Geology topics

Clint C. Muhlfeld

Publications and source records attributed to Clint C. Muhlfeld.

At least 19 recordsLinked to original sources

USGS2026

An integrated drought early warning system to support coldwater fisheries management

Low streamflow resulting from drought and human water use is a threat to freshwater fisheries throughout western North America, creating a need for effective tools to aid management and fisheries use. We developed a drought early warning framework that forecasts river conditions that could result in temporary fishery closures and restrictions across Montana’s renowned trout fisheries. This tool provides reach-specific, probabilistic decision support for proactive management under drought conditions. We calibrated statistical models using historical streamflow and stream temperature data from U.S. Geological Survey (USGS) gauges to predict the likelihood of exceeding the low-flow and high-temperature thresholds for fisheries closure within 1- to 4-week outlooks during the warm season (May–October). These forecasts demonstrated consistently high model performance in predicting the criteria for low-flow fishing closure across all rivers (4-week outlook: mean R 2 = 0.96, IQR [interquartile range]: 0.94–0.97) and variable but often high model performance for temperature-based restriction criteria (mean R 2 = 0.80, IQR: 0.55–0.86), particularly at sites that frequently experience higher stream temperature conditions. This drought early warning system—available via the web-based tool TroutCast ( https://www.usgs.gov/apps/troutcast/ )—provides daily updated seasonal forecasts to help anticipate effects to recreational fishing opportunities. By quantifying forecast uncertainty and providing reach-specific probabilities, the system supports proactive management, improves coordination between fisheries and water managers, and provides stakeholders with actionable information on probable future effects on fishing access within a framework that is broadly applicable to other freshwater systems and water resource management challenges.

Montana↗

USGS2026

Invasive hybridization has unpredicted and variable effects on trout survival in contrasting environments

Invasive hybridization between native and introduced species is widespread, especially in fishes, yet its effects on fitness-related traits across environments remain poorly understood. We combined individual genetic admixture estimates with capture–recapture data to quantify how hybridization between native Westslope Cutthroat Trout ( Oncorhynchus lewisi ) and invasive Rainbow Trout ( Oncorhynchus mykiss ) influences survival. We measured individual survival of 5186 trout across three populations in contrasting environments. Non-native admixture significantly affected survival in two populations, with positive effects during summer and negative effects during winter. Prior research has shown hybridization increases with stream temperature; however, survival patterns did not follow this trend. In a warmer stream, native trout in all size-classes had ≥20% higher annual survival than hybrids, whereas in a cooler stream, juvenile native trout had ≥20% lower survival than hybrids. These findings indicate that hybridization effects on survival are complex and vary among populations, environments, and size-classes. Landscape patterns of hybridization may therefore not reflect local survival (or fitness) outcomes, emphasizing that measures fitness-related traits across populations and environments could elucidate the eco-evolutionary consequences of invasive hybridization.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2025

Aridity reduces lag times between aquatic and terrestrial dry-down among watersheds and across years in the northwest US

Landscapes encompass both aquatic and terrestrial ecosystems that experience the same climate but may respond to climate in divergent ways. For example, the time lag between seasonal dry-down of terrestrial soil moisture and decline in streamflow has important implications for species and ecosystem processes across the aquatic–terrestrial interface. How these lags between aquatic and terrestrial hydrology vary with climate and spatial location within watersheds remains largely unexplored. Here, we examine seasonal patterns of aquatic–terrestrial dry-down across seven watersheds in the northwestern USA, spanning a wide range of aridity. We compared daily streamflow data from USGS gages at watershed outlets with simulated daily soil moisture (1979–2020) from multiple locations within each watershed. In all watersheds, annual dry cycles progressed sequentially through the following features: evapotranspiration, precipitation, shallow soil moisture, deep soil moisture, and finally streamflow. Seasonal streamflow minima lagged behind soil moisture minima for shorter durations in more arid watersheds and drier years. Within watersheds, lag times varied spatially due to interactions between elevation and aridity, with short lags in low-elevation soils near streams in arid watersheds and longer lags in less arid watersheds. Collectively, these results indicate shorter lags between seasonal aquatic and terrestrial dry periods in drier watersheds and years, and show that these tighter linkages are spatially aggregated in drier watersheds. The co-occurrence of seasonally dry conditions in both aquatic and terrestrial systems under increasing aridification is likely to intensify stressors on ecosystems and services. Recognizing these patterns may be critical for predicting ecosystem vulnerabilities and informing adaptation strategies to mitigate the impacts of seasonally dry conditions.

Montana, Oregon, Wyoming↗

USGS2025

Non-native prey availability and over-compensatory density dependence drive population dynamics of a native fish predator

Understanding the factors that regulate population dynamics is crucial for conserving imperiled species. Bull trout ( Salvelinus confluentus ), a piscivorous salmonid and one of North America's most threatened cold-water species, has declined significantly due to habitat loss, overfishing, invasive species, and climate change. While recovery efforts have primarily targeted these threats, the role of prey availability in influencing bull trout population dynamics under multiple stressors remains poorly understood. Using a stage-based integrated population model, we quantified the effects of non-native prey availability (kokanee; Oncorhynchus nerka ), angling pressure, climatic variation, and density-dependent processes on bull trout population dynamics in Lake Koocanusa, a transboundary reservoir and river system (United States and Canada), over a 40-year period (1980–2023). Our results show that bull trout populations are regulated by density-dependent processes, including over-compensation in sub-adult recruitment and reduced adult survival at high densities. Increased kokanee biomass and restricted harvest significantly enhanced bull trout survival and abundance, whereas reduced water availability had a limited negative effect on sub-adult production. Model simulations indicate that as kokanee biomass availability increases, the number of bull trout that can be sustainably harvested also increases. In fact, a modest annual fishery (300 individuals) can be sustained, especially under moderate to high kokanee biomass conditions. These results underscore the importance of prey availability, including non-native species, in supporting bull trout populations. Effective management of threatened apex fish predators like bull trout requires addressing the complex interplay between environmental threats, prey dynamics, and density-dependent mechanisms across all life stages.

British Columbia, Montana↗

USGS2024

Climate change vulnerability of Arctic char across Scandinavia

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 pronounced, face the challenge of coping with changing abiotic and biotic conditions or risk extinction. Here, we use an extensive fish community and environmental dataset for 1762 lakes sampled across Scandinavia (mid-1990s) to evaluate the climate vulnerability of Arctic char ( Salvelinus alpinus ), the world's most cold-adapted and northernly distributed freshwater fish. Machine learning models show that abiotic and biotic factors strongly predict the occurrence of Arctic char across the region with an overall accuracy of 89 percent. Arctic char is less likely to occur in lakes with warm summer temperatures, high dissolved organic carbon levels (i.e., browning), and presence of northern pike ( Esox lucius ). Importantly, climate warming impacts are moderated by habitat (i.e., lake area) and amplified by the presence of competitors and/or predators (i.e., northern pike). Climate warming projections under the RCP8.5 emission scenario indicate that 81% of extant populations are at high risk of extirpation by 2080. Highly vulnerable populations occur across their range, particularly near the southern range limit and at lower elevations, with potential refugia found in some mountainous and coastal regions. Our findings highlight that range shifts may give way to range contractions for this cold-water specialist, indicating the need for pro-active conservation and mitigation efforts to avoid the loss of Arctic freshwater biodiversity.

Global Change Biology↗

USGS2024

Local environments, not invasive hybridization, influence cardiac performance of native trout under acute thermal stress

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-driven increases in water temperature. It has been postulated that invasive hybridization may enhance physiological tolerance to climate-induced thermal stress because laboratory studies indicate that rainbow trout have a higher thermal tolerance than cutthroat trout. Here, we assessed whether invasive hybridization improves cardiac performance response to acute water temperature stress of native wild trout populations. We collected trout from four streams with a wide range of non-native admixture among individuals and with different temperature and streamflow regimes in the upper Flathead River drainage, USA. We measured individual cardiac performance (maximum heart rate, “MaxHR”, and temperature at arrhythmia, “ArrTemp”) during laboratory trials with increasing water temperatures (10–28°C). Across the study populations, we observed substantial variation in cardiac performance of individual trout when exposed to thermal stress. Notably, we found significant differences in the cardiac response to thermal regimes among native cutthroat trout populations, suggesting the importance of genotype-by-environment interactions in shaping the physiological performance of native cutthroat trout. However, rainbow trout admixture had no significant effect on cardiac performance (MaxHR and ArrTemp) within any of the three populations. Our results indicate that invasive hybridization with a warmer-adapted species does not enhance the cardiac performance of native trout under warming conditions. Maintaining numerous populations across thermally and hydrologically diverse stream environments will be crucial for native trout to adapt and persist in a warming climate.

Montana↗

USGS2023

Mountain glaciers influence biogeochemical and ecological characteristics of high-elevation lakes across the northern Rocky Mountains, USA

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 nutrient concentrations, stoichiometry, water clarity, chlorophyll, and zooplankton communities. Total phosphorus (TP) and soluble reactive phosphorus were two times higher in glacial lakes than in non-glacial lakes, while nitrate concentrations were three times higher. However, organic carbon concentrations in glacial lakes were two times lower than in non-glacial lakes. The carbon-to-phosphorus ratio and the nitrogen-to-phosphorus ratio of lake seston increased with water clarity in glacial lakes, suggesting that turbidity from glacial flour increases light limitation and increases stoichiometric food quality for zooplankton in newly formed lakes. However, chlorophyll a concentrations did not differ between lake types. Through structural equation modeling, we found that glaciers exhibit a bidirectional association with nitrate and TP concentrations, perhaps mediated through landscape vegetation and lake clarity. Zooplankton communities in high-turbidity glacial lakes were largely composed of cyclopoid copepods and rotifers (i.e., non-filter feeders), while non-glacial lakes tended to be dominated by calanoid copepods and cladocerans (i.e., filter feeders). Our results show that glacier-influenced lakes have biogeochemical and ecological characteristics distinct from snow-fed mountain lakes. Sustained studies are needed to assess the dynamics of these unique features as the influence of the alpine cryosphere fades under ongoing climate change.

Montana↗

USGS2023

Validation of a species-specific probe-based qPCR assay for the threatened meltwater stonefly, Lednia tumana, in environmental samples

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 174.2, respectively). The assay’s utility was demonstrated in situ on water samples with concomitant manual invertebrate surveys from a wide range of alpine streams across L. tumana ’s native range.

Conservation Genetics Resources↗

USGS2022

High dispersal rates in hybrids drive expansion of maladaptive hybridization

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 genetic introgression increases reproductive dispersal using a human-mediated hybrid zone between native cutthroat trout ( Oncorhynchus clarkii ) and invasive rainbow trout ( Oncorhynchus mykiss ) in a large and connected river system. We quantified the propensity for individuals to migrate from natal rearing habitats (migrate), reproduce in non-natal habitats (stray), and the joint probability of dispersal as a function of genetic ancestry. Hybrid trout with predominantly non-native rainbow trout ancestry were more likely to migrate as juveniles and to stray as adults. Overall, hybrids with greater than 50% rainbow trout ancestry were 5.7 times more likely to disperse than native or hybrid trout with small amounts of rainbow trout ancestry. Our results show a genetic basis for increased dispersal in hybrids that is likely contributing to the rapid expansion of invasive hybridization between these species. Management actions that decrease the probability of hybrid dispersal may mitigate the harmful effects of invasive hybridization on native biodiversity.

Montana↗

USGS2022

Rapid SNP genotyping, sex identification, and hybrid-detection in threatened bull trout

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 with high heterozygosity ( H > 0.30). We developed 63 high-heterozygosity bull trout polymorphic SNPs and one sex-identification SNP and tested them on range-wide samples. In addition, we tested previously published SNP assays including 11 species-diagnostic SNPs differentiating bull trout from brook trout and 3 brook trout variable SNPs on a broad set of range-wide samples. Genotypes from the sex-identification SNP showed 95% agreement with the field sex identification across 113 samples. The eleven species-diagnostic loci reliably discriminated between known brook trout, bull trout, and F 1 hybrid control samples. These SNP assays will facilitate genotyping of partially degraded museum fin clips, and tissues with low DNA content such as scales and otoliths. Finally, these loci will allow rapid genotyping for improved resolution of bull trout population structure, sex ratios, movement patterns, and introgressive hybridization with non-native brook trout for a wide range of management questions.

British Columbia, Idaho, Montana, Nevada, Oregon, ↗

USGS2022

Stoneflies in the genus Lednia (Plecoptera: Nemouridae): Sentinels of climate change impacts on mountain stream biodiversity

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 glacier cover, Lednia has emerged as a sentinel of climate change threats to high-elevation aquatic biodiversity. Lednia tumana , which is endemic to Glacier National Park, USA and the surrounding mountains, is the most well-studied species in the genus and in 2019 became federally protected under the U.S. Endangered Species Act (ESA) due to climate-induced loss of meltwater habitats. Three other Lednia species have also been described, and like L. tumana , each is endemic to a mountain region of western North America: Lednia sierra in the Sierra Nevada, Lednia borealis in the Cascade Range, and Lednia tetonica in the Teton Range. In this review, we provide a comprehensive overview of Lednia ecology, genetics, and physiology, with an emphasis on the conservation outlook for the group and species with similar headwater distributions. We highlight substantial progress made in the last decade to better understand the ecology and evolution of Lednia , including the identification of 140 Lednia- containing streams (an increase from 12 streams in 2010), and a more complete understanding of the degree to which warming streams may imperil species in the genus. In light of the ESA listing of L. tumana , we show that similar conservation threats likely face all extant Lednia species. However, substantial gaps in our knowledge remain, primarily centering around their distributions (and the potential for as yet undescribed species), life history, ecophysiology, and trophic ecology. We conclude by describing pressing questions for Lednia that when addressed will expand knowledge of the genus and its conservation as well as broader understanding of climate risks to mountain stream biodiversity worldwide.

California, Montana, Washington, Wyoming↗

USGS2022

Socioeconomic resilience to climatic extremes in a freshwater fishery

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 of spatial scales in rivers of the northern Rocky Mountains, USA, over the past three decades. Fishers opportunistically shifted from drought-sensitive to drought-resistant rivers during periods of low streamflows and warm temperatures. This adaptive behavior stabilized fishing pressure and expenditures by a factor of 2.6 at the scale of the regional fishery (i.e., portfolio effect). However, future warming is predicted to homogenize habitat options that enable adaptive behavior by fishers, putting ~30% of current spending at risk across the region. Maintaining a diverse portfolio of fishing opportunities that enable people to exploit shifting resources provides an important resilience mechanism for mitigating the socioeconomic impacts of climate change on fisheries.

Montana↗

USGS2022

Stream size, temperature, and density explain body sizes of freshwater salmonids across a range of climate conditions

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. Hierarchical spatial modeling across a gradient of habitats (5221 sites) illustrated the importance of watershed effects, which explained 17%–45% of the of the variation in body size across taxa. Stream size had a strong, positive relationship with body size, yet there was approximately tenfold difference in the strength of the relationship across taxa. Trout body size consistently declined with increasing density across taxa. Despite reliance on cold water, we found positive relationships between summer stream temperature and trout body size across most taxa. Our results highlight how providing trout access to larger, productive rivers for the expression of growth and life-history variation would promote body size diversity within and across populations.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2021

Testing a generalizable machine learning workflow for aquatic invasive species on Rainbow Trout (Oncorhynchus mykiss) in northwest Montana

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 existing invasive species occurrence data via machine learning models to provide the proactive spatial risk analysis necessary for implementing coordinated and agile management paradigms across large scales. We present a workflow that generates rapid spatial risk assessments on aquatic invasive species using occurrence data, spatially explicit environmental data, and an ensemble approach to species distribution modeling using five machine learning algorithms. For proof of concept and validation, we tested this workflow using extensive spatial and temporal hybridization and occurrence data from a well-studied, ongoing, and climate-driven species invasion in the upper Flathead River system in northwestern Montana, USA. Rainbow Trout (RBT; Oncorhynchus mykiss), an introduced species in the Flathead River basin, compete and readily hybridize with native Westslope Cutthroat Trout (WCT; O. clarkii lewisii), and the spread of RBT individuals and their alleles has been tracked for decades. We used remotely sensed and other geospatial data as key environmental predictors for projecting resultant habitat suitability to geographic space. The ensemble modeling technique yielded high accuracy predictions relative to 30-fold cross-validated datasets (87% 30-fold cross-validated accuracy score). Both top predictors and model performance relative to these predictors matched current understanding of the drivers of RBT invasion and habitat suitability, indicating that temperature is a major factor influencing the spread of invasive RBT and hybridization with native WCT. The congruence between more time-consuming modeling approaches and our rapid machine-learning approach suggest that this workflow could be applied more broadly to provide data-driven management information for early detection of potential invaders.

Alberta, British Columbia, Montana↗

USGS2021

Species invasion progressively disrupts the trophic structure of native food webs

Species invasions can have substantial impacts on native species and ecosystems, with important consequences for biodiversity. How these disturbances drive changes in the trophic structure of native food webs through time is poorly understood. Here, we quantify trophic disruption in freshwater food webs to invasion by an apex fish predator, lake trout, using an extensive stable isotope dataset across a natural gradient of uninvaded and invaded lakes in the northern Rocky Mountains, USA. Lake trout invasion increased fish diet variability (trophic dispersion), displaced native fishes from their reference diets (trophic displacement), and reorganized macroinvertebrate communities, indicating strong food web disruption. Trophic dispersion was greatest 25 to 50 y after colonization and dissipated as food webs stabilized in later stages of invasion (>50 y). For the native apex predator, bull trout, trophic dispersion preceded trophic displacement, leading to their functional loss in late-invasion food webs. Our results demonstrate how invasive species progressively disrupt native food webs via trophic dispersion and displacement, ultimately yielding biological communities strongly divergent from those in uninvaded ecosystems.

Montana↗

USGS2021

Climate change and expanding invasive species drive widespread declines of native trout in the northern Rocky Mountains, USA

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 trout species throughout the northern Rocky Mountains, USA. We found that the occupancy of native bull trout and cutthroat trout declined by 18 and 6%, respectively (1993–2018), and was predicted to decrease by an additional 39 and 16% by 2080. However, reasons for these occupancy reductions markedly differed among species: Climate-driven increases in water temperature and decreases in summer flow likely caused declines of bull trout, while climate-induced expansion of invasive species largely drove declines of cutthroat trout. Our results demonstrate that climate change can affect ecologically similar, co-occurring native species through distinct pathways, necessitating species-specific management actions.

Montana↗

USGS2021

Influence of water temperature and biotic interactions on the distribution of westslope cutthroat trout (Oncorhynchus clarkii lewisi) in a population stronghold under climate change

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 biotic factors (bull trout presence, Salvelinus confluentus ) on distributions of westslope cutthroat trout ( Oncorhynchus clarkii lewisi ; WCT) in the North Fork Flathead River, USA and Canada. The probability of WCT presence increased with stream temperature and decreased with channel gradient and bull trout presence, yet the effect of bull trout was reduced with increasing pool densities. Combining this model with spatially explicit stream temperature projections, we predict a 29% increase in suitable habitat under high emissions through 2075, with gains at mid-elevation sites predicted to exceed bull trout thermal tolerances and high-elevation sites expected to become more thermally suitable for WCT. Our study illustrates the importance of considering abiotic and biotic drivers to assess species response to climate change, helping to guide local-scale climate adaptation and management.

Alberta, British Columbia, Montana↗

USGS2020

Detecting population declines via monitoring the effective number of breeders (Nb)

Estimating the effective population size and effective number of breeders per year ( N b ) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one-sample LDNe estimator of N b in age-structured populations using a range of published species life history types, sample sizes, and DNA markers. N b estimates were biased by ~5%–10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence N b estimation. Precision was higher for 100 SNPs ( H ≈ 0.30) than for 15 microsatellites ( H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when N b was small ( N b < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe ) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that N b = 50 when the true N b = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject N b = 500 when the true N b = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in N b when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate N b for age structured populations ( https://github.com/popgengui/agestrucnb/ ), which should help biologists develop sensitive monitoring programmes for early detection of changes in N b and population declines.

Molecular Ecology Resources↗