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Daniel J. Isaak

Dan Isaak - Research Fish Biologist

Research Fish Biologist

322 East Front Street, Suite 401
Boise, ID 83702
Contact Daniel J. Isaak

Current Research

Understanding effects of climate change on stream habitats and fish communities, Development and implementation of basinscale and regional monitoring programs for bull trout and other aquatic organisms. Development and implementation of basinscale and regional stream temperature models and monitoring protocols . Effects of fire and disturbance on streams. Development of bioclimatic models to predict distributions of trout species to climate scenarios at regional and basinscales.

For more information, please see:

The Rangewide Bull Trout eDNA Project

The National Stream Internet

Climate Shield Cold-Water Refuge Streams for Native Trout

Climate Change, Crowd-Sourcing, and Conserving Aquatic Biotas in the Rocky Mountains This Century

Adaptation for Wildland Aquatic Resources - Science Briefing

Bull Trout and Climate Change - Science Briefing

Bull Trout Monitoring - Science Briefing

Application of a Spatially Explicit Decision Framework for Fish Conservation - Science Briefing

Climate Change and Rocky Mountain Native Trout - Science Briefing

Climate Change and Wildfires: Effects on Stream Temperatures and Thermal Habitat - Science Briefing

A National Stream Internet - Science Briefing

NorWeST: A Regional Stream Temperature Database and Modeled Climate Scenarios – Science Briefing

Pilot Watershed Vulnerability Assessment Project - Science Briefing

Spatial Statistical Modeling Tools for Stream Networks - Science Briefing

Species Distribution Uncertainty - Science Briefing

Stream Isotherm Shifts From Climate Change - Briefing Paper

Stream Temperature Modeling and Monitoring - Science Briefing

Using Underwater Epoxy To Install Temperature Sensors - Science Briefing

Research Interests

My primary research interest is in understanding how climate change, disturbance, and biophysical interactions across spatial and temporal scales affect population dynamics of aquatic organisms and their habitats in mountain streams.

The National Stream Internet - The NSI is a network of people, data, and analytical techniques that interact synergistically to create information about streams. This website is a hub designed to connect users with software, data, and tools for creating that information. As better information is developed, it should enable stronger science, management, and conservation as pertains to stream ecosystems.

Cold Water Climate Shield - The Climate Shield website hosts geospatial data and related information that describes specific locations of cold-water refuge streams for native Cutthroat Trout and Bull Trout across the northwestern U.S. Forecasts about the locations of refugia could enable the protection of key watersheds, be used to rally support among multiple stakeholders, and provide a foundation for planning climate-smart conservation networks that improve the odds of preserving native trout populations through the 21st century.

Climate- Aquatics Blog: This website archives blogs periodically written by the scientist that describe research pertaining to climate change effects on aquatic resources.

Stream Temperature Modeling and Monitoring Website: This website acts as central repository for information pertaining to monitoring and modeling of stream temperatures that the scientist and his collaborators develop.

SSN & STARS: Tools for Spatial Statistical Modeling on Stream Networks: This website hosts freeware statistical software and GIS tools for implementing a new class of spatial statistical models applicable to data measured on stream networks.

NorWest Stream Temperature- Regional Database and Model: This website hosts a comprehensive interagency stream temperature database and high resolution climate scenarios for the Northwest U.S.

Please click here if interested in following on Twitter.

RMRS Scientist Profile Video (YouTube) - Dr. Dan Isaak talks about building the publically-accessible NorWeST stream temperature database and Its applications for identifying climate refugia for cold-water fish.

Past Research

Assessing spatial and temporal variation in demographic and genetic characteristics of Chinook salmon populations in central Idaho. Landscape ecology and relationships between trout abundance and distributions relative to landscape characteristics. Radio telemetry and distributional assessments of northern pikeminnow in the Lower Snake River.

Please see also:

2011 Climate- Aquatics Workshop

2009 Western Watersheds and Climate Change Workshop

2008 Bull Trout and Climate Change Symposium

Why This Research is Important

Many natural resources are at risk from human development of natural landscapes and the effects of climate change. My research attempts to provide better understanding and predictive models of stream ecosystems so that managers can respond proactively and more effectively to these threats.


  • South Dakota State University, B.S., Wildlife and Fisheries Sciences, 1991
  • University of Idaho, M.S., Fisheries Resources, 1994
  • University of Wyoming, Ph.D., Zoology and Physiology, 2001
  • Featured Publications


    Young, Michael K.; Isaak, Daniel J.; Spaulding, Scott; Thomas, Cameron A.; Barndt, Scott A.; Groce, Matthew C.; Horan, Dona; Nagel, David E., 2018. Climate vulnerability of native cold-water salmonids in the Northern Rockies Region [Chapter 5]
    Isaak, Daniel J.; Young, Michael K.; McConnell, Callie; Roper, Brett B.; Archer, Eric K.; Staab, Brian; Hirsch, Christine; Nagel, David E.; Schwartz, Michael K.; Chandler, Gwynne L., 2018. Crowd-sourced databases as essential elements for Forest Service partnerships and aquatic resource conservation
    Isaak, Daniel J.; Young, Michael K.; Tait, Cynthia; Duffield, Daniel; Horan, Dona; Nagel, David E.; Groce, Matthew C., 2018. Effects of climate change on native fish and other aquatic species [Chapter 5]
    Wilcox, Taylor M.; Young, Michael K.; McKelvey, Kevin S.; Isaak, Daniel J.; Horan, Dona; Schwartz, Michael K., 2018. Fine-scale environmental DNA sampling reveals climate-mediated interactions between native and invasive trout species
    Isaak, Daniel J.; Luce, Charles H.; Horan, Dona; Chandler, Gwynne L.; Wollrab, Sherry P.; Nagel, David E., 2018. Global warming of salmon and trout rivers in the northwestern U.S.: Road to ruin or path through purgatory?
    Leasure, Douglas R.; Wenger, Seth J.; Chelgren, Nathan D.; Neville, Helen M.; Dauwalter, Daniel C.; Bjork, Robin; Fesenmyer, Kurt A.; Dunham, Jason B.; Peacock, Mary M.; Luce, Charles H.; Lute, Abby C.; Isaak, Daniel J., 2018. Hierarchical multi-population viability analysis
    Isaak, Daniel J.; Luce, Charles H.; Chandler, Gwynne L.; Horan, Dona; Wollrab, Sherry P., 2018. Principal components of thermal regimes in mountain river networks
    Cooke, Brian; Battaglia, Mike; Dwire, Kathleen A.; Isaak, Daniel J.; Joyce, Linda A.; Merritt, David; Oropeza, Jill; Regan, Claudia; Reynolds, Lindsay; Rice, Janine; Schillie, Trey, 2018. Warming and warnings: Assessing climate change vulnerability in the Rocky Mountain Region
    Clifton, Caty F.; Day, Kate T.; Dello, Kathie; Grant, Gordon E.; Halofsky, Jessica E.; Isaak, Daniel J.; Luce, Charles H.; Safeeq, Mohammad; Staab, Brian P.; Stevenson, John, 2017. Climate change and hydrology in the Blue Mountains [Chapter 3]
    Isaak, Daniel J.; Ramsey, Katherine; Chatel, John C.; Konnoff, Deborah L.; Gecy, Robert A.; Horan, Dona, 2017. Climate change, fish, and aquatic habitat in the Blue Mountains [Chapter 5]
    Young, Michael K.; Isaak, Daniel J.; McKelvey, Kevin S.; Wilcox, Taylor M.; Campbell, Matthew R.; Corsi, Matthew P.; Horan, Dona; Schwartz, Michael K., 2017. Ecological segregation moderates a climactic conclusion to trout hybridization
    Isaak, Daniel J.; Wenger, Seth J.; Peterson, Erin E.; Ver Hoef, Jay M.; Nagel, David E.; Luce, Charles H.; Hostetler, Steven W.; Dunham, Jason B.; Roper, Brett B.; Wollrab, Sherry P.; Chandler, Gwynne L.; Horan, Dona; Payne (Parkes) , Sharon L., 2017. The NorWeST summer stream temperature model and scenarios for the western U.S.: A crowd-sourced database and new geospatial tools foster a user community and predict broad climate warming of rivers and streams
    Vose, James M.; Miniat, Chelcy Ford; Luce, Charles H.; Asbjornsen, Heidi; Caldwell, Peter V.; Campbell, John L.; Grant, Gordon E.; Isaak, Daniel J.; Loheide, Steven P. II; Sun, Ge, 2016. Echohydrological implications of drought for forests in the United States
    Benjankar, Rohan; Tonina, Daniele; Marzadri, Alessandra; McKean, James (Jim) A.; Isaak, Daniel J., 2016. Effects of habitat quality and ambient hyporheic flows on salmon spawning site selection
    Carnie, Ryan; Tonina, Daniele; McKean, James (Jim) A.; Isaak, Daniel J., 2016. Habitat connectivity as a metric for aquatic microhabitat quality: Application to Chinook salmon spawning habitat
    Isaak, Daniel J.; Young, Michael K.; Luce, Charles H.; Hostetler, Steven W.; Wenger, Seth J.; Peterson, Erin E.; Ver Hoef, Jay M.; Groce, Matthew C.; Horan, Dona; Nagel, David E., 2016. Slow climate velocities of mountain streams portend their role as refugia for cold-water biodiversity
    Williams, J. E.; Isaak, Daniel J.; Imhof, J.; Hendrickson, D. A.; McMillan, J. R., 2015. Cold-water fishes and climate change in North America
    Isaak, Daniel J.; Peterson, Erin E.; Ver Hoef, Jay M.; Wenger, Seth J.; Falke, Jeffrey A.; Torgersen, Christian E.; Sowder, Colin; Steel, E. Ashley; Fortin, Marie-Josee; Jordan, Chris E.; Ruesch, Aaron S.; Som, Nicholas; Monestiez, Pascal., 2014. Applications of spatial statistical network models to stream data
    Stamp, Jen; Hamilton, Anna; Craddock, Michelle; Parker, Laila; Roy, Allison H.; Isaak, Daniel J.; Holden, Zach; Passmore, Margaret; Bierwagen, Britta G., 2014. Best practices for continuous monitoring of temperature and flow in wadeable streams
    Isaak, Daniel J., 2014. Blogging fish science
    Isaak, Daniel J.; Young, Michael K.; Nagel, David E.; Horan, Dona, 2014. Cold water as a climate shield to preserve native trout through the 21st Century
    Holsinger, Lisa M.; Keane II, Robert E.; Isaak, Daniel J.; Eby, Lisa; Young, Michael K., 2014. Relative effects of climate change and wildfires on stream temperatures: A simulation modeling approach in a Rocky Mountain watershed
    Luce, Charles H.; Staab, Brian; Kramer, Marc; Wenger, Seth; Isaak, Daniel J.; McConnell, Callie, 2014. Sensitivity of summer stream temperatures to climate variability in the Pacific Northwest
    Al-Chokhachy, Robert; Wenger, Seth J.; Isaak, Daniel J.; Kershner, Jeffrey L., 2013. Characterizing the thermal suitability of instream habitat for salmonids: A cautionary example from the Rocky Mountains
    Peterson, Douglas P.; Wenger, Seth J.; Rieman, Bruce E.; Isaak, Daniel J., 2013. Linking climate change and fish conservation efforts using spatially explicit decision support tools
    Peterson, Erin E.; Ver Hoef, Jay M.; Isaak, Daniel J.; Falke, Jeffrey A.; Fortin, Marie-Josee; Jordan, Chris E.; McNyset, Kristina; Monestiez, Pascal; Ruesch, Aaron S.; Sengupta, Aritra; Som, Nicholas; Steel, E. Ashley; Theobald, David M.; Torgersen, Christian E.; Wenger, Seth J., 2013. Modelling dendritic ecological networks in space: An integrated network perspective
    Goode, Jaime R.; Buffington, John M.; Tonina, Daniele; Isaak, Daniel J.; Thurow, Russ F.; Wenger, Seth; Nagel, David E.; Luce, Charles H.; Tetzlaff, Doerthe; Soulsby, Chris, 2013. Potential effects of climate change on streambed scour and risks to salmonid survival in snow-dominated mountain basins
    Wenger, Seth J.; Som, Nicholas A.; Dauwalter, Daniel C.; Isaak, Daniel J.; Neville, Helen M.; Luce, Charles H.; Dunham, Jason B.; Young, Michael K.; Fausch, Kurt D.; Rieman, Bruce E., 2013. Probabilistic accounting of uncertainty in forecasts of species distributions under climate change
    Luce, Charles H.; Morgan, Penny; Dwire, Kathleen A.; Isaak, Daniel J.; Holden, Zachary; Rieman, Bruce, 2012. Climate change, forests, fire, water, and fish: Building resilient landscapes, streams, and managers
    Isaak, Daniel J.; Muhlfeld, Clint C.; Todd, Andrew S.; Al-Chokhachy, Robert; Roberts, James; Kershner, Jeffrey L.; Fausch, Kurt D.; Hostetler, Steven W., 2012. The past as prelude to the future for understanding 21st-Century climate effects on Rocky Mountain trout
    Wenger, Seth J.; Isaak, Daniel J.; Luce, Charles H.; Neville, Helen M.; Fausch, Kurt D.; Dunham, Jason B.; Dauwalter, Daniel C.; Young, Michael K.; Elsner, Marketa M.; Rieman, Bruce E.; Hamlet, Alan F.; Williams, Jack E., 2011. Flow regime, temperature, and biotic interactions drive differential declines of trout species under climate change [includes Supporting Information]
    Wenger, Seth J.; Isaak, Daniel J.; Dunham, Jason B.; Fausch, Kurt D.; Luce, Charles H.; Neville, Helen M.; Rieman, Bruce E.; Young, Michael K.; Nagel, David E.; Horan, Dona; Chandler, Gwynne L., 2011. Role of climate and invasive species in structuring trout distributions in the interior Columbia River Basin, USA
    Isaak, Daniel J.; Rieman, Bruce; Horan, Dona, 2009. A watershed-scale monitoring protocol for bull trout
    Courbois, Jean-Yves; Katz, Stephen L.; Isaak, Daniel J.; Steel, E. Ashley; Thurow, Russ F.; Rub, A. Michelle Wargo; Olsen, Tony; Jordan, Chris E., 2008. Evaluating probability sampling strategies for estimating redd counts: an example with Chinook salmon (Oncorhynchus tshawytscha)
    Rieman, Bruce E.; Isaak, Daniel J.; Adams, Susan; Horan, Dona; Nagel, David E.; Luce, Charles H.; Myers, Deborah, 2007. Anticipated climate warming effects on bull trout habitats and populations across the interior Columbia River basin
    Isaak, Daniel J.; Thurow, Russ F.; Rieman, Bruce E.; Dunham, Jason B., 2007. Chinook salmon use of spawning patches: Relative roles of habitat quality, size, and connectivity
    fishing on snake river
    Anyone familiar with the Columbia River’s massive salmon die-off a few summers ago might also be concerned about how climate change will affect fish habitats. The 2015 die-off killed more than 250,000 fish and was blamed on record low streamflows and high water temperatures. While coldwater fish such as salmon and trout can adjust to slightly warmer-than-normal temperatures for short periods, abnormally high temperatures for prolonged periods lower oxygen levels, increase the likelihood of deadly diseases, and cause life-threatening physiological stress.
    National Genomics Center stream water filter setup for eDNA sample collection
    The National Genomics Center for Wildlife and Fish Conservation pioneered development of eDNA sampling of aquatic environments at their laboratory in Missoula, MT. The Center has partnered with dozens of National Forests, as well as other state, federal, tribal, and private natural resource organizations to assist in the collection and processing of eDNA samples. Thousands of eDNA samples are collected annually and constitute a rapidly growing biodiversity archive that provides precise information about native and non-native species distributions, temporal trends in those distributions, and the efficacy of species and habitat restoration and conservation efforts. eDNA sampling provides a low-cost & sensitive method for determining which species occur in water bodies. Rapid adoption of eDNA sampling by many natural resource agencies led to an exponential increase in data and the need for an open-access database. The website and open-access database were launched in June 2018 with approximately 6,000 samples and is updated semi-annually with newly processed samples.
    Concerns about climate change effects on cold-water biodiversity sparked broad multi-agency collaborative efforts throughout the American West. U.S. Forest Service research teams led development of massive interagency databases that now enable precise mapping of critical habitats and species distributions in streams flowing through 101 National Forests.
    Westslope cutthroat trout, native to the Columbia River and upper Missouri River hybridize with introduced rainbow trout and have been extirpated from large portions of their historical range.
    Hybridization between westslope cutthroat trout and both rainbow trout and Yellowstone cutthroat trout is a major conservation concern for the species.  A new broad-scale analysis of hybridization patterns found many pure populations of westslope cutthroat trout in headwaters streams.
    Native trout are culturally and ecologically important, but climate change is likely to shrink the cold-water environments they require. Much can be done to preserve these fish but efficient planning and targeting of conservation resources has been hindered by a lack of broad-scale datasets and precise information about which streams are most likely to support native trout populations later this century. The Climate Shield is a useful took for aquatic fisheries conservation planning.
    The bull trout is an ESA-listed species that relies on cold stream environments across the Northwest and is expected to decline with climate change. Resource managers from dozens of agencies are charged with maintaining bull trout in thousands of streams, but monitoring this species is difficult. Environmental DNA (eDNA) is much faster, easier, and more sensitive than traditional fish sampling methods and provides an opportunity to better delineate populations of federally threatened species like bull trout.
    The website provides: 1) A large list of supporting science behind eDNA sampling. 2) The recommended field protocol for eDNA sampling and the equipment loan program administered by the NGC. 3) A systematically-spaced sampling grid for all flowing waters of the U.S. in a downloadable format that includes unique database identifiers and geographic coordinates for all sampling sites. Available for download in an Geodatabase or available by ArcGIS Online map. This sampling grid can be used to determine your field collection sites to contribute. 4) The lab results of eDNA sampling at those sites where project partners have agreed to share data.
    Flow gages* record discharge in streams and rivers across the U.S. but the extent and adequacy of this monitoring network relative to USFS lands has not been documented. To address that deficiency, the medium resolution National Hydrography Layer was used with gage location information from the National Water Information System to describe the monitoring network and how it has changed through time. Summaries were made for eight USFS regions that describe the number and locations of gages relative to USFS lands and network characteristics such as elevation and watershed area.
    Knowing how environments might influence the degree and location of hybridization between these species represents a potentially powerful tool for managers. To address that need, we modeled how hybridization between westslope cutthroat trout and rainbow trout is influenced by stream characteristics that favor each species. On the Cutthroat trout-rainbow trout hybridization website, we describe that model, and provide high-resolution digital maps in user-friendly formats of the predictions of different levels of hybridization across the native range of westslope cutthroat trout in the Northern Rocky Mountains, representing both current conditions and those associated with warmer stream temperatures. Our goal is to help decision-makers gauge the potential for hybridization between cutthroat trout and rainbow trout when considering management strategies for conserving cutthroat trout.
    The bull trout has a historical range that encompasses many waters across the Northwest. Though once abundant, bull trout have declined in many locations and is now federally listed and protected under the Endangered Species Act. Rocky Mountain Research Station scientists initiated the range-wide bull trout eDNA project in partnership with biologists from more than 20 organizations to create sound and precise information about the distribution of bull trout in thousands of streams across their range.
    External DNA released by animals in aquatic environments, called environmental DNA (eDNA), can be used to determine whether a species is present without actually capturing or seeing an individual. Because of its greater efficiency and reduced cost, eDNA sampling may revolutionize the monitoring and assessment of freshwater species.
    Fishes of the genus Cottus –the sculpins- have long been a challenge for fish managers and ichthyologists in the West. They share streams, rivers, and lakes with trout and salmon, and depend on the same kinds of habitats with relatively cold, clean water. Yet we don’t know how many kinds of sculpins there are.