, https://doi.org/10.1002/aqc.2259.
Benjamin, J.R., Connolly, P.J., Romine, J.G., Perry, R.W., 2013, Potential effects of changes in temperature and food resources on life history trajectories of juvenile Oncorhynchus mykiss: Transactions of the American Fisheries Society, v. 142, p. 208-220, https://doi.org/10.1080/00028487.2012.728162.
Benjamin, J.R., Lepori, F., Baxter, C.V., Fausch, K.D., 2013, Can replacement of native by non-native trout alter stream-riparian food webs?: Freshwater Biology, v. 58, p. 1694-1709, https://doi.org/10.1111/fwb.12160.
Benjamin, J.R., Wetzel, L.A., Martens, K., Larsen, K., Connolly, P.J., 2014, Spatio-temporal variability in movement, age, and growth of mountain whitefish (Prosopium williamsoni) in a river network based upon PIT tagging and otolith chemistry: Canadian Journal Fisheries and Aquatic Sciences, v. 71, p. 131-140, https://doi.org/10.1139/cjfas-2013-0279.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
*Disclaimer: Listing outside positions with professional scientific organizations on this Staff Profile are for informational purposes only and do not constitute an endorsement of those professional scientific organizations or their activities by the USGS, Department of the Interior, or U.S. Government