Daniel J. Isaak, PhD
Treesearch Publications
- Michael Dumelle, Erin E. Peterson, Jay M. Ver Hoef, Alan Pearse, Daniel J. Isaak. 2025. SSN2: The next generation of spatial stream network modeling in R
- Daniel J. Isaak, Michael Dumelle, Dona Horan, Daniel Mason, Thomas W. Franklin, David E. Nagel, Jay M. Ver Hoef, Michael K. Young. 2025. Improving species distribution models for stream networks by incorporating spatial autocorrelation in multi-sourced datasets: A range-wide assessment of Idaho giant salamander status and future risk
- Daniel J. Isaak, Dona Horan, David E. Nagel. 2025. The importance of trimming National Hydrography Dataset streamline networks when delineating potential habitats and species distributions for fish and amphibians in broad geographical applications
- David E. Nagel, Erin Peterson, Daniel J. Isaak, Michael Dumelle, Jay Ver Hoef, Dona Horan. 2024. National Stream Internet Protocol and User Guide
- M. R. Fuller, N. E. Detenbeck, P. Leinenbach, R. Labiosa, Daniel J. Isaak. 2024. Scenario planning management actions to restore cold water stream habitat: Comparing mechanistic and statistical modeling approaches
- Daniel J. Isaak, Dona Horan, Sherry P. Wollrab. 2024. Air temperature data source affects inference from statistical stream temperature models in mountainous terrain
- Joy Drohan, Daniel J. Isaak, Charlie H. Luce, Michael K. Young, Dona Horan, David E. Nagel, Sherry P. Wollrab, Gwynne L. Chandler, Scott Barndt, Yvette Converse, Sean Finn, Scott Spaulding, Brian Staab. 2024. Some good news on climate change: High mountain streams act as strongholds for cold-water species
- Edgar Santos-Fernandez, Jay M. Ver Hoef, James McGree, Daniel J. Isaak, Kerrie Mengersen, Erin E. Peterson. 2023. SSNbayes: An R Package for Bayesian spatio-temporal modelling on stream networks
- Jay M. Ver Hoef, Michael DumelleI, Matt Higham, Erin E. Peterson, Daniel J. Isaak. 2023. Indexing and partitioning the spatial linear model for large data sets
- Matthew R. Fuller, Naomi E. Detenbeck, Peter Leinenbach, Rochelle Labiosa, Daniel J. Isaak. 2023. Spatial and temporal variability in stream thermal regime drivers for three river networks during the summer growing season
- Daniel J. Isaak, Michael K. Young. 2023. Cold-water habitats, climate refugia, and their utility for conserving salmonid fishes
- Neil J. Mochnacz, Mark K. Taylor, Margaret F. Docker, Daniel J. Isaak. 2023. An ecothermal paradox: Bull trout populations diverge in response to thermal landscapes across a broad latitudinal gradient
- Daniel J. Isaak, Charlie H. Luce. 2023. Elevation-dependent warming of streams in mountainous regions: implications for temperature modeling and headwater climate refugia
- Michael K. Young, Rebecca Smith, Kristine L. Pilgrim, Daniel J. Isaak, Kevin S. McKelvey, Sharon L. Payne, Jacob Egge, Michael K. Schwartz. 2022. A molecular taxonomy of Cottus in western North America
- Michael K. Young, Daniel J. Isaak, David E. Nagel, Dona Horan, Kellie Carim, Thomas W. Franklin, Victoria Zeller, Brett Roper, Michael K. Schwartz. 2022. Broad-scale eDNA sampling for describing aquatic species distributions in running waters: Pacific lamprey Entosphenus tridentatus in the upper Snake River, USA
- Gregory R. Jacobs, Russ F. Thurow, John M. Buffington, Daniel J. Isaak, Seth J. Wenger. 2022. Erratum: Climate, fire regime, geomorphology, and conspecifics influence the spatial distribution of Chinook salmon redds
- Daniele Tonina, James A. McKean, Daniel J. Isaak, Rohan M. Benjankar, Chunling Tang, Qiuwen Chen. 2022. Climate change shrinks and fragments salmon habitats in a snow-dependent region
- Daniel J. Isaak, Michael K. Young, Dona Horan, David E. Nagel, Michael K. Schwartz, Kevin S. McKelvey. 2022. Do metapopulations and management matter for relict headwater bull trout populations in a warming climate?
- Matthew R. Fuller, Peter Leinenbach, Naomi E. Detenbeck, Rochelle Labiosa, Daniel J. Isaak. 2022. Riparian vegetation shade restoration and loss effects on recent and future stream temperatures
- Edgar Santos-Fernandez, Jay M. Ver Hoef, Erin E. Peterson, James McGree, Daniel J. Isaak, Kerrie Mengersen. 2022. Bayesian spatio-temporal models for stream networks
- William L. Gaines, Paul F. Hessburg, Gregory H. Aplet, Paul Henson, Susan J. Prichard, Derek J. Churchill, Gavin M. Jones, Daniel J. Isaak, Carly Vynne. 2022. Climate change and forest management on federal lands in the Pacific Northwest, USA: Managing for dynamic landscapes
- David S. Pilliod, Robert S. Arkle, Russ F. Thurow, Daniel J. Isaak. 2022. Hydroclimatic conditions, wildfire, and species assemblages influence co‐occurrence of bull trout and tailed frogs in northern Rocky Mountain streams
- Craig Paukert, Julian D. Olden, Abigail J. Lynch, David D. Breshears, R. Christopher Chambers, Cindy Chu, Margaret Daly, Kimberly L. Dibble, Jeff Falke, Daniel J. Isaak, Peter Jacobson, Olaf P. Jensen, Daphne Munroe. 2021. Climate change effects on North American fish and fisheries to inform adaptation strategies
- William Jeff Reeder, Frank Gariglio, Ryan Carnie, Chunling Tang, Daniel J. Isaak, Qiuwen Chen, Zhongbo Yu, James A. McKean, Daniele Tonina. 2021. Some (fish might) like it hot: Habitat quality and fish growth from past to future climates
- Helen M. Neville, Douglas R. Leasure, Daniel C. Dauwalter, Jason B. Dunham, Robin Bjork, Kurt A. Fesenmyer, Nathan D. Chelgren, Mary M. Peacock, Charlie H. Luce, Daniel J. Isaak, Lee Ann Carranza, Jon Sjoberg, Seth J. Wenger. 2020. Application of multiple-population viability analysis to evaluate species recovery alternatives
- Daniel J. Isaak, Michael K. Young. 2020. One year after launch, eDNAtlas proves its worth
- Michael T. LeMoine, Lisa A. Eby, Chris G. Clancy, Leslie G. Nyce, Michael J. Jakober, Daniel J. Isaak. 2020. Landscape resistance mediates native fish species distribution shifts and vulnerability to climate change in riverscapes
- Gregory R. Jacobs, Russ F. Thurow, John M. Buffington, Daniel J. Isaak, Seth J. Wenger. 2020. Climate, fire regime, geomorphology, and conspecifics influence the spatial distribution of Chinook Salmon redds
- Daniel J. Isaak, Charlie H. Luce, Dona Horan, Gwynne L. Chandler, Sherry P. Wollrab, William B. Dubois, David E. Nagel. 2020. Thermal regimes of perennial rivers and streams in the western United States
- Charlie H. Luce, Daniel J. Isaak. 2018. Fishing for climate data: How recent research is helping to forecast changes in salmon and trout habitat
- Daniel J. Isaak, Charlie H. Luce, Gwynne L. Chandler, Dona Horan, Sherry P. Wollrab. 2018. Principal components of thermal regimes in mountain river networks
- Douglas R. Leasure, Seth J. Wenger, Nathan D. Chelgren, Helen M. Neville, Daniel C. Dauwalter, Robin Bjork, Kurt A. Fesenmyer, Jason B. Dunham, Mary M. Peacock, Charlie H. Luce, Abby C. Lute, Daniel J. Isaak. 2018. Hierarchical multi-population viability analysis
- Taylor M. Wilcox, Michael K. Young, Kevin S. McKelvey, Daniel J. Isaak, Dona Horan, Michael K. Schwartz. 2018. Fine-scale environmental DNA sampling reveals climate-mediated interactions between native and invasive trout species
- Daniel J. Isaak, Michael K. Schwartz. 2018. From expensive to efficient: New eDNAtlas shares nationwide aquatic species information
- Daniel J. Isaak, Michael K. Young, Callie McConnell, Brett B. Roper, Eric K. Archer, Brian Staab, Christine Hirsch, David E. Nagel, Michael K. Schwartz, Gwynne L. Chandler. 2018. Crowd-sourced databases as essential elements for Forest Service partnerships and aquatic resource conservation
- Brian Cooke, Michael A. Battaglia, Kathleen A. Dwire, Daniel J. Isaak, Linda A. Joyce, David Merritt, Jill Oropeza, Claudia Regan, Lindsay Reynolds, Janine Rice, Trey Schillie. 2018. Warming and warnings: Assessing climate change vulnerability in the Rocky Mountain Region
- Daniel J. Isaak, Michael K. Young, Cynthia Tait, Daniel Duffield, Dona Horan, David E. Nagel, Matthew C. Groce. 2018. Effects of climate change on native fish and other aquatic species [Chapter 5]
- Daniel J. Isaak, Charlie H. Luce, Dona Horan, Gwynne L. Chandler, Sherry P. Wollrab, David E. Nagel. 2018. Global warming of salmon and trout rivers in the northwestern U.S.: Road to ruin or path through purgatory?
- Michael K. Young, Daniel J. Isaak, Scott Spaulding, Cameron A. Thomas, Scott A. Barndt, Matthew C. Groce, Dona Horan, David E. Nagel. 2018. Climate vulnerability of native cold-water salmonids in the Northern Rockies Region [Chapter 5]
- Daniel J. Isaak, Michael K. Young. 2017. Delineating climate refugia for native aquatic species with big crowd-sourced databases
- Daniel J. Isaak, Seth J. Wenger, Erin E. Peterson, Jay M. Ver Hoef, David E. Nagel, Charlie H. Luce, Steven W. Hostetler, Jason B. Dunham, Brett B. Roper, Sherry P. Wollrab, Gwynne L. Chandler, Dona Horan, Sharon L. Payne. 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
- Michael K. Young, Daniel J. Isaak, Kevin S. McKelvey, Taylor M. Wilcox, Matthew R. Campbell, Matthew P. Corsi, Dona Horan, Michael K. Schwartz. 2017. Ecological segregation moderates a climactic conclusion to trout hybridization
- Daniel J. Isaak, Katherine Ramsey, John C. Chatel, Deborah L. Konnoff, Robert A. Gecy, Dona Horan. 2017. Climate change, fish, and aquatic habitat in the Blue Mountains [Chapter 5]
- Caty F. Clifton, Kate T. Day, Kathie Dello, Gordon Grant, Jessica E. Halofsky, Daniel J. Isaak, Charlie H. Luce, Mohammad Safeeq, Brian P. Staab, John Stevenson. 2017. Climate change and hydrology in the Blue Mountains [Chapter 3]
- Daniel J. Isaak, Seth J. Wenger, Michael K. Young. 2017. Big biology meets microclimatology: Defining thermal niches of ectotherms at landscape scales for conservation planning
- Daniel J. Isaak, Jay M. Ver Hoef, Erin E. Peterson, Dona Horan, David E. Nagel. 2017. Scalable population estimates using spatial-stream-network (SSN) models, fish density surveys, and national geospatial database frameworks for streams
- Michael K. Young, Daniel J. Isaak, Kevin S. McKelvey, Taylor M. Wilcox, Daniel M. Bingham, Kristine L. Pilgrim, Kellie Carim, Matthew R. Campbell, Matthew P. Corsi, Dona Horan, David E. Nagel, Michael K. Schwartz. 2016. Climate, demography, and zoogeography predict introgression thresholds in salmonid hybrid zones in Rocky Mountain streams
- Rohan Benjankar, Daniele Tonina, Alessandra Marzadri, Jim A. McKean, Daniel J. Isaak. 2016. Effects of habitat quality and ambient hyporheic flows on salmon spawning site selection
- Daniel J. Isaak, Michael K. Young, Charlie H. Luce, Steven W. Hostetler, Seth J. Wenger, Erin E. Peterson, Jay M. Ver Hoef, Matthew C. Groce, Dona Horan, David E. Nagel. 2016. Slow climate velocities of mountain streams portend their role as refugia for cold-water biodiversity
- James Vose, Chelcy F. Miniat, Charles H. Luce, Heidi Asbjornsen, Peter V. Caldwell, John Campbell, Gordon Grant, Daniel J. Isaak, Steven P. Loheide, Ge Sun. 2016. Echohydrological implications of drought for forests in the United States
- Ryan Carnie, Daniele Tonina, Jim A. McKean, Daniel J. Isaak. 2016. Habitat connectivity as a metric for aquatic microhabitat quality: Application to Chinook salmon spawning habitat
- J. E. Williams, Daniel J. Isaak, J. Imhof, D. A. Hendrickson, J. R. McMillan. 2015. Cold-water fishes and climate change in North America
- Daniel J. Isaak, Michael K. Young, David E. Nagel, Dona Horan, Matthew C. Groce. 2015. The cold-water climate shield: Delineating refugia for preserving salmonid fishes through the 21st century
- Daniel J. Isaak, Michael K. Young, David E. Nagel, Dona Horan. 2014. Cold water as a climate shield to preserve native trout through the 21st Century
- Sarah J. Hines, Daniel J. Isaak, Charlie H. Luce, Michael K. Young. 2014. Climate change, crowd-sourcing, and conserving aquatic biotas in the Rocky Mountains this century
- Daniel J. Isaak. 2014. Blogging fish science
- Jen Stamp, Anna Hamilton, Michelle Craddock, Laila Parker, Allison H. Roy, Daniel J. Isaak, Zach Holden, Margaret Passmore, Britta G. Bierwagen. 2014. Best practices for continuous monitoring of temperature and flow in wadeable streams
- Daniel J. Isaak. 2014. Climate change and the future of freshwater fisheries
- Lisa M. Holsinger, Robert E. Keane, Daniel J. Isaak, Lisa Eby, Michael K. Young. 2014. Relative effects of climate change and wildfires on stream temperatures: A simulation modeling approach in a Rocky Mountain watershed
- Charlie H. Luce, Brian Staab, Marc Kramer, Seth Wenger, Daniel J. Isaak, Callie McConnell. 2014. Sensitivity of summer stream temperatures to climate variability in the Pacific Northwest
- Daniel J. Isaak, Erin E. Peterson, Jay M. Ver Hoef, Seth J. Wenger, Jeffrey A. Falke, Christian E. Torgersen, Colin Sowder, E. Ashley Steel, Marie-Josee Fortin, Chris E. Jordan, Aaron S. Ruesch, Nicholas Som, Pascal Monestiez. 2014. Applications of spatial statistical network models to stream data
- Robert Al-Chokhachy, Seth J. Wenger, Daniel J. Isaak, Jeffrey L. Kershner. 2013. Characterizing the thermal suitability of instream habitat for salmonids: A cautionary example from the Rocky Mountains
- Daniel J. Isaak, Dona Horan, Sherry P. Wollrab. 2013. A simple protocol using underwater epoxy to install annual temperature monitoring sites in rivers and streams
- Seth J. Wenger, Nicholas A. Som, Daniel C. Dauwalter, Daniel J. Isaak, Helen M. Neville, Charlie H. Luce, Jason B. Dunham, Michael K. Young, Kurt D. Fausch, Bruce E. Rieman. 2013. Probabilistic accounting of uncertainty in forecasts of species distributions under climate change
- Erin E. Peterson, Jay M. Ver Hoef, Daniel J. Isaak, Jeffrey A. Falke, Marie-Josee Fortin, Chris E. Jordan, Kristina McNyset, Pascal Monestiez, Aaron S. Ruesch, Aritra Sengupta, Nicholas Som, E. Ashley Steel, David M. Theobald, Christian E. Torgersen, Seth J. Wenger. 2013. Modelling dendritic ecological networks in space: An integrated network perspective
- Douglas P. Peterson, Seth J. Wenger, Bruce E. Rieman, Daniel J. Isaak. 2013. Linking climate change and fish conservation efforts using spatially explicit decision support tools
- Jaime Goode, John M. Buffington, Daniele Tonina, Daniel J. Isaak, Russ F. Thurow, Seth Wenger, David E. Nagel, Charlie H. Luce, Doerthe Tetzlaff, Chris Soulsby. 2013. Potential effects of climate change on streambed scour and risks to salmonid survival in snow-dominated mountain basins
- Daniel J. Isaak, Bruce E. Rieman. 2013. Stream isotherm shifts from climate change and implications for distributions of ectothermic organisms
- Daniel J. Isaak, Clint C. Muhlfeld, Andrew S. Todd, Robert Al-Chokhachy, James Roberts, Jeffrey L. Kershner, Kurt D. Fausch, Steven W. Hostetler. 2012. The past as prelude to the future for understanding 21st-Century climate effects on Rocky Mountain trout
- Charlie H. Luce, Penny Morgan, Kathleen A. Dwire, Daniel J. Isaak, Zachary Holden, Bruce Rieman. 2012. Climate change, forests, fire, water, and fish: Building resilient landscapes, streams, and managers
- Daniel J. Isaak, Sherry P. Wollrab, Dona Horan, Gwynne L. Chandler. 2011. Climate change effects on stream and river temperatures across the northwest U.S. from 1980-2009 and implications for salmonid fishes
- Seth J. Wenger, Daniel J. Isaak, Jason B. Dunham, Kurt D. Fausch, Charlie H. Luce, Helen M. Neville, Bruce E. Rieman, Michael K. Young, David E. Nagel, Dona Horan, Gwynne L. Chandler. 2011. Role of climate and invasive species in structuring trout distributions in the interior Columbia River Basin, USA
- Seth J. Wenger, Daniel J. Isaak, Charlie H. Luce, Helen M. Neville, Kurt D. Fausch, Jason B. Dunham, Daniel C. Dauwalter, Michael K. Young, Marketa M. Elsner, Bruce E. Rieman, Alan F. Hamlet, Jack E. Williams. 2011. Flow regime, temperature, and biotic interactions drive differential declines of trout species under climate change [includes Supporting Information]
- Daniel J. Isaak. 2011. Stream temperature monitoring and modeling: Recent advances and new tools for managers
- Daniel J. Isaak, Dona Horan. 2011. An evaluation of underwater epoxies to permanently install temperature sensors in mountain streams
- Bruce E. Rieman, Daniel J. Isaak. 2010. Climate change, aquatic ecosystems, and fishes in the Rocky Mountain West: implications and alternatives for management
- Seth J. Wenger, Charlie H. Luce, Alan F. Hamlet, Daniel J. Isaak, Helen M. Neville. 2010. Macroscale hydrologic modeling of ecologically relevant flow metrics
- Daniel J. Isaak, Charlie H. Luce, Bruce E. Rieman, David E. Nagel, Erin E. Peterson, Dona Horan, Sharon L. Payne, Gwynne L. Chandler. 2010. Effects of climate change and wildfire on stream temperatures and salmonid thermal habitat in a mountain river network
- Daniel J. Isaak, Bruce Rieman, Dona Horan. 2009. A watershed-scale monitoring protocol for bull trout
- Jim A. McKean, Daniel J. Isaak, Wayne Wright. 2009. Improving stream studies with a small-footprint green lidar
- Jean-Yves Courbois, Stephen L. Katz, Daniel J. Isaak, E. Ashley Steel, Russ F. Thurow, A. Michelle Wargo Rub, Tony Olsen, Chris E. Jordan. 2008. Evaluating probability sampling strategies for estimating redd counts: an example with Chinook salmon (Oncorhynchus tshawytscha)
- Bruce E. Rieman, Daniel J. Isaak, Susan B. Adams, Dona Horan, David E. Nagel, Charlie H. Luce, Deborah Myers. 2007. Anticipated climate warming effects on bull trout habitats and populations across the interior Columbia River basin
- Helen Neville, Daniel J. Isaak, Russ F. Thurow, Jason Dunham, Bruce Rieman. 2007. Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytcha) within a Snake River watershed
- Daniel J. Isaak, Russ F. Thurow, Bruce E. Rieman, Jason B. Dunham. 2007. Chinook salmon use of spawning patches: Relative roles of habitat quality, size, and connectivity
- H. M. Neville, Daniel J. Isaak, J. B. Dunham, Russ F. Thurow, B. E. Rieman. 2006. Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: Insights from spatial autocorrelation analysis of individual genotypes
- Daniel J. Isaak, Russ F. Thurow. 2006. Network-scale spatial and temporal variation in Chinook salmon (Oncorhynchus tshawytscha) redd distributions: patterns inferred from spatially continuous replicate surveys
- Daniel J. Isaak, Wayne A. Hubert. 2004. Nonlinear response of trout abundance to summer stream temperatures across a thermally diverse montane landscape
- Daniel J. Isaak, Russ F. Thurow, B. E. Rieman, J. B. Dunham. 2003. Temporal variation in synchrony among chinook salmon (Oncorhynchus tshawytscha) redd counts from a wilderness area in central Idaho
Citations of Non-Forest Service Publications
- Chandler, G.L.; Wollrab, S.P.; Horan, D. L.; Nagel, D. E.; Parkes, S.L.; Isaak, D.J.; Horan, D.L; Wenger, S.J.; Peterson, E.E.; Ver Hoef, J.M.; Hostetler, S.W.; Luce, C.H.; Dunham, J.B.; Kershner, J.L.; Roper, B.B. 2016. NorWeST stream temperature data summaries for the western U.S. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2016-0032.
- Isaak, D.J.; Wenger, S.J.; Peterson, E.E.; Ver Hoef, J.M.; Hostetler, S.W.; Luce, C.H.; Dunham, J.B.; Kershner, J.L.; Roper, B.B.; Nagel, D.E.; Chandler, G.L.; Wollrab, S.P.; Parkes, S.L.; Horan, D.L. 2016. NorWeST modeled summer stream temperature scenarios for the western U.S. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2016-0033.
- Young, Michael K.; Isaak, Daniel J.; McKelvey, Kevin S.; Schwartz, Michael K.; Carim, Kellie J.; Fredenberg, Wade; Wilcox, Taylor M.; Franklin, Thomas W.; Chandler, Gwynne L.; Nagel, David E.; Parkes-Payne, Sharon L.; Horan, Dona L.; Wollrab, Sherry P. 2017. Species occurrence data from the Range-Wide Bull Trout eDNA Project. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2017-0038.
- Schwartz, M. K., Young, M.K., McKelvey, K.S., Isaak, D.J., Nagel, D.E., Franklin, T.W., Greaves, S.E., Dysthe, J.C., Chandler, G.L., Wollrab, S.P., Carim, K.J., Wilcox, T.M., Parkes-Payne, S.L., Horan, D.L. 2018. Species occurrence data from the Aquatic eDNAtlas database. Fort Collins, CO: Forest Service Research Data Archive. DOI Pending.
Data and Tools
- 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
Last updated March 10, 2026