Clint Muhlfeld

• PhD
• Researcher at U.S. Geological Survey

Trout are one of the most culturally, economically, and ecologically important taxonomic groups of freshwater fishes worldwide. Native to all continents in the Northern Hemisphere, trout belong to seven genera, which are distributed across 52 countries. Despite their broad importance as societal icons and as indicators of biodiversity, many of the...

Glaciers are important drivers of environmental heterogeneity and biological diversity across mountain landscapes. Worldwide, glaciers are receding rapidly due to climate change, with important consequences for biodiversity in mountain ecosystems. However, the effects of glacier loss on biodiversity have never been quantified across a mountainous r...

Significance Invasive species are a leading cause of biodiversity loss, yet the mechanisms by which invaders progressively disrupt ecosystems and native species remain unclear. Using an extensive isotope dataset across multiple ecosystems and stages of invasion, we show that an invasive fish predator (lake trout) disrupted food webs by forcing nati...

Climate change and invasive species are major threats to native biodiversity, but few empirical studies have examined their combined effects at large spatial and temporal scales. Using 21,917 surveys collected over 30 years, we quantified the impacts of climate change on the past and future distributions of five interacting native and invasive trou...

Heterogeneity is a central feature of ecosystem resilience, but how this translates to socioeconomic resilience depends on people's ability to track shifting resources in space and time. Here, we quantify how climatic extremes have influenced how people (fishers) track economically valuable ecosystem services (fishing opportunities) across a range...

Climate change is anticipated to cause species to shift their ranges upward and poleward, yet space for tracking suitable habitat conditions may be limited for range‐restricted species at the highest elevations and latitudes of the globe. Consequently, range‐restricted species inhabiting Arctic freshwater ecosystems, where global warming is most pr...

Climate‐induced expansion of invasive hybridization (breeding between invasive and native species) poses a significant threat to the persistence of many native species worldwide. In the northern U.S. Rocky Mountains, hybridization between native cutthroat trout and non‐native rainbow trout has increased in recent decades due, in part, to climate‐dr...

Mountain glaciers are retreating rapidly due to climate change, leading to the formation of downstream lakes. However, little is known about the physical and biogeochemical conditions in these lakes across a range of glacial influence. We surveyed alpine lakes fed by both glacial and snowpack meltwaters and those fed by snowpack alone to compare nu...

A probe-based quantitative real-time PCR assay was developed to detect meltwater stonefly (Lednia tumana) environmental (e)DNA in water samples. The limits of detection and quantification, respectively, were 12.1 and 58.4 gene copies for calibration standards and these values were similarly low in a relevant environmental sample matrix (8.6 and 174...

Hybridization between native and invasive species, a major cause of biodiversity loss, can spread rapidly even when hybrids have reduced fitness. This paradox suggests that hybrids have greater dispersal rates than non-hybridized individuals, yet this mechanism has not been empirically tested in animal populations. Here, we test if non-native genet...

We developed new bull trout genetic markers using Restriction-site Associated DNA sequencing (RAD-seq) to improve our ability to address questions important for their conservation and management. Samples from across the species range were sequenced and 5020 high quality single nucleotide polymorphism (SNP) loci were discovered, including hundreds w...

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. Hierarchi...

Rapid recession of glaciers and snowfields is threatening the habitats of cold-water biodiversity worldwide. In many ice-sourced headwaters of western North America, stoneflies in the genus Lednia (Plecoptera: Nemouridae) are a prominent member of the invertebrate community. With a broad distribution in mountain streams and close ties to declining...

Biological invasions are accelerating worldwide, causing major ecological and economic impacts in aquatic ecosystems. The urgent decision-making needs of invasive species managers can be better met by the integration of biodiversity big data with large-domain models and data-driven products. Remotely sensed data products can be combined with existi...

Brad Shepard died suddenly and unexpectedly on September 23, 2021, while going fishing on his island on the Yellowstone River with his favorite fishing partner, his son Ben, by his side. Bradley Bernard Shepard was born June 12, 1952, in Dayton, Ohio. He found his passion very early in life; fishing with his grandfather at the age of 2 years. He he...

Climate warming is expected to have substantial impacts on native trout across the Rocky Mountains, but there is little understanding of how these changes affect future distributions of co-occurring native fishes within population strongholds. We used mixed-effects logistic regression to investigate the role of abiotic (e.g., temperature) and bioti...

Climate change vulnerability assessments of cold-water species have focused on protecting cold summer habitats in high-elevation streams. Now, a study shows that seasonally warm rivers can provide the majority of growth potential for cold-water fishes, unveiling a notable blind spot in freshwater climate research and planning.

Human‐mediated hybridization threatens many native species, but the effects of introgressive hybridization on life history expression are rarely quantified, especially in vertebrates. We quantified the effects of non‐native rainbow trout admixture on important life history traits including growth and partial migration behavior in three populations...

With the rise of large-scale environmental models comes new challenges for how we best utilize this information in research, management and decision making. Interactive data visualizations can make large and complex datasets easier to access and explore, which can lead to knowledge discovery, hypothesis formation and improved understanding. Here, w...

Estimating the effective population size and effective number of breeders per year (Nb) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one‐sample ldne estimator of Nb in age‐structured populations using a range of published species life history types, sample sizes, and DNA m...

Climate change may facilitate the expansion of non-native invasive species (NIS) in aquatic and terrestrial systems. However, empirical evidence remains scarce and poorly synthesized at scales necessary for effective management. We conducted a literature synthesis to assess the state of research on the observed and predicted effects of climate chan...

Compensatory growth—when individuals in poor condition grow rapidly to catch up to conspecifics—may be a mechanism that allows individuals to tolerate stressful environmental conditions, both abiotic and biotic. This phenomenon has been documented fairly widely in laboratory and field experiments, but evidence for compensatory growth in the wild is...

Climate change is increasing the severity and extent of extreme droughts events, posing a critical threat to freshwater ecosystems, particularly with increasing human demands for diminishing water supplies. Despite the importance of drought as a significant driver of ecological and evolutionary dynamics, current understanding of drought consequence...

Alpine streams are dynamic habitats harboring substantial biodiversity across small spatial extents. The diversity of alpine stream biota is largely reflective of environmental heterogeneity stemming from varying hydrological sources. Globally, alpine stream diversity is under threat as meltwater sources recede and stream conditions become increasi...

The effect of climate change on stream temperature regimes is of significant concern to natural resource managers focused on protecting cold-water-dependent species. Nevertheless, understanding of how human land-use activities may act to exacerbate the effects of climate change on stream temperature regimes is limited. Using extensive stream temper...

We used redd count data from 88 bull trout (Salvelinus confluentus) populations in the upper Columbia River basin to quantify local and regional patterns in population dynamics, including adult abundance, long-term trend, and population synchrony. We further used this information to assess conservation risk of metapopulations using eight population...

Riverscapes are complex, landscape-scale mosaics of connected river and stream habitats embedded in diverse ecological and socioeconomic settings. Social–ecological interactions among stakeholders often complicate natural-resource conservation and management of riverscapes. The management challenges posed by the conservation and restoration of wild...

Stream temperature has direct and indirect effects on stream ecology and is critical in determining both abiotic and biotic system responses across a hierarchy of spatial and temporal scales. Temperature variation is primarily driven by solar radiation, while landscape topography, geology, and stream reach processes across ecosystem scales contribu...

Aim Climate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome‐s...

Climate warming is expected to increase stream temperatures in mountainous regions of western North America, yet the degree to which future climate change may influence seasonal patterns of stream temperature is uncertain. In this study, a spatially explicit statistical model framework was integrated with empirical stream temperature data (approxim...

We appreciate the comments of Young et al. (2017) on our recent paper (Muhlfeld et al., 2017) concerning spatiotemporal dynamics of hybridization between native westslope cutthroat trout (Oncoryhnchus clarkii lewisi; WCT) and introduced coastal rainbow trout (O. mykiss irideus; RBT). Nevertheless, we believe there is no evidence for “ecological seg...

Hybridization between invasive and native species, a significant threat to worldwide biodiversity, is predicted to increase due to climate-induced expansions of invasive species. Long-term research and monitoring are crucial for understanding the ecological and evolutionary processes that modulate the effects of invasive species. Using a large, mul...

Fisheries managers have implemented suppression programmes to control non-native lake trout, Salvelinus namaycush (Walbaum), in several lakes throughout the western United States. This study determined the feasibility of experimentally suppressing lake trout using gillnets in an isolated backcountry lake in Glacier National Park, Montana, USA, for...

Climate change vulnerability assessments (CCVAs) are important tools to plan for and mitigate potential impacts of climate change. However, CCVAs often lack scientific rigor, which can ultimately lead to poor conservation prioritization and associated ecological and economic costs. We discuss the need to improve comparability and consistency of CCV...

To address the issue of drought and build long-term resilience to drought at local, regional, and national levels, the USGS has developed a coordinated and integrated drought science plan. The plan presents a new path for understanding the complexity of drought issues and the impact of drought on human and natural systems. This understanding can in...

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural sele...

Climate warming is causing rapid loss of glaciers and snowpack in mountainous regions worldwide. These changes are predicted to negatively impact the habitats of many range-restricted species, particularly endemic, mountaintop species dependent on the unique thermal and hydrologic conditions found only in glacier-fed and snowmelt-driven alpine stre...

Invasive hybridization is one of the greatest threats to the persistence of Westslope Cutthroat Trout Oncorhynchus clarkii lewisi. Large protected areas, where nonhybridized populations are interconnected and express historical life history and genetic diversity, provide some of the last ecological and evolutionary strongholds for conserving this s...

Climate change is an additional stressor in a complex suite of threats facing freshwater biodiversity, particularly for cold‐water fishes. Research addressing the consequences of climate change on cold‐water fish has generally focused on temperature limits defining spatial distributions, largely ignoring how climatic variation influences population...

[This corrects the article DOI: 10.1371/journal.pone.0157386.].

There is an urgent need to consider more aggressive and direct interventions for the conservation of freshwater fishes that are threatened by invasive species, habitat loss, and climate change. Conservation introduction (moving a species outside its indigenous range to other areas where conditions are predicted to be more suitable) is one type of t...

Much remains unknown about the genetic status and population connectivity of high-elevation and high-latitude freshwater invertebrates, which often persist near snow and ice masses that are disappearing due to climate change. Here we report on the conservation genetics of the meltwater stonefly Lednia tumana (Ricker) of Montana, USA, a cold-water o...

Gravel-bed river floodplains in mountain landscapes disproportionately concentrate diverse habitats, nutrient cycling, productivity of biota, and species interactions. Although stream ecologists know that river channel and floodplain habitats used by aquatic organisms are maintained by hydrologic regimes that mobilize gravel-bed sediments, terrestr...

Pacific trout Oncorhynchus spp. in western North America are strongly valued in ecological, socioeconomic, and cultural views, and have been the subject of substantial research and conservation efforts. Despite this, the understanding of their evolutionary histories, overall diversity, and challenges to their conservation is incomplete. We review t...

Despite increasing concern that climate change may negatively impact trout—a globally distributed group of fish with major economic, ecological, and cultural value—a synthetic assessment of empirical data quantifying relationships between climatic variation and trout ecology does not exist. We conducted a systematic review to describe how temporal...

Climate change vulnerability assessments (CCVAs) are valuable tools for assessing species' vulnerability to climatic changes, yet failure to include measures of adaptive capacity and to account for sources of uncertainty may limit their effectiveness. Here, we provide a more comprehensive CCVA approach that incorporates all three elements used for...

Environmental variation and landscape features affect ecological processes in fluvial systems; however, assessing effects at management-relevant temporal and spatial scales is challenging. Genetic data can be used with landscape models and traditional ecological assessment data to identify biodiversity hotspots, predict ecosystem responses to anthr...

CDFISH is now available on GITHUB https://github.com/ComputationalEcologyLab?tab=repositories

Samples are organized by river basin and population. Temp is the mean August stream temperature from NoRWeST (http://www.fs.fed.us/rm/boise/AWAE/projects/NorWeST.html) or lake surface temperature (°C). N is the number of individuals included in RADseq genotying, Nfilter is the number of individuals (from a total of 339) used in subsequent analyses,...

Samples are organized by river basin and population. Temp is the mean August stream temperature from NoRWeST (http://www.fs.fed.us/rm/boise/AWAE/projects/NorWeST.html) or lake surface temperature (°C). N is the number of individuals included in RADseq genotying, Nfilter is the number of individuals (from a total of 339) used in subsequent analyses,...

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity, and persistence. We used riverscape genetics modeling to assess whether climatic and habitat variables were related to neutral and...

AbstractHybridization between introduced and native fauna is a risk to native species and may threaten the long-term persistence of numerous taxa. Rainbow Trout Oncorhynchus mykiss has been one of the most widely introduced species around the globe and often hybridizes with native Cutthroat Trout O. clarkii in the Rocky Mountains. Previous work has...

We welcome Phillips and Baird's strenuous critique of our opinion article, which identifies some uncertainties regarding the role of spatial sorting in the spread of invasive hybridization. We acknowledged several of these sources of uncertainty in our article and we emphasized the need for more empirical work.

Invasive hybridization is causing loss of biodiversity worldwide. The spread of such introgression can occur even when hybrids have reduced Darwinian fitness, which decreases the frequency of hybrids due to low survival or reproduction through time. This paradox can be partially explained by spatial sorting, where genotypes associated with dispersa...

In this article we describe the current status and conservation of interior (potamodromous) Redband Trout Oncorhynchus mykiss sspp. throughout its range in the western United States using extant data and expert opinion provided by fish managers. Redband Trout historically occupied 60,295 km of stream habitat and 152 natural lakes. Currently, Redban...

Climate warming poses a serious threat to alpine-restricted species worldwide, yet few studies have empirically documented climate-induced changes in distributions. The rare stonefly, Zapada glacier (Baumann and Gaufin), endemic to alpine streams of Glacier National Park (GNP), Montana, was recently petitioned for listing under the US Endangered Spec...

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we t...

Invasive hybridization and introgression pose a serious threat to the persistence of many native species. Understanding the effects of hybridization on native populations (e.g., fitness consequences) requires numerous species-diagnostic loci distributed genome-wide. Here we used RAD sequencing to discover thousands of single-nucleotide polymorphism...

The intention of this document is to provide Glacier National Park (GLAC) a watershed-scale prioritization tool to assist with finer scale monitoring or management decisions. This document relies on existing data to provide a comprehensive overview of the ecosystem condition of GLAC’s watersheds. The models within this document may be used to asses...

Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between enviro...

Hybridization between native and non-native species has serious biological consequences, but our understanding of how dispersal and selection interact to influence invasive hybridization is limited. Here, we document the spread of genetic introgression between a native (Oncorhynchus clarkii) and invasive (Oncorhynchus mykiss) trout, and identify th...

We investigated multiscale hydrogeomorphic influences on the distribution and abundance of bull trout (Salvelinus confluentus) spawning in snowmelt-dominated streams of the upper Flathead River basin, northwestern Montana. Within our study reaches, bull trout tended to spawn in the finest available gravel substrates. Analysis of the mobility of the...

Climate change will decrease worldwide biodiversity through a number of potential pathways, including invasive hybridization (cross-breeding between invasive and native species). How climate warming influences the spread of hybridization and loss of native genomes poses difficult ecological and evolutionary questions with little empirical informati...

Quantifying the effectiveness of management actions to mitigate the effects of changing climatic conditions (i.e., climate adaptation) can be difficult, yet critical for conservation. We used population genetic data from 1984 to 2011 to assess the degree to which ambient climatic conditions and targeted suppression of sources of nonnative Rainbow T...

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 impa...

Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially explicit, individual-based, demographi...

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 ecosyste...

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-le...

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, eleva...

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...

Introduction The role of restoration goals in guiding watershed assessments Assessing causes of habitat and biological degradation Assessing habitat alteration Assessing changes in biota Assessing potential effects of climate change Identifying restoration opportunities Case studies Summary References

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 alt...

Non-native lake trout threaten native salmonid populations in western North America. Glacier National Park (GNP) contains about one-third of the natural lakes supporting threatened bull trout in the United States, yet several populations are at high risk of extirpation due to the invasion and establishment of non-native lake trout from Flathead Lak...

Climate change is rapidly altering the biodiversity of aquatic ecosystems worldwide. Trend data indicate that the Northern Rocky Mountains are experiencing earlier and more rapid snowmelt in the spring, warmer drier summers, increased winter flooding, and extensive loss of snow and ice masses. These changes are likely to shift patterns in distribut...

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...