Robert Al-Chokhachy

• PhD, Aquatic Ecology
• Researcher at United States Geological Survey

Warming rivers and interactions with non-native species impact salmonid species globally. Understanding how hydroclimatic conditions synergistically and independently interact with non-native species is critical for effectively managing salmonids into the future. We used a 10-year mark–recapture dataset to assess how native Yellowstone cutthroat tr...

Despite > 700,000 km of unpaved roads in the western United States, our knowledge of how roads impact instream sediment is unclear. We combined two studies, including (1) a regional analysis linking stream habitat data from a large‐scale monitoring program with road density data to identify generalizable relationships between roads and streambed se...

Objective Our aim was to determine the movement patterns of three abundant salmonids—Brown Trout Salmo trutta , Mountain Whitefish Prosopium williamsoni , and Rainbow Trout Oncorhynchus mykiss —in the Smith River watershed of Montana. Methods We tagged 7172 fish with passive integrated transponder (PIT) tags, monitored their movements past 15 stat...

Prioritizing restoration opportunities effectively across entire riverscape networks (i.e., riverine landscape including floodplain and stream channel networks) can be difficult when relying on in‐channel, reach‐scale monitoring data, or watershed‐level summaries that fail to capture riverscape heterogeneity and the information necessary to impleme...

Redd counts are commonly applied to estimate spawning population size for salmonids and allow for broad spatial and temporal coverage in monitoring efforts. However, the utility of redd counts may be compromised by observation error, particularly with respect to superimposition, where later arriving spawners construct redds overlapping existing red...

Accurately estimating stream channel characteristics is essential for managing and restoring populations and aquatic ecosystems. Reach-based sampling designs have been used extensively to collect fisheries related data; however, few studies have examined accuracy and precision of scaling up reach-based sampling designs to stream habitat assessments...

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 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...

In arid ecosystems, available water is a critical, yet limited resource for human consumption, agricultural use, and ecosystem processes—highlighting the importance of developing management strategies to meet the needs of multiple users. Here, we evaluated how water availability influences stream thermal regimes and life-history expressions of Laho...

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...

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...

Fish managers must weigh trade‐offs among cost, speed, efficiency, and ecological adaptation when deciding how to translocate native salmonids to either establish or genetically augment populations. Remote site incubators (RSIs) appear to be a reasonable strategy, but large‐scale evaluations of this method have been limited. We used 129 RSIs to inc...

Climate change and non-native species are considered two of the biggest threats to native salmonids in North America. We evaluated how non-native salmonids and stream temperature and discharge were associated with Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) distribution, abundance, and body size to gain a more complete understanding...

The potential to provide inferences about fish abundance from environmental (e)DNA samples has generated great interest. However, the accuracy of these abundance estimates is often low and variable across species and space. A plausible refinement is the use of common aquatic habitat monitoring data to account for attributes that influence eDNA dyna...

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...

Many freshwater fish populations have been greatly reduced, with particular loss of migratory fishes. Recovering depleted populations is challenging as threats are often plentiful and complex, especially in arid environments where demands for water resources are high. Here, we describe how a collaborative, multifaceted approach has spurred natural...

Like many other salmonids, Bull Trout Salvelinus confluentus migratory life‐history expressions are becoming increasingly rare. A critical step in effectively refining management and conservation strategies is a robust assessment of the effectiveness of such strategies and key biological information used in monitoring and recovery planning. To addr...

Environmental DNA (eDNA) detection probability increases with volume of water sampled. Common approaches for collecting eDNA samples often require many samples since these approaches usually use fine filters, which restrict the volume of water that can be sampled. An alternative to collecting many, small volume water samples using fine filters may...

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...

Introduced species can have important effects on the component species and processes of native ecosystems. However, effective introduced species management can be complicated by technical and social challenges. We identify “social–ecological mismatches” (that is, differences between the scales and functioning of interacting social and ecological sy...

Coldwater fishes are sensitive to abiotic and biotic stream factors, which can be influenced by climate. Distributions of inland salmonids in North America have declined significantly, with many of the current strongholds located in small headwater systems that may serve as important refugia as climate change progresses. We investigated the effects...

Nonnative trout are a considerable threat to native salmonids yet our understanding of the mechanisms behind interspecific interactions remains limited. We evaluated the impacts of nonnative Brown Trout Salmo salar on a population of Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri in Montana, USA. We contrasted diets, growth, and survival...

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...

Preserving remaining non‐hybridized Cutthroat Trout populations is a conservation priority often requiring management action. Although proactive Rainbow Trout and hybrid suppression programs offer a flexible tool, particularly in large interconnected river basins, this management approach is used less frequently than alternatives (barriers and pisc...

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...

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...

Despite the importance of hydrologic regimes to the phenology, demography, and abundance of fishes such as salmonids, there have been surprisingly few syntheses that holistically assess regional, species-specific trends in hydrologic regimes within a framework of climate change. Here, we consider hydrologic regimes within the Greater Yellowstone Ar...

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...

Temporal symmetry models (TSM) represent advances in the analytical application of mark–recapture data to population status assessments. For a population of char, we employed 10 years of active and passive mark–recapture data to quantify population growth rates using different data sources and analytical approaches. Estimates of adult population gr...

The Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri is native to the Rocky Mountains and has declined in abundance and distribution as a result of habitat degradation and introduced salmonid species. Many of its remaining strongholds are in headwater basins with minimal human disturbances. Understanding the life histories, vital rates, an...

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...

Global climate change is altering freshwater ecosystems and affecting fish populations and communities. Underpinning changes in fish distribution and assemblage-level responses to climate change are individual-level physiological constraints. In this review, we synthesize the mechanistic effects of climate change on neuroendocrine, cardiorespirator...

Freshwater wetlands are particularly vulnerable to climate change. Specifically, changes in temperature, precipitation, and evapotranspiration (i.e., climate drivers) are likely to alter flooding regimes of wetlands and affect the vital rates, abundance, and distributions of wetland-dependent species. Amphibians may be among the most climate-sensit...

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...

Unpaved forest roads remain a pervasive disturbance on public lands and mitigating sediment from road networks remains a priority for management agencies. Restoring roaded landscapes is becoming increasingly important for many native coldwater fishes that disproportionately rely on public lands for persistence. However, effectively targeting restor...

Understanding how climate change may facilitate species turnover is an important step in identifying potential conservation strategies. We used data from 33 sites in western Montana to quantify climate associations with native bull trout (Salvelinus confluentus) and non-native brown trout (Salmo trutta) abundance and population growth rates (λ). We...

Effects of climate change over the next century will have important consequences for freshwater fish distributions and abundance. A fish’s body temperature closely mirrors that of its environment. Consequently, the physiology, ontogeny, and life histories of freshwater fishes are regulated by the timing and magnitude of streamflow and temperature r...

Knowledge of climatic variability at small spatial extents (< 50 km) is needed to assess vulnerabilities of biological reserves to climate change. We used empirical and modeled weather station data to test if climate change has increased the synchrony of surface air temperatures among 50 sites within the Greater Yellowstone Area (GYA) of the interi...

Results and discussion for data sets 2–5. (PDF)

The proportion of sites in each season with significant trends for each descriptive statistic for minimum and maximum temperature distributions using the modeled SNOTEL + COOP data, 1948–2012. (PDF)

Description of snowpack telemetry (SNOTEL) and Cooperative Observer Network (COOP) weather stations used in this study. (PDF)

Slopes and intercepts for seasonal Tmin and Tmax distribution metrics using the modeled SNOTEL + COOP data, 1948–2012. (PDF)

Slopes and intercepts for monthly Tmin and Tmax distribution metrics using the modeled SNOTEL + COOP data, 1948–2012. (PDF)

Management prioritization of species relative to their climate change sensitivity. (PDF)

Habitat fragmentation, which affects many native salmonid species, is one of the major factors contributing to the declines in distribution and abundance of Bull Trout Salvelinus confluentus. Increasingly, managers are considering options to maintain and enhance the persistence of isolated local populations through active management strategies. Und...

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...

We completed a multi-year synthesis of the data and analyses for the Walla Walla River to help broadly prioritize conservation actions and inform the conservation of bull trout. • The assessment provides fundamental and critical information on bull trout growth, movement patterns, and survival rates. At the population level we assess abundance, str...

Little is known about the variability in the spatial and temporal distribution of spawning potamodromous trout despite decades of research directed at salmonid spawning ecology and the increased awareness that conserving life history diversity should be a focus of management. We monitored a population of fluvial–resident Bonneville Cutthroat Trout...

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...

Exotic plant invasions into riparia often result in shifts in vegetative composition, altered stream function, and cascading effects to biota at multiple scales. Characterizing the distribution patterns of exotic plants is an important step in directing targeted research to identify mechanisms of invasion and potential management strategies. In thi...

We combine large observed data sets and dynamically downscaled climate data to explore historic and future (2050-2069) stream temperature changes over the topographically diverse Greater Yellowstone Ecosystem (elevation range = 824 - 4,017 m). We link future stream temperatures with fish growth models to investigate how changing thermal regimes cou...

Understanding a species' thermal niche is becoming increas-ingly important for management and conservation within the con-text of global climate change, yet there have been surprisingly few efforts to compare assessments of a species' thermal niche across methods. To address this uncertainty, we evaluated the differences in model performance and in...

The Upper Snake River represents one of the largest remaining strongholds of Yellowstone cutthroat across its native range. Understanding the effects of restoration activities and the diversity of life-history patterns and factors influencing such patterns remains paramount for long-term conservation strategies. In 2011, we initiated a project to q...

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...

Habitat fragmentation, hybridization, and competition with nonnative salmonids are viewed as major threats to Lahontan cutthroat trout Oncorhynchus clarkii henshawi . Understanding Lahontan cutthroat trout behavior and survival is a necessary step in the reintroduction and establishment of naturally reproducing populations of Lahontan cutthroat tro...

Understanding the factors associated with the current distribution of Yellowstone cutthroat trout is an imperative step in the design and implementation of future conservation and management strategies, particularly given emerging potential stressors associated with regional climate change. Despite substantial interagency effort to develop rangewid...

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...

Background/Question/Methods Conceptual models outlining anthropogenic stressors and their hypothesized impacts to biological integrity are critical to the design of effectiveness monitoring programs. Benthic macroinvertebrates (BMI) are one of the primary tools for quantifying the cumulative impacts of land management activities on biological int...

Aquatic invasive species present unique ecological threats. Pervasive habitat modification and the ease of global transportation have facilitated their spread, and they are now a leading threat to native species and to the functioning of entire ecosystems. Various researchers have suggested steps to take in treating aquatic invasive species, and in...

Habitat degradation and introduction of non-native salmonids have caused substantial declines in abundance and distribution of Yellowstone cutthroat trout. Additionally, global climate change is expected to exacerbate current threats through changes to thermal regimes, hydrology, stream productivity, and distributions of non-native species. Underst...

The invasion of nonnative fishes is often facilitated through a complex interaction of biotic and abiotic factors operating at multiple spatial and temporal scales within riverscapes. Human-mediated hybridization can be a major consequence of nonnative species invasions and is a leading cause of biodiversity loss worldwide. How hybridization affect...

Understanding the factors associated with the current distribution of Yellowstone cutthroat trout is an imperative step in the design and implementation of future conservation and management strategies, particularly given emerging potential stressors associated with regional climate change. Despite substantial interagency effort to develop rangewid...

Publication of the RiverScapes paper in 2002 by Fausch et al. presaged rapid advances in the ability to monitor and model lotic ecosystems and the natural world. In the decade since, new techniques have emerged that provide high-resolution spatial and temporal mapping, modeling, and monitoring of biophysical attributes, which fill important deficie...

The quality and quantity of stream habitat can have profound impacts on the distribution and abundance of aquatic species. Stream networks, however, are dynamic in their response to natural- and human-induced disturbance regimes, which results in spatially explicit patterns of temporal variability. Quantifying spatial patterns in habitat (temporal)...

We illustrate how the variability in data collected within and among habitat sampling protocols can profoundly affect the interpretation of habitat quality and quantity, along with the development of habitat-to-fish population metrics. We input data collected from two standardized survey techniques, as well as data collected using one standardized...

Identifying the overall status of freshwater streams is an important step in evaluating effects of land management and prioritizing restoration activities. To address these needs, we developed an index of physical habitat condition for headwater streams based on physical stream habitat data (2003–2007) and evaluated the condition status of 217 refe...

An understanding of habitat relationships for bull trout Salvelinus confluentus remains an important component for identifying future restoration, management, and recovery efforts. We examined past efforts through a comprehensive synthesis of peer-reviewed articles evaluating bull trout habitat relationships, and we used field data within classific...

We evaluated the potential for reintroducing Lahontan cutthroat trout Oncorhynchus clarkii henshawi, a species listed under the Endangered Species Act, into a lacustrine system where the biotic community has changed dramatically since the species' extirpation there. Since 2002, 76,547 Lahontan cutthroat trout have been reintroduced into Fallen Leaf...

The Puerto Rican terrestrial frog (Eleutherodactylus coqui) has received considerable attention in Hawaii because of its rapid spread, loud mating calls, and its potential threat to native species. Thus far, its invasion potential on the Island of Hawaii remains poorly understood. Critical components for determining this potential are robust estima...

Using empirical field data for bull trout (Salvelinus confluentus), we evaluated the trade-off between power and sampling effortcost using Monte Carlo simulations of commonly collected markrecaptureresight and count data, and we estimated the power to detect changes in abundance across different time intervals. We also evaluated the effects of moni...

The Puerto Rican frog (Eleutherodactylus coqui) is an invasive pest in Hawaii. Citric acid is approved for controlling these frogs, but has been limited to terrain accessible by foot or vehicle. We determined the effectiveness of helicopter applications of 16% citric acid and repeated 11% citric acid treatments for eradicating and/or reducing densi...

Identification of the factors limiting inland salmonid populations, such as those of the threatened bull trout Salvelinus confluentus in the Pacific Northwest, can be particularly challenging due to substantial gaps in our understanding of population demographics, population structure in the presence of multiple life history forms, and vital rates....

Increasing concerns about management and recovery of the threatened bull trout (Salvelinus confluentus) prompted the Bull Trout Committee of Western Division American Fisheries Society to survey scientists working most closely with bull trout in Pacific Northwest drainages of the contiguous United States. We solicited scientific and judgment-based...

The management and recovery of populations of bull trout Salvelinus confluentus requires a comprehensive understanding of habitat use across different systems, life stages, and life history forms. To address these needs, we collected microhabitat use and availability data in three fluvial populations of bull trout in eastern Oregon. We evaluated di...

For salmonids that exhibit multiple life history forms within a single population, it may be necessary to evaluate the inconsistencies associated with population monitoring techniques. We compared mark– resight population estimates with those based on annual redd counts for bull trout Salvelinus confluentus in eastern Oregon. Our data suggest that...