Clint Muhlfeld, Ph.D.
I am a Research Aquatic Ecologist for the USGS Northern Rocky Mountain Science Center stationed in Glacier National Park and Associate Research Professor at the University of Montana’s Flathead Lake Biological Station.
Research interests
My general research interests encompass the fields of aquatic ecology, fisheries biology, and conservation biology. My research goal is to understand how aquatic species interact with physical and biological templates over space and time to inform conservation and management. Specifically, my applied research focuses on assessing how human stressors – invasive species, habitat modification, and climate change – influence native salmonids and rare alpine macroinvertebrates in the Rocky Mountains of United States and Canada.
My research spans a range of scientific and conservation issues from examining evolutionary and ecological impacts of invasive species on native fishes, assessing life history and genetic diversity of native salmonids, assessing the status of threatened freshwater species, investigating the impacts of dams and barriers on aquatic species and ecosystems, developing quantitative models (e.g., stream temperature, instream flow/habitat, bioenergetics, riverscape connectivity, population viability) to predict species’ responses to environmental change, to understanding and predicting the impacts of climate change on freshwater species and ecosystems.
I particularly enjoy collaboration and multidisciplinary research, and advising and educating graduate students working on freshwater ecology and conservation biology projects. Currently, I actively participate on several regional, national, and international science teams that address natural resource issues facing aquatic ecosystems. My hope is that the ecological integrity of aquatic ecosystems will be conserved for future generations through research-informed management and education.
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
Affiliations and Memberships*
Flathead Lake Biological Station, University of Montana
Science and Products
Aquatic invasive species: Lessons from cancer research
Thermal tolerance of meltwater stonefly Lednia tumana nymphs from an alpine stream in Waterton–Glacier International Peace Park, Montana, USA
Estimating thermal regimes of bull trout and assessing the potential effects of climate warming on critical habitats
Factors influencing the distribution of native bull trout and westslope cutthroat trout in western Glacier National Park, Montana
Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
The past as prelude to the future for understanding 21st-century climate effects on Rocky Mountain Trout
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
RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
CDFISH: an individual-based, spatially-explicit, landscape genetics simulator for aquatic species in complex riverscapes
Estimating westslope cutthroat trout (Oncorhynchus clarkii lewisi) movements in a river network using strontium isoscapes
A fine-scale assessment of using barriers to conserve native stream salmonids: a case study in Akokala Creek, Glacier National Park, USA
Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi: implications for conservation
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.
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Aquatic invasive species: Lessons from cancer research
Aquatic invasive species are disrupting ecosystems with increasing frequency. Successful control of these invasions has been rare: Biologists and managers have few tools for fighting aquatic invaders. In contrast, the medical community has long worked to develop tools for preventing and fighting cancer. Its successes are marked by a coordinated research approach with multiple steps: prevention, eaAuthorsAdam J. Sepulveda, Andrew Ray, Robert K. Al-Chokhachy, Clint C. Muhlfeld, Robert E. Gresswell, Jackson A. Gross, Jeffrey L. KershnerThermal tolerance of meltwater stonefly Lednia tumana nymphs from an alpine stream in Waterton–Glacier International Peace Park, Montana, USA
Global climate change threatens to affect negatively the structure, function, and diversity of aquatic ecosystems worldwide. In alpine systems, the thermal tolerances of stream invertebrates can be assessed to understand better the potential effects of rising ambient temperatures and continued loss of glaciers and snowpack on alpine stream ecosystems. We measured the critical thermal maximum (CTM)AuthorsHilary G. Billman, J. Joseph Giersch, K.M. Kappenman, Clint C. Muhlfeld, Molly A. H. WebbEstimating thermal regimes of bull trout and assessing the potential effects of climate warming on critical habitats
Understanding the vulnerability of aquatic species and habitats under climate change is critical for conservation and management of freshwater systems. Climate warming is predicted to increase water temperatures in freshwater ecosystems worldwide, yet few studies have developed spatially explicit modelling tools for understanding the potential impacts. We parameterized a nonspatial model, a spatiaAuthorsLeslie A. Jones, Clint C. Muhlfeld, Lucy A. Marshall, Brian L. McGlynn, Jeffrey L. KershnerFactors influencing the distribution of native bull trout and westslope cutthroat trout in western Glacier National Park, Montana
The widespread declines of native bull trout (Salvelinus confluentus) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations prompted researchers to investigate factors influencing their distribution and status in western Glacier National Park, Montana. We evaluated the association of a suite of abiotic factors (stream width, elevation, gradient, large woody debris density, pool dAuthorsVincent S. D'Angelo, Clint C. MuhlfeldGenomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'superAuthorsPaul A. Hohenlohe, Mitch D. Day, Stephen J. Amish, Michael R. Miller, Nick Kamps-Hughes, Matthew C. Boyer, Clint C. Muhlfeld, Fred W. Allendorf, Eric A. Johnson, Gordon LuikartThe 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 warming climateAuthorsDaniel J. Isaak, Clint C. Muhlfeld, Andrew S. Todd, Robert Al-chokhachy, James Roberts, Jeffrey L. Kershner, Kurt D. Fausch, Steven W. HostetlerAssessing 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 threatenedAuthorsClint C. Muhlfeld, Leslie A. Jones, D. Kotter, William J. Miller, Doran Geise, Joel Tohtz, Brian MarotzRAD 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 sequencingAuthorsStephen J. Amish, Paul A. Hohenlohe, Sally Painter, Robb F. Leary, Clint C. Muhlfeld, Fred W. Allendorf, Gordon LuikartCDFISH: 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 individuals in subpoAuthorsErin L. Landguth, Clint C. Muhlfeld, Gordon LuikartEstimating 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) within andAuthorsClint C. Muhlfeld, Simon R. Thorrold, Thomas E. McMahon, Brian MarotzA 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 approach toAuthorsClint C. Muhlfeld, Vincent S. D'Angelo, S.T. Kalinowski, Erin L. Landguth, C.C. Downs, J. Tohtz, Jeffrey L. KershnerGenetic 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 least. NeigAuthorsDaniel P. Drinan, Steven T. Kalinowski, Ninh V. Vu, Bradley B. Shepard, Clint C. Muhlfeld, Matthew R. CampbellNon-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.
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*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