The study of the cutthroat trout in the Logan River drainage was initiated in cooperation with the Utah Cooperative Wildlife Research Unit and the Utah Fish and Game Department during May of 1948. The first field work began that month. The taking of fish was terminated in November, 1949, although several trips were made into the study area as late as January, 1950.

Nine hemoglobins have been isolated from the blood of cutthroat trout. All nine hemoglobins bind oxygen cooperatively and appear to be tetramers with molecular weights of -64,000. The oxygen equilibria and subunit structures of the purified hemoglobins were studied. In addition, the red blood cells of cutthroat trout were examined for the presence of ATP and GTP, which are known to be physiological modulators of hemoglobins in fishes. Five hemoglobins with isoelectric points from 9.1 to 7.0 are classified as cathodal hemoglobins. These five hemoglobins have identical oxygen binding properties by the criteria tested. All have oxygen equilibria which are unaffected by protons and ATP and essentially independent of temperature, with overall enthalpies of oxygenation ~0. Two hemoglobins with isoelectric points near 6.5, classified as a nodal hemoglobins, have oxygen binding properties distinctly different from those of the cathodal hemoglobins. Both are characterized by a Root effect, displaying non-cooperative oxygen binding and low oxygen affinity at pH 6.2. ATP causes a large reduction in the oxygen affinity without affecting the cooperativity of oxygen binding. GTP has a similar but slightly larger effect on both hemoglobins. The oxygen equilibria of the anodal hemoglobins are temperature dependent, with the oxygen affinity being reduced as temperature increases. The overall enthalpy of oxygenation is -14 kcal/mol for both hemoglobins. The two remaining hemoglobins represent only a small percentage of the total hemoglobin. These hemoglobins are tentatively designated as embryonic hemoglobins based primarily on a comparison of their properties to those observed for hemoglobins from newly-hatched rainbow trout (Iuchi, I. (1973) Comp. Biochem. Physiol. 44B, 1087-1101). These two hemoglobins have isoelectric points near 5.9 and oxygen binding properties similar to those of the cathodal hemoglobins. With the possible exception of one of the embryonic hemoglobins (for which globins were not obtained), all the hemoglobins are composed of two different types of globin chains. Six are ∝_2 β_2 tetramers, while two of the cathodal hemoglobins are hybrid tetramers of the type 〖∝∝'β〗_2 and ∝∝'ββ. Red blood cells of cutthroat trout contain both ATP and GTP, suggesting that, in contrast to rainbow trout, both nucleotides may be important physiological modulators of hemoglobin oxygen affinity in this fish.

Sixteeen sets of original laboratory data collected by many investigators for various Cutthroat flume sizes are thoroughly reviewed and organized. Best-fit discharge parameters are obtained by performing the free-flow analysis and the submerged-flow analysis. Then, the transition submergence can be calculated. Afterwards, the unified free-flow and submerged-flow discharge parameter s are developed for each flume size in order to generalize the calibrations for Cutthroat flumes. This is a very tedious process requiring a trial-and-error approach. Finally, comparisons are made of the measured laboratory discharges with the predicted discharges for both free flow and submerged flow using both the best-fit and the unified discharge parameters. The results proved quite good as measured by the standard deviation for each flume size. In most cases, the average standard deviation using the unified discharge parameters was only slightly greater than when using the best-fit discharge parameters. However, there is a significant difference in the accuracy of free-flow measurements compared with submerged-flow measurements. Using the unified discharge parameters, the mean standard deviation for all of the flumes was 2.1 percent for free flow and 6.5 percent for submerged flow.

Movement patterns and habitat use of Bonneville cutthroat trout (Oncorhynchus clarki Utah) in tributaries of the Logan River watershed are greatly affected by habitat alterations created by North American Beaver (Castor canadensis). Evaluation of cutthroat trout habitat use in these watersheds is also complicated by biotic interactions with invasive brown trout (Salmo trutta) and brook trout (Salvelinus fontinalis). My objectives in this thesis were to 1.) Evaluate the passage of beaver dams by each trout species in the Temple Fork watershed and 2.) Evaluate the habitat use of cutthroat trout in the presence of brown trout and brook trout over a range of spatial scales. To address these objectives, 1381 trout were fitted with passive integrated transponder tags. Their locations were recorded using a combination of annual capture/recapture surveys, stationary in-stream antennas, and monthly continuous mobile antenna surveys. To address objective 1, fish were located above and below 22 beaver dams to establish whether fish passed dams and to identify downstream and upstream passage; 187 individual trout were observed making 481 passes of all 22 beaver dams. Native Bonneville cutthroat trout passed dams more frequently than both non-native brown trout and brook trout. It was determined that spawning timing affected seasonal changes in dam passage for each species. Physical characteristics of dams such as height and upstream location affected the passage of each species. Movement behaviors of each trout species were also evaluated to help ex- plain dam passage. These data suggest beaver dams are not acting as barriers to movement for cutthroat and brook trout but may be impeding the movements of invasive brown trout. To address objective 2, a hierarchical classification of stream habitat was created using the River Styles framework. The River Styles framework not only establishes a relationship between habitats at different scales, but also attempts to understand the processes that create and maintain those habitats. The location of each fish observation was associated with habitats at the stream, landscape unit, River Style, and geomorphic unit levels. Habitat use of each species of fish was evaluated at each spatial scale using all fish observations over the four-year study period. Hotspot locations, or locations used consistently by a species of fish consistently through time, were also evaluated across the entire study period and over each year. It was found that brook trout almost exclusively use the beaver ponds and beaver-altered habitats in Spawn Creek. Brown trout were not found in the upper- most parts of both Spawn Creek and Temple Fork. They were also found more than the other species in pools created by bedrock or man-made control features, suggesting that they select highly stable habitats. Cutthroat trout were found more than brown trout in beaver-altered habitats and lateral scour pools, suggesting that they select more dynamic, naturally occurring habitats.

Stream restoration has become a popular management tool for attempting to increase and/or restore fish populations by improving habitat. A section of the Strawberry River, Utah recently underwent a stream restoration project, where the main goals of the project included increasing spawning activity, rearing potential, and resident populations of Bear Lake cutthroat trout Oncorhynchus clarkia utah. The impact of the restoration project on cutthroat trout was investigated by first characterizing preferred habitat for different life stages, investigating habitat as a limiting factor in the system, and then assessing the quality of available habitat by comparing restored/unrestored sections of stream and pre-restoration/post-restoration of the same sections of stream. Results indicated cutthroat trout in the Strawberry River preferred faster water velocities, shallower depths, moderate substrates sizes, and riffle habitat types for spawning. In contrast, juvenile and adult life stages preferred deeper sections of stream, the presence of cover, and pool habitat types. Limiting factor analyses suggested spawner abundance may be limiting in the Strawberry River and maximum daily temperatures during the summer may be the strongest limiting habitat factor for juvenile and resident adult cutthroat trout. Restoration generally appeared to initiate a shift towards more favorable habitat, especially in terms of increasing near-bed velocity and increasing the proportion of preferred substrate sizes for spawning, and increasing the percentage of pools for juvenile and resident adult life stages. The potential benefits of the restoration remained somewhat ambiguous, a result of relatively small differences observed between study reaches, limited pre-restoration data, high spatial and inter-annual variability within and among control study reaches, and the inherently delayed reaction of ecological responses to physical changes from restoration. However, these issues can be resolved through continued monitoring. Long-term monitoring would allow for the accounting of natural variability to further tease out differences resulting from restoration and differences resulting from natural fluctuations. Additional monitoring would also capture long-term responses, which has the potential to be significant considering the relatively slow response of riparian vegetation to restoration. This study also provides a baseline dataset and template for future long-term monitoring efforts.

The distribution of Lahontan cutthroat trout Oncorhynchus clarki henshawi was assessed in a high-desert stream in southeastern Oregon where beaver Castor canadensis are abundant. Longitudinal patterns of beaver ponds, habitat, temperature, and Lahontan cutthroat trout age group distribution were identified throughout Willow Creek. Three distinct stream segments were classified based on geomorphological characteristics. Four beaver-pond and four free-flowing sample sections were randomly located in each of the three stream segments. Beavers substantially altered the physical habitat of Willow Creek increasing the depth and width of available habitat. In contrast, there was no measurable effect on water temperature. The total number of Lahontan cutthroat trout per meter was significantly higher in beaver ponds than free-flowing sections. Although density (fish/m��) showed no statistically significant (P<0.05) increase, values in beaver ponds were two-fold those of free-flowing sections. Age-1 and young-of-the-year trout were absent or in very low numbers in lower Willow Creek because of elevated temperatures, but high numbers of age-2 and 3 (adults) Lahontan cutthroat trout were found in beaver ponds where water temperatures reached lethal levels (>24��C). Apparently survival is greater in beaver ponds than free-flowing sections as temperatures approach lethal limits. / Graduation date: 2003

This thesis addresses the issue of hybridization between native westslope cutthroat trout (Oncorhynchus clarkii lewisi) and introduced rainbow trout (O. mykiss), giving strong consideration to their differing glacial refugia during the Wisconsin Glaciation. We hypothesize that having more recently derived from an anadromous form O. mykiss will possess life history characteristics more typical of a highly anadromous species. This hypothesis would also predict hybrids to be intermediate in these characteristics. In a comparison of growth rates and survivorship (Chapter 2) O. clarkii lewisi were found to employ a slower growing, longer lived strategy than O. mykiss, with hybrids typically being intermediate. Additionally, O. mykiss were also found to have aerobic and anaerobic metabolic capacities superior to O. clarkii lewisi in a first time comparison of these species (Chapter 3). These results support the glacial refuge hypothesis, but furthermore provide a potential explanation of the establishment of the elevational gradient commonly observed in hybridization studies. It would seem likely that O. mykiss would require more productive reaches being a faster growing, shorter lived species with higher metabolic costs. This study confirmed the gradient of O. mykiss persisting at lower elevations, trending through a hybrid zone to pure O. clarkii lewisi in headwater reaches and above migratory barriers (Chapter 2). A similar gradient was also reported when considering only the hybrid population, supporting the notion that habitat preference is under some genotypic control. The importance of migratory barriers was found to decrease with elevation suggesting potential additional limiting factors. Hybrid individuals were also found to be intermediate in morphological characteristics (Chapter 4). The confidence in differentiating between pure and non-pure O. clarkii lewisi was found to increase with the number of O. mykiss alleles (degree of hybridization) an individual possessed. Morphological-based identification was found to be an efficient, cost-friendly, preliminary assessment tool that could be useful in limiting the number of sites needing detailed genetic assessment. / 152 leaves : ill. (some col.) ; 29 cm.

Computational fluid dynamics software was used to simulate the hydraulic behavior of 51 Cutthroat flume (CTF) sizes under various flow conditions, including 24 standard sizes with throat widths (W) from 0.051 to 1.219 m (2 inches to 4 ft), flume scale lengths (L) ranging from 0.457 to 2.743 m (1.5 - 9 ft), constriction ratios (W/L) of 1/9, 2/9, 3/9, and 4/9, and 27 non-standard flumes of intermediate sizes. The validity and accuracy of the simulation results were demonstrated using laboratory data from other studies for 16 of the standard flume sizes and three non-standard sizes. By using the depth-discharge data for 24 standard CTFs obtained from the modeling, a series of "best-fit" calibrations of existing separate free- and submerged-flow rating equations were performed for each of the 24 standard-sized CTFs. A new unified rating equation for free- and submerged-flow conditions for the standard CTF sizes was proposed by comparing a set of empirical equations. The performance of the unified rating equation was also analyzed in order to determine the technical desirability of the equations as substitutes for the existing separate free- and submerged-flow rating equations. For the free-flow rating, the discharge parameters in the traditional equation are generalized to be applicable to any of the CTF sizes with flume lengths ranging from 0.457 to 2.743 m (1.5 - 9 ft), and the constriction ratio ranging from 1/9 to 4/9. This allows the application of CTFs with greater accuracy than the previously available equation. With the new generic-fit equations for the free-flow rating parameters, the discharge error is 4% from the standard discharge, with an average error of 2.2% for full-scale discharge. The generic unified rating equations proposed herein are also applicable to any of the CTF sizes, varying among the 24 standard sizes with flume lengths ranging from 0.457 to 2.743 m (1.5 - 9 ft) and the constriction ratio ranging from 1/9 to 4/9. With the generic-fit equations for the calibration parameters as derived herein, the discharge error is 6 - 8% compared to the standard discharge, and 2 - 3% for full-scale discharge.

Colorado River cutthroat trout, Oncorhyncus clarki pleuriticus , occupy less than 12% of their historic range. Restoration and conservation of this species are currently under way across the upper Colorado River basin, but guidance to inform management decisions related to the impacts of climate change on cutthroat is lacking. Shifts in the thermal distribution of freshwater fish have been documented, and will continue to occur as cold water habitat is threatened by warming water temperatures. Coupled air and water temperature data allow for an estimation of potential resistance and resilience to warming, determining the effect that local air has on stream temperature. The United States Forest Service, cooperating with federal agencies, state agencies and private landowners, placed temperature loggers in the water and two air locations at 50 sites. To select a representative subset of sites, six habitat characteristics of each Colorado River cutthroat trout core conservation population were considered. These characteristics include solar input, elevation, watershed area, riparian vegetation, groundwater input, and the 30-year mean maximum July air temperature. Results from coupled temperature loggers indicate that the relationship between air and water temperature in the upper Colorado River basin is neither linear, nor one-to-one. Using Mohseni's (2003) equation, the relationship between air and water temperature was fit to a nonlinear regression curve. Analysis shows that the median rise in daily maximum water temperature is only 0.41°C for a 1.0°C increase in the median daily maximum air temperature. Air temperature exerts the most influence over water temperature; however, these results indicate that there are other characteristics that influence stream temperature. To determine these characteristics, analysis of the six habitat characteristics used for site selection in addition to aspect, slope, and latitude were used to model multiple temperature metrics. The best model, nonlinear water to air temperature relationship, had an R2 between actual and predicted values of 0.71. It also became clear that using multi-metric analysis would provide a much more robust indicator of resistance. This work will allow managers to consider potential climate change resistance or resilience in project prioritization, by understanding potential habitat characteristics to buffer stream warming.

Through a myriad of practices, anthropogenic land and water use has caused the localized extirpation or complete elimination of many native fishes throughout North America. Specifically, native salmonids have seen substantial declines in population sizes and geographic distributions due to a number of factors, including habitat loss or degradation, overharvest, or the introduction of non-native competitors and predators. Among those affected, the 14 subspecies of cutthroat trout found across western North America have been subject to two extinctions and five listings as Threatened as per the Endangered Species Act. Lahontan cutthroat trout Oncorhynchus clarkii henshawi have experienced marked reductions throughout their native range in the western Great Basin, U.S. In Pyramid Lake, Nevada, where they were once locally extirpated due to overfishing, water loss, and degraded spawning habitat, Lahontan cutthroat trout have been successfully stocked and managed, though they do not routinely reach their pre-extirpation sizes. With little research to determine the factors influencing Lahontan cutthroat trout in Pyramid Lake, I used a suite of modeling tools and empirical data to elucidate the influence of the current surrounding environment on Lahontan cutthroat trout in Pyramid Lake. To identify important food web interactions that may affect the availability of food to Lahontan cutthroat trout, I used diet composition and stable isotope analyses of carbon and nitrogen to understand dietary trends. Large Lahontan cutthroat trout (>400 mm TL), along with non-native Sacramento perch Ambloplites interruptus, relied most heavily on fish prey, yet neither species showed signs of cannibalism or preying on the other species. Diet composition and stable isotope analyses also indicated that Lahontan cutthroat trout rely mostly on tui chub Gila bicolor and other fish for food. I also used results from bioenergetic and hydroacoustic analyses to compare the number of tui chub consumed by trout to the number of tui chub in the lake, during the time of this study. Results from these analyses suggest that trout consume well below the number of tui chub available in the lake, indicating that trout are not limited by the availability of tui chub. Lastly, I used a number of biotic and abiotic predictors to determine which factors influence the distribution, and subsequently abundance, of trout in Pyramid Lake and found that biotic factors were very weak predictors of trout distribution, further indicating that trout are not limited by food resources in Pyramid Lake.