Geology Reports⌕ Search

Geology topics

Robert Al-Chokhachy

Publications and source records attributed to Robert Al-Chokhachy.

At least 19 recordsLinked to original sources
USGS2026

Riverscape heterogeneity shapes population diversity for a migratory fish

Habitat patch dynamics can scale up to influence population demography and diversity with implications for resilience to environmental stochasticity. But how the spatial arrangement and size of habitat patches interact with other components of habitat heterogeneity to shape population diversity at larger spatial scales is not well understood. For riverine fishes, there is increasing evidence that tributary streams provide critical demographic support to main stem rivers. However, the extent to which main stem rivers rely on demographic contributions from tributaries, and the factors underlying this dependence, have not been assessed. Here, we used genetic stock identification to evaluate the effect of tributaries on population diversity of Yellowstone cutthroat trout ( Oncorhynchus virginalis bouvieri ) occupying the main stem Snake River, Wyoming, USA. We found that the main stem relied almost entirely on tributaries for demographic support, but main stem composition varied spatially among river sections. Distance between habitat patches, catchment area, and groundwater availability acted in concert to determine the contribution of specific tributaries to the main stem, but contributions were ultimately modulated by habitat connectivity. We also found evidence for multi-scale spatial structure in tributary contributions, providing insight into untested drivers of main stem river population diversity. Our results demonstrate how spatially discrete and distributed riverscape attributes influence population diversity at broader spatial scales, illustrating how ecosystem resilience emerges from the dynamic, two-way exchange of individuals and energy across habitat networks. Management plans for large rivers that address the ecological contributions of tributaries may be needed to achieve optimal outcomes. Similarly, conservation strategies that exclusively focus on headwater streams may fail to capture the broader habitat requirements necessary to maintain robust cold-water fish populations and associated recreational fisheries, particularly under global environmental change.

Wyoming↗
USGS2026

Establishing conservation benchmarks for threatened Bull Trout using spawner-recruitment relationships

Understanding the relationship between breeding adults and juvenile recruitment is fundamental to conserving at-risk species. Knowing whether recruitment is depensatory or compensatory at low adult abundances can aid in developing conservation strategies and recovery goals. However, this relationship requires long-term monitoring of two life stages, which can be costly and uncommon, especially for non-commercially harvested fish species, such as Bull Trout ( Salvelinus confluentus ). Listed as threatened in the United States and Canada, Bull Trout have declined throughout their range due to anthropogenic disturbances. Although spawner–recruitment relationships can create realistic recovery goals, this relationship is poorly characterized for Bull Trout. We used redd counts and juvenile densities from 11 Bull Trout populations to (1) establish spawner-recruitment dynamics, (2) assess environmental influences on productivity, and (3) derive recovery benchmarks. Bull Trout exhibited high recruitment productivity at low adult abundances and clear recruitment limitations at high abundances. Recruitment productivity varied across populations but was not associated with environmental covariates. We highlight strong compensatory capacity at low adult abundances, indicating possible recovery if limiting factors beyond spawning and rearing habitats are addressed.

Montana↗
USGS2025

Groundwater structures fish growth and production across a riverscape

Landscapes are composed of habitat patches and conditions that vary across space and time. While habitat variability and complexity can support important ecological processes and ecosystem services, the dynamic nature of habitats can also constrain organismal growth and production as optimal conditions are fleeting. In riverine ecosystems, groundwater discharge to streams stabilises water temperature and flow regimes, thus mediating how habitat complexity is expressed. Yet, how stable habitats structure growth and production within the broader landscape matrix is not well understood. In this study, we explored the effects of groundwater on spatiotemporal variation in growth and production for juvenile Yellowstone cutthroat trout ( Oncorhynchus virginalis bouvieri ) across the upper Snake River catchment, Wyoming, USA. We combined machine learning techniques and remotely sensed landscape data to estimate groundwater availability across the river network, which we linked to stream temperature regimes and conspecific density. We then used Bayesian hierarchical models to quantify the effects of temperature, density and groundwater on spatiotemporal variation in fish growth and production in 52 focal reaches. Finally, we predicted body size trajectories and trends in total production continuously over both space and time to understand the effect of groundwater at the riverscape scale. Groundwater discharged to streams where topography changes abruptly in valley-bottom areas underlain by coarse glacial deposits. Groundwater stabilised temperature regimes and was associated with high trout densities. Temperature and density, in turn, interacted to influence growth rates: growth increased strongly with temperature, but this effect was reduced when density was high. Accordingly, variation in groundwater availability among stream reaches diversified growth and production regimes. In reaches with low groundwater availability, growth and production declined over time from summer maxima. In contrast, in reaches with high groundwater availability, temporal trends in growth and production were hump-shaped—peaking in autumn—and mean production was greater. At the riverscape scale, temporal asynchrony in growth rates generated convergent spatial variation in growth capacity, but—when combined with density—led to the formation of distinct hotspots of production. Our results demonstrate how groundwater, an important driver of aquatic ecosystem heterogeneity, structures trout growth and production across space and time. Importantly, rare, but stable habitats may disproportionately affect ecological processes and serve as key sources of population diversity at larger spatial scales.

Wyoming↗
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

Impacts of lake elevation decline on spawning habitat of a critical, native forage species

Objective Lake elevation decline is a global phenomenon with pronounced effects in arid regions that changes the characteristics of nearshore habitat area available to lacustrine spawners, potentially impacting recruitment and whole-lake food web dynamics. Our objective was to understand the potential effects of lake elevation decline on spawning habitat for the Tui Chub Siphateles bicolor , a lacustrine spawner and critical component of the native food web in Pyramid Lake, Nevada. Methods We explored the distribution of ripe Tui Chub in nearshore habitat by associating habitat characteristics to ripe Tui Chub CPUE from a custom gill-net configuration, with data analyzed using generalized linear mixed-effects models. We then explored potential spawning habitat availability at all potential lake elevations using an elevation-explicit model of the basin that we developed based on several bathymetric and geospatial data sets and the knowledge of spawner distribution gained in the first component of the study. Results Ripe Tui Chub catch was primarily predicted by temperature, reaching a maximum between 14.2°C and 24.8°C found at less than 15 m of depth in Pyramid Lake throughout the summer spawning period. We estimated that with a contemporary decline in lake elevation of 8 m, Pyramid Lake will host the minimum area of spawning habitat based on morphometry alone at a 40% decrease from a theoretical maximum. Conclusions A decrease in lake elevation or an increase in lake temperatures—both of which are probable events based on future climate scenarios and estimates of water extraction upstream of Pyramid Lake—is likely to further restrict Tui Chub spawning habitat area. Our results have important implications for ecological water demand in Pyramid Lake and provide managers with information facilitating a science-based approach to managing the fish community.

Nevada↗
USGS2025

Principles of riverscape health

Riverscapes are the integration of terrestrial and aquatic systems from headwaters to estuaries that provide habitat and ecosystem benefits when in good health. However, current riverscape degradation is pervasive, impairing the function and resulting benefits of these systems. Healthy riverscapes are adaptive and some can ‘heal’ after disturbance with minimal to no human assistance. As riverscape health is threatened, a need exists to address current degradation and understand the potential for riverscape restoration—concisely communicating what comprises healthy riverscapes is essential to direct limited resources and increase efficacy of restoration and conservation efforts. Healthy riverscapes have (i) space to interact within their valley bottom; (ii) natural flow, sediment, and vegetation regimes appropriate to the biophysical setting and river type; and (iii) structural forcing to support diversity and that creates varied residence times for water, sediment, and vegetation. These three principles are grounded in interdisciplinary science and lessons from riverscape scientists and restoration practitioners across the world. Understanding the context, anthropogenic influences, boundary conditions, and legacy effects influencing riverscapes is essential for the appropriate application of these principles in pursuit of achieving riverscape health. Emphasizing a holistic, biogeomorphic view of riverscapes through these principles can guide policies, restoration actions, and monitoring frameworks that ensure that riverscapes remain capable of accommodating and adjusting to disturbances while continuing to support biodiversity and human benefits.

WIREsWATER (Wiley Interdisciplinary Reviews Primer↗
USGS2025

Native Yellowstone cutthroat trout Oncorhynchus virginalis bouvieri growth and survival in a headwater stream primarily driven by warming stream temperatures, with non-native brown trout Salmo trutta posing an additional threat to survival

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 trout (YCT) Oncorhynchus virginalis bouvieri and non-native brown trout Salmo trutta growth rates and apparent survival were affected by hydroclimatic conditions and (for YCT) the presence of brown trout in a tributary. Growth (YCT) and survival (both species across size classes) were negatively related to warming stream temperatures. Brown trout growth was positively related to increasing daily streamflow variability (a proxy for streamflow), but this variable was not included in the top YCT growth model. Density-dependent effects appeared to be non-existent (growth) or weakly positive (survival). When sympatric with brown trout, YCT displayed worse survival than allopatric YCT across environmental conditions. Broadly, we found native and non-native trout respond to different hydroclimatic conditions that shift with changing climatic conditions, and brown trout represent an additional threat to YCT survival.

Montana↗
USGS2025

The effects of unpaved roads on instream sediment: Patterns and challenges for monitoring

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 sediment distributions and (2) a targeted field study to evaluate the responses of streambed and suspended sediment collected at locations above and below road–stream connection points to better understand the consistency of responses. Regional analyses indicated a significant positive relationship between road density and fine sediment in pool tails and a significant negative relationship between road density and median particle size. We also found significant relationships between landscape, climate, and local covariates and streambed sediment metrics, where most of the parameter estimates of the covariates were equal to or stronger than those for road density. Field studies suggested higher suspended sediment levels across the seasonal hydrologic regime where roads were open to travel year-round. However, sediment responses to road–stream connection points varied by metric and site. Together, our results indicated negative relationships between increasing road densities and sediment size distributions, but detecting road effects at site scales will be challenging given the effects of covariates that can overwhelm sediment signals.

Montana↗
USGS2025

Appendix B: Patterns of bull trout Salvelinus confluentus demography, life history, abundance, and trends in the Lewis River

Declines in the distribution and abundance of bull trout ( Salvelinus confluentus ) across much of the historical range in the Pacific Northwest region of Canada and the United States have been well documented (Post and Johnston 2002; Rieman et al. 1997). Recent estimates of population trends appear to vary considerably across regions with large numbers of migratory and resident populations exhibiting substantial declines in adult abundance (Al-Chokhachy et al. 2016; Kovach et al. 2018), whereas others remain stable or potentially increasing (Erhardt and Scarnecchia 2014; Meyer et al. 2014). For example, 61% of the core populations in Alberta, Canada, are considered declining, and 39% are stable or increasing (Alberta Sustainable Resource Development 2012). The variability in population status and trends highlights the importance of population-specific data. Much of our understanding of bull trout life history has stemmed from a few, well-studied populations, and continuing to improve our knowledge of the variability in life-history expressions (e.g., Starcevich et al. 2012) can support directing local and regional conservation efforts (sensu Schindler et al. 2010). Here, we consider the life history, demographic patterns, and assess potential threats for an adfluvial population of bull trout in the upper Lewis River basin in Washington, USA. We synthesized recent monitoring efforts and field studies to refine our understanding of bull trout life-history expressions (i.e., migration patterns), demographics, and genetic status. We further evaluated the potential threats of brook trout ( S. fontinalis ), a species that is not native to the Lewis River, but which was recently documented in bull trout monitoring efforts (Al-Chokhachy et al. 2024). Our specific objectives included evaluating: (1) trends in size structure of subadults and adult bull trout (2014 – 2024); (2) patterns of adult migration and life-history and climate drivers of migration patterns (2011 – 2024); (3) the within-year temporal patterns of bull trout and coho salmon ( Oncorhynchus kisutch ) spawning and superimposition of bull trout redds by spawning coho salmon (2024); (4) temporal trends in abundance for adult and juvenile bull trout from annual monitoring methods (2008 – 2024); and (5) the current (2024) extent of non-native brook trout in wetland habitat adjacent to Yale Lake.

Washington↗
USGS2024

Spatial and temporal variability of movements among sympatric salmonids in an unfragmented inland watershed

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 stationary PIT arrays over 4 years, and located tagged fish between arrays by conducting mobile surveys. Result Movement patterns varied seasonally, among species, and among locations. Movement was greatest in the middle portion of the watershed, which included a pristine main‐stem canyon and lower reaches of major tributaries. Fish rarely left the canyon, but movement into the canyon from other regions was common. Mountain Whitefish were most likely to move, and Brown Trout were least likely to move. Most fish travelled less than 10 km, but some fish travelled over 100 km. Distinct movement patterns were not evident; rather, a continuous spectrum of movement behaviors was apparent. Movements by Mountain Whitefish and Rainbow Trout increased during their spawning periods. Movements peaked when mean daily water temperatures were between 11.3 and 17.1°C. Conclusion Movements were diverse and probably contributed to metapopulation dynamics, population resiliency, and species diversity. Fish movements along stream networks connect populations across diverse landscapes, and therefore, protecting and restoring stream connectivity along inland streams such as the Smith River is critical to maintaining productive fish assemblages.

Montana↗
USGS2024

From pixels to riverscapes: How remote sensing and geospatial tools can prioritize riverscape restoration at multiple scales

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 implement restoration actions. Leveraging remote sensing and geospatial tools to develop spatially continuous information across nested hierarchical scales may support increased understanding of local riverscape reaches in their broader network context. Using riparian (vegetation) and geomorphic (elevation) indicators to assess status of riverscape health, along with a measure of restoration capacity (valley bottom area), could be adapted to fit specific management goals related to riverscape restoration. Frameworks using remotely sensed vegetation and elevation data to prioritize restoration continuously across riverscapes at restoration-relevant, reach-scales may uphold the ecosystem services provided by riverscapes. By incorporating local knowledge and identifying caveats for using these datasets, continuous inferences can be applied at network scales (watershed to regional extent and reach-scale resolution) to prioritize restoration over a wide variety of ecoregions.

California, Nevada↗
USGS2023

Shrinking body size and climate warming: Many freshwater salmonids do not follow the rule

Declining body size is believed to be a universal response to climate warming and has been documented in numerous studies of marine and anadromous fishes. The Salmonidae are a family of coldwater fishes considered to be among the most sensitive species to climate warming; however, whether the shrinking body size response holds true for freshwater salmonids has yet to be examined at a broad spatial scale. We compiled observations of individual fish lengths from long-term surveys across the Northern Hemisphere for 12 species of freshwater salmonids and used linear mixed models to test for spatial and temporal trends in body size (fish length) spanning recent decades. Contrary to expectations, we found a significant increase in length overall but with high variability in trends among populations and species. More than two-thirds of the populations we examined increased in length over time. Secondary regressions revealed larger-bodied populations are experiencing greater increases in length than smaller-bodied populations. Mean water temperature was weakly predictive of changes in body length but overall minimal influences of environmental variables suggest that it is difficult to predict an organism's response to changing temperatures by solely looking at climatic factors. Our results suggest that declining body size is not universal, and the response of fishes to climate change may be largely influenced by local factors. It is important to know that we cannot assume the effects of climate change are predictable and negative at a large spatial scale.

Global Change Biology↗
USGS2023

Timing of reproduction underlies fitness tradeoffs for a salmonid fish

Life history diversity is generated and maintained in part by density-dependent fitness tradeoffs that inhibit a single trait value from reaching fixation. While central to our understanding of evolution, demonstrating density dependence in the strength of fitness tradeoffs is difficult in natural systems. The timing of reproduction is a key life history trait that determines access to breeding habitat and exposure of offspring to competitive interactions and environmental conditions. Understanding the processes underlying diversity in reproductive timing will aid efforts to increase adaptive capacity under global environmental change. Here, we used detailed field studies, genetic parentage assignment, and simulation modeling to evaluate the fitness tradeoffs associated with the timing of reproduction for Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri in groundwater-dominated tributaries to the upper Snake River, Wyoming, USA. We conducted our study across two years to understand how the strength of tradeoffs changes with population density. We found that early breeders experienced reduced reproductive success relative to later breeders due to the negative impact of nest superimposition (where later breeders construct nests overlapping those constructed previously) on embryo survival. However, as the risk of superimposition declined in the low-density year and early breeders experienced fewer losses, reproductive success became more similar among individuals breeding at different times. Further, in the spring following the critical period for growth and survival, offspring of early breeders had experienced longer growing seasons, attained larger body sizes, and were equally abundant relative to those of later breeders, suggesting that fitness losses due to superimposition may be offset by size-dependent competitive ability and overwinter survival. Our results illustrate a mechanism underlying diversity in the timing of reproduction for salmonids. This type of life history diversity will help to ensure the resilience and stability of salmonid populations attempting to adapt to changing local stressors associated with global climate change.

Oikos↗
USGS2023

Using continuous surveys to evaluate precision and bias of inferences from design-based reach-scale sampling of stream habitat

Accurately estimating stream 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 the effectiveness of reach-based sampling designs for stream habitat assessments. Here, we used continuous habitat surveys to census stream attributes in tributaries in the upper Lewis River, WA and better understand the potential bias and precision of reach-based designs. We used resampling analyses via bootstrapping to create simulated outcomes of different sampling designs including simple random with equal probability, simple random with unequal probability, and a generalized random tessellation stratified design (GRTS). We found precision of estimates of habitat attributes (large woody debris, residual pool depth, and grain size) increased with sampling intensity; however, the effort needed to achieve reasonable precision (CV = 0.20) varied across streams, attributes, and designs. Bias was relatively low, but also varied across streams and attributes. Our findings illustrate the challenges of using reach-based designs for stream habitat assessments and the need for novel approaches for broader data collection.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2023

Redd superimposition mediates the accuracy, precision, and significance of redd counts for cutthroat trout

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 redds. Here, we provide a mechanistic evaluation of the effects of superimposition on the error structure and biological significance of redd count data for Yellowstone cutthroat trout ( Oncorhynchus clarkii bouvieri ) spawning within tributaries to the Snake River, Wyoming. We used a Bayesian framework to parse observation error into distinct components and found low detection of redd clusters (i.e., areas of superimposition) was offset by overestimates of the number of redds per cluster, such that observed counts accurately reflected census redd abundance. However, a saturating relationship between redd counts and spawner abundance indicated that counts is best interpreted as effective reproductive effort rather than spawner abundance. Our results provide a mechanistic understanding of redd count data that can be used to assess their application and interpretation for monitoring.

Wyoming↗
USGS2023

Vital sign monitoring is good medicine for parks

Nearly 70 years ago a young ranger naturalist working in Yellowstone National Park (YNP), Frederick B. Turner, became fascinated with the abundance of frogs next to his cabin at “Soldier Creek” (known as Lodge Creek today). This interest blossomed into Turner’s PhD research and his publication in 1960 about the local population of Columbia spotted frogs (shown to right) became a classic for herpetologists. Unfortunately, the frog population Turner studied had a less positive future in store. Research by Idaho State University biologists in the 1990s revealed the Lodge Creek population had dwindled by 80%. Now, most of Turner’s study area is bereft of spotted frogs, and the remnant population near Yellowstone Lake is affected by a steep decline in reproduction and frequent disease outbreaks. Meanwhile, amphibian population declines documented worldwide, including in national parks of the western U.S., have become common. In YNP and neighboring Grand Teton National Park, we face the important questions of whether widespread amphibian declines are occurring here and if so, what do they portend. Can amphibians inform us about the health and changing conditions of wetlands in YNP? What are the implications of diminishing wetlands for other water-dependent species? And, more broadly, can amphibian and other living organisms serve as reliable indicators or vital signs for park health? In this issue of Yellowstone Science, we discuss how ecosystem science is taking cues from the medical field by relying on vital sign monitoring programs to assess ecosystem health.

Yellowstone Science↗
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↗