Geology topics

Bradley B. Shepard

Publications and source records attributed to Bradley B. Shepard.

At least 19 recordsLinked to original sources

USGS2021

Evaluation of remote site incubators to incubate wild- and hatchery-origin Westslope Cutthroat Trout embryos

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 incubate >35,700 eyed embryos of Westslope Cutthroat Trout Oncorhynchus clarkii lewisi at eight sites within the upper 30 km of the Cherry Creek basin (Madison River, Montana) from 2007 to 2010, after using piscicides to remove all fish. We obtained gametes from 258 parental-pair crosses (164 females and 258 males) from four wild populations and two hatchery broods. All embryos were incubated to the eyed stage in two hatcheries prior to placing them in RSIs. Green-to-eyed egg survivals were higher for progeny of wild-spawned adults (median, 91.0%; 95% CI, 88.7–93.7%) than for progeny of hatchery-spawned adults (median, 81.7%; 95% CI, 74.9–88.4%), and this difference was highly significant ( P < 0.01). Over 26,500 fry were counted leaving RSIs. Median embryo-to-fry survival was 75.6% (95% CI, 72.2–79.0%). Fry exited individual RSIs from 8 to 45 d after embryo translocation. Fry survivals differed among years and sites, and year was more important than site in explaining variation in survival. The success of RSI fry introductions was confirmed by annual monitoring of fish abundance, which indicated that abundances of Westslope Cutthroat Trout 5 to 9 years after RSI introductions were equal to or higher than abundances of nonnative salmonids prior to their removal using piscicides.

Montana↗

USGS2021

The interactive effects of stream temperature, stream size, and non-native species on Yellowstone cutthroat trout

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 of the existing threats to native populations. Allopatric Yellowstone cutthroat trout were distributed across a wide range of average August temperatures (3.2 to 17.7 °C), but occurrence significantly declined at colder temperatures (<10 °C) with increasing numbers of non-natives. At warmer temperatures, occurrence remained high, despite sympatry with non-natives. Yellowstone cutthroat trout relative abundance was significantly reduced with increasing abundance of non-natives, with the greatest impacts at colder temperatures. Body sizes of large Yellowstone cutthroat trout (90th percentile) significantly increased with warming temperatures and larger stream size, highlighting the importance of access to these more productive stream segments. Considering multiple population-level attributes demonstrates the complexities of how native salmonids (such as Yellowstone cutthroat trout) are likely to be affected by shifting climates.

Idaho, Wyoming↗

USGS2019

Consistent compensatory growth offsets poor condition in trout populations

1. 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 scarce. 2. Cutthroat trout (Oncorhynchus clarkii subsp) are cold-water specialists that inhabit streams in montane ecosystems where seasonal conditions can be harsh and growth rates vary greatly among seasons. Understanding if individuals compensate for periods of reduced growth and body condition will improve understanding of the requirements of fish throughout their life-cycle and across freshwater habitats. 3. We quantified compensatory growth of juvenile cutthroat trout using extensive mark-recapture data from 11 stream populations (1,125 individuals) and two subspecies inhabiting a wide range of ecological settings in the northern Rocky Mountains, USA. Our objectives were to determine how growth was linked across seasons and determine if individuals behaviorally compensated for depressed body condition via emigration. 4. Fish in relatively poor condition consistently demonstrated compensatory growth in mass during subsequent seasons. In contrast, fish in relatively better condition responded with positive growth in length during the summer signaling these fish may be better suited to headwater environments; no compensatory growth in length was found during the winter. Furthermore, we found no evidence that individual condition mediated migration tendencies of fish to seek more favorable habitat. 5. Across a wide range of environmental conditions, we found consistent empirical support for compensatory growth in mass in the wild. A critical next step is to quantify how changing abiotic and biotic conditions influence the ability of stream fishes to compensate for locally or seasonally challenging conditions, thereby affecting long-term resiliency, viability, and adaptation in the face of changing environmental conditions.

Montana, Wyoming↗

USGS2018

Microhabitat use of native fishes in the Kootenai River: A fine‐scale evaluation of large‐scale habitat rehabilitation efforts

Fish and microhabitat data were collected at 542 prepositioned electrofishing sites (surface area of each site = 4 m 2 ) in the Kootenai River, Idaho, during 2014 and 2015 to evaluate small‐scale habitat use by fishes, as it relates to large‐scale habitat rehabilitation efforts. Samples were collected from a 12‐km braided segment of river that had received localized habitat rehabilitation treatments since 2011. Fish and microhabitat data were collected to investigate habitat drivers related to the occurrence and relative abundance of fishes. Each sampling location was selected at random and characterized as “treated” (i.e., rehabilitated) or “untreated” based on proximity to habitat treatments. Fishes sampled from backwaters composed 71% of the overall catch and 84% of the catch from locally untreated areas of the river. Species‐specific regression models suggested that water depth and current velocity influenced the occurrence and abundance of fishes. In particular, shallow habitats with low current velocities were important for small‐bodied native fishes and likely serve as important rearing areas for juvenile fish. These habitat conditions typically characterize backwater and channel‐margin habitats that are vulnerable to anthropogenic perturbation. Prioritizing process‐based rehabilitation of these areas in large, regulated rivers would allow natural channel‐forming processes for the benefit of native fishes.

Idaho↗

USGS2018

A portfolio framework for prioritizing conservation efforts for Yellowstone Cutthroat Trout populations

Managing and conserving native taxa are becoming increasingly challenging because of mounting threats and limited resources, predicating the need for frameworks to prioritize conservation actions. We integrated attributes of population persistence, genetic status, threats from nonnative species, and threats from climatic shifts to prioritize conservation actions for Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri . We used the individual attributes to rank populations and provide a framework for identifying the benefits of individual conservation actions. The majority of extant populations (57%) had a high probability (>0.75) of persistence, but nearly 70% of populations were either slightly hybridized or sympatric with nonnative species, and 44% of extant populations occupied habitat with low climatic resilience. Overall, we found that 36% of populations ranked as high (>0.75) conservation priority, and these populations primarily occupied large, relatively high‐elevation habitats. The prioritization framework provides a platform for identifying and ranking actions with the greatest conservation effectiveness.

Idaho, Montana, Nevada, Utah, Wyoming↗

USGS2018

Comparison of a prepositioned areal electrofishing device and fixed underwater videography for sampling riverine fishes

Prepositioned areal electrofishing devices (PAEDs) are used to evaluate microhabitat use by fishes because they minimize fright biases associated with traditional electrofishing techniques (e.g., boat electrofishing). Similarly, fixed underwater videography (FUV) is commonly used to minimize the effect of observers on fish behavior. The specific objectives of this research were to evaluate estimates of taxonomic occurrence and diversity between PAEDs and FUV and determine an appropriate time interval between positioning and electrifying of a PAED to reduce effects of PAED positioning on fish occurrence. Video cameras were positioned instream at 28 locations on the Kootenai River, Idaho, prior to PAED deployment such that the entire immobilization zone of the PAED was captured on camera. Following a 4-min acclimation period, cameras recorded fish behavior approximately 15 min prior to and 20 min following PAED deployment. Electrical current was applied to the PAEDs for 20 s immediately following the FUV procedure, and immobilized fishes were collected and processed. Video footage was subsampled in the laboratory, and fishes in the video were identified and enumerated in 5-s or 20-s intervals. Fixed underwater videography sampled more taxa than PAEDs at any given site. However, fishes sampled with FUV were difficult to identify, and most individuals were classified as “unidentifiable.” Consequently, direct comparisons between FUV and PAEDs are limited. Our results indicate that PAEDs should remain undisturbed for a minimum of 12 min before the equipment is electrified. Both PAEDs and FUV provide an estimate of taxonomic occurrence, but logistical and financial constraints along with project objectives must be considered when selecting between these 2 gear types. Results from this study provide information on the effectiveness of each gear type as it relates to the characterization of riverine fish assemblages at a small spatial scale.

Western North American Naturalist↗

USGS2017

Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout

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, multi-decade genetics dataset (N = 582 sites, 12,878 individuals) with high-resolution climate predictions and extensive stocking records, we evaluate the spatiotemporal dynamics of hybridization between native cutthroat trout and invasive rainbow trout, the world’s most widely introduced invasive fish, across the northern Rocky Mountains of the United States. Historical effects of stocking and contemporary patterns of climatic variation were strongly related to the spread of hybridization across space and time. The probability of occurrence, extent of, and temporal changes in hybridization increased at sites in close proximity to historical stocking locations with greater rainbow trout propagule pressure, warmer water temperatures, and lower spring precipitation. Although locations with warmer water temperatures were more prone to hybridization, cold sites were not protected from invasion; 58% of hybridized sites had cold mean summer water temperatures (<11 ° C). Despite cessation of stocking over 40 years ago, hybridization increased over time at half (50%) of the locations with long-term data, the vast majority of which (74%) were initially non-hybridized, emphasizing the chronic, negative impacts of human-mediated hybridization. These results show that effects of climate change on biodiversity must be analyzed in the context of historical human impacts that set ecological and evolutionary trajectories.

Global Change Biology↗

USGS2016

Life history characteristics and vital rates of Yellowstone Cutthroat Trout in two headwater basins

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, and behaviors of Yellowstone Cutthroat Trout within headwater stream networks remains limited yet is critical for effective management and conservation. We estimated annual relative growth in length and weight, annual survival rates, and movement patterns of Yellowstone Cutthroat Trout from three tributaries of Spread Creek, Wyoming, and two tributaries of Shields River, Montana, from 2011 through 2013 using PIT tag antennas within a mark–recapture framework. Mean annual growth rates varied among tributaries and size-classes, but were slow compared with populations of Yellowstone Cutthroat Trout from large, low-elevation streams. Survival rates were relatively high compared with those of other Cutthroat Trout subspecies, but we found an inverse relationship between survival and size, a pattern contrary to what has been reported for Cutthroat Trout in large streams. Mean annual survival rates ranged from 0.32 (SE = 0.04) to 0.68 (SE = 0.05) in the Spread Creek basin and from 0.30 (SE = 0.07) to 0.69 (SE = 0.10) in the Shields River basin. Downstream movements from tributaries were substantial, with as much as 26.5% of a tagging cohort leaving over the course of the study. Integrating our growth, survival, and movement results demonstrates the importance of considering strategies to enhance headwater stream habitats and highlights the importance of connectivity with larger stream networks.

North American Journal of Fisheries Management↗

USGS2016

Conservation of native Pacific trout diversity in western North America

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 the state of knowledge on these important issues, focusing on Pacific trout in the genus Oncorhynchus. Although most research on salmonid fishes emphasizes Pacific salmon, we focus on Pacific trout because they share a common evolutionary history, and many taxa in western North America have not been formally described, particularly in the southern extent of their ranges. Research in recent decades has led to the revision of many hypotheses concerning the origin and diversification of Pacific trout throughout their range. Although there has been significant success at addressing past threats to Pacific trout, contemporary and future threats represented by nonnative species, land and water use activities, and climate change pose challenges and uncertainties. Ultimately, conservation of Pacific trout depends on how well these issues are understood and addressed, and on solutions that allow these species to coexist with a growing scope of human influences.

Fisheries↗

USGS2016

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout ( Salvelinus fontinalis ) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection > 0.99 at densities of ≥ 3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.

Montana↗

USGS2016

Electrofishing effort requirements for estimating species richness in the Kootenai River, Idaho

This study was conducted on the Kootenai River, Idaho to provide insight on sampling requirements to optimize future monitoring effort associated with the response of fish assemblages to habitat rehabilitation. Our objective was to define the electrofishing effort (m) needed to have a 95% probability of sampling 50, 75, and 100% of the observed species richness and to evaluate the relative influence of depth, velocity, and instream woody cover on sample size requirements. Sidechannel habitats required more sampling effort to achieve 75 and 100% of the total species richness than main-channel habitats. The sampling effort required to have a 95% probability of sampling 100% of the species richness was 1100 m for main-channel sites and 1400 m for side-channel sites. We hypothesized that the difference in sampling requirements between main- and side-channel habitats was largely due to differences in habitat characteristics and species richness between main- and side-channel habitats. In general, main-channel habitats had lower species richness than side-channel habitats. Habitat characteristics (i.e., depth, current velocity, and woody instream cover) were not related to sample size requirements. Our guidelines will improve sampling efficiency during monitoring effort in the Kootenai River and provide insight on sampling designs for other large western river systems where electrofishing is used to assess fish assemblages.

Idaho↗

USGS2015

Patterns of fish assemblage structure and habitat use among main- and side-channel environments in the lower Kootenai River, Idaho

The lower Kootenai River, Idaho, was sampled during the summers of 2012 and 2013 to evaluate its fish assemblage structure at seven sites within main- and side-channel habitats where large-scale habitat rehabilitation was undertaken. Understanding the current patterns of fish assemblage structure and their relationships with habitat is important for evaluating the effects of past and future rehabilitation projects on the river. Species-specific habitat associations were modeled, and the variables that best explained the occurrence and relative abundance of fish were identified in order to guide future habitat rehabilitation so that it benefits native species. The results indicated that the side-channel habitats supported higher species richness than the main-channel habitats and that nonnative fishes were closely associated with newly rehabilitated habitats. This research provides valuable insight on the current fish assemblages in the Kootenai River and the assemblage-level responses that may occur as a result of future rehabilitation activities.

Idaho↗

USGS2015

Effects of hybridization between nonnative Rainbow Trout and native Westslope Cutthroat Trout on fitness-related traits

Hybridization between introduced and native fauna is a risk to native species and may threaten the long-term persistence of numerous taxa. Rainbow Trout Oncorhynchus mykiss has been one of the most widely introduced species around the globe and often hybridizes with native Cutthroat Trout O. clarkii in the Rocky Mountains. Previous work has shown that hybridization negatively affects reproductive success, but identification of the traits contributing to that reduction has been elusive. In this study, we used a combination of field and laboratory techniques to assess how hybridization with Rainbow Trout affects seven traits during several stages of Westslope Cutthroat Trout development: embryonic survival, ova size, ova energy concentration, sperm motility, juvenile weight, juvenile survival, and burst swimming endurance. Rainbow Trout admixture was correlated with an increase in embryonic survival and ova energy concentration but with a decrease in juvenile weight and burst swimming endurance. These correlations differed from previously observed patterns of reproductive success and likely do not explain the declines in reproductive success associated with admixture. Future investigation of additional, unstudied traits and the use of different environments may shed light on the traits responsible for reproductive success in admixed Cutthroat Trout.

Transactions of the American Fisheries Society↗

USGS2015

Status and conservation of interior Redband Trout in the western United States

In this article we describe the current status and conservation of interior (potamodromous) Redband Trout Oncorhynchus mykiss sspp. throughout its range in the western United States using extant data and expert opinion provided by fish managers. Redband Trout historically occupied 60,295 km of stream habitat and 152 natural lakes. Currently, Redband Trout occupy 25,417 km of stream habitat (42% of their historical range) and 124 lakes or reservoirs. Nonhybridized populations are assumed to occupy 11,695 km (46%) of currently occupied streams; however, fish from only 4,473 km (18%) have been genetically tested. Approximately 47% of the streams occupied by Redband Trout occur on private land, 45% on government lands, and 8% in protected areas. A total of 210 Redband Trout populations, occupying 15,252 km of stream habitat (60% of the current distribution) and 95,158 ha of lake habitat (52%), are being managed as “conservation populations.” Most conservation populations have been designated as weakly to strongly connected metapopulations (125; 60%) and occupy much more stream length (14,112 km; 93%) than isolated conservation populations (1,141 km; 7%). The primary threats to Redband Trout include invasive species, habitat degradation and fragmentation, and climate change. Although the historical distribution of interior Redband Trout has declined dramatically, we conclude that the species is not currently at imminent risk of extinction because it is still widely distributed with many populations isolated by physical barriers and active conservation efforts are occurring for many populations. However, the hybridization status of many populations has not been well quantified, and introgression may be more prevalent than documented here. We recommend (1) collecting additional genetic data and estimating distribution and abundance by means of a more rigorous spatial sampling design to reduce uncertainties, (2) collecting additional information to assess and predict the impacts of climate on populations, and (3) continuing to use this database to evaluate the status of Redband Trout and inform conservation efforts through time.

North American Journal of Fisheries Management↗

USGS2014

Factors influencing successful eradication of nonnative brook trout from four small Rocky Mountain streams using electrofishing

We successfully eradicated nonnative Brook Trout Salvelinus fontinalis by electrofishing from 2.4- to 3.0-km treatment reaches of four Rocky Mountain streams in Montana to conserve sympatric populations of native Westslope Cutthroat Trout Oncorhynchus clarkii lewisi . At least 6, and as many as 14, removal treatments of two to four electrofishing passes per treatment were required to successfully eradicate Brook Trout from these treatment reaches. We increased success by modifying our treatment efforts during this study from single annual treatments to several treatments a year to take advantage of autumn spawning and winter aggregating behavior. Eradication by electrofishing cost US \$3,500 to \$5,500 per kilometer where no riparian vegetation or woody debris clearing was necessary, increasing to \$8,000 to \$9,000 per kilometer where clearing was needed. Treatment costs without stream clearing were similar to costs of eradication using piscicides. Eradication by electrofishing may be preferable where native fish occur in sympatry with nonnative fish in smaller streams (base flow wetted widths

Montana↗

USGS2013

Juvenile movement among different populations of cutthroat trout introduced as embryos to vacant habitat

Translocations are frequently used to increase the abundance and range of endangered fishes. One factor likely to affect the outcome of translocations is fish movement. We introduced embryos from five Westslope Cutthroat Trout Oncorhynchus clarkii lewisi populations (both hatchery and wild) at five different locations within a fishless watershed. We then examined the movement of age‐1 and age‐2 fish and looked for differences in movement distance among source populations and among introduction sites; we also examined the interactions among age, population, and introduction site. At age 1, most individuals (90.9%) remained within 1,000 m their introduction sites. By age 2, the majority of individuals (58.3%) still remained within 1,000 m of their introduction site, but considerably more individuals had moved downstream, some more than 6,000 m from their introduction site. We observed a significant interaction between age and source population ( F 4, 1077 = 15.45, P < 0.0001) as well as between age and introduction site ( F 41, 1077 = 11.39, P < 0.0008), so we presented results in the context of these interactions. Within age‐groups, we observed differences in movement behavior among source populations and among donor populations of Westslope Cutthroat Trout. We discuss these findings in light of previous research on juvenile salmonid movement.

Montana↗

USGS2012

Evidence of local adaptation in westslope cutthroat trout

An understanding of the process of local adaptation would allow managers to better protect and conserve species. Many salmonids are in need of such efforts, and because they often persist in differing, isolated environments, they are useful organisms for studying local adaptation. In addition, the temperature sensitivity of salmonids provides a likely target for natural selection. We studied thermal adaptation in four wild populations and one hatchery stock of westslope cutthroat trout Oncorhynchus clarkii lewisi . The mean summer temperatures of source streams ranged from 6.7°C to 11.2°C. Embryos were collected from the wild, and embryonic development, embryonic survival, and juvenile growth were determined. A significant relationship between median embryonic survival and source stream temperature was detected. Based on a rank test, populations from colder streams had a greater decline in median embryonic survival at warm temperatures than populations from warmer streams. Embryonic development and juvenile growth did not appear to be influenced by source. These findings suggest that populations are thermally adapted to their source streams and this should be considered by managers. However, further study is necessary to sort out the potential confounding factors, whether genetic or epigenetic.

Transactions of the American Fisheries Society↗

USGS2012

Evaluating a fish monitoring protocol using state-space hierarchical models

Using data collected from three river reaches in Montana, we evaluated our ability to detect population trends and predict fish future fish abundance. Data were collected as part of a long-term monitoring program conducted by Montana Fish, Wildlife and Parks to primarily estimate rainbow (Oncorhynchus mykiss) and brown trout (Salmo trutta) abundance in numerous rivers across Montana. We used a hierarchical Bayesian mark-recapture model to estimate fish abundance over time in each of the three river reaches. We then fit a state-space Gompertz model to estimate current trends and future fish populations. Density dependent effects were detected in 1 of the 6 fish populations. Predictions of future fish populations displayed wide credible intervals. Our simulations indicated that given the observed variation in the abundance estimates, the probability of detecting a 30% decline in fish populations over a five-year period was less than 50%. We recommend a monitoring program that is closely tied to management objectives and reflects the precision necessary to make informed management decisions.

Montana↗