My research is focused on landscape ecology of aquatic ecosystems, conservation biology of focal species, ecology of natural disturbance, biological invasions, and monitoring.
Education and Certifications
Ph.D. Ecology Evolution and Conservation Biology, University of Nevada, Reno, NV
Science and Products
Aquatic & Landscape Ecology Research Team (FRESC)
Updated classifications of flow permanence on streams in the Colville National Forest
USGS science supporting the Elwha River Restoration Project
Controls on Habitat for Native Lampreys in the Umpqua River Basin
Controls on Salmon and Lamprey Habitat along the Siletz River
Probability of Streamflow Permanence (PROSPER)
Aquatic & Landscape Ecology Research Team (FRESC)
Threat of Invasives to Native Species and Ecosystems
Restoration and Management of Aquatic Ecosystems
Climate and Aquatic Ecosystems
Life Histories of Aquatic Species
Landscape Ecology of Aquatic Ecosystems
Webinar: Understanding Water Availability Across Landscapes in a Time of Increasing Drought
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.
Fishes of the Harney Basin revisited: A contemporary assessment of the distribution of fish fauna throughout the Harney Basin from 1990 to 2019 (ver. 2.0, April 2022)
Air and stream temperature and pressure for HJ Andrews Experimental Forest, Western Oregon, 2020
Stream Temperature in the Northern Great Basin region of Southeastern Oregon, 2016-2021
FLOwPER Database: StreamFLOw PERmanence field observations, April 2020 - Nov 2020
Stream Temperature in the Lahontan Basin of Nevada and California, 2017-2019
Stream Temperature and Water Presence Models of Willow/Whitehorse and Willow/Rock Watersheds, Oregon and Nevada
FLOwPER Database: StreamFLOw PERmanence field observations, August 2019 - October 2019
Stream Temperature in the Northern Great Basin region of Southeastern Oregon, 2016-2019
Geomorphic and larval lamprey surveys in tributaries of the Umpqua River, Oregon
Stream temperature and drying data from Willow/Whitehorse watersheds, southeast Oregon, 2014-16, and Willow/Rock/Frazer watersheds, northern Nevada, 2015-2016
Stream temperature data from Willow-Whitehorse and Little Blitzen watersheds, southeast Oregon, 2011-2015
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.
Evolutionary and ecological connectivity in westslope cutthroat trout (Oncorhynchus clarkii lewisi) and mountain whitefish (Prosopium williamsoni) in relation to the potential influences of Boundary Dam, Washington, Idaho, and parts of British Columbia
Tough places and safe spaces: Can refuges save salmon from a warming climate?
Passage of adult coho salmon (Oncorhynchus kisutch) over Lake Creek Falls, Oregon, 2019
Influence of riparian thinning on trophic pathways supporting stream food webs in forested watersheds
Engaging stakeholders to develop a decision support model of conservation risk and management capacity to prioritize investments in Bull Trout recovery
Resist, accept, and direct responses to biological invasions: A social–ecological perspective
Dammed water quality — Longitudinal stream responses below beaver ponds in the Umpqua River Basin, Oregon
Stream size, temperature, and density explain body sizes of freshwater salmonids across a range of climate conditions
Controlling invasive fish in fluctuating environments: Model analysis of common carp (Cyprinus carpio) in a shallow lake
Pathways of productivity and influences on top consumers in forested streams
A riverscape approach reveals downstream propagation of stream thermal responses to riparian thinning at multiple scales
Fish response to successive clearcuts in a second-growth forest from the central Coast range of Oregon
Non-USGS Publications**
**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.
To request an interview, contact fresc_outreach@usgs.gov or call (541) 750-1030.
Science and Products
- Science
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...Filter Total Items: 16Updated classifications of flow permanence on streams in the Colville National Forest
The Issue: Streamflow permanence refers to the probability that a stream will lose surface flow (become a dry channel), as well as the timing, duration, and frequency of drying. Patterns of streamflow permanence drive important decisions regarding forest management and other land uses. The Colville National Forest Land and Resource Management Plan (2019), for example, specifies riparian management...USGS science supporting the Elwha River Restoration Project
The Elwha River Restoration Project has reconnected the water, salmon, and sediment of a pristine river and coast of the Olympic Peninsula of Washington.Controls on Habitat for Native Lampreys in the Umpqua River Basin
Native lampreys are culturally significant fishes for tribal communities in Oregon. As such, the USGS has begun working with the Cow Creek Band of Umpqua Tribe of Indians to study changes that may be affecting habitat for native Pacific and western brook lampreys in the Umpqua River basin.Controls on Salmon and Lamprey Habitat along the Siletz River
Chinook Salmon and Pacific Lamprey are culturally significant fishes to the Tribal community along the Siletz River, Oregon. The USGS has begun studying how streamflow and bedload conditions may influence mainstem spawning habitats.Probability of Streamflow Permanence (PROSPER)
PRObability of Streamflow PERmanence (PROSPER) Rivers and streams are constantly changing. Streamflows can change throughout the year and between years due to snowmelt, precipitation, diversions, and return flows. For many streams, these fluctuations determine whether a stream has year-round flow or not. PROSPER is a project initiated to better understand what causes these fluctuations in...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...Threat of Invasives to Native Species and Ecosystems
Invasive species are a growing threat to native species and ecosystem processes in fresh waters. The Introducing non-native fish into an area may have no effect, little current effect, or the potential to seriously impact the native species, possibly resulting in their extinction. We conduct research to address the causes of invasions and their impacts. We also provide technical support for...Restoration and Management of Aquatic Ecosystems
Restoration of aquatic ecosystems involves a broad spectrum of active and passive efforts. Passive efforts rely on natural recovery of ecosystems, such as land use practices that protect riparian zones and sources of wood and sediment that drive the geomorphic and associated biological functions in streams. Active efforts involve more direct intervention, usually applied to specific locations, to...Climate and Aquatic Ecosystems
Effects of changing climate on aquatic ecosystems requires understanding a complex series of interactions between terrestrial climates, their corresponding impacts on hydrological processes, and ultimately a suite of biological responses. These uncertainties stand in contrast to the urgent need for reliable information to be used in developing long-term strategies for climate adaptation to...Life Histories of Aquatic Species
Many species exhibit diverse behaviors that translate into different patterns of habitat use and demography. Diversity within species can be related to a complex array of processes, including genetic and maternal influences, and external environmental drivers. Our work addresses life history diversity in salmon and trout, including Pacific salmon, steelhead and rainbow trout, cutthroat trout, and...Landscape Ecology of Aquatic Ecosystems
Landscape ecology has only a short history as a recognized discipline, but it has transformed our thinking about the interplay between pattern and process. We now understand that many smaller-scale phenomena are driven by spatial processes, such as the proximity of different habitats to one another, the ability of organisms to move through landscapes, and the dynamics of natural disturbance such...Webinar: Understanding Water Availability Across Landscapes in a Time of Increasing Drought
View this webinar to learn about a new initiative to address knowledge gaps in water availability at the landscape scale. - Data
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.
Fishes of the Harney Basin revisited: A contemporary assessment of the distribution of fish fauna throughout the Harney Basin from 1990 to 2019 (ver. 2.0, April 2022)
We compiled electrofishing and habitat data sampled from 1990 to 2019 in the Harney Basin by the US Geological Survey (USGS), Oregon Department of Fish and Wildlife (ODFW) and the High Desert Partnership (HDP) to describe native and non-native fish distributions and their habitat associations. USGS collected eDNA data in 2019 to refine the known distributions of common carp (Cyprinus carpio). SiteAir and stream temperature and pressure for HJ Andrews Experimental Forest, Western Oregon, 2020
This dataset includes temperature and pressure data from 26 sites in the HJ Andrews Experimental Forest in western Oregon. Stream and Air data loggers were deployed in June of 2020 and downloaded in October 2020. The HJ_Andrews_Temperature file contains temperature data (in C) by logger serial number, site, and usage for the study period. The HJ_Andrews_Pressure file contains pressure data (in kPaStream Temperature in the Northern Great Basin region of Southeastern Oregon, 2016-2021
This dataset includes hourly stream and air temperature data from 124 sites throughout the Northern Great Basin region of SE Oregon. Data loggers were deployed June through September of 2016 and downloaded each subsequent summer through 2021. The SE_OR_Stream_Temps and SE_OR_Air_Temps files contain temperature data (in degrees Celsius) by logger serial number and site for the study period. The SE_FLOwPER Database: StreamFLOw PERmanence field observations, April 2020 - Nov 2020
IMPORTANT NOTE: This dataset includes spatial locations where streamflow permanence observations (continuous flow, discontinuous flow, and dry) were recorded using the FLOwPER (FLOw PERmanence) field survey available in the Survey 123 and S1 mobile application. Additional information to describe the field conditions are included as part of the survey. Field observations in the FLOwPER Database havStream Temperature in the Lahontan Basin of Nevada and California, 2017-2019
This dataset includes hourly stream temperature data for 139 temperature logger sites throughout the Lahontan Basin Region of Northern Nevada and Eastern California. Data loggers were part a study beginning in 2017, with data available through 2019 for most locations. The spatial data layer contains site locations, geographic information, data summaries, mean August stream temperatures, and modeleStream Temperature and Water Presence Models of Willow/Whitehorse and Willow/Rock Watersheds, Oregon and Nevada
This data release contains spatial stream network (SSN) objects and R scripts to run SSN models to predict mean monthly stream temperature between May and August and water presence on May 15, June 15, July 15, and August 15 in the Willow/Whitehorse watershed during 2015, 2016, and 2017 and the Willow/Rock watershed during 2016 and 2017. Functions referenced within the script may accessed in the SSFLOwPER Database: StreamFLOw PERmanence field observations, August 2019 - October 2019
IMPORTANT NOTE: More recent versions of these data release are available at this link. This dataset includes spatial locations where streamflow permanence observations (continuous flow, discontinuous flow, and dry) were recorded using the FLOwPER (FLOw PERmanence) field survey available in the Survey 123 and S1 mobile application. Additional information to describe the field conditions are includStream Temperature in the Northern Great Basin region of Southeastern Oregon, 2016-2019
This data release is superseded by Thorson, J.M., Dunham, J.B., Heck, M.P., Hockman-Wert, D.P., and Mintz, J.M., 2022, Stream Temperature in the Northern Great Basin region of Southeastern Oregon, 2016-2021: U.S. Geological Survey data release, https://doi.org/10.5066/P9EDM6L6. Please contact fresc_outreach@usgs.gov for original data set. This dataset includes hourly stream and air temperature daGeomorphic and larval lamprey surveys in tributaries of the Umpqua River, Oregon
Interactions between geomorphic processes at multiple scales shape the distributions of habitats, species, and life stages that a river can support. Understanding these hierarchical processes may be helpful for proactive monitoring and restoration of native Western Brook Lamprey (Lampetra richardsoni) and Pacific Lamprey (Entosphenus tridentatus) in Pacific Northwest rivers. The processes creatingStream temperature and drying data from Willow/Whitehorse watersheds, southeast Oregon, 2014-16, and Willow/Rock/Frazer watersheds, northern Nevada, 2015-2016
These tabular, spatial, and code data sets were created in support of a stream temperature and drying study that took place in the Willow and Whitehorse watersheds of southeastern Oregon from 2014-2016 and the Willow, Rock, and Frazer watersheds of northern Nevada from 2015-2016. A prior data release of stream temperature data and associated spatial data from the Willow and Whitehorse watersheds oStream temperature data from Willow-Whitehorse and Little Blitzen watersheds, southeast Oregon, 2011-2015
This dataset includes stream temperatures from two data loggers installed at one site in the Little Blitzen River of SE Oregon as part of a redband trout (Oncorhynchus mykiss gairdnerii) study. The site was used as an undisturbed reference in comparison with similar temperature monitoring sites in the Willow-Whitehorse watershed that experienced a 2012 fire that burned nearly the entire watershed. - Multimedia
- Publications
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: 124Evolutionary and ecological connectivity in westslope cutthroat trout (Oncorhynchus clarkii lewisi) and mountain whitefish (Prosopium williamsoni) in relation to the potential influences of Boundary Dam, Washington, Idaho, and parts of British Columbia
In this report, we consider evolutionary and ecological connectivity for westslope cutthroat trout (Oncorhynchus clarkii lewisi) and mountain whitefish (Prosopium williamsoni) within the Pend Oreille River in northeastern Washington State, northern Idaho, and adjacent portions of southeastern British Columbia, Canada. Specifically, we focused on the rationale for active translocation of individualTough places and safe spaces: Can refuges save salmon from a warming climate?
The importance of thermal refuges in a rapidly warming world is particularly evident for migratory species, where individuals encounter a wide range of conditions throughout their lives. In this study, we used a spatially explicit, individual-based simulation model to evaluate the buffering potential of cold-water thermal refuges for anadromous salmon and trout (Oncorhynchus spp.) migrating upstrePassage of adult coho salmon (Oncorhynchus kisutch) over Lake Creek Falls, Oregon, 2019
Across the Pacific Northwest, there are many examples of artificial structures created to allow passage of upstream-migrating salmon over natural barriers. We studied upstream passage across three structures installed in 1989 to allow passage of salmon over Lake Creek Falls, a series of three natural waterfalls at the outlet of Triangle Lake on Lake Creek, in the central Oregon Coast Range (lat 12Influence of riparian thinning on trophic pathways supporting stream food webs in forested watersheds
Resource managers seek to thin second-growth riparian forests to address multiple stream and riparian management objectives, including enhancing aquatic productivity via light-mediated trophic pathways in watersheds of the Pacific Northwest (USA). However, such increases in aquatic productivity depend on complex food web dynamics that link riparian forests and streams. To evaluate how riparian forEngaging stakeholders to develop a decision support model of conservation risk and management capacity to prioritize investments in Bull Trout recovery
Rarely are sufficient resources available to support the full suite of management actions to promote recovery of a species across their entire distribution. Decision support models are a tool that can inform natural resource management decisions with consideration of the perspectives from a variety of stakeholders who work across large geographic and jurisdictional extents. We offer an example ofResist, 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 land-use chaDammed water quality — Longitudinal stream responses below beaver ponds in the Umpqua River Basin, Oregon
Beaver-related restoration (BRR) has gained popularity as a means of improving stream ecosystems, but the effects are not fully understood. Studies of dissolved oxygen (DO) and water temperature, key water quality metrics for salmonids, have demonstrated improved conditions in some cases, but warming and decreased DO have been more commonly reported in meta-analyses. These results point to the conStream size, temperature, and density explain body sizes of freshwater salmonids across a range of climate conditions
Climate change and anthropogenic activities are altering the body sizes of fishes, yet our understanding of factors influencing body size for many taxa remains incomplete. We evaluated the relationships between climate, environmental, and landscape attributes and the body size of different taxa of freshwater trout (Salmonidae) in the USA. Hierarchical spatial modeling across a gradient of habitatsControlling invasive fish in fluctuating environments: Model analysis of common carp (Cyprinus carpio) in a shallow lake
Climate change can act to facilitate or inhibit invasions of non-native species. Here, we address the influence of climate change on control of non-native common carp (hereafter, carp), a species recognized as one of the “world's worst” invaders across the globe. Control of this species is exceedingly difficult, as it exhibits rapid population growth and compensatory density dependence. In many loPathways 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 responses toA riverscape approach reveals downstream propagation of stream thermal responses to riparian thinning at multiple scales
Hydrological connectivity in river networks influences their response to environmental changes as local effects may extend downstream via flowing water. For example, localized changes in riparian forest conditions can affect stream temperatures, and these effects may propagate downstream. However, studies evaluating stream temperature responses to riparian forest management have not considered cumFish response to successive clearcuts in a second-growth forest from the central Coast range of Oregon
Research dating back to the 1950 s has documented negative effects from harvesting of primeval forests on stream ecosystems of the Pacific Northwest. By the early 1990 s, state and federal forest practice rules governing timber harvest were modified throughout North America to better protect aquatic habitats and biotic resources, principally salmonids. These rules inspired a generation of studiesNon-USGS Publications**
Rosenberger, A.E., Dunham, J.B., 2005, Validation of abundance estimates from mark-recapture and removal techniques for rainbow trout captured by electrofishing in small streams: North American Journal of Fisheries Management, v. 25, p. 1395-1410.Dunham, J.B., Pilliod, D.S., Young, M., 2004, Assessing the Consequences of Nonnative Trout in Headwater Ecosystems in Western North America: Fisheries, v. 29, no. 6, p. 18-26, https://doi.org/http://dx.doi.org/10.1577/1548-8446(2004)29[18:ATCONT]2.0.CO;2.Meeuwig, M.H., Dunham, J.B., Hayes, J.P., Vinyard, G.L., 2004, Effects of constant and cyclical thermal regimes on growth and feeding of juvenile cutthroat trout of variable sizes: Ecology of Freshwater Fish, v. 13, p. 208-216.Poole, G.C., Dunham, J.B., Keenan, D.M., Sauter, S.T., McCullough, D.A., Mebane, C., Lockwood, J.C., Essig, D.A., Hicks, M.P., Sturdevant, D.J., Materna, E.J., Spalding, M., Risley, J., Deppman, M., 2004, The case for regime-based water quality standards: BioScience, v. 54, no. 2, p. 155-161.Peterson, J., Dunham, J.B., 2003, Combining inferences from models of capture efficiency, detectability, and suitable habitat to classify landscapes for conservation of threatened bull trout: Conservation Biology, v. 17, no. 4, p. 1070-1077.Dunham, J.B., Schroeter, R., Rieman, B.E., 2003, Influence of maximum water temperature on occurence of Lahotan cutthroat trout within streams: North American Journal of Fisheries Management, v. 23, p. 1042-1049.Dunham, J.B., Rieman, B.E., Chandler, G.L., 2003, Influences of temperature and environmental variable on the distribution of bull trout within streams at the southern margin of its range: North American Journal of Fisheries Management, v. 23, p. 894-904, https://doi.org/http://dx.doi.org/10.1577/M02-028.Isaak, D.J., Thurow, R.F., Rieman, B.E., Dunham, J.B., 2003, Temporal variation in synchrony among Chinook salmon (Oncorhynchus tshawytscha) redd counts from a wilderness area in central Idaho: Canadian Journal of Fisheries and Aquatic Sciences, v. 60, p. 840-848.Dunham, J.B., Adams, S.B., Schroeter, R., Novinger, D.C., 2002, Alien invasions in aquatic ecosystems - Toward an understanding of brook trout invasions and potential impacts on inland cutthroat trout in western North America: Reviews in Fish Biology and Fisheries, v. 12, p. 373-391.Dunham, J.B., Cade, B.S., Terrell, J.W., 2002, Influences of spatial and temporal variation on fish-habitat relationships defined by regression quantiles: Transactions of the American Fisheries Society, v. 131, p. 86-98.Sauter, S.T., McMillan, J.R., Dunham, J.B., 2001, Salmonid behavior and water temperature: US Environmental Protection Agency, Region 10 EPA-910-D-01-001, p. 36.Dunham, J.B., Rieman, B.E., Davis, K., 2001, Sources and magnitude of sampling error in redd counts for bull trout: North American Journal of Fisheries Management, v. 21, p. 343-352.Dunham, J.B., 2000, Book Review - Metapopulations and Ecology by I. Hanksi. Oxford University Press, New York: Ecology, v. 81, no. 6, p. 1757-1758, https://doi.org/10.1890/0012-9658(2000)081[1757:MAE]2.0.CO;2.Dunham, J.B., Rahn, M.E., Schroeter, R., Breck, S.W., 2000, Diets of sympatric Lahontan cutthroat trout and nonnative brook trout- implications for species interactions: Western North American Naturalist, v. 60, no. 3, p. 304-310.Dunham, J.B., Dickerson, B.G., Beever, E.A., Duncan, R.D., Vinyard, G.L., 2000, Effects of food limitation and emigration on self-thinning in experimental minnow cohorts: Journal of Animal Ecology, v. 69, p. 927-934.Rieman, B.E., Dunham, J.B., 2000, Metapopulations and salmonids - A synthesis of life history patterns and empirical observations: Ecology of Freshwater Fish, v. 9, p. 51-64.Dunham, J.B., Peacock, M., Rieman, B.E., Schroeter, R., Vinyard, G.L., 1999, Local and geographic variability in the distribution of stream-living Lahontan cutthroat trout: Transactions of the American Fisheries Society, v. 128, p. 875-889.Dunham, J.B., Rieman, B.E., 1999, Metapopulation structure of bull trout - Influences of physical, biotic, and geometrical landscape characteristics: Ecological Applications, v. 9, no. 2, p. 642-655, https://doi.org/10.1890/1051-0761(1999)009[0642:MSOBTI]2.0.CO;2.Dunham, J.B., Minckley, W.L., 1998, Allozymic variation in desert pupfish from natural and artificial habitats- Genetic conservation in fluctuating populations: Biological Conservation, v. 84, p. 7-15.Dunham, J.B., Vinyard, G.L., Rieman, B.E., 1997, Habitat fragmentation and extinction risk of Lahontan cutthroat trout: North American Journal of Fisheries Management, v. 17, p. 1126-1133.Dunham, J.B., Vinyard, G.L., 1997, Incorporating stream level variability into analysis of site level fish habitat relationships- some cautionary examples: Transactions of the American Fisheries Society, v. 126, p. 323-329.Dunham, J.B., Vinyard, G.L., 1997, Relationships between body mass, population density, and the self thinning rule in stream-living salmonids: Canadian Journal of Fisheries and Aquatic Sciences, v. 54, no. 5, p. 1025-1030, https://doi.org/10.1139/f97-012.Luce, C.H., Rieman, B.E., Dunham, J.B., Clayton, J., King, J.G., and Black, T.A., 2001, Incorporating aquatic ecology into decisions on prioritization of road decommissioning: Water Resources Impact, v. 3, no. 3, p. 8-14.**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.
- News
To request an interview, contact fresc_outreach@usgs.gov or call (541) 750-1030.
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