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USGS2015

Fish assemblages in the Upper Esopus Creek, NY: Current status, variability, and controlling factors

The Upper Esopus Creek receives water diversions from a neighboring basin through the Shandaken Tunnel (the portal) from the Schoharie Reservoir. Although the portal is closed during floods, mean flows and turbidity of portal waters are generally greater than in Esopus Creek above their confluence. These conditions could potentially affect local fish assemblages, yet such effects have not been assessed in this highly regulated stream. We studied water quality, hydrology, temperature, and fish assemblages at 18 sites in the Upper Esopus Creek during 2009–2011 to characterize the effects of the portal input on resident-fish assemblages and to document the status of the fishery resource. In general, fish-community richness increased by 2–3 species at mainstem sites near the portal, and median density and biomass of fish communities at sites downstream of the portal were significantly lower than they were at sites upstream of the portal. Median densities of Salmo trutta (Brown Trout) and all trout species were significantly lower than at mainstem sites downstream from the portal—25.1 fish/0.1 ha and 148.9 fish/0.1 ha, respectively—than at mainstem sites upstream from the portal—68.8 fish/0.1 ha and 357.7 fish/0.1 ha, respectively—yet median biomass for Brown Trout and all trout did not differ between sites from both reaches. The median density of young-of-year Brown Trout at downstream sites (9.3 fish/0.1 ha) was significantly lower than at upstream sites (33.9 fish/0.1 ha). Waters from the portal appeared to adversely affect the density and biomass of young-of-year Brown Trout, but lower temperatures and increased flows also improved habitat quality for mature trout at downstream sites during summer. These findings, and those from companion studies, indicate that moderately turbid waters from the portal had few if any adverse impacts on trout populations and overall fish communities in the Upper Esopus Creek during this study.

New York↗

USGS2022

Monitoring fish abundance and behavior, using multi-beam acoustic imaging sonar, at a Selective Water Withdrawal structure in Lake Billy Chinook, Deschutes River, Oregon, 2020

Collection of juvenile salmonids at Round Butte Dam is a critical part of the effort to enhance populations of anadromous fish species in the upper Deschutes River because fish that are not collected at the dam may either incur increased mortality during dam passage or remain landlocked and lost to the anadromous fish population. Adaptive resolution imaging sonar systems were used to assess the behavior, abundance, and timing of fish at the entrance to the Selective Water Withdrawal (SWW) intake and fish collection structure located in the forebay of Round Butte Dam during the spring of 2020. The purpose of the SWW is to direct surface currents in the forebay to attract and collect downriver migrating juvenile salmonid smolts (Chinook salmon [ Oncorhynchus tshawytscha ], sockeye salmon [ O. nerka ], and steelhead [ O. mykiss ]) from Lake Billy Chinook and to enable operators of the SWW to withdraw water from surface and benthic elevations in the reservoir to manage downriver water temperatures. The objective of this study was to assess the abundance and behaviors of smolt-size fish (95–300 millimeters) observed near the SWW and to determine if the presence of bull trout ( Salvelinus confluentus; >350 millimeters), the predominant predator of juvenile salmonids, influenced the behavior of downriver migrants. Two imaging sonar units were deployed during the spring of 2020 smolt out-migration period. One unit monitored fish movements near the entrances and one unit monitored in one of the collection flumes of the SWW. The imaging sonar technology was informative for assessing abundance and spatial and temporal behaviors of smolt and bull trout-size fish. Smolt and bull trout-size fish were regularly observed near the entrance to and in the collection flume. Increased abundances were observed during the night, with corresponding increased discharge through the SWW, compared to during the day when discharge was reduced. Behavioral differences also were observed at different discharge rates, with smolt-size fish exhibiting more directed movement toward the collector during periods of increased discharge. Additionally, the presence of bull trout-size fish may have affected the behavior of smolt-size fish because a greater percentage of smolt-size fish were observed traveling away from the SWW when bull trout-size fish were present than when bull trout-size fish were absent. Increased counts of bull trout-size fish coincided with the increased abundances of smolt-size fish. Overall, the results indicate that smolt-size fish are more abundant near the entrance and in the flume of the SWW during periods of increased discharge, and bull trout-size fish were present at the SWW and may have affected smolt collection.

Oregon↗

USGS2020

Carbon dioxide-induced mortality of four species of North American fishes

Fisheries managers have a growing interest in the use of carbon dioxide (CO 2 ) as a tool for controlling invasive fishes. However, limited published data exist on susceptibility of many commonly encountered species to elevated CO 2 concentrations. Our objective was to estimate the 24-h 50% lethal concentration (LC 50 ) and 95% lethal concentration (LC 95 ) of CO 2 for four fishes (Rainbow Trout Oncorhynchus mykiss , Common Carp Cyprinus carpio , Channel Catfish Ictalurus punctatus , and Westslope Cutthroat Trout Oncorhynchus clarkii lewisi ). In the laboratory, we exposed juvenile fish to a range of CO 2 concentrations for 24 h in unpressurized, flow-through tanks. We developed a Bayesian hierarchical model to estimate the dose-response relationship for each fish species with associated uncertainty, and estimated 24-h LC 50 and LC 95 values based on laboratory trials for each species. The minimum concentration inducing mortality differed among cold water–adapted species and warm water–adapted species groups: 150 mg CO 2 /L for Westslope Cutthroat Trout and Rainbow Trout and 225 mg CO 2 /L for Common Carp and Channel Catfish. We observed complete mortality at 275 mg CO 2 /L (38,672 microatmospheres [μatm]), 225 mg CO 2 /L (30,711 μatm), and 495 mg CO 2 /L (65,708 μatm [Common Carp]; 77,213 μatm [Channel Catfish]) for Westslope Cutthroat Trout, Rainbow Trout, and both Common Carp and Channel Catfish, respectively. There was evidence of a statistical difference between the 24-h LC 95 values of Westslope Cutthroat Trout and Rainbow Trout (245.0 [222.2–272.2] and 190.6 [177.2–207.8] mg CO 2 /L, respectively). Additionally, these values were almost half the estimated 24-h LC 95 values for Common Carp and Channel Catfish (422.5 [374.7–474.5] and 434.2 [377.2–492.2] mg CO 2 /L, respectively). Although the experimental findings show strong relationships between increased CO 2 concentration and higher mortality, additional work is required to assess the efficacy and feasibility of a CO 2 application in a field setting.

Journal of Fish and Wildlife Management↗

USGS2001

Effects of dissolved carbon dioxide on the physiology and behavior of fish artificial streams

A new technology for treating waters contaminated with acid mine drainage involves the dissolution of limestone particles using carbon dioxide at pressures above ambient. Because of the fish health risks associated with episodes of high carbon dioxide levels in treated waters, we subjected three species of fish, brook trout ( Salvelinus fontinalis ), slimy sculpin ( Cottus cognatus ), and blacknose dace ( Rhinichthys atratulus ), to 24 h exposures of elevated dissolved carbon dioxide (CO 2 ) at three levels, ranging from 1.0 (low) to 6.3 (high)%, under laboratory conditions. We measured blood physiological variables as well as behavior, including feeding responses, before, during, and after exposure. Physiological responses differed by species, but all species had elevated hematocrits after 1 h of exposure. Brook trout hematocrits were higher at medium and high levels of CO 2 than in a control group (0.0% CO 2 ) after 24 h of exposure. Slimy sculpin hematocrits were higher in medium- and high-level exposure groups than in controls after 1 h, but not after 24 h, of exposure. Blacknose dace hematocrits were higher in all three exposure groups than in controls after 1 h but only in medium-level exposure groups after 24 h. Brook trout plasma glucose was significantly higher in medium- and high-level exposure groups after 1 h, and in the high-level group after 24 h, than in controls. Slimy sculpin plasma glucose was not significantly different in elevated CO 2 exposure groups from that of controls throughout exposure. Branchial ventilation was significantly greater in all species at elevated CO 2 during exposure, indicating stress; however, no difference was observed between treatment and control groups of blacknose dace after 24 h, indicating acclimation. Pectoral fin beats and cough rates were not consistently related to CO 2 exposure throughout the study. Brook trout had the longest lasting reaction to stress at lower levels of CO 2 among the three species tested. Many of the 11 observed behavioral variables, related to swimming, feeding, social, and illness factors, were affected by elevations of dissolved CO 2 . Two to seven behavioral variables (18–64% of those measured) were affected by treatment level of dissolved CO 2 with a trend by species for the number of variables affected: brook trout>blacknose dace>slimy sculpin. However, behavioral sensitivity to treatment level was greatest in blacknose dace. Recovery to pre-treatment activity rates for most behavior patterns (including feeding) was observed 24 h after cessation of exposure in all three species. Recovery was independent of treatment level, was most rapid in blacknose dace, and was slowest in brook trout. Overall, slimy sculpin was least affected behaviorally by elevated CO 2 . Although all three species showed stress response and changes in behavior at moderate levels of CO 2 (≥2%), brook trout and blacknose dace showed evidence of ability to avoid harmful CO 2 levels by swimming out of affected waters, whereas the slimy sculpin showed minimal behavioral changes despite remaining in place during exposure. Thus, predation risk and other sources of mortality seem minimal in the event of technological malfunction at a stream treatment site involving the use of CO 2 under pressure.

Environmental Toxicology↗

USGS2022

Informing management of Henrys Lake, Idaho using an integrated catch-at-age model

Henrys Lake, Idaho, supports a popular fishery for Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri and Yellowstone Cutthroat Trout × Rainbow Trout O. mykiss hybrids. A majority of the adult population of fish in Henrys Lake are of hatchery origin that were stocked as fingerlings. The fishery is closed to angling during the late winter and spring months, but fisheries managers are considering opening the fishery year-round with catch-and-release-only regulations or with a two-fish bag limit during the extended season. However, there is concern that the proposed management actions may negatively affect the current fishery. Therefore, we developed an integrated catch-at-age model to estimate population parameters for trout in Henrys Lake and used a simulation model to evaluate alternative management actions. Results of this study suggest that catch and release of both Yellowstone Cutthroat Trout and hybrids would increase and that abundance of trout in the spring (i.e., the start of the traditional season) would decrease under both proposed bag limits. Losses in abundance can be mitigated by stocking additional fish as long as no more than approximately 1,520,000 Yellowstone Cutthroat Trout are stocked annually. If catch-and-release-only regulations are implemented during the newly proposed season, total harvest is expected to decrease compared to the current fishery due to additional catch-and-release mortality. Ultimately, managers will need to prioritize harvest or catch-and-release opportunity, both of which provide additional utility to anglers, when choosing how to proceed with bag limit regulations.

Idaho↗

USGS2020

Comparison of underwater video with electrofishing and dive‐counts for stream fish abundance estimation

Advances in video technology enable new strategies for stream fish research. We compared juvenile (age‐0) and adult (age 1+) Brook Trout Salvelinus fontinalis abundance estimates from underwater video with backpack electrofishing and dive‐count methods across a series of stream pools in Shenandoah National Park, Virginia ( n = 41). Video methods estimated greater mean abundance of adult trout than 1‐pass electrofishing but were not different than 3‐pass electrofishing or dive‐count methods in this regard. In contrast, videos underestimated abundance of juvenile trout, and we suggest this is because predator avoidance‐behaviors by juvenile trout limit their use of microhabitat locations visible to cameras. Integrated abundance estimates from 2 cameras increased correspondence to comparison methods relative to single cameras, demonstrating the importance of an expanded field of view for video sampling in streams. Geomorphic features helped explain method‐wise differences: more adult trout were estimated with video than 3‐pass electrofishing as riffle crest depth and boulder composition increased, indicating habitat associations with trout escapement from electrofishing. Our results demonstrated that video techniques can provide a robust alternative or supplement to traditional methods for estimating adult trout abundance in stream pools.

Virgiinia↗

USGS2010

Founding population size of an aquatic invasive species

Non-native species of fish threaten native fishes throughout North America, and in the Rocky Mountains, introduced populations of lake trout threaten native populations of bull trout. Effective management of lake trout and other exotic species require understanding the dynamics of invasion in order to either suppress non-native populations or to prevent their spread. In this study, we used microsatellite genetic data to estimate the number of lake trout that invaded a population of bull trout in Swan Lake, MT. Examination of genetic diversity and allele frequencies within the Swan Lake populations showed that most of the genes in the lake trout population are descended from two founders. This emphasizes the importance of preventing even a few lake trout from colonizing new territory.

Conservation Genetics↗

USGS2018

Identifying cost-effective invasive species control to enhance endangered species populations in the Grand Canyon, USA

Recovering endangered species populations when confronted with the threat of invasive species is an ongoing natural resource management challenge. While eradication of the invasive species is often the optimal economic solution, it may not be a feasible nor desirable management action in other cases. For example, when invasive species are desired in one area, but disperse into areas managed for endangered species, managers may be interested in persistent, but cost-effective means of managing dispersers rather than eradicating the source. In the Colorado River, a nonnative rainbow trout ( Oncorhynchus mykiss ) sport fishery is desired within Glen Canyon National Recreation Area, however, dispersal downriver into the Grand Canyon National Park is not desired as rainbow trout negatively affect endangered humpback chub ( Gila cypha ). Here, we developed a bioeconomic model incorporating population abundance goals and cost-effectiveness analyses to approximate the optimal control strategies for invasive rainbow trout conditional on achieving endangered humpback chub adult population abundance goals. Model results indicated that the most cost-effective approach to achieve target adult humpback chub abundance was a high level of rainbow trout control over moderately high rainbow trout population abundance. Adult humpback chub abundance goals were achieved at relatively low rainbow trout abundance and control measures were not cost-effective at relatively high rainbow trout abundance. Our model considered population level dynamics, species interaction and economic costs in a multi-objective decision framework to provide a preferred solution to long-run management of invasive and native species.

Grand Canyon↗

USGS2021

Comparisons among three diet analyses demonstrate multiple patterns in the estimated adult diet of a freshwater piscivore, Salvelinus namaycush

Understanding trophic interactions is critical for successful resource management. However, studying diet patterns (e.g., spatial and seasonal changes) can require extensive effort. Using individual analyses to interpret patterns may be further complicated by assumptions and limitations of the analytical approach. We investigated and compared predicted adult lake trout (Salvelinus namaycush) diet composition and patterns using stomach content analysis (SCA), fatty acid analysis (FAS), and stable isotope analysis (SIA) individually and simultaneously. The three analyses were conducted for fall-captured fish in Lake Ontario and provided different diet composition estimates; SCA suggested alewife (Alosa pseudoharengus) was dominant by frequency and mass, while FAA and SIA suggested rainbow smelt (Osmerus mordax) contributed the most based on similarity among fatty acid signatures and two-stable isotope (carbon and nitrogen) mixing models, respectively. We hypothesize the disagreement among diet estimates is a result of a seasonal shift in diet variably expressed due to differing extent of time reflected by the diet metric: hours to days for SCA, weeks to months for FAA and several months for SIA. Despite variability in diet composition estimates among methods, similar patterns in lake trout diet were observed among the three diet analyses; the contribution of alewife in lake trout diet was greater for larger individuals and for males compared to females, particularly in the east and northeast regions of the lake where alewife density was relatively low. Thus, the complementary results from the three analyses suggest that length, location, sex, and season all influence lake trout diet. Individually, analyses often failed to identify these patterns in lake trout diet with significance, and some of the patterns have not been observed in previous studies of lake trout diet in Lake Ontario. The thorough description of lake trout diet obtained from a single sampling season demonstrates how simultaneous use of multiple diet analyses may allow investigation of spatial and seasonal diet composition and with reduced sampling effort.

Lake Ontario↗

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↗

USGS2023

Pelagic food web interactions in a large invaded ecosystem: Implications for reintroducing a native top predator

A series of species introductions, overexploitation, and habitat modification preceded the extirpation of Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi; LCT), historically the apex predator, from Lake Tahoe, California-Nevada, USA. Studies evaluating limiting factors for LCT emphasise the need to elucidate food web interactions, yet important knowledge gaps regarding trophic interactions among nonnative pelagic fishes and invertebrates remain. We quantified the abundance and consumption demand of planktivores with an emphasis on kokanee ( Oncorhynchus nerka ) and Mysis diluviana . We synthesised this new information with existing information for lake trout ( Salvelinus namaycush ). The seasonal supply of copepods satisfied the consumption demand of kokanee, but only supported low feeding and growth rates. Kokanee relied heavily on Mysis as prey, an unusual result. Mysis exhibited a high degree of herbivory initially followed by heavier consumption on copepods by larger individuals. Consumption demand for Mysis on copepods exceeded that of kokanee during all seasons. Mysis contributed to over 50% of the annual energy budget for lake trout up to 625 mm. Consumption of Mysis by lake trout and kokanee represented a significant source of mortality when compared to the production of Mysis . Predation on kokanee was sustainable, only involved lake trout >625 mm, and was focused on prespawning aggregations. Despite the presence of Mysis -fueled lake trout, kokanee have persisted; a noteworthy pattern when considering the negative responses of kokanee to nonnative lake trout and Mysis observed elsewhere. This pattern suggests that there may still be an effective niche for LCT in the invaded Lake Tahoe ecosystem.

California, Nevada↗

USGS2012

Long-term impacts of invasive species on a native top predator in a large lake system

1. Declining abundances of forage fish and the introduction and establishment of non-indigenous species have the potential to substantially alter resource and habitat exploitation by top predators in large lakes. 2. We measured stable isotopes of carbon (δ 13 C) and nitrogen (δ 15 N) in field-collected and archived samples of Lake Ontario lake trout ( Salvelinus namaycush ) and five species of prey fish and compared current trophic relationships of this top predator with historical samples. 3. Relationships between δ 15 N and lake trout age were temporally consistent throughout Lake Ontario and confirmed the role of lake trout as a top predator in this food web. However, δ 13 C values for age classes of lake trout collected in 2008 ranged from 1.0 to 3.9‰ higher than those reported for the population sampled in 1992. 4. Isotope mixing models predicted that these changes in resource assimilation were owing to the replacement of rainbow smelt ( Osmerus mordax ) by round goby ( Neogobius melanostomus ) in lake trout diet and increased reliance on carbon resources derived from nearshore production. This contrasts with the historical situation in Lake Ontario where δ 13 C values of the lake trout population were dominated by a reliance on offshore carbon production. 5. These results indicate a reduced capacity of the Lake Ontario offshore food web to support the energetic requirements of lake trout and that this top predator has become increasingly reliant on prey resources that are derived from nearshore carbon pathways.

Freshwater Biology↗

USGS2025

Mixed natal origins present management challenges for a non-native fish established throughout a modified river network

Expansion of non-native brown trout ( Salmo trutta ) in the Colorado River below Glen Canyon Dam motivated reevaluation of suppression strategies to minimize potential impacts to native fishes in the Grand Canyon, Arizona, USA. Brown trout are one of several non-native fish species of management concern in this river reach, and understanding their natal sources and movement patterns may assist managers in planning suppression strategies. We identified trace elements in brown trout otoliths, which, when coupled with location-specific water chemistry data, identified brown trout natal origins over 19 years. Strontium and manganese concentrations revealed distinct emigration patterns from natal tributary streams and the mainstem Colorado River over two periods. Adult brown trout collected from throughout our study area showed mixed tributary and mainstem natal origins, which persisted during suppression efforts in a known spawning tributary. Unexpectedly, we found evidence of brown trout reproduction in the Colorado River for at least a decade before documentation through field monitoring. Our findings may inform but complicate the development of management strategies for system-wide brown trout suppression.

Arizona↗

USGS1983

Resistance of salmonids to Aeromonas salmonicida: Relation between agglutinins and neutralizing activities

Serum of furunculosis‐resistant rainbow trout Salmo gairdneri, when injected into brook trout Salvelinus fontinalis, increased resistance of the brook trout to virulent challenges of Aeromonas salmonicida, the furunculosis pathogen. Serum from susceptible Atlantic salmon Salmo salar did not confer passive resistance on brook trout although natural agglutinin titers in Atlantic salmon serum were equal to those in rainbow trout. Further analyses indicated that rainbow trout serum neutralized toxic components produced by A. salmonicida, but that Atlantic salmon serum did not. When 11 strains of rainbow trout were challenged with 10 9 virulent cells of A. salmonicida, a range of mortality from 0 to 83% resulted. Although no correlation was observed between the natural serum agglutinin level of a particular strain and its relative resistance to experimental pathogen challenge, an inverse relation was apparent between cytotoxic serum‐neutralization activity and resistance to furunculosis.

Transactions of the American Fisheries Society↗

USGS1996

Episodic acidification of small streams in the northeastern United states: Effects on fish populations

As part of the Episodic Response Project (ERP), we studied the effects of episodic acidification on fish in 13 small streams in the northeastern United States: four streams in the Adirondack region of New York, four streams in the Catskills, New York, and five streams in the northern Appalachian Plateau, Pennsylvania. In situ bioassays with brook trout (Salvelinus fontinalis) and a forage fish species (blacknose dace (Rhinichthys atratulus), mottled sculpin (Cottus bairdi), or slimy sculpin (Cottus cognatus), depending on the region) measured direct toxicity. Movements of individual brook trout, in relation to stream chemistry, were monitored using radiotelemetry. Electrofishing surveys assessed fish community status and the density and biomass of brook trout in each stream. During low flow, all streams except one had chemical conditions considered suitable for the survival and reproduction of most fish species (median pH 6.0-7.2 during low flow; inorganic Al < 60 μg/L). ERP streams with suitable conditions during low flow, but moderate-to-severe episodic acidification during high flow, had higher fish mortality in bioassays, net down-stream movement of brook trout during events, and lower brook trout density and biomass compared to nonacidic streams, and lacked acid-sensitive fish species (blacknose dace and sculpin). Movement of trout into refugia (areas with higher pH and lower Al) during episodes partially mitigated the adverse effects of episodes. Recolonization from alkaline tributaries or microhabitats can maintain low densities of fish in streams that experience severe acidic episodes, but it is not sufficient to sustain fish densities and community composition at levels expected in the absence of these episodes. Fish responses to acid-base chemistry were fairly consistent across regions. In general, trout abundance was reduced and acid-sensitive fish species were absent from ERP streams with median pH < 5.0-5.2 during high flow and inorganic Al > 100-200 μg/L. We conclude that episodic acidification can have long-term effects on fish communities in small streams.

Ecological Applications↗

USGS2003

Reconnaissance-level application of physical habitat simulation in the evaluation of physical habitat limits in the Animas Basin, Colorado

The Animas River is in southwestern Colorado and flows mostly to the south to join the San Juan River at Farmington, New Mexico (Figure 1). The Upper Animas River watershed is in San Juan County, Colorado and is located in the San Juan Mountains. The lower river is in the Colorado Plateau country. The winters are cold with considerable snowfall and little snowmelt in the mountains in the upper part of the basin. The lower basin has less snow but the winters are still cold. The streamflows during the winter are low and reasonably stable. The native trout in the Animas Basin is the cutthroat trout. Few native trout remain and the trout found in the upper watershed are brook trout with rainbow and brown trout in the lower river. There is considerable metal contamination in the upper basin near Silverton but a brook trout fishery does exist in the Animas River from just above Howardsville to where the Animas joins Cement Creek in Silverton. There are two principle objectives of the habitat studies in the Animas Basin: (1) to improve understanding of the fate of sediment from mining operations from the view point of physical habitat impacts, and (2) to determine if reconnaissance level physical habitat studies can be useful in understanding the impacts of mining on the aquatic ecosystem. Part of the project was to apply the Physical Habitat Simulation System (PHABSIM) to selected locations in the Upper Animas River Basin, Colorado in order to demonstrate the importance of physical habitat in evaluating the efficacy of mined land remediation activities. Physical habitat analysis included the use of sedimentation variables in physical habitat simulations. A map of the Upper Animas Basin is presented in Figure 2. The project involves collecting data for the following locations: Animas River above Magee Creek; Animas River above Howardsville; Animas River below Howardsville; Animas River above Silverton at Hillsdale Cemetery; Animas River at Silverton; Cement Creek above Silverton; Cement Creek at Silverton; Mineral Creek at Powerline above Silverton; Mineral Creek at Campground; South Mineral Creek at Overflow Campground; Mineral Creek above Bear Creek; Mineral Creek at Silverton; Animas River below Silverton; and Animas River at Elk Park. Bed material samples were collected at each site. These included samples of the armour, the substrate, and sand and fines deposited on the surface. At selected sites the stream morphology was measured. These measurements included one to three cross sections, stream discharge, and water surface elevations. The data are located in the files of the Fort Collins Science Center.

Colorado, New Mexico↗

USGS2007

Longitudinal patterns of fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River, Oregon

The Lower Crooked River is a remarkable groundwater-fed stream flowing through vertical basalt canyons in the Deschutes River Valley ecoregion in central Oregon (Pater and others, 1998). The 9-mile section of the river between the Crooked River National Grasslands boundary near Ogden Wayside and river mile (RM) 8 is protected under the National Wild and Scenic Rivers Act (16 U.S.C. 1271-1287) for its outstandingly remarkable scenic, recreational, geologic, hydrologic, wildlife, and botanical values (ORVs), and significant fishery and cultural values. Groundwater springs flow directly out of the canyon walls into the Lower Crooked River and create a unique hydrologic setting for native coldwater fish, such as inland Columbia Basin redband trout (Oncorhynchus mykiss gairdneri). To protect and enhance the ORVs that are the basis for the wild and scenic designation, the Bureau of Land Management (BLM) has identified the need to evaluate, among other conditions, fish presence and habitat use of the Lower Crooked River. The results of this and other studies will provide a scientific basis for communication and cooperation between the BLM, Oregon Water Resources Department, Oregon Department of Fish and Wildlife (ODFW) and all water users within the basin. These biological studies initiated by the BLM in the region reflect a growing national awareness of the impacts of agricultural and municipal water use on the integrity of freshwater ecosystems. Biological surveys are needed to better understand the aquatic ecosystem of the Lower Crooked River. This baseline information will be valuable to public land managers whose task is to balance resource use while protecting the unique attributes (that is, ORVs) of the Lower Crooked River. The habitat requirements of coldwater fishes in this section of stream are of particular interest due to state and federal regulation of water temperature in order to protect and restore fish populations. Historical data on the distribution and abundance of stream fishes in the Lower Crooked River are limited to point observations by fishermen and local biologists because steep canyon walls have limited access to most of the river. Surveys of aquatic habitat (channel morphology and substrate composition) have been conducted for the BLM by the ODFW (Oregon Department of Fish and Wildlife, 1997), U.S. Forest Service (United States Forest Service, 2003), and the U.S. Fish and Wildlife Service (USFWS), but fish surveys using electrofishing gear have never been conducted in the isolated 11-mile section of the Crooked River Gorge, and visual observations with mask and snorkel have only been made at isolated point locations where hiking trails provide access to the river (K. Jones, Steve Marx, and Brett Hodgson, ODFW; P. Lickwar, USFWS; pers. comm.). Thus, there is a poor understanding of stream fish presence and distribution throughout Lower Crooked River. Information on fish assemblages is available for the Deschutes River basin and applies generally to the Lower Crooked River because the two rivers were connected historically (Zimmerman and Ratliff 2003). The construction of dams throughout the Deschutes River basin has eliminated historic runs of salmon and steelhead and prevented migration of bull trout and Pacific lamprey into the Crooked River system. Native fish species expected to occur in the Lower Crooked River include Columbia Basin redband trout ( Oncorhynchus mykiss gairdneri ), mountain whitefish ( Prosopium williamsoni ), sculpin ( Cottus spp.), two species of dace ( Rhinichthys spp.), two species of sucker ( Catostomus spp.), northern pikeminnow ( Ptychocheilus oregonensis ), chiselmouth ( Acrocheilus alutaceus ), and redside shiner ( Richardsonius balteatus ). Threespine stickleback ( Gasterosteus aculeatus ), a species native to western Oregon, also occurs in the basin but is believed to be introduced (D. Markle, Department of Fisheries and Wildlife, Oregon State University, personnel commun.). Extensive stocking of rainbow trout has contributed to a large population of naturalized fish of hatchery origin in the Lower Crooked River. Due to the difficulty of differentiating between wild redband trout and naturalized rainbow trout of hatchery origin, the general classification of rainbow trout ( Oncorhynchus mykiss ) is used throughout this report to describe the fish that were observed in the Lower Crooked River. Exotic fish species expected to occur in the Lower Crooked River include large- and smallmouth bass ( Micropterus spp.), yellow perch ( Perca flavescens ), and brown bullhead (Ameiurus nebulosis) (Zimmerman and Ratliff 2003). The goal of this project was to examine longitudinal patterns in fish assemblages, aquatic habitat, and water temperature in the Lower Crooked River during summer conditions. Specific objectives were to (1) characterize the spatial distribution of native and non-native fishes, (2) describe variation in channel morphology, substrate composition, and water temperature, and (3) evaluate the associations between fishes, aquatic habitat, and water temperature.

Oregon↗

USGS2003

Aquatic assemblages and their relation to temperature variables of least-disturbed streams in the Salmon River basin, central Idaho, 2001

In the late 1990s, Idaho’s established stream temperature criteria for the protection of coldwater biota and salmonid spawning were considered inadequate because the criteria did not agree with observed biological conditions in many instances and did not allow for variability in environmental condition or species diversity across a broad area such as the entire State of Idaho. In 2001, benthic invertebrate and fish assemblages in 34 least-disturbed streams in the Salmon River Basin, central Idaho, were evaluated in relation to stream temperature and other environmental variables. The Salmon River Basin retains watersheds that are minimally affected by human activities. These “natural” stream conditions provide a basis for deriving attainable stream temperatures that can be used to set new, and revise existing, water-quality criteria for stream habitats affected by human activities. During July through September 2001, data were collected to document the thermal regime of least-disturbed streams, characterize the distribution of aquatic biota at streams representing a gradient of temperature, and describe the relations between environmental variables and benthic invertebrate and fish assemblages. Nine stream temperature metrics were compared with the U.S. Environmental Protection Agency’s criterion of 10 ° C (degrees Celsius) for bull trout spawning and juvenile rearing. The maximum weekly-maximum temperature at all 33 sites where temperature data were available exceeded this criterion. The maximum daily-maximum temperature (MDMT) at 30 of the sites exceeded the Idaho Department of Environmental Quality (IDEQ) criterion of 13.0 ° C for the protection of salmonid spawning; and the maximum daily-average temperature at all 33 sites exceeded the 9.0 ° C criterion for the protection of salmonid spawning. The thermal regime at most sites did not exceed the IDEQ criteria for the protection of coldwater biota. Nine environmental variables—water-surface gradient, discharge, wetted channel width, width:depth ratio, aspect, total seasonal thermal input, open canopy, riparian canopy density, and elevation were selected for correlation with the nine stream temperature metrics. Elevation showed the strongest inverse correlation with the stream temperature metrics. Two hundred and one benthic invertebrate taxa from the 34 sampling sites were identified. The most abundant taxa were Baetis tricaudatus , Oligochaeta, Tvetenia bavarica gr., Acari, Rhithrogena , Cinygmula , Heterlimnius , Micropsectra , Eukiefferiella devonica gr., Drunella doddsi , and Cricotopus . Of the 201 benthic invertebrate taxa collected during this study, 57 taxa (present at a minimum of 5 sampling sites) were significantly correlated with one or more of the stream temperature metrics. Among the invertebrate taxa collected, 32 were identified as coldwater taxa. Of the coldwater taxa collected, Zapada oregonensis gr. showed the strongest inverse correlation with the stream temperature metrics and was collected at sites where maximum weekly-maximum temperature (based on date of sample and 6 days prior) ranged from 11.3 ° to 18.5 °C. Ten species of fish in the families Salmonidae, Cottidae, and Cyprinidae were collected. Two species (bull trout and chinook salmon) listed as threatened under the U.S. Fish and Wildlife Service Endangered Species Act were collected. Among all species, bull trout showed the strongest inverse correlation between relative fish abundance and stream temperature. Bull trout and juvenile bull trout densities were inversely correlated with stream temperature. The probability of occurrence of juvenile bull trout was significantly correlated with MDMT on the basis of results from a logistic regression model developed during this study. However, this model differed from a similar model developed by the U.S. Forest Service on the basis of regional data collected in the Pacific Northwest. The regression model based on data collected during this study showed higher probabilities of occurrence of bull trout at colder stream temperatures (10 ° to 15 ° C) and lower probabilities of occurrence at warmer stream temperatures (16 ° to 21 ° C) than did the model based on regional data. The model comparisons suggest that regional or local differences need to be considered when deriving stream temperature criteria.

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