Clint Muhlfeld, Ph.D.
I am a Research Aquatic Ecologist at the USGS Northern Rocky Mountain Science Center (NOROCK) in West Glacier, Montana. I currently serve as the Acting Center Director of NOROCK in Bozeman, Montana.
Research interests
As a Research Aquatic Ecologist, I study the ecology, evolution, and conservation of freshwater species and ecosystems. My research examines how climate variability, hydrologic change, biological invasions, and habitat alteration influence freshwater biodiversity and ecosystem processes, with particular expertise in cold-water biota. I have led ecological and evolutionary studies across freshwater systems ranging from glacier-fed mountain streams and large river networks to lakes, as well as regional and global assessments of trout and char. My research combines long-term ecological studies, field research, genetics, and quantitative modeling and draws on multiple disciplines, including ecology, fisheries science, genetics, and hydrology.
Education and Certifications
Ph.D. 2008. Fish and Wildlife Biology, Montana State University, Bozeman
M.S. 1999. Fishery Resources, University of Idaho, Moscow
B.S. 1994. Aquatic Biology, University of Montana, Missoula; University of Maine, Orono
Science and Products
Filter Total Items: 24
Filter Total Items: 96
The past as prelude to the future for understanding 21st-century climate effects on Rocky Mountain Trout The past as prelude to the future for understanding 21st-century climate effects on Rocky Mountain Trout
Bioclimatic models predict large reductions in native trout across the Rocky Mountains in the 21st century but lack details about how changes will occur. Through five case histories across the region, we explore how a changing climate has been affecting streams and the potential consequences for trout. Monitoring records show trends in temperature and hydrographs consistent with a...
Authors
Daniel J. Isaak, Clint C. Muhlfeld, Andrew S. Todd, Robert Al-chokhachy, James Roberts, Jeffrey L. Kershner, Kurt D. Fausch, Steven W. Hostetler
Assessing the impacts of river regulation on native bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) habitats in the upper Flathead River, Montana, USA Assessing the impacts of river regulation on native bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) habitats in the upper Flathead River, Montana, USA
Hungry Horse Dam on the South Fork Flathead River, Montana, USA, has modified the natural flow regimen for power generation, flood risk management and flow augmentation for anadromous fish recovery in the Columbia River. Concern over the detrimental effects of dam operations on native resident fishes prompted research to quantify the impacts of alternative flow management strategies on...
Authors
Clint C. Muhlfeld, Leslie A. Jones, D. Kotter, William J. Miller, Doran Geise, Joel Tohtz, Brian Marotz
RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single-nucleotide polymorphism (SNP) markers based on RAD...
Authors
Stephen J. Amish, Paul A. Hohenlohe, Sally Painter, Robb F. Leary, Clint C. Muhlfeld, Fred W. Allendorf, Gordon Luikart
CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes
We introduce Cost Distance FISHeries (CDFISH), a simulator of population genetics and connectivity in complex riverscapes for a wide range of environmental scenarios of aquatic organisms. The spatially-explicit program implements individual-based genetic modeling with Mendelian inheritance and k-allele mutation on a riverscape with resistance to movement. The program simulates...
Authors
Erin L. Landguth, Clint C. Muhlfeld, Gordon Luikart
Estimating westslope cutthroat trout (Oncorhynchus clarkii lewisi) movements in a river network using strontium isoscapes Estimating westslope cutthroat trout (Oncorhynchus clarkii lewisi) movements in a river network using strontium isoscapes
We used natural variation in the strontium concentration (Sr:Ca) and isotope composition (87Sr:86Sr) of stream waters and corresponding values recorded in otoliths of westslope cutthroat trout (Oncorhynchus clarkii lewisi) to examine movements during their life history in a large river network. We found significant spatial differences in Sr:Ca and 87Sr:86Sr values (strontium isoscapes)...
Authors
Clint C. Muhlfeld, Simon R. Thorrold, Thomas E. McMahon, Brian Marotz
A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA
Biologists are often faced with the difficult decision in managing native salmonids of where and when to install barriers as a conservation action to prevent upstream invasion of nonnative fishes. However, fine-scale approaches to assess long-term persistence of populations within streams and watersheds chosen for isolation management are often lacking. We employed a spatially-explicit...
Authors
Clint C. Muhlfeld, Vincent S. D'Angelo, S.T. Kalinowski, Erin L. Landguth, C.C. Downs, J. Tohtz, Jeffrey L. Kershner
Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi: implications for conservation Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi: implications for conservation
Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the...
Authors
Daniel P. Drinan, Steven T. Kalinowski, Ninh V. Vu, Bradley B. Shepard, Clint C. Muhlfeld, Matthew R. Campbell
Seasonal movements of non-native lake trout in a connected lake and river system Seasonal movements of non-native lake trout in a connected lake and river system
Non-native lake trout, Salvelinus namaycush (Walbaum), threaten native salmonid populations in the western United States. Effective management of lake trout requires understanding movements within connected lake and river systems. This study determined the seasonal movements of subadult lake trout in the Flathead River upstream of Flathead Lake, Montana, USA using radio telemetry. The
Authors
Clint C. Muhlfeld, J. Joseph Giersch, Brian Marotz
The distribution and abundance ofa nuisance native alga, Didymosphenia geminata,in streams of Glacier National Park: Climate drivers and management implications The distribution and abundance ofa nuisance native alga, Didymosphenia geminata,in streams of Glacier National Park: Climate drivers and management implications
Didymosphenia geminata (didymo) is a freshwater alga native to North America, including Glacier National Park, Montana. It has long been considered a cold-water species, but has recently spread to lower latitudes and warmer waters, and increasingly forms large blooms that cover streambeds. We used a comprehensive monitoring data set from the National Park Service (NPS) and USGS models of...
Authors
Clint C. Muhlfeld, Leslie A. Jones, E. William Schweiger, Isabel W. Ashton, Loren L. Bahls
Climate change links fate of glaciers and an endemic alpine invertebrate Climate change links fate of glaciers and an endemic alpine invertebrate
Climate warming in the mid- to high-latitudes and high-elevation mountainous regions is occurring more rapidly than anywhere else on Earth, causing extensive loss of glaciers and snowpack. However, little is known about the effects of climate change on alpine stream biota, especially invertebrates. Here, we show a strong linkage between regional climate change and the fundamental niche...
Authors
Clint C. Muhlfeld, J. Joseph Giersch, F. Richard Hauer, Gregory T. Pederson, Gordon Luikart, Douglas P. Peterson, Christopher C. Downs, Daniel B. Fagre
Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: Implications for conservation Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: Implications for conservation
Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the...
Authors
D.P. Drinan, S.T. Kalinowski, N.V. Vu, B.B. Shepard, C.C. Muhlfeld, M. R. Campbell
The distribution and abundance of a nuisance native alga, Didymosphen Didymosphenia geminata, in streams of Glacier National Park: Climate drivers and management implications The distribution and abundance of a nuisance native alga, Didymosphen Didymosphenia geminata, in streams of Glacier National Park: Climate drivers and management implications
Didymosphenia geminata (didymo) is a freshwater alga native to North America, including Glacier National Park, Montana. It has long been considered a cold-water species, but has recently spread to lower latitudes and warmer waters, and increasingly forms large blooms that cover streambeds. We used a comprehensive monitoring data set from the National Park Service (NPS) and USGS models of...
Authors
Schweiger E. William, I.W. Ashton, C.C. Muhlfeld, L.A. Jones, L.L. Bahls
Non-USGS Publications**
Muhlfeld, Clint C., Thomas E. McMahon, and Durae Belcer. 2009. Spatial and temporal dynamics of spawning between native westslope cutthroat trout (Oncorhynchus clarkii lewisi), introduced rainbow trout (O. mykiss), and their hybrids. Canadian Journal of Fisheries and Aquatic Sciences 66:1153-1168.
Muhlfeld, Clint C., Thomas E. McMahon, Matthew C. Boyer, and Robert E. Gresswell. 2009. Local-habitat, watershed, and biotic factors in the spread of hybridization between native westslope cutthroat trout and introduced rainbow trout. Transactions of the American Fisheries Society 138:1036-1051.
Boyer, Matthew C., Clint C. Muhlfeld, and Fred Allendorf. 2008. Rainbow trout invasion and the spread of hybridization with westslope cutthroat trout. Canadian Journal of Fisheries and Aquatic Sciences 65:658-669.
Muhlfeld, Clint C., David H. Bennett, Kirk Steinhorst, Brian Marotz, and Matthew C. Boyer. 2008. Using bioenergetics modeling to estimate consumption of native juvenile salmonids by nonnative northern pike in the upper Flathead River system, Montana. North American Journal of Fisheries Management 28:636-648.
**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
Filter Total Items: 24
Filter Total Items: 96
The past as prelude to the future for understanding 21st-century climate effects on Rocky Mountain Trout The past as prelude to the future for understanding 21st-century climate effects on Rocky Mountain Trout
Bioclimatic models predict large reductions in native trout across the Rocky Mountains in the 21st century but lack details about how changes will occur. Through five case histories across the region, we explore how a changing climate has been affecting streams and the potential consequences for trout. Monitoring records show trends in temperature and hydrographs consistent with a...
Authors
Daniel J. Isaak, Clint C. Muhlfeld, Andrew S. Todd, Robert Al-chokhachy, James Roberts, Jeffrey L. Kershner, Kurt D. Fausch, Steven W. Hostetler
Assessing the impacts of river regulation on native bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) habitats in the upper Flathead River, Montana, USA Assessing the impacts of river regulation on native bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) habitats in the upper Flathead River, Montana, USA
Hungry Horse Dam on the South Fork Flathead River, Montana, USA, has modified the natural flow regimen for power generation, flood risk management and flow augmentation for anadromous fish recovery in the Columbia River. Concern over the detrimental effects of dam operations on native resident fishes prompted research to quantify the impacts of alternative flow management strategies on...
Authors
Clint C. Muhlfeld, Leslie A. Jones, D. Kotter, William J. Miller, Doran Geise, Joel Tohtz, Brian Marotz
RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single-nucleotide polymorphism (SNP) markers based on RAD...
Authors
Stephen J. Amish, Paul A. Hohenlohe, Sally Painter, Robb F. Leary, Clint C. Muhlfeld, Fred W. Allendorf, Gordon Luikart
CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes
We introduce Cost Distance FISHeries (CDFISH), a simulator of population genetics and connectivity in complex riverscapes for a wide range of environmental scenarios of aquatic organisms. The spatially-explicit program implements individual-based genetic modeling with Mendelian inheritance and k-allele mutation on a riverscape with resistance to movement. The program simulates...
Authors
Erin L. Landguth, Clint C. Muhlfeld, Gordon Luikart
Estimating westslope cutthroat trout (Oncorhynchus clarkii lewisi) movements in a river network using strontium isoscapes Estimating westslope cutthroat trout (Oncorhynchus clarkii lewisi) movements in a river network using strontium isoscapes
We used natural variation in the strontium concentration (Sr:Ca) and isotope composition (87Sr:86Sr) of stream waters and corresponding values recorded in otoliths of westslope cutthroat trout (Oncorhynchus clarkii lewisi) to examine movements during their life history in a large river network. We found significant spatial differences in Sr:Ca and 87Sr:86Sr values (strontium isoscapes)...
Authors
Clint C. Muhlfeld, Simon R. Thorrold, Thomas E. McMahon, Brian Marotz
A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA
Biologists are often faced with the difficult decision in managing native salmonids of where and when to install barriers as a conservation action to prevent upstream invasion of nonnative fishes. However, fine-scale approaches to assess long-term persistence of populations within streams and watersheds chosen for isolation management are often lacking. We employed a spatially-explicit...
Authors
Clint C. Muhlfeld, Vincent S. D'Angelo, S.T. Kalinowski, Erin L. Landguth, C.C. Downs, J. Tohtz, Jeffrey L. Kershner
Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi: implications for conservation Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi: implications for conservation
Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the...
Authors
Daniel P. Drinan, Steven T. Kalinowski, Ninh V. Vu, Bradley B. Shepard, Clint C. Muhlfeld, Matthew R. Campbell
Seasonal movements of non-native lake trout in a connected lake and river system Seasonal movements of non-native lake trout in a connected lake and river system
Non-native lake trout, Salvelinus namaycush (Walbaum), threaten native salmonid populations in the western United States. Effective management of lake trout requires understanding movements within connected lake and river systems. This study determined the seasonal movements of subadult lake trout in the Flathead River upstream of Flathead Lake, Montana, USA using radio telemetry. The
Authors
Clint C. Muhlfeld, J. Joseph Giersch, Brian Marotz
The distribution and abundance ofa nuisance native alga, Didymosphenia geminata,in streams of Glacier National Park: Climate drivers and management implications The distribution and abundance ofa nuisance native alga, Didymosphenia geminata,in streams of Glacier National Park: Climate drivers and management implications
Didymosphenia geminata (didymo) is a freshwater alga native to North America, including Glacier National Park, Montana. It has long been considered a cold-water species, but has recently spread to lower latitudes and warmer waters, and increasingly forms large blooms that cover streambeds. We used a comprehensive monitoring data set from the National Park Service (NPS) and USGS models of...
Authors
Clint C. Muhlfeld, Leslie A. Jones, E. William Schweiger, Isabel W. Ashton, Loren L. Bahls
Climate change links fate of glaciers and an endemic alpine invertebrate Climate change links fate of glaciers and an endemic alpine invertebrate
Climate warming in the mid- to high-latitudes and high-elevation mountainous regions is occurring more rapidly than anywhere else on Earth, causing extensive loss of glaciers and snowpack. However, little is known about the effects of climate change on alpine stream biota, especially invertebrates. Here, we show a strong linkage between regional climate change and the fundamental niche...
Authors
Clint C. Muhlfeld, J. Joseph Giersch, F. Richard Hauer, Gregory T. Pederson, Gordon Luikart, Douglas P. Peterson, Christopher C. Downs, Daniel B. Fagre
Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: Implications for conservation Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: Implications for conservation
Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the...
Authors
D.P. Drinan, S.T. Kalinowski, N.V. Vu, B.B. Shepard, C.C. Muhlfeld, M. R. Campbell
The distribution and abundance of a nuisance native alga, Didymosphen Didymosphenia geminata, in streams of Glacier National Park: Climate drivers and management implications The distribution and abundance of a nuisance native alga, Didymosphen Didymosphenia geminata, in streams of Glacier National Park: Climate drivers and management implications
Didymosphenia geminata (didymo) is a freshwater alga native to North America, including Glacier National Park, Montana. It has long been considered a cold-water species, but has recently spread to lower latitudes and warmer waters, and increasingly forms large blooms that cover streambeds. We used a comprehensive monitoring data set from the National Park Service (NPS) and USGS models of...
Authors
Schweiger E. William, I.W. Ashton, C.C. Muhlfeld, L.A. Jones, L.L. Bahls
Non-USGS Publications**
Muhlfeld, Clint C., Thomas E. McMahon, and Durae Belcer. 2009. Spatial and temporal dynamics of spawning between native westslope cutthroat trout (Oncorhynchus clarkii lewisi), introduced rainbow trout (O. mykiss), and their hybrids. Canadian Journal of Fisheries and Aquatic Sciences 66:1153-1168.
Muhlfeld, Clint C., Thomas E. McMahon, Matthew C. Boyer, and Robert E. Gresswell. 2009. Local-habitat, watershed, and biotic factors in the spread of hybridization between native westslope cutthroat trout and introduced rainbow trout. Transactions of the American Fisheries Society 138:1036-1051.
Boyer, Matthew C., Clint C. Muhlfeld, and Fred Allendorf. 2008. Rainbow trout invasion and the spread of hybridization with westslope cutthroat trout. Canadian Journal of Fisheries and Aquatic Sciences 65:658-669.
Muhlfeld, Clint C., David H. Bennett, Kirk Steinhorst, Brian Marotz, and Matthew C. Boyer. 2008. Using bioenergetics modeling to estimate consumption of native juvenile salmonids by nonnative northern pike in the upper Flathead River system, Montana. North American Journal of Fisheries Management 28:636-648.
**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.