Cutthroat Trout Research Articles

Quantifying thermal refugia connectivity by combining temperature modeling, distributed temperature sensing, and thermal infrared imaging

Abstract. Watershed-scale stream temperature models are often one-dimensional because they require fewer data and are more computationally efficient than two- or three-dimensional models. However, one-dimensional models assume completely mixed reaches and ignore small-scale spatial temperature variability, which may create temperature barriers or refugia for cold-water aquatic species. Fine spatial- and temporal-resolution stream temperature monitoring provides information to identify river features with increased thermal variability. We used distributed temperature sensing (DTS) to observe small-scale stream temperature variability, measured as a temperature range through space and time, within two 400 m reaches in summer 2015 in Nevada's East Walker and main stem Walker rivers. Thermal infrared (TIR) aerial imagery collected in summer 2012 quantified the spatial temperature variability throughout the Walker Basin. We coupled both types of high-resolution measured data with simulated stream temperatures to corroborate model results and estimate the spatial distribution of thermal refugia for Lahontan cutthroat trout and other cold-water species. Temperature model estimates were within the DTS-measured temperature ranges 21 % and 70 % of the time for the East Walker River and main stem Walker River, respectively, and within TIR-measured temperatures 17 %, 5 %, and 5 % of the time for the East Walker, West Walker, and main stem Walker rivers, respectively. DTS, TIR, and modeled stream temperatures in the main stem Walker River nearly always exceeded the 21 ∘C optimal temperature threshold for adult trout, usually exceeded the 24 ∘C stress threshold, and could exceed the 28 ∘C lethal threshold for Lahontan cutthroat trout. Measured stream temperature ranges bracketed ambient river temperatures by −10.1 to +2.3 ∘C in agricultural return flows, −1.2 to +4 ∘C at diversions, −5.1 to +2 ∘C in beaver dams, and −4.2 to 0 ∘C at seeps. To better understand the role of these river features on thermal refugia during warm time periods, the respective temperature ranges were added to simulated stream temperatures at each of the identified river features. Based on this analysis, the average distance between thermal refugia in this system was 2.8 km. While simulated stream temperatures are often too warm to support Lahontan cutthroat trout and other cold-water species, thermal refugia may exist to improve habitat connectivity and facilitate trout movement between spawning and summer habitats. Overall, high-resolution DTS and TIR measurements quantify temperature ranges of refugia and augment process-based modeling.

Environmental DNA in lake sediment reveals biogeography of native genetic diversity

Understanding the historical distributions of species is vital to the conservation and restoration of native species, yet such information is often qualitative. We show that the paleolimnological history of threatened freshwater fishes can be reconstructed using species‐diagnostic markers amplified from environmental DNA deposited in lake sediments (lake sedDNA). This method was validated through the detection of lake sedDNA from non‐native trout (Yellowstone cutthroat trout, Oncorhynchus clarkii bouvieri), which corroborated historical records of human‐mediated introductions. We also discovered native trout (westslope cutthroat trout, Oncorhynchus clarkii lewisi) lake sedDNA that predated human‐mediated introductions of freshwater fishes in a watershed with high topographical relief. This unexpected result revealed that the westslope population was of native origin and requires immediate conservation protection. Our findings demonstrate that lake sedDNA can be used to determine the colonization history of freshwater fishes and the structure of ecosystems, aiding in the identification of native ranges, novel native diversity, and introductions of non‐native species.

Comparing correlative and bioenergetics‐based habitat suitability models for drift‐feeding fishes

Abstract Quantitative habitat suitability models (HSMs) are frequently used to inform the conservation and management of lotic organisms, often in the context of instream flow management. Correlative statistical models relating hydraulic variables to habitat preferences (habitat suitability curves based on use:availability ratios) are the most common form of HSM, but face significant criticism on the grounds that habitat preference may not reflect the fitness consequences of habitat use. Consequently, there has been a drive to develop mechanistic approaches that link habitat to direct correlates of fitness. Bioenergetic foraging models relating hydraulic conditions to energy balance are particularly well‐developed for drift‐feeding fishes (e.g. salmonids) and show promise as a more mechanistic approach to modelling suitability. However, these models are rarely validated empirically or quantitatively compared with correlative HSMs. We addressed these gaps by comparing the ability of a bioenergetics‐based HSM and two correlative HSMs (a traditional suitability index and a resource selection function) to predict density and growth of stream salmonids (juvenile steelhead, Oncorhynchus mykiss, and coastal cutthroat trout, Oncorhynchus clarki). Suitability estimates differed between the approaches, with both correlative models predicting higher suitability relative to the bioenergetic model at shallow depths and low to intermediate velocities, but lower suitability as depth increased. The bioenergetic model explained over 90% of variation in trout growth, compared to c. 50% for the correlative model. The bioenergetic model was also better at predicting fish density; however, the improvement was less striking and a high proportion of variation remained unexplained by either method. Differences in suitability estimates between approaches probably reflect biotic interactions (e.g. territorial displacement or predation risk) that decouple realised habitat use from energetics‐based estimates of habitat quality. Results highlight fundamental differences between correlative HSMs, based on observed habitat use, and mechanistic HSMs, based on the physiology and behaviour of the focal taxa. They also suggest that mechanistic bioenergetics‐based models provide more rigorous estimates of habitat suitability for drift‐feeding stream fishes. The bioenergetics approach is readily accessible to instream flow practitioners because model predictions are expressed in terms of traditional habitat suitability curves.

Cutthroat Trout: Evolutionary Biology and Taxonomy. Edited by PatrickTrotter, PeterBisson, LukeSchultz, and BrettRoper. American Fisheries Society, Special Publication 36, Bethesda, Maryland. 2018. 386 pages. US$79 ($55 for American Fisheries Society members) (paper).

Cutthroat Trout: Evolutionary Biology and Taxonomy. Edited by PatrickTrotter, PeterBisson, LukeSchultz, and BrettRoper. American Fisheries Society, Special Publication 36, Bethesda, Maryland. 2018. 386 pages. US$79 ($55 for American Fisheries Society members) (paper).

カットスロートトラウト(Oncorhynchus clarki)雌の肝臓におけるエストラジオール-17β応答性遺伝子の生殖周期に伴う発現解析

カットスロートトラウト(Oncorhynchus clarki)雌の肝臓におけるエストラジオール-17β応答性遺伝子の生殖周期に伴う発現解析

Parallel introgression and selection on introduced alleles in a native species.

As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that thedegree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome-wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.

Salmon species identification via direct DNA sequencing of single amplicons

For Pacific salmonids, a key fisheries forensics and management goal is to identify individuals to specific species and potentially specific populations or geographic regions within species. Genetic variation can be used for both species and individual identification, and variation at single nucleotide polymorphisms (SNPs) within two specific DNA amplicons was used to distinguish among coho salmon (Oncorhynchus kisutch), Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon (Oncorhynchus nerka), chum salmon (Oncorhynchus keta), pink salmon (Oncorhynchus gorbuscha), masu salmon (Oncorhynchus masou), steelhead/rainbow trout (Oncorhynchus mykiss), cutthroat trout (Oncorhynchus clarkii), and Atlantic salmon (Salmo salar). A total of 2510 individuals was evaluated from a Pacific rim distribution of populations for sockeye salmon, chum salmon, and pink salmon, whereas masu salmon samples were genotyped only from Japanese populations. Coho salmon, Chinook salmon, steehead trout, cutthroat trout, and Atlantic salmon samples were genotyped only from North American populations. All individual salmonids genotyped were assigned with 100% accuracy to their respective species via diagnostic homozygous SNP genotypes for each species except for cutthroat trout, where no diagnostic SNP genotypes were observed in the two amplicons evaluated.

Assessing thermal adaptation using family-based association and FST outlier tests in a threatened trout species.

Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full-sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family-based genome-wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p<0.05 and p<0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance-related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p<0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.

Population connectivity of adfluvial and stream-resident Lahontan cutthroat trout: implications for resilience, management, and restoration

Population connectivity between resident and migratory cutthroat trout (Oncorhynchus clarkii ssp.) is understudied, but has implications for population viability and management. We examined evidence for stream residency, studied the spatial patterns of stream use by adfluvial and stream-resident trout, and measured migration rates with changing stream depth for Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) in the Summit Lake Basin, Nevada (USA). Passive integrated transponder technology and a fry trap were used to track fish movements and identify the distribution of resident and adfluvial trout. Stream residents were distributed throughout the network. Adfluvial spawners concentrated in lower reaches, but also migrated up to 12.9 km. Adfluvial juveniles migrated to the lake from lower reaches and from upstream of adfluvial spawners. High stream depths coincided with more adfluvial juveniles migrating to the lake and more adfluvial spawners moving into the stream, which led to more accessing the upper watershed. This work shows that connectivity is central to adfluvial–resident Lahontan cutthrout trout population dynamics and may lead to increased probability of persistence — a characteristic of these isolated, threatened trout populations.

Predatory fish invasion induces within and across ecosystem effects in Yellowstone National Park.

Predatory fish introduction can cause cascading changes within recipient freshwater ecosystems. Linkages to avian and terrestrial food webs may occur, but effects are thought to attenuate across ecosystem boundaries. Using data spanning more than four decades (1972-2017), we demonstrate that lake trout invasion of Yellowstone Lake added a novel, piscivorous trophic level resulting in a precipitous decline of prey fish, including Yellowstone cutthroat trout. Plankton assemblages within the lake were altered, and nutrient transport to tributary streams was reduced. Effects across the aquatic-terrestrial ecosystem boundary remained strong (log response ratio ≤ 1.07) as grizzly bears and black bears necessarily sought alternative foods. Nest density and success of ospreys greatly declined. Bald eagles shifted their diet to compensate for the cutthroat trout loss. These interactions across multiple trophic levels both within and outside of the invaded lake highlight the potential substantial influence of an introduced predatory fish on otherwise pristine ecosystems.

Distinct Phenotypes of Native Cutthroat Trout Emerge under a Molecular Model of Lineage Distributions

AbstractRecent molecular investigations using contemporary and century‐old museum specimens questioned the traditional four‐subspecies taxonomic arrangement of Cutthroat Trout Oncorhynchus clarkii in the southern Rocky Mountains and revealed six lineages, including two that are likely extinct. We examined extant lineage specimens to determine whether morpho‐meristic taxonomic approaches better classified Cutthroat Trout under (1) the traditional Geographic Model, which recognizes different subspecies east and west of the Continental Divide and in the Rio Grande basin; or (2) the Molecular Model, which uses genotypes to assign populations to four lineages. Classification success of the Molecular Model was higher than that of the Geographic Model, whether comparisons involved single‐trait, principal components, or discriminant function analyses. Native east slope South Platte River trout (putative Greenback Cutthroat Trout O. clarkii stomias) were distinct and correctly classified, as were 83% of Rio Grande Cutthroat Trout O. clarkii virginalis populations. In all, 100% of the Blue Lineage populations of Colorado River Cutthroat Trout O. clarkii pleuriticus (putative west slope native of the White, Yampa, Green, and downstream Colorado River drainages) and 71% of the Green Lineage populations of Colorado River Cutthroat Trout (native to west slope Gunnison and Dolores River drainages and Colorado River headwaters) were correctly classified (89% overall) under the Molecular Model. Green Lineage misclassifications were mainly from morphologically and genetically distinct populations located east of the Continental Divide, whose native status remains unknown. In contrast, only 63% of those east slope and west slope Cutthroat Trout populations were correctly classified under the Geographic Model. Cohesion of distinct phenotypes and genotypes of present‐day native Cutthroat Trout lineages was remarkable given widespread and massive early stocking of various lineages outside of their native ranges. Strong congruence of morphological and molecular patterns demonstrated the power of joint morphological and molecular analyses. We encourage management that preserves diversity of these rare Cutthroat Trout lineages that evolved in concert with their environment.

Effects of Air Exposure During Simulated Catch‐and‐Release Angling on Survival and Fitness of Yellowstone Cutthroat Trout

AbstractConcerns have been raised regarding the practice of exposing fish to air during catch‐and‐release (C&amp;R) angling. The purpose of this study was to evaluate the effects of air exposure on short‐ and long‐term survival and progeny production of Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri. Prespawn adults were sampled at a weir during upstream migration in 2016 and 2017, exposed to a simulated angling event of 102 s, and then exposed to air for a randomly selected duration of 0, 30, or 60 s. An additional control group was added during 2017 in which fish were not exposed to simulated angling or air. In total, 1,519 fish were sampled in 2016, and 744 fish were sampled in 2017. Additionally, age‐0 fish (2016: n = 2,924; 2017: n = 1,492) were collected to evaluate the effects of air exposure on the production of progeny. No effect of angling itself or of angling and air exposure was observed on short‐term (≤60 d posttreatment) or long‐term (&gt;1 year posttreatment) survival of adults, with one exception. During 2016, fish that had been air exposed for 60 s had a statistically higher short‐term survival rate than fish that received no air exposure. Air exposure had no effect on the proportion of fish that successfully spawned. Regression analysis revealed that neither angling nor air exposure affected progeny production. Considering that much of the literature, as well as this study, reports little to no influence of air exposure on salmonid mortality or reproductive success, it seems highly unlikely that air exposure of less than 60 s during C&amp;R angling would have negative population‐level effects.

Performance of Diploid and Triploid Westslope Cutthroat Trout Fry Stocked into Idaho Alpine Lakes

AbstractAnglers value alpine lakes as providing a scenic, backcountry fishing experience that is seldom found in other fisheries. However, trout introduced into alpine lakes often pose a risk to native salmonids in downstream habitats by establishing source populations in headwater locations. Although the stocking of sterile triploid trout can reduce this risk, poststocking performance should be equivalent to that of diploid fish before fisheries managers and anglers consider triploid stocking to be ideal. In this study, three different mechanical pressure treatments were tested to create mixed‐sex triploid Westslope Cutthroat Trout Oncorhynchus clarkii lewisi; at 65,500.19 kPa (9,500 psi) applied for 5 min at 300 Celsius‐minutes after fertilization, triploid induction rates were 100%, and egg survival to eye‐up was only 8% lower than that for diploids. Fry were stocked into 51 alpine lakes (25 with triploids and 26 with diploids), and fish were sampled 3 years later. Gill‐net catch rates, growth, and condition did not differ between stocked diploid and triploid fish. General linear models revealed that test fish were larger and in better condition in lakes with fewer total fish (indicating a density‐dependent influence on growth and condition) and were also in better condition in lower‐elevation lakes containing a higher percentage of shallow habitat. Ploidy level was not included in the most plausible model for any of the response variables. Our results indicate that triploid Westslope Cutthroat Trout can easily be created by using pressure treatment of fertilized eggs and appear to be a suitable alternative to diploids in alpine lake stocking programs. Our study suggests that the use of triploid Westslope Cutthroat Trout in alpine lakes similar to those we studied would prevent hybridization with native salmonids in adjacent habitats without reducing the abundance, size, or condition of fish available to anglers in the lakes where they are stocked.

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.

Drought impacts to trout and salamanders in cool, forested headwater ecosystems in the western Cascade Mountains, OR

Climate change projections for the western United States suggest that many regions will experience increasing frequency and severity of droughts. In summer 2015, the Pacific Northwest experienced a drought with early onset of stream low flows, reduced summer discharge, and elevated temperatures. We evaluated population responses of two dominant stream predators—coastal cutthroat trout (Oncorhynchus clarkii clarkii) and coastal giant salamander (Dicamptodon tenebrosus)—across nine Cascade Mountain streams. Drought conditions impacted both trout and salamanders, but their responses differed. Adult trout abundance and biomass were significantly lower in 2015 relative to 2014, a year with discharge and temperature closer to historical norms. Juvenile trout abundance did not differ between years but juveniles were significantly larger in 2015. Salamander abundance and biomass were not significantly different between years but body condition was lower in all nine streams in 2015. Differences in temperature among streams did not explain trout or salamander responses. Habitat was important for trout responses with trout abundance and biomass experiencing smaller declines in systems with more deep pool area. Despite notable short-term drought impacts to trout and salamanders in 2015, populations recovered to pre-drought conditions within two years in all but the smallest stream.

Application of multistate modeling to estimate salmonid survival and movement in relation to spatial and temporal variation in metal exposure in a mining-impacted river

Multistate modeling was used to estimate survival and movement of brown trout (Salmo trutta) and westslope cutthroat trout (Oncorhynchus clarkii lewisi) in relation to copper concentrations in the mining-impacted Clark Fork River, Montana. Survival probability in the uppermost river segment, where dissolved copper concentrations frequently exceeded acute criteria for aquatic life (range: 31–60 days &gt; 13.4 μg·L–1), was 2.1 times lower for brown trout and 122 times lower for westslope cutthroat trout compared with survival rates in the lowermost segment that had relatively low dissolved copper (0 days exceedance of acute concentration). Lowest survival for both species occurred in the spring–summer period when dissolved copper concentrations were elevated coincident with higher discharge. Movement among study segments was generally low, and cutthroat trout showed low movement into the uppermost river segment with the most elevated copper levels. Both species showed high rates of movement into tributaries, which coincided with their respective spawning migrations rather than as an apparent avoidance of elevated copper levels. The linkage between survival rate and level of copper exposure for both trout species suggests that additional removal of tailings deposits could improve survival rates.

Juvenile Salmonid Assemblages at the Mirror Lake Complex in the Lower Columbia River before and after a Culvert Modification

AbstractThis study examined salmonid assemblages upstream of a culvert connecting the Mirror Lake Complex with the lower Columbia River before and after the culvert was modified to improve habitat connectivity and fish passage. Initially the culvert limited water flow between the Columbia River and the Mirror Lake Complex. The outlet and interior of the culvert were reconfigured to create a more “natural” and suitable passageway for salmonids through the removal of riprap and the strategic placement of boulders, cobbles, gravels, baffles, and weirs. Prior to the culvert modification, three sites were sampled monthly between April and August of 2008, 5.0 and 0.5 km upstream of the culvert and immediately downstream of the culvert. After the culvert modification, the same sites were sampled from 2009 to 2012, with two additional sites added in 2010. Sites near the culvert supported Chinook Salmon Oncorhynchus tshawytscha, Coho Salmon O. kisutch, and Chum Salmon O. keta, while sites further from the culvert supported unmarked Coho Salmon and Rainbow Trout O. mykiss, steelhead (anadromous Rainbow Trout), and Cutthroat Trout O. clarkii. Clear trends in salmonid occurrence were not observed, although densities of Chinook Salmon tended to be higher in years postmodification than before modification. Culvert modifications should focus on alleviating site‐specific fish passage conditions to result in substantial changes to habitat connectivity.

Effects of A Severe Drought On Summer Abundance, Growth, and Movement of Cutthroat Trout In A Western Oregon Headwater Stream

Winter snowpack depth, snowmelt timing, and snowmelt duration are projected to change in the future, leading to increased frequency and severity of drought in the Pacific Northwest. In summer 2015, stream flows throughout the Pacific Northwest were at record low levels because of low winter snowpack conditions consistent with these climate projections. We explored effects of the 2015 low-snowpack-associated drought on Coastal Cutthroat Trout (Oncorhynchus clarkii clarkii) abundance, growth, and movement patterns in two 100m reaches ( 350 y old forests) of an unnamed perennial western Oregon headwater stream before (2 y) and during a severe drought. We found that the abundance of Cutthroat Trout declined substantially during the drought year, regardless of habitat availability, riparian forest age, or stream wood structure. Fish growth during summer was consistently negative during all 3 y of the study in both reaches. During the drought year, estimated abundance and total biomass of Cutthroat Trout declined in both reaches compared to the 2y prior. In all 3 y, the majority (76%) of fish in the reach with a young riparian forest stand moved >2 m from their release point. In contrast, across the 3 study years, only 26% of fish on average moved >2 m from their release point in the old-growth reach, which had more large wood and pool area. Across both reaches, in the non-drought years, most fish moved into pools (32.4%), but some moved to riffles (23.3%). During the drought year, of the fish that were recaptured, only upstream movement to pools were observed. There were no observed movements of recaptured fish to riffles. Overall, study results suggest that increasing severity of summer drought in the Pacific Northwest is likely to reduce the abundance of fish in small headwater streams, and the remaining fish preferentially use pool habitats such as those found in structurally complex streams.

Impacts of Nonnative Brown Trout on Yellowstone Cutthroat Trout in a Tributary Stream

AbstractNonnative trout are a considerable threat to native salmonids, yet our understanding of the mechanisms behind interspecific interactions remains limited. We evaluated the impacts of nonnative Brown TroutSalmo salaron a population of Yellowstone Cutthroat TroutOncorhynchus clarkii bouvieriin Montana. We contrasted diets, growth, and survival of Yellowstone Cutthroat Trout occurring in allopatry (i.e., where no Brown Trout were present) with individuals sympatric (i.e., co‐occurring) with nonnative Brown Trout. We assessed summer and autumn diets using gastric lavage methods and survival and growth using mark–recapture analyses. Overlap in diets at sites where Yellowstone Cutthroat Trout were sympatric with Brown Trout was high during July (Horn's index:H = 0.94) and October (H = 0.83). In the presence of Brown Trout, Yellowstone Cutthroat Trout growth rates were significantly lower for juvenile (&lt;175 mm) length and adult (≥175 mm) length and mass than in allopatric sites. Allopatric Yellowstone Cutthroat Trout survival was greater across size‐classes; the most pronounced difference was in the age‐2 size‐class (125–175 mm). Together, these results in concert with observed changes in length‐frequency data, indicating a considerable lack of Yellowstone Cutthroat Trout recruitment where they are sympatric with Brown Trout, suggest the negative implications of Brown Trout are notable.

Hierarchical multi-population viability analysis.

Population viability analysis (PVA) uses concepts from theoretical ecology to provide a powerful tool for quantitative estimates of population dynamics and extinction risks. However, conventional statistical PVA requires long-term data from every population of interest, whereas many species of concern exist in multiple isolated populations that are only monitored occasionally. We present a hierarchical multi-population viability analysis model that increases inference power from sparse data by sharing information among populations to assess extinction risks while accounting for incomplete detection and sampling biases with explicit observation and sampling sub-models. We present a case study in which we customized this model for historical population monitoring data (1985-2015) from federally threatened Lahontan cutthroat trout populations in the Great Basin, USA. Data were counts of fish captured during backpack electrofishing surveys from locations associated with 155 isolated populations. Some surveys (25%) included multi-pass removal sampling, which provided valuable information about capture efficiency. GIS and remote sensing were used to estimate August stream temperatures, peak flows, and riparian vegetation condition in each population each year. Field data were used to derive an annual index of nonnative trout densities. Results indicated that population growth rates were higher in colder streams and that nonnative trout reduced carrying capacities of native trout. Extinction risks increased with more environmental stochasticity and were also related to population extent, water temperatures, and nonnative densities. We developed a graphical user interface to interact with the fitted model results and to simulate future habitat scenarios and management actions to assess their influence on extinction risks in each population. Hierarchical multi-population viability analysis bridges the gap between site-level field observations and population-level processes, making effective use of existing datasets to support management decisions with robust estimates of population dynamics, extinction risks, and uncertainties.