Bonneville Cutthroat Research Articles

Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies (Oncorhynchus clarkii).

For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species-level consideration if other recent species elevations are retained.

Trends in the Abundance of Bonneville Cutthroat Trout and Nonnative Trout in the Bear River Basin of Idaho

Trends in the Abundance of Bonneville Cutthroat Trout and Nonnative Trout in the Bear River Basin of Idaho

Reduced complexity models for regional aquatic habitat suitability assessment

AbstractGeneralizable methods that identify suitable aquatic habitat across large river basins and regions are needed to inform resource management. Habitat suitability models intersect environmental variables to predict species occurrence, but are often data intensive and thus are typically developed at small spatial scales. This study estimated mean monthly aquatic habitat suitability throughout Utah (USA) for Bonneville Cutthroat Trout (Oncorhynchus clarkii utah) and Bluehead Sucker (Catostomus discobolus) with publicly available, geospatial datasets. We evaluated 15 habitat suitability models using unique combinations of percent of mean annual discharge, velocity, gradient, and stream temperature. Environmental variables were validated with observed conditions and species presence observations to verify habitat suitability estimates. Stream temperature, gradient, and discharge best predicted Bonneville Cutthroat Trout presence, and gradient and discharge best predicted Bluehead Sucker presence. Simple aquatic habitat suitability models outperformed models that used only streamflow to estimate habitat for both species, and are useful for conservation planning and water resources decision‐making. This modeling approach could enable resource managers to prioritize stream restoration across vast regions within their management domain, and is potentially compatible with water management modeling to improve ecological objectives in management models.

Population Dynamics and Harvest Management of the Bonneville Cutthroat Trout Fishery in Bear Lake, Idaho–Utah

AbstractLand‐use disturbances and associated losses in habitat quantity and quality negatively affected the Bonneville Cutthroat Trout (BCT) Oncorhynchus clarkii utah population in Bear Lake, Idaho–Utah, in the early 1900s. Bear Lake BCT follow an adfluvial life history strategy, and without access to suitable spawning habitat, the population of wild BCT was nearly extirpated by the early 1950s. In response to this decline, supplementation of the population with hatchery BCT began in 1973. Production of wild BCT was minimal until conservation efforts shifted towards improving fish habitat and access to spawning tributaries. In 2002, only 5% of the population consisted of wild fish; by 2017, nearly 70% of BCT in annual population surveys were wild. As a result, rule changes have been proposed to allow for regulated harvest of wild BCT. However, gaining a comprehensive understanding of the population dynamics of BCT in Bear Lake is critical before changes are made to management of the fishery. The objectives of this study were to describe the population dynamics of wild and hatchery BCT in Bear Lake and evaluate different management options. We evaluated population demographics of hatchery and wild BCT in Bear Lake and used age‐structured population models to assess a variety of management scenarios associated with wild fish harvest regulations (e.g., bag limits). Bonneville Cutthroat Trout grew at relatively fast rates, and females began to mature at age 5. We observed considerable differences in the length and age structure of the hatchery population (i.e., exploited) versus the wild population (i.e., unexploited) of BCT. In general, BCT in Bear Lake were larger and older than Cutthroat Trout O. clarkii in other systems. The current rate of exploitation for hatchery BCT was estimated as 0.27 (i.e., two‐fish daily limit). If the limit were changed to a six‐fish daily limit, the rate of exploitation would be approximately 0.47. A yield‐per‐recruit model evaluating spawning potential ratio indicated that a limit of two wild fish would be a sustainable level of exploitation, whereas a six‐wild‐fish limit would result in recruitment overfishing. This research has provided baseline population dynamics of BCT in Bear Lake that will provide insight for future monitoring efforts. Under current conditions, allowing harvest of either origin BCT in Bear Lake would satisfy angler values while ensuring the persistence of an ecologically and recreationally important population.

Occurrence, Abundance, Movement, and Habitat Associations of Bonneville Cutthroat Trout in Tributaries to Bear Lake, Idaho–Utah

AbstractBonneville Cutthroat Trout (BCT) Oncorhynchus clarkii utah in Bear Lake, Idaho–Utah, is an important endemic and recreational species and plays a vital ecological role in systems throughout the basin. Although the distribution and abundance of BCT have declined due to anthropogenic disturbances, production of wild BCT in Bear Lake has increased over the past decade as a result of extensive habitat improvement in spawning tributaries. The objective of this study was to assess the occurrence, distribution, and out‐migration of BCT in tributaries of Bear Lake. Surveys were conducted at 75 stream reaches across three study streams (i.e., St. Charles, Fish Haven, and Swan creeks) during 2019 and 2020. A total of 1,064 BCT was sampled from 55 of 75 total reaches (73%). Total length of BCT varied from 22 to 650 mm, and the average TL was 117 mm (SE = 2.2). Regression models were used to identify abiotic and biotic features associated with BCT distribution, abundance, and probability of out‐migration. Regardless of the tributary, elevation was negatively related to BCT occurrence and relative abundance. Other habitat characteristics associated with the presence and abundance of BCT were similar to those of other Cutthroat Trout species. For example, BCT were often associated with large substrates, instream cover, canopy cover, and heterogeneity in several habitat characteristics. The probability of a BCT out‐migrating was positively associated with fish length and age but negatively related to distance to Bear Lake and number of downstream irrigation diversions. Results from this study provide critical information on the ecology and early life history characteristics of BCT that can be used to guide additional conservation and management efforts (i.e., removal of nonnative fish species; continued habitat restoration efforts).

Detecting Rainbow Trout Introgression in Bonneville Cutthroat Trout of the Bear River Basin Using Field-Based Phenotypic Characteristics

Cutthroat trout Oncorhynchus clarkii × rainbow trout O. mykiss hybrids (hereafter hybrids) are difficult to visually distinguish from parental taxa, yet identifying phenotypic traits to separate hybrids from cutthroat trout is needed for conservation and management purposes. We compared phenotypic characteristics against genotype (using 34 species-diagnostic single nucleotide polymorphism loci) for 316 Bonneville cutthroat trout O. clarkii utah, rainbow trout and hybrids in Bear River tributaries. Our phenotypic classifications of fish were 91% accurate for Bonneville cutthroat trout but only 68% accurate for rainbow trout and hybrids combined. Classification errors based on phenotype were observed between parental taxa and hybrids but not between cutthroat trout and rainbow trout. The most useful phenotypic traits for distinguishing Bonneville cutthroat trout from hybrids were the absence of a white leading edge on the pelvic fin, the presence of fewer than 7 spots on the top of the head, and the presence of a prominent throat slash. The degree of hybridization in individual hybrids was associated with the number of spots on the top of their head. However, 16% of >F1 hybrids with a higher proportion of cutthroat trout ancestry and 6% of F1 hybrids exhibited all the phenotypic characteristics of cutthroat trout. The ability to visually detect admixture in hybrids was not related to fish length but was related to admixture level, with logistic regression model results predicting that, for individual hybrids when the proportion of alleles assigned to rainbow trout was >18% (95% CI, 11% to 26%), biologists were more than 50% likely to visually detect O. mykiss traits. While we encourage the use of genetic-based assessments for Bonneville cutthroat trout populations when feasible, our results suggest that phenotypic traits can assist in identifying hybridized populations and hybrid individuals, which will benefit the management and conservation of this species. However, our study included Bonneville cutthroat trout from only the Bear River basin, and further work is needed from the southern portion of the subspecies' range to support or refute our findings.

Conflicts among protected native birds and valuable sport fishes: potential pelican predation effects

Reservoirs are examples of novel ecosystems that have developed into popular sport fisheries; these systems are also becoming seasonal refuges for migratory birds, including the piscivorous American white pelican ( Pelecanus erythrorhynchos). We (1) investigated the proportion of cutthroat trout ( Oncorhynchus clarkii utah) and other species consumed by pelicans, (2) compared whether pelicans have an adverse effect on cutthroat trout spawning movement, and (3) determined the importance of pelican predation relative to other sources of fish mortality in Strawberry Reservoir, Utah, USA. Pelican diet samples consisted of >85% Utah sucker ( Catostomus ardens), 6% Utah chub ( Gila atraria), and 3% cutthroat trout. Based on bioenergetics, we estimated that pelicans consumed 384–3020 individual cutthroat trout (0.17%–1.3% of population), in contrast to 14 166–27 196 nongame sucker and chub. Bird-related mortality rate ranged from 1% to 6% for stocked, PIT (passive integrated transponder)-tagged adult cutthroat trout and from 4% to 16% for subadult cutthroat trout. Based on these results, any management action taken to control pelican predation would need to be weighed against the benefits of nongame fish removal and the protected status of pelicans.

Resilient and rapid recovery of native trout after removal of a non‐native trout

AbstractWhile the importance of reducing impacts of non‐native species is increasingly recognized in conservation, the feasibility of such actions is highly dependent upon several key uncertainties including stage of invasion, size of the ecosystem being restored, and magnitude of the restoration activity. Here, we present results of a multi‐year, non‐native brown trout (Salmo trutta) removal and native Bonneville cutthroat trout (Oncorhynchus clarkii utah) response to this removal in a small tributary in the Intermountain West, United States. We monitored trout for 10 years prior to the onset of eradication efforts, which included 2 years of mechanical removal followed by 2 years of chemical treatment. Cutthroat trout were then seeded with low numbers of both eggs and juvenile trout. We monitored demographics and estimated population growth rates and carrying capacities for cutthroat trout from long‐term depletion estimate data, assuming logistic population growth. Following brown trout eradication and initial seeding efforts, cutthroat trout in this tributary have responded rapidly and have approached their estimated carrying capacity within 6 years. Population projections suggest a 95% probability that cutthroat trout will be at or above 90% of their carrying capacity within 10 years of the eradication of brown trout. Additionally, at least four age‐classes are present including adults large enough to satisfy angling demand. These results demonstrate native trout species have substantial capacity to rapidly recover following removal of invasive species in otherwise minimally altered habitats. While tributaries such as like this study location are likely limited in extent individually, collectively they may serve such as source populations for larger connected systems. In such cases, these source populations may provide additional conservation potential through biotic resistance.

A Multifaceted Reconstruction of the Population Structure and Life History Expressions of a Remnant Metapopulation of Bonneville Cutthroat Trout: Implications for Maintaining Intermittent Connectivity

AbstractFishes that evolutionarily demonstrated a fluvial life history expression and migrated to spawning and rearing habitat by using lotic corridors are increasingly impacted by fragmentation. The overall goal of this study was to identify the contemporary importance of main‐stem connectivity and tributaries for maintaining life history expression, population structure, and viability of a large metapopulation of Bonneville Cutthroat Trout (BCT) Oncorhynchus clarkii utah persisting in the highly fragmented Weber River, Utah. We used a multifaceted approach, including active sampling, mark–recapture, passive PIT tag detection, otolith microchemistry, and genetics. We collected BCT in all tributaries and the main stem, encountering age‐0 fish in three tributaries, indicating successful reproduction. In tributaries, the size structure was bimodal and consisted of smaller fish that were classified as resident and larger fish that were deemed to be fluvial, whereas all sizes and ages (age ≥ 1) were present in the main stem. We identified up to eight age‐classes; tributaries were dominated by ages 2 and 8, and the main stem was dominated by ages 2, 5, 6, and 7. Tributary BCT had lower growth rates than BCT in the main stem. We observed a surprising degree of fluvial life history expression, and fish also demonstrated very complex movement patterns across their life span. Average apparent survival (33%) was within the range estimated in similar studies for BCT, and the resight rate was best explained by angler management regulations. The fact that BCT in the Weber River and tributaries still reproduce successfully in most years and are still able to grow into large, fluvial fish suggests that connectivity must be occasionally available despite considerable fragmentation. Therefore, this metapopulation may need little further human intervention if barriers to fish passage can be removed, thereby improving connectivity, and it represents a high‐priority metapopulation for conservation, thus highlighting the utility of our approach.

The influence of multiyear drought and associated reduction in tributary connectivity on an adfluvial fish species

AbstractMultiyear drought is projected to increase in frequency and duration in arid and semiarid regions across the world, threatening native species and ecosystem function. The effects of multiyear drought are often exacerbated by human water use, which manifest in reduced lake elevation, reduced stream discharge, and disruption in hydrologic connectivity for aquatic species. Here, we demonstrate that drought‐driven decreasing lake levels reduce the connectivity between tributaries and lakes by creating an elevation‐explicit tributary distance map. We combined long‐term fish catch data and a lake elevation time‐series with our elevation‐explicit tributary distance map to test whether population demographics are related to drought‐driven changes in tributary connectivity. We surveyed the littoral zone of Bear Lake, Utah and Idaho, USA, from full pool to a depth of >12 m, totalling 94.86 km2 surveyed. As lake elevation decreased from full pool to the lowest historical elevation, tributary channel distance increased by 3.5 km. Bear Lake Bonneville Cutthroat Trout (Oncorhynchus clarkii utah) catch per unit effort was strongly negatively correlated with tributary channel distance, though individual growth rates were not influenced by drought metrics. We predicted the response of age 0 to age 10 cutthroat under high and low cobble availability, estimating up to a 61% decline in cutthroat CPUE when tributary channel distance is at its maximum historical value. Our study provided a unique opportunity to identify quantitative linkages between climate‐driven changes in habitat connectivity and an ecologically important endemic sportfish, expanding our understanding of potential pathways through which climate change may affect lentic ecosystems and fishes.

Dynamic Habitat Disturbance and Ecological Resilience (DyHDER): modeling population responses to habitat condition

AbstractUnderstanding how populations respond to spatially heterogeneous habitat disturbance is as critical to conservation as it is challenging. Here, we present a new, free, and open‐source metapopulation model: Dynamic Habitat Disturbance and Ecological Resilience (DyHDER), which incorporates subpopulation habitat condition and connectivity into a population viability analysis framework. Modeling temporally dynamic and spatially explicit habitat disturbance of varying magnitude and duration is accomplished through the use of habitat time‐series data and a mechanistic approach to adjusting subpopulation vital rates. Additionally, DyHDERuses a probabilistic dispersal model driven by site‐specific habitat suitability, density dependence, and directionally dependent connectivity. In the first application of DyHDER, we explore how fragmentation and projected climate change are predicted to impact a well‐studied Bonneville cutthroat trout metapopulation in the Logan River (Utah,USA). The DyHDERmodel predicts which subpopulations are most susceptible to disturbance, as well as the potential interactions between stressors. Further, the model predicts how populations may be expected to redistribute following disturbance. This information is valuable to conservationists and managers faced with protecting populations of conservation concern across landscapes undergoing changing disturbance regimes. The DyHDERmodel provides a valuable and generalizable new tool to explore metapopulation resilience to spatially and temporally dynamic stressors for a diverse range of taxa and ecosystems.

Prioritizing Stream Barrier Removal to Maximize Connected Aquatic Habitat and Minimize Water Scarcity

AbstractInstream barriers, such as dams, culverts, and diversions, alter hydrologic processes and aquatic habitat. Removing uneconomical and aging instream barriers is increasingly used for river restoration. Historically, selection of barrier removal projects used score‐and‐rank techniques, ignoring cumulative change and the spatial structure of stream networks. Likewise, most water supply models prioritize either human water uses or aquatic habitat, failing to incorporate both human and environmental water use benefits. Here, a dual‐objective optimization model identifies barriers to remove that maximize connected aquatic habitat and minimize water scarcity. Aquatic habitat is measured using monthly average streamflow, temperature, channel gradient, and geomorphic condition as indicators of aquatic habitat suitability. Water scarcity costs are minimized using economic penalty functions while a budget constraint specifies the money available to remove barriers. We demonstrate the approach using a case study in Utah's Weber Basin to prioritize removal of instream barriers for Bonneville cutthroat trout, while maintaining human water uses. Removing 54 instream barriers reconnects about 160 km of quality‐weighted habitat and costs approximately US$10 M. After this point, the cost‐effectiveness of removing barriers to connect river habitat decreases. The modeling approach expands barrier removal optimization methods by explicitly including both economic and environmental water uses.

Modeling the fish community population dynamics and forecasting the eradication success of an exotic fish from an alpine stream

Management actions aimed at eradicating exotic fish species from riverine ecosystems can be better informed by forecasting abilities of mechanistic models. We illustrate this point with an example of the Logan River, Utah, originally populated with endemic cutthroat trout (Oncorhynchus clarkii utah), which compete with exotic brown trout (Salmo trutta). The coexistence equilibrium was disrupted by a large scale, experimental removal of the exotic species in 2009–2011 (on average, 8.2% of the stock each year), followed by an increase in the density of the native species. We built a spatially-explicit, reaction-diffusion model encompassing four key processes: population growth in heterogeneous habitat, competition, dispersal, and a management action. We calibrated the model with detailed long-term monitoring data (2001–2016) collected along the 35.4-km long river main channel. Our model, although simple, did a remarkable job reproducing the system steady state prior to the management action. Insights gained from the model independent predictions are consistent with available knowledge and indicate that the exotic species is more competitive; however, the native species still occupies more favorable habitat upstream. Dynamic runs of the model also recreated the observed increase of the native species following the management action. The model can simulate two possible distinct long-term outcomes: recovery or eradication of the exotic species. The processing of available knowledge using Bayesian methods allowed us to conclude that the chance for eradication of the invader was low at the beginning of the experimental removal (0.7% in 2009) and increased (20.5% in 2016) by using more recent monitoring data. We show that accessible mathematical and numerical tools can provide highly informative insights for managers (e.g., outcome of their conservation actions), identify knowledge gaps, and provide testable theory for researchers.

Adfluvial salmonids have engineering but not fertilization impacts in tributaries of a central Utah reservoir

Migratory fishes can affect tributary ecosystem properties given their potential to introduce nutrients (fertilize) and physically modify habitat (engineer) during spawning. Nonetheless, migrant effects are frequently context-dependent, and it is useful to understand their strength relative to other potential ecosystem drivers. We examined whether tributary ecosystem properties varied in response to migrations of two adfluvial salmonids, taking advantage of differences in migration timing and reproductive strategy between species, as well as hydrogeomorphic differences between a pair of tributaries. For analyses, we used a model comparison approach to evaluate migrant effects relative to other possible drivers. We observed that Bonneville cutthroat trout (Oncorhynchus clarkii utah) engineered benthic chlorophyll a in redds, with reduction (51% ± 16% decrease) generally occurring during migrations. Contrary to expectations, migrant fertilization effects were not pronounced even in the more retentive tributary during migration by species (kokanee, Oncorhynchus nerka) that exhibited high postspawning mortality. Based on multimodel comparisons, isolated migrant effects were not the primary influence on measured ecosystem properties. Our findings underscore the need to consider different biotic and abiotic conditions that can mediate migratory fish effects.

Earning their Stripes: The Potential of Tiger Trout and Other Salmonids as Biological Controls of Forage Fishes in a Western Reservoir

AbstractMaintaining a balance between predator and prey populations can be an ongoing challenge for fisheries managers, especially in managing artificial ecosystems such as reservoirs. In a high‐elevation Utah reservoir, the unintentional introduction of the Utah Chub Gila atraria and its subsequent population expansion prompted managers to experimentally shift from exclusively stocking Rainbow Trout Oncorhynchus mykiss to also stocking tiger trout (female Brown Trout Salmo trutta × male Brook Trout Salvelinus fontinalis) and Bonneville Cutthroat Trout O. clarkii utah (hereafter, Cutthroat Trout) as potential biological control agents. We measured a combination of diet, growth, temperature, and abundance and used bioenergetic simulations to quantify predator demand versus prey supply. Utah Chub were the predominant prey type for tiger trout, contributing up to 80% of the diet depending on the season. Utah Chub represented up to 70% of the total diet consumed by Cutthroat Trout. Although Utah Chub dominated the fish biomass in the reservoir, we still estimated abundances of 238,000 tiger trout, 214,000 Cutthroat Trout, and 55,000 Rainbow Trout. Consequently, when expanded to the population level of each predator, tiger trout and Cutthroat Trout consumed large quantities of Utah Chub on an annual basis: tiger trout consumed 508,000 kg (2,660 g/predator) of the standing prey population, and Cutthroat Trout consumed an estimated 322,000 kg (1,820 g/predator). The estimated combined consumption by Cutthroat Trout and tiger trout exceeded the estimate of Utah Chub annual production. As such, our results suggest that the high rates of piscivory exhibited by Cutthroat Trout and tiger trout in artificial lentic ecosystems are likely sufficient to effectively reduce the overall abundance of forage fishes and to prevent forage fishes from dominating fish assemblages. Collectively, this research provides the first documented findings on tiger trout ecology and performance, which will aid managers in designing and implementing the best stocking strategy to optimize sport fish performance, control undesirable forage fish, and enhance and maintain angler satisfaction.Received April 1, 2016; accepted November 8, 2016 Published online March 8, 2017

Terrestrial–aquatic linkages in spring-fed and snowmelt-dominated streams

ABSTRACTThe importance of trophic linkages between aquatic and terrestrial ecosystems is predicted to vary as a function of subsidy quantity and quality relative to in situ resources. To test this prediction, I used multi-year diet data from Bonneville cutthroat trout Oncorhynchus clarki Utah in spring-fed and snowmelt-driven streams in the high desert of western North America. I documented that trout in spring-fed streams consumed more (number and weight) aquatic than terrestrial invertebrates, while trout in snowmelt-driven streams consumed a similar number of both prey types but consumed more terrestrial than aquatic invertebrates by weight. Trout in spring-fed streams consumed more aquatic invertebrates than trout in snowmelt streams and trout consumed more terrestrial invertebrates in snowmelt than in spring-fed streams. Up to 93% of trout production in spring-fed streams and 60% in snowmelt streams was fueled by aquatic invertebrates, while the remainder of trout production in each stream type was from terrestrial production. I found that the biomass and occurrence of consumed terrestrial invertebrates were not related to our measures of in situ resource quality or quantity in either stream type. These empirical data highlight the importance of autotrophic-derived production to trout in xeric regions.

Assessing conditions influencing the longitudinal distribution of exotic brown trout (Salmo trutta) in a mountain stream: a spatially-explicit modeling approach

Trout species often segregate along elevational gradients, yet the mechanisms driving this pattern are not fully understood. On the Logan River, Utah, USA, exotic brown trout (Salmo trutta) dominate at low elevations but are near-absent from high elevations with native Bonneville cutthroat trout (Onchorhynchus clarkii utah). We used a spatially-explicit Bayesian modeling approach to evaluate how abiotic conditions (describing mechanisms related to temperature and physical habitat) as well as propagule pressure explained the distribution of brown trout in this system. Many covariates strongly explained redd abundance based on model performance and coefficient strength, including average annual temperature, average summer temperature, gravel availability, distance from a concentrated stocking area, and anchor ice-impeded distance from a concentrated stocking area. In contrast, covariates that exhibited low performance in models and/or a weak relationship to redd abundance included reach-average water depth, stocking intensity to the reach, average winter temperature, and number of days with anchor ice. Even if climate change creates more suitable summer temperature conditions for brown trout at high elevations, our findings suggest their success may be limited by other conditions. The potential role of anchor ice in limiting movement upstream is compelling considering evidence suggesting anchor ice prevalence on the Logan River has decreased significantly over the last several decades, likely in response to climatic changes. Further experimental and field research is needed to explore the role of anchor ice, spawning gravel availability, and locations of historical stocking in structuring brown trout distributions on the Logan River and elsewhere.

Isolation, Migration, and Local Recruitment Drive Persistence of Cutthroat Trout in Tributaries near American Falls Reservoir

AbstractWe analyzed 67 SNPs to describe the genetics of Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri in seven tributaries near American Falls Reservoir, Idaho. We detected Yellowstone Cutthroat Trout in all but one site despite significant historical stocking of Rainbow Trout O. mykiss. Three of four relatively low‐elevation sites near the reservoir contained Yellowstone Cutthroat Trout in sympatry with early‐generation hybrids and Rainbow Trout yet contained no physical barriers to admixture. A posteriori assignment tests suggested that migrants from a nearby headwater population in Ross Fork Creek and possibly recruitment by local‐origin Yellowstone Cutthroat Trout with fluvial or adfluvial life histories drive persistence in these sites. In contrast, hybridization was rare or absent in headwater populations and was associated with complete or apparent physical isolation. We also compared genetic diversity of our samples with Yellowstone basin Yellowstone Cutthroat Trout and Bear River Bonneville Cutthroat Trout O. c. utah to examine possible historical gene flow resulting from hydrogeological connections during the Pleistocene. Multivariate analysis showed that most genetic variation among individuals was explained by divergence of Yellowstone basin Yellowstone Cutthroat Trout from our samples and Bear River Bonneville Cutthroat Trout, which supports recent mtDNA studies and a possible change in taxonomic nomenclature. Our results indicate that, due to relative isolation and downstream emigration, headwater populations are critical to the persistence of Yellowstone Cutthroat Trout and thus loss of such populations would likely threaten the subspecies throughout the region. Management actions to reduce threats from established, nonnative Rainbow Trout populations will likely have to be multifaceted and may include a combination of targeted removal of Rainbow Trout and hybrids and the use of physical barriers to prevent further dispersal.Received April 19, 2015; accepted February 7, 2016 Published online May 31, 2016

The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus.

Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O. clarkii bouvieri), and rainbow trout (O. mykiss), which are of conservation interest both as native species and as invasive species across each other’s native ranges. We found that local polymorphisms within westslope cutthroat trout and rainbow trout posed a challenge to designing assays that are generally applicable across the range of these widely-distributed species. Further, poorly-resolved taxonomies of Yellowstone cutthroat trout and Bonneville cutthroat trout (O. c. utah) prevented design of an assay that distinguishes these recognized taxa. The issues of intraspecific polymorphism and unresolved taxonomy for eDNA assay design addressed in this study are likely to be general problems for closely-related taxa. Prior to field application, we recommend that future studies sample populations and test assays more broadly than has been typical of published eDNA assays to date.

Exploring Crowded Trophic Niche Space in a Novel Reservoir Fish Assemblage: How Many is Too Many?

AbstractIn highly managed reservoir systems, species interactions within novel fish assemblages can be difficult to predict. In high‐elevation Scofield Reservoir in Utah the unintentional introduction of Utah Chub Gila atraria and subsequent population expansion prompted a shift from stocking exclusively Rainbow Trout Oncorhynchus mykiss to include tiger trout (female Brown Trout Salmo trutta × male Brook Trout Salvelinus fontinalis) and Bonneville Cutthroat Trout O. clarkii utah, which composed a novel suite of top predators and potential competitors. We examined the interspecific interactions among Scofield Reservoir piscivores using a multifaceted approach including gut analyses, stable isotopes, and gape limitation. Large Cutthroat Trout consumed 50–100% Utah Chub and tiger trout consumed 45–80%. In contrast, small and large Rainbow Trout consumed primarily invertebrate prey and exhibited significant overlap with small tiger trout, Cutthroat Trout, and Utah Chub. Large Cutthroat Trout and tiger trout occupy a top piscivore trophic niche and are more littoral, while Rainbow Trout occupy an omnivore niche space and are more pelagic. Both Cutthroat and tiger trout varied in niche space with respect to size‐class, demonstrating an ontogenetic shift to piscivory at approximately 350 mm TL. Cutthroat Trout and tiger trout are capable of consuming prey up to 50% of their own size, which is larger than predicted based on their theoretical gape limit. Because it appears food resources (Utah Chub) are not limited, and performance metrics are high, competition is unlikely between Cutthroat Trout and tiger trout. In contrast, apparent survival of Rainbow Trout has recently declined significantly, potentially due to shared food resources with Utah Chub or negative behavioral interactions with other members of the community. Collectively, this research aids in understanding biotic interactions within a top‐heavy and novel fish community and assists towards developing and implementing suitable management strategies to control nuisance species.