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• 8461. [Article] Survival Rates and Cause-Specific Mortality of Mule Deer in South-Central Oregon

  It is critical for wildlife managers to understand the population dynamics of a harvested species, particularly for ungulates, which are a valuable wildlife resource. Due to concerns that mule deer (Odocoileus ...

  Citation × Citation Citation Abstract Copy Title: Survival Rates and Cause-Specific Mortality of Mule Deer in South-Central Oregon Author: Mulligan, Elizabeth M. It is critical for wildlife managers to understand the population dynamics of a harvested species, particularly for ungulates, which are a valuable wildlife resource. Due to concerns that mule deer (Odocoileus hemionus) populations in Oregon were declining, more comprehensive data on population vital rates and the factors potentially affecting them were needed by resource managers. To meet this research need, Oregon Department of Fish and Wildlife implemented a seven year study to investigate habitat use and survival of mule deer in eastern Oregon. From 2005-2012, the agency radiocollared 621 mule deer in south-central Oregon in order to gain more comprehensive information about seasonal movement, seasonal and annual survival, and changes in habitat use for the population. I used the radio-telemetry data from this larger study to investigate mule deer survival rates and cause-specific mortality and the effects of deer seasonal distributions, movement behavior, and environmental factors such as annual and climatic variation. I used known-fate data for 408 adult female radio-collared mule deer to estimate monthly survival rates and to investigate a variety of factors that might affect these rates including seasonal distribution, temporal effects (seasonal, annual, and trends across season and year), movement behavior, and climatic covariates on differing scales. Variation in survival rates for this population of female mule deer in eastern Oregon was best explained by an additive effect of migration behavior, fall migration period, and precipitation levels on individual winter ranges. Survival was significantly higher for migratory deer than residents. Both groups had lower survival during the fall migration period (Oct-Nov) and a positive linear relationship between survival and winter precipitation in individual winter ranges. Annual survival estimates for migrants ranged from 0.81-0.82, which is similar to other findings, but survival rates for residents (0.76- 0.77) were low in comparison to survival rates for adult female mule deer in other parts of their range. I used a nonparametric cumulative incidence function estimator (NPCIFE) to generate annual cumulative incidence functions separately for males and females due to differing risks associated with each sex. The four competing sources of mortality I included in this analysis for males were legal harvest, illegal harvest, predation, and starvation, disease, vehicle or fence-collision combined as one category (i.e., other). For females in investigated predation, human-associated mortality (vehicle or fence), illegal harvest, and natural causes (starvation and disease). Annual risk functions were pooled across all years of the study to maximize sample size. For males, the cumulative risk was highest for legal harvest (0.249, 95%CI=0.172-0.326), with predation the next highest cause of mortality for this sex (0.104, 95%CI=0.042-0.611). For females, the cumulative risk was highest for predation, (0.044, 95%CI=0.028-0.065) with anthropogenic causes (0.038, 95%CI=0.021-0.054) and illegal harvest (0.031, 95%CI=0.17-0.054) also important sources of mortality. Higher monthly survival rates of migrants compared to residents (across all months of the biological cycle) suggested that leaving for potentially higher quality summer foraging grounds outweighed the cost of traveling through unfamiliar habitats and energy expenditure from migration. Conversely, it may also imply that the summer ranges for residents had a negative effect on survival due to habitat quality or human disturbance. Both migrants and residents had lower monthly survival during the fall migration period (Oct - Nov). Female mule deer were excluded from the state-managed bow and rifle hunting season during this study, but females may experience the negative effects of human disturbance associated with fall hunting activities. This time of year is also energetically costly for females, being that some may still be nursing, which could have an additive effect to the energy used to migrate or avoid human disturbance. Winter precipitation also had positive effect on survival for both groups, possibly because increased average winter precipitation resulted in increased winter forage quantity and quality. My results suggest that female survival rates observed during my study are on the low end of the range reported for this species and may be contributing to population declines of mule deer in Oregon. Annual estimates of male survival were also low, but it is unclear how that might contribute to overall population declines without more information on annual and seasonal variation in male survival. Surprisingly, I observed high levels of illegal harvest on female deer and evidence that female survival during the fall migration period, which overlaps Oregon’s legal harvest season, was lower than other times of the year. It is unclear why the fall migration period negatively affects both migrants and resident deer similarly, but future research should attempt to determine the specific factors that are negatively impacting mule deer survival during this time period in south-central Oregon. In addition, as human development in the area continues to grow, it is important to consider migration paths and the habitat quality of both summer and winter ranges. My results suggested that conditions may differ between summer ranges in particular, for residents vs. migrants, and understanding these differences may be the key to increasing survival of female mule deer in Oregon. Sharing information from this study with law enforcement and the general public may be the first step towards increasing awareness of, and thereby reducing, the relatively high levels of illegal harvest I documented for the female population. Future research should focus on investigating the differences in habitat quality for residents versus migrants, the factors that decrease survival during fall migration for both groups, and the social and economic factors that contribute to the illegal harvest of female mule deer in eastern Oregon. Title: Survival Rates and Cause-Specific Mortality of Mule Deer in South-Central Oregon Author: Mulligan, Elizabeth M. It is critical for wildlife managers to understand the population dynamics of a harvested species, particularly for ungulates, which are a valuable wildlife resource. Due to concerns that mule deer (Odocoileus hemionus) populations in Oregon were declining, more comprehensive data on population vital rates and the factors potentially affecting them were needed by resource managers. To meet this research need, Oregon Department of Fish and Wildlife implemented a seven year study to investigate habitat use and survival of mule deer in eastern Oregon. From 2005-2012, the agency radiocollared 621 mule deer in south-central Oregon in order to gain more comprehensive information about seasonal movement, seasonal and annual survival, and changes in habitat use for the population. I used the radio-telemetry data from this larger study to investigate mule deer survival rates and cause-specific mortality and the effects of deer seasonal distributions, movement behavior, and environmental factors such as annual and climatic variation. I used known-fate data for 408 adult female radio-collared mule deer to estimate monthly survival rates and to investigate a variety of factors that might affect these rates including seasonal distribution, temporal effects (seasonal, annual, and trends across season and year), movement behavior, and climatic covariates on differing scales. Variation in survival rates for this population of female mule deer in eastern Oregon was best explained by an additive effect of migration behavior, fall migration period, and precipitation levels on individual winter ranges. Survival was significantly higher for migratory deer than residents. Both groups had lower survival during the fall migration period (Oct-Nov) and a positive linear relationship between survival and winter precipitation in individual winter ranges. Annual survival estimates for migrants ranged from 0.81-0.82, which is similar to other findings, but survival rates for residents (0.76- 0.77) were low in comparison to survival rates for adult female mule deer in other parts of their range. I used a nonparametric cumulative incidence function estimator (NPCIFE) to generate annual cumulative incidence functions separately for males and females due to differing risks associated with each sex. The four competing sources of mortality I included in this analysis for males were legal harvest, illegal harvest, predation, and starvation, disease, vehicle or fence-collision combined as one category (i.e., other). For females in investigated predation, human-associated mortality (vehicle or fence), illegal harvest, and natural causes (starvation and disease). Annual risk functions were pooled across all years of the study to maximize sample size. For males, the cumulative risk was highest for legal harvest (0.249, 95%CI=0.172-0.326), with predation the next highest cause of mortality for this sex (0.104, 95%CI=0.042-0.611). For females, the cumulative risk was highest for predation, (0.044, 95%CI=0.028-0.065) with anthropogenic causes (0.038, 95%CI=0.021-0.054) and illegal harvest (0.031, 95%CI=0.17-0.054) also important sources of mortality. Higher monthly survival rates of migrants compared to residents (across all months of the biological cycle) suggested that leaving for potentially higher quality summer foraging grounds outweighed the cost of traveling through unfamiliar habitats and energy expenditure from migration. Conversely, it may also imply that the summer ranges for residents had a negative effect on survival due to habitat quality or human disturbance. Both migrants and residents had lower monthly survival during the fall migration period (Oct - Nov). Female mule deer were excluded from the state-managed bow and rifle hunting season during this study, but females may experience the negative effects of human disturbance associated with fall hunting activities. This time of year is also energetically costly for females, being that some may still be nursing, which could have an additive effect to the energy used to migrate or avoid human disturbance. Winter precipitation also had positive effect on survival for both groups, possibly because increased average winter precipitation resulted in increased winter forage quantity and quality. My results suggest that female survival rates observed during my study are on the low end of the range reported for this species and may be contributing to population declines of mule deer in Oregon. Annual estimates of male survival were also low, but it is unclear how that might contribute to overall population declines without more information on annual and seasonal variation in male survival. Surprisingly, I observed high levels of illegal harvest on female deer and evidence that female survival during the fall migration period, which overlaps Oregon’s legal harvest season, was lower than other times of the year. It is unclear why the fall migration period negatively affects both migrants and resident deer similarly, but future research should attempt to determine the specific factors that are negatively impacting mule deer survival during this time period in south-central Oregon. In addition, as human development in the area continues to grow, it is important to consider migration paths and the habitat quality of both summer and winter ranges. My results suggested that conditions may differ between summer ranges in particular, for residents vs. migrants, and understanding these differences may be the key to increasing survival of female mule deer in Oregon. Sharing information from this study with law enforcement and the general public may be the first step towards increasing awareness of, and thereby reducing, the relatively high levels of illegal harvest I documented for the female population. Future research should focus on investigating the differences in habitat quality for residents versus migrants, the factors that decrease survival during fall migration for both groups, and the social and economic factors that contribute to the illegal harvest of female mule deer in eastern Oregon. Close

• 8462. [Article] Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models : a case study from the Marennes-Oléron Estuary, France

  This thesis presents two related studies on the methodology for creating, and subsequently analyzing, an inverse food web model of an intertidal seagrass bed. The first study (Chapter 2) describes, for ...

  Citation × Citation Citation Abstract Copy Title: Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models : a case study from the Marennes-Oléron Estuary, France Author: Pacella, Stephen Roger This thesis presents two related studies on the methodology for creating, and subsequently analyzing, an inverse food web model of an intertidal seagrass bed. The first study (Chapter 2) describes, for the first time in the literature, a method for incorporating isotopic information gained from Bayesian mixing models into an inverse food web model. The second study (Chapter 3) analyzes the results of this food web model from an ecological perspective, which includes the first complete description of the carbon budget of an intertidal seagrass food web incorporating isotopic information. Linear inverse modeling (LIM) is a technique that estimates a complete network of flows in an under-determined system (e.g., a food web) using a combination of site-specific data and previously published data. This estimation of complete flow networks of food webs in marine ecosystems is becoming more recognized as a powerful tool for understanding ecosystem functioning. However, diets and consumption rates of organisms are often difficult or impossible to accurately and reliably measure in the field, resulting in a large amount of uncertainty in the magnitude of consumption flows and resource partitioning in food web models. In order to address this issue, Chapter 2 utilized stable isotope data to help aid in estimating these unknown flows. δ¹³C and δ¹⁵N isotope data of consumers and producers in the Marennes-Oleron seagrass system were used in Bayesian mixing models; the output of which were then used to constrain consumption flows in an inverse analysis food web model of the seagrass ecosystem. We hypothesized that incorporating the diet information gained from the stable isotope mixing models would result in a more constrained food web model. In order to test this, two inverse food web models were built to track the flow of carbon through the seagrass food web on an annual basis, with units of mg C m⁻² d⁻¹. The first model (Traditional LIM) included all available data, with the exception of the diet constraints formed from the stable isotope mixing models. The second model (Isotope LIM) was identical to the Traditional LIM, but included the SIAR diet constraints. Both models were identical in structure, and intended to model the same Marennes- Oleron intertidal seagrass bed. Each model consisted of 27 compartments (24 living, 3 detrital) and 175 flows. Comparisons between the outputs of the models showed the addition of the SIAR-derived isotopic diet constraints further constrained the solution range of all food web flows on average by 26%. Flows that were directly affected by an isotopic diet constraint were 45% further constrained on average. These results confirmed our hypothesis that incorporation of the isotope information would result in a more constrained food web model, and demonstrated the benefit of utilizing multi-tracer stable isotope information in ecosystem models. In Chapter 3, Ecological Network Analysis (ENA) was used to investigate the functional ecology of the system. The majority of seagrass food web studies thus far have relied on trophic marker analyses (i.e. stable isotopes, fatty acids) to investigate food sources and trophic positions, and as a result, few studies have examined seagrass beds from a perspective of whole-ecosystem functioning. By quantifying the Marennes- Oleron seagrass food web using linear inverse modeling coupled with results from isotopic mixing models, this study investigated the relative trophic importance of primary producers in the system, the trophic structure of the seagrass bed flora and fauna, the relative importance of allochthonous versus autochthonous carbon, and both the sequestration and export of organic carbon to the surrounding environment. Additionally, results of these analyses were compared with other coastal systems, including a neighboring bare mudflat located in the Marennes-Oleron estuary. Grazing rates indicated that microphytobenthos was directly consumed about 7 times more than Zostera, while a novel metric of total food web dependency derived from network analysis showed the consumer compartments relied upon microphytobenthos 22 time more than on Z. noltii via direct and indirect pathways. Meiofauna was found to provide an important link between primary production and detritus with upper trophic levels (i.e. fish). Autochthonous carbon was utilized over 4 times more than allochthonous carbon by the seagrass food web in total, and the system was shown to be a net carbon sink. Our analysis supported the concept that seagrass meadows have a high metabolic capacity and the ability to accumulate large sedimentary carbon pools (e.g., carbon sequestration), which are important climate-regulating ecosystem services. ENA revealed the Oleron seagrass bed to be a relatively mature, stable system internally, with strong connections via energy transport to and from surrounding environments. To the best of the authors' knowledge, this study was the first to fully characterize the carbon budget of an intertidal seagrass food web utilizing probabilistic methods. Title: Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models : a case study from the Marennes-Oléron Estuary, France Author: Pacella, Stephen Roger This thesis presents two related studies on the methodology for creating, and subsequently analyzing, an inverse food web model of an intertidal seagrass bed. The first study (Chapter 2) describes, for the first time in the literature, a method for incorporating isotopic information gained from Bayesian mixing models into an inverse food web model. The second study (Chapter 3) analyzes the results of this food web model from an ecological perspective, which includes the first complete description of the carbon budget of an intertidal seagrass food web incorporating isotopic information. Linear inverse modeling (LIM) is a technique that estimates a complete network of flows in an under-determined system (e.g., a food web) using a combination of site-specific data and previously published data. This estimation of complete flow networks of food webs in marine ecosystems is becoming more recognized as a powerful tool for understanding ecosystem functioning. However, diets and consumption rates of organisms are often difficult or impossible to accurately and reliably measure in the field, resulting in a large amount of uncertainty in the magnitude of consumption flows and resource partitioning in food web models. In order to address this issue, Chapter 2 utilized stable isotope data to help aid in estimating these unknown flows. δ¹³C and δ¹⁵N isotope data of consumers and producers in the Marennes-Oleron seagrass system were used in Bayesian mixing models; the output of which were then used to constrain consumption flows in an inverse analysis food web model of the seagrass ecosystem. We hypothesized that incorporating the diet information gained from the stable isotope mixing models would result in a more constrained food web model. In order to test this, two inverse food web models were built to track the flow of carbon through the seagrass food web on an annual basis, with units of mg C m⁻² d⁻¹. The first model (Traditional LIM) included all available data, with the exception of the diet constraints formed from the stable isotope mixing models. The second model (Isotope LIM) was identical to the Traditional LIM, but included the SIAR diet constraints. Both models were identical in structure, and intended to model the same Marennes- Oleron intertidal seagrass bed. Each model consisted of 27 compartments (24 living, 3 detrital) and 175 flows. Comparisons between the outputs of the models showed the addition of the SIAR-derived isotopic diet constraints further constrained the solution range of all food web flows on average by 26%. Flows that were directly affected by an isotopic diet constraint were 45% further constrained on average. These results confirmed our hypothesis that incorporation of the isotope information would result in a more constrained food web model, and demonstrated the benefit of utilizing multi-tracer stable isotope information in ecosystem models. In Chapter 3, Ecological Network Analysis (ENA) was used to investigate the functional ecology of the system. The majority of seagrass food web studies thus far have relied on trophic marker analyses (i.e. stable isotopes, fatty acids) to investigate food sources and trophic positions, and as a result, few studies have examined seagrass beds from a perspective of whole-ecosystem functioning. By quantifying the Marennes- Oleron seagrass food web using linear inverse modeling coupled with results from isotopic mixing models, this study investigated the relative trophic importance of primary producers in the system, the trophic structure of the seagrass bed flora and fauna, the relative importance of allochthonous versus autochthonous carbon, and both the sequestration and export of organic carbon to the surrounding environment. Additionally, results of these analyses were compared with other coastal systems, including a neighboring bare mudflat located in the Marennes-Oleron estuary. Grazing rates indicated that microphytobenthos was directly consumed about 7 times more than Zostera, while a novel metric of total food web dependency derived from network analysis showed the consumer compartments relied upon microphytobenthos 22 time more than on Z. noltii via direct and indirect pathways. Meiofauna was found to provide an important link between primary production and detritus with upper trophic levels (i.e. fish). Autochthonous carbon was utilized over 4 times more than allochthonous carbon by the seagrass food web in total, and the system was shown to be a net carbon sink. Our analysis supported the concept that seagrass meadows have a high metabolic capacity and the ability to accumulate large sedimentary carbon pools (e.g., carbon sequestration), which are important climate-regulating ecosystem services. ENA revealed the Oleron seagrass bed to be a relatively mature, stable system internally, with strong connections via energy transport to and from surrounding environments. To the best of the authors' knowledge, this study was the first to fully characterize the carbon budget of an intertidal seagrass food web utilizing probabilistic methods. Close

• 8463. [Article] The Responses of Slope-spawning Flatfish to Environmental Variability in the Eastern Bering Sea

  When adult spawning and juvenile settling locations of marine fishes are geographically separated, their early life history stages must rely on transport and their own behavior to move them toward suitable ...

  Citation × Citation Citation Abstract Copy Title: The Responses of Slope-spawning Flatfish to Environmental Variability in the Eastern Bering Sea Author: Vestfals, Cathleen D. When adult spawning and juvenile settling locations of marine fishes are geographically separated, their early life history stages must rely on transport and their own behavior to move them toward suitable habitats for successful recruitment to the juvenile phase. Variations in climate may reduce the availability of spawning and juvenile nursery habitats and alter ocean circulation patterns, which can disrupt dispersal pathways and affect life cycle closure. This research focused on two commercially- and ecologically-important flatfish species in the eastern Bering Sea (EBS), Greenland halibut (Reinhardtius hippoglossoides) and Pacific halibut (Hippoglossus stenolepis), which may be especially sensitive to climate variability due to strong seasonally and ontogenetically variable distributions and extended pelagic larval phases. Data from fishery-dependent and fishery-independent sources were analyzed to determine the influence of environmental variability on adult habitat use, thus gaining a uniquely comprehensive range of seasonal and geographic coverage of each species' distribution. Transport along and across the Bering Slope was characterized from 23 years (1982 - 2004) of simulations from a Regional Ocean Modeling System (ROMS) ocean circulation model, with the expectation that changes in the strength and position of the Bering Slope Current (BSC) would affect recruitment, and that circulation features along and across the shelf edge would be strongly influenced by atmospheric forcing. To understand the physical mechanisms of larval delivery to shelf nursery areas, Greenland and Pacific halibut dispersal pathways were simulated from their source (e.g., spawning areas over the continental slope) to settlement locations (e.g., juvenile nursery areas on the continental shelf) using DisMELS (Dispersal Model for Early Life Stages), an individual-based particle-tracking model. Spatial patterns of dispersal were characterized for each species and for years with contrasting settlement success to understand the influence of local oceanographic and atmospheric conditions on dispersal corridor use. Adult Greenland and Pacific halibut exhibited strong and contrasting responses to changes in temperature on the shelf, with catches decreasing and increasing, respectively, at approximately 1°C. The effect of temperature was not as prominent along the slope, suggesting that slope habitats may provide some insulation from shelf-associated environmental variability, particularly for Greenland halibut. With warming, Greenland halibut exhibited more of a bathymetric shift in distribution, while the shift was more latitudinal for Pacific halibut. Habitat partitioning may, in part, explain differences in Greenland and Pacific halibut adult distributions. Analysis of modeled circulation revealed strong variations in the strength and position of the BSC, with changes in along-shelf and cross-shelf flow associated with changes in recruitment. Greenland halibut benefitted from decreased along-shelf and on-shelf flow, while Pacific halibut benefitted from on-shelf flows through Bering and Pribilof canyons. Variability in transport and the BSC position was strongly influenced by winds, ice cover, and large-scale climatic drivers. Greenland and Pacific halibut dispersal pathways varied between years, with distinct differences in dispersal characteristics found between the two species. In general, Greenland halibut connected to shelf nursery areas via more northern corridors, while Pacific halibut connected through more southern ones. In years with poor settlement success, the reverse pattern was observed. Greenland halibut dispersal metrics were strongly correlated with along- and cross-shelf transport, as well as NW along-shelf winds and ice, while Pacific halibut had strong associations with SW onshelf winds. Spawning time and location, along with climate-induced changes in circulation, appear to differentially affect Greenland and Pacific halibut dispersal pathways, which can lead to variations in their recruitment. Overall, Greenland and Pacific halibut had contrasting responses to similar environmental forcing, and predicted climate change is expected to impact these species in different ways. With increasing warming on the EBS shelf, they will likely further partition their habitats, with Greenland halibut finding colder refuges along the slope and Pacific halibut inhabiting larger portions of the shelf. Climate-induced changes in circulation were found to affect the transport of halibut eggs and larvae and their recruitment to the juvenile phase, which suggests an important role in their slope-shelf connectivity. Results of this study suggest that Greenland and Pacific halibut use different mechanisms to move from their spawning locations along the slope to their settlement areas on the shelf, and that environmental conditions that increase slope-shelf connectivity for one species will likely result in reduced connectivity for the other. This research improves our understanding of how slopespawning flatfish respond to a changing ocean environment, which is important for effective management of their populations, as predicted climate change will likely alter their habitat use and population dynamics. Title: The Responses of Slope-spawning Flatfish to Environmental Variability in the Eastern Bering Sea Author: Vestfals, Cathleen D. When adult spawning and juvenile settling locations of marine fishes are geographically separated, their early life history stages must rely on transport and their own behavior to move them toward suitable habitats for successful recruitment to the juvenile phase. Variations in climate may reduce the availability of spawning and juvenile nursery habitats and alter ocean circulation patterns, which can disrupt dispersal pathways and affect life cycle closure. This research focused on two commercially- and ecologically-important flatfish species in the eastern Bering Sea (EBS), Greenland halibut (Reinhardtius hippoglossoides) and Pacific halibut (Hippoglossus stenolepis), which may be especially sensitive to climate variability due to strong seasonally and ontogenetically variable distributions and extended pelagic larval phases. Data from fishery-dependent and fishery-independent sources were analyzed to determine the influence of environmental variability on adult habitat use, thus gaining a uniquely comprehensive range of seasonal and geographic coverage of each species' distribution. Transport along and across the Bering Slope was characterized from 23 years (1982 - 2004) of simulations from a Regional Ocean Modeling System (ROMS) ocean circulation model, with the expectation that changes in the strength and position of the Bering Slope Current (BSC) would affect recruitment, and that circulation features along and across the shelf edge would be strongly influenced by atmospheric forcing. To understand the physical mechanisms of larval delivery to shelf nursery areas, Greenland and Pacific halibut dispersal pathways were simulated from their source (e.g., spawning areas over the continental slope) to settlement locations (e.g., juvenile nursery areas on the continental shelf) using DisMELS (Dispersal Model for Early Life Stages), an individual-based particle-tracking model. Spatial patterns of dispersal were characterized for each species and for years with contrasting settlement success to understand the influence of local oceanographic and atmospheric conditions on dispersal corridor use. Adult Greenland and Pacific halibut exhibited strong and contrasting responses to changes in temperature on the shelf, with catches decreasing and increasing, respectively, at approximately 1°C. The effect of temperature was not as prominent along the slope, suggesting that slope habitats may provide some insulation from shelf-associated environmental variability, particularly for Greenland halibut. With warming, Greenland halibut exhibited more of a bathymetric shift in distribution, while the shift was more latitudinal for Pacific halibut. Habitat partitioning may, in part, explain differences in Greenland and Pacific halibut adult distributions. Analysis of modeled circulation revealed strong variations in the strength and position of the BSC, with changes in along-shelf and cross-shelf flow associated with changes in recruitment. Greenland halibut benefitted from decreased along-shelf and on-shelf flow, while Pacific halibut benefitted from on-shelf flows through Bering and Pribilof canyons. Variability in transport and the BSC position was strongly influenced by winds, ice cover, and large-scale climatic drivers. Greenland and Pacific halibut dispersal pathways varied between years, with distinct differences in dispersal characteristics found between the two species. In general, Greenland halibut connected to shelf nursery areas via more northern corridors, while Pacific halibut connected through more southern ones. In years with poor settlement success, the reverse pattern was observed. Greenland halibut dispersal metrics were strongly correlated with along- and cross-shelf transport, as well as NW along-shelf winds and ice, while Pacific halibut had strong associations with SW onshelf winds. Spawning time and location, along with climate-induced changes in circulation, appear to differentially affect Greenland and Pacific halibut dispersal pathways, which can lead to variations in their recruitment. Overall, Greenland and Pacific halibut had contrasting responses to similar environmental forcing, and predicted climate change is expected to impact these species in different ways. With increasing warming on the EBS shelf, they will likely further partition their habitats, with Greenland halibut finding colder refuges along the slope and Pacific halibut inhabiting larger portions of the shelf. Climate-induced changes in circulation were found to affect the transport of halibut eggs and larvae and their recruitment to the juvenile phase, which suggests an important role in their slope-shelf connectivity. Results of this study suggest that Greenland and Pacific halibut use different mechanisms to move from their spawning locations along the slope to their settlement areas on the shelf, and that environmental conditions that increase slope-shelf connectivity for one species will likely result in reduced connectivity for the other. This research improves our understanding of how slopespawning flatfish respond to a changing ocean environment, which is important for effective management of their populations, as predicted climate change will likely alter their habitat use and population dynamics. Close

• 8464. [Article] Implications of cougar prey selection and demography on population dynamics of elk in northeast Oregon

  Mule deer (Odocoileus hemionus hemionus) and Rocky Mountain elk (Cervus canadensis nelsoni; hereafter elk) populations in northeast Oregon have declined in the past 10 to 20 years. Concurrent with these ...

  Citation × Citation Citation Abstract Copy Title: Implications of cougar prey selection and demography on population dynamics of elk in northeast Oregon Author: Clark, Darren A. Mule deer (Odocoileus hemionus hemionus) and Rocky Mountain elk (Cervus canadensis nelsoni; hereafter elk) populations in northeast Oregon have declined in the past 10 to 20 years. Concurrent with these declines, cougar (Puma concolor) populations have apparently increased, leading to speculation that predation by cougars may be responsible for declining ungulate populations. However, empirical data on cougar diets, kill rates, and prey selection are lacking to support this speculation. Furthermore, the common assumption that cougar populations have increased in northeast Oregon may not be well founded because cougar populations in other areas within the Pacific Northwest region have declined in recent years. My primary research objectives were to (1) estimate kill rates and prey selection by cougars in northeast Oregon, (2) document causes of mortality and estimate survival rates for cougars, (3) estimate population growth rates of cougars in northeast Oregon and simulate the effects of hypothetical lethal control efforts on the cougar population, and (4) investigate the relative influence of top-down, bottom-up, and climatic factors for limiting population growth rates of elk in northeast Oregon. Results from my research will help guide cougar and elk management in northeast Oregon and provide a framework for assessing relative effects of top-down, bottom-up, and abiotic factors on population growth rates of ungulates in this and other areas. I implemented a 3-year study in northeast Oregon to investigate diets, kill rates, and prey selection of cougars in a multiple-prey system to better understand mechanisms by which cougars may influence ungulate populations. During my research, 25 adult cougars were captured and fitted with Global Positioning System (GPS) collars to identify kill sites. I monitored predation sequences of these cougars for 7,642 days and located the remains of 1,213 prey items killed by cougars. Cougars killed ungulates at an average rate of 1.03 per week (95% CI = 0.92 – 1.14); however, ungulate kill rates were variable and influenced by the season and demographic classification of cougars. Cougars killed ungulates 1.55 (95% CI = 1.47 – 1.66) times more frequently during summer (May-Oct) than during winter (Nov-Apr), but killed similar amounts of ungulate biomass (8.05 kg/day; 95% CI = 6.74 – 9.35) throughout the year. Cougars killed ungulates more frequently in summer because juvenile ungulates comprised most of the diet and were smaller on average than ungulate prey killed in winter. Female cougars with kittens killed more frequently (kills/day) than males or solitary females. After accounting for the additional biomass of kittens in cougar family groups, male cougars killed on average more biomass of ungulate prey per day than did females (R = 0.41, P < 0.001), and female cougars killed more biomass of prey per day as a function of the number and age of their kittens (R = 0.60, P < 0.001). Patterns of prey selection were influenced by season and demographic classification of cougars. Female cougars selected elk calves during summer and deer fawns during winter. In contrast, male cougars selected elk calves and yearling elk during summer and elk calves during winter. My results strongly supported the hypothesis that cougar predation is influenced by season, gender, and reproductive status of the cougar and these patterns in cougar predation may be generalizable among ecosystems. The observed selection for juvenile elk and deer suggested a possible mechanism by which cougars could negatively affect population growth rates of ungulates. I investigated survival and documented causes of mortality for radio-collared cougars at 3 study areas in Oregon during 1989 – 2011. Mortality due to hunter harvest was the most common cause of death for cougars in the Catherine Creek study area and the study area combining Wenaha, Sled Springs, and Mt. Emily Wildlife Management Units (WSM study area) in northeast Oregon. In contrast, natural mortality was the most common cause of death for cougars in the Jackson Creek study area in southwest Oregon. Annual survival rates of adult males were lowest at Catherine Creek when it was legal to hunt cougars with dogs (Ŝ = 0.57), but increased following the prohibition of this hunting practice (Ŝ = 0.86). This latter survival rate was similar to those observed at Jackson Creek (Ŝ = 0.78) and WSM (Ŝ = 0.82). Regardless of whether hunting of cougars with dogs was permitted, annual survival rates of adult females were similar among study areas (Catherine Creek Ŝ = 0.86; WSM Ŝ = 0.85; Jackson Creek Ŝ = 0.85). I did not document an effect of age on cougar survival rates in the Catherine Creek study area, which I attributed to selective harvest of prime-aged, male cougars when it was legal to hunt cougars with dogs. In contrast, I observed an effect of age on annual survival in both the WSM and Jackson Creek study areas. These results indicate that sub-adult males had significantly lower survival rates than sub-adult females, but survival rates of males and females were similar by age 4 or 5 years. My results suggest that survival rates of cougars in areas where hunting cougars with dogs is illegal should be substantially higher than areas where use of dogs is legal. I used estimates of cougar vital rates from empirical data collected in northeast Oregon to parameterize a Leslie projection matrix model to estimate deterministic and stochastic population growth rates of cougars in northeast Oregon when hunting cougars with dogs was legal (1989 - 1994) and illegal (2002 - 2011). A model cougar population in northeast Oregon that was hunted with dogs increased at a mean stochastic growth rate of 21% per year (λ[subscript s] = 1.21). Similarly, I found that a model cougar population that was subjected to hunting without dogs increased at a rate of 17% per year (λ[subscript s] = 1.17). Given that hunting cougars with dogs typically results in increased harvest and reduced survival rates of cougars, it was unexpected that the cougar population subjected to hunting with dogs was increasing at a faster rate than one that was not hunted with dogs. However, cougar populations in Oregon were subjected to low harvest rates when hunting cougars with dogs was legal and harvest was male biased. This resulted in high survival rates of female cougars and correspondingly high population growth rates. The Oregon Cougar Management Plan allows the Oregon Department of Fish and Wildlife to administratively reduce cougar populations to benefit ungulate populations, reduce human-cougar conflicts, and limit livestock depredation. Consequently, I was interested in modeling the effects of a hypothetical lethal control effort on a local cougar population. Using empirically-derived vital rates and a deterministic Leslie matrix model, I found that the proportion of the cougar population that would need to be removed annually to achieve a 50% population reduction within 3 years was 28% assuming a closed population, and 48% assuming maximum immigration rates into the population. Using a stochastic Leslie matrix model, I also determined that the model cougar population would likely return to its pre-removal size in 6 years assuming a closed population, and 2 years assuming maximum immigration rates. These model results indicate that current management practices and harvest regulations, combined with short-term, intensive, and localized population reductions, are unlikely to negatively affect the short-term viability of cougar populations in northeast Oregon. However, at this time, it is not known if intensive lethal control efforts funded by state agencies will be cost-effective (i.e., increased sales of tags to hunt deer and elk will offset the costs of control efforts). Further research is needed to investigate the cost-effectiveness of cougar control efforts in Oregon. I developed a Leslie matrix population model, parameterized with empirically-derived vital rates for elk in northeast Oregon, to investigate the relative influence on elk population growth rates of (1) survival and pregnancy, and (2) top-down, bottom-up, and climatic variables. I then estimated the effect of varying the strength of top-down factors on growth rates of elk populations. Growth rates of the model elk population were most sensitive to changes in adult female survival, but due to the inherent empirical variation in juvenile survival rates explained the overwhelming majority of variation in model population growth rates (r² = 0.92). Harvest of female elk had a strong negative effect on model population growth rates of elk (r² = 0.63). An index of cougar density was inversely related to population growth rates of elk in my model (r² = 0.38). A delay in mean date of birth was associated with reduced juvenile survival, but this had a minimal effect on population growth rates in my model (r² = 0.06). Climatic variables, which were used as surrogates for nutritional condition of females, had minimal effects on population growth rates. Likewise, elk density had almost no effect on population growth rates (r² = 0.002). The results of my model provided a novel finding that cougars can be a strong limiting factor on elk populations. Wildlife managers should consider the potential top-down effects of cougars and other predators as a limiting factor on elk populations. Title: Implications of cougar prey selection and demography on population dynamics of elk in northeast Oregon Author: Clark, Darren A. Mule deer (Odocoileus hemionus hemionus) and Rocky Mountain elk (Cervus canadensis nelsoni; hereafter elk) populations in northeast Oregon have declined in the past 10 to 20 years. Concurrent with these declines, cougar (Puma concolor) populations have apparently increased, leading to speculation that predation by cougars may be responsible for declining ungulate populations. However, empirical data on cougar diets, kill rates, and prey selection are lacking to support this speculation. Furthermore, the common assumption that cougar populations have increased in northeast Oregon may not be well founded because cougar populations in other areas within the Pacific Northwest region have declined in recent years. My primary research objectives were to (1) estimate kill rates and prey selection by cougars in northeast Oregon, (2) document causes of mortality and estimate survival rates for cougars, (3) estimate population growth rates of cougars in northeast Oregon and simulate the effects of hypothetical lethal control efforts on the cougar population, and (4) investigate the relative influence of top-down, bottom-up, and climatic factors for limiting population growth rates of elk in northeast Oregon. Results from my research will help guide cougar and elk management in northeast Oregon and provide a framework for assessing relative effects of top-down, bottom-up, and abiotic factors on population growth rates of ungulates in this and other areas. I implemented a 3-year study in northeast Oregon to investigate diets, kill rates, and prey selection of cougars in a multiple-prey system to better understand mechanisms by which cougars may influence ungulate populations. During my research, 25 adult cougars were captured and fitted with Global Positioning System (GPS) collars to identify kill sites. I monitored predation sequences of these cougars for 7,642 days and located the remains of 1,213 prey items killed by cougars. Cougars killed ungulates at an average rate of 1.03 per week (95% CI = 0.92 – 1.14); however, ungulate kill rates were variable and influenced by the season and demographic classification of cougars. Cougars killed ungulates 1.55 (95% CI = 1.47 – 1.66) times more frequently during summer (May-Oct) than during winter (Nov-Apr), but killed similar amounts of ungulate biomass (8.05 kg/day; 95% CI = 6.74 – 9.35) throughout the year. Cougars killed ungulates more frequently in summer because juvenile ungulates comprised most of the diet and were smaller on average than ungulate prey killed in winter. Female cougars with kittens killed more frequently (kills/day) than males or solitary females. After accounting for the additional biomass of kittens in cougar family groups, male cougars killed on average more biomass of ungulate prey per day than did females (R = 0.41, P < 0.001), and female cougars killed more biomass of prey per day as a function of the number and age of their kittens (R = 0.60, P < 0.001). Patterns of prey selection were influenced by season and demographic classification of cougars. Female cougars selected elk calves during summer and deer fawns during winter. In contrast, male cougars selected elk calves and yearling elk during summer and elk calves during winter. My results strongly supported the hypothesis that cougar predation is influenced by season, gender, and reproductive status of the cougar and these patterns in cougar predation may be generalizable among ecosystems. The observed selection for juvenile elk and deer suggested a possible mechanism by which cougars could negatively affect population growth rates of ungulates. I investigated survival and documented causes of mortality for radio-collared cougars at 3 study areas in Oregon during 1989 – 2011. Mortality due to hunter harvest was the most common cause of death for cougars in the Catherine Creek study area and the study area combining Wenaha, Sled Springs, and Mt. Emily Wildlife Management Units (WSM study area) in northeast Oregon. In contrast, natural mortality was the most common cause of death for cougars in the Jackson Creek study area in southwest Oregon. Annual survival rates of adult males were lowest at Catherine Creek when it was legal to hunt cougars with dogs (Ŝ = 0.57), but increased following the prohibition of this hunting practice (Ŝ = 0.86). This latter survival rate was similar to those observed at Jackson Creek (Ŝ = 0.78) and WSM (Ŝ = 0.82). Regardless of whether hunting of cougars with dogs was permitted, annual survival rates of adult females were similar among study areas (Catherine Creek Ŝ = 0.86; WSM Ŝ = 0.85; Jackson Creek Ŝ = 0.85). I did not document an effect of age on cougar survival rates in the Catherine Creek study area, which I attributed to selective harvest of prime-aged, male cougars when it was legal to hunt cougars with dogs. In contrast, I observed an effect of age on annual survival in both the WSM and Jackson Creek study areas. These results indicate that sub-adult males had significantly lower survival rates than sub-adult females, but survival rates of males and females were similar by age 4 or 5 years. My results suggest that survival rates of cougars in areas where hunting cougars with dogs is illegal should be substantially higher than areas where use of dogs is legal. I used estimates of cougar vital rates from empirical data collected in northeast Oregon to parameterize a Leslie projection matrix model to estimate deterministic and stochastic population growth rates of cougars in northeast Oregon when hunting cougars with dogs was legal (1989 - 1994) and illegal (2002 - 2011). A model cougar population in northeast Oregon that was hunted with dogs increased at a mean stochastic growth rate of 21% per year (λ[subscript s] = 1.21). Similarly, I found that a model cougar population that was subjected to hunting without dogs increased at a rate of 17% per year (λ[subscript s] = 1.17). Given that hunting cougars with dogs typically results in increased harvest and reduced survival rates of cougars, it was unexpected that the cougar population subjected to hunting with dogs was increasing at a faster rate than one that was not hunted with dogs. However, cougar populations in Oregon were subjected to low harvest rates when hunting cougars with dogs was legal and harvest was male biased. This resulted in high survival rates of female cougars and correspondingly high population growth rates. The Oregon Cougar Management Plan allows the Oregon Department of Fish and Wildlife to administratively reduce cougar populations to benefit ungulate populations, reduce human-cougar conflicts, and limit livestock depredation. Consequently, I was interested in modeling the effects of a hypothetical lethal control effort on a local cougar population. Using empirically-derived vital rates and a deterministic Leslie matrix model, I found that the proportion of the cougar population that would need to be removed annually to achieve a 50% population reduction within 3 years was 28% assuming a closed population, and 48% assuming maximum immigration rates into the population. Using a stochastic Leslie matrix model, I also determined that the model cougar population would likely return to its pre-removal size in 6 years assuming a closed population, and 2 years assuming maximum immigration rates. These model results indicate that current management practices and harvest regulations, combined with short-term, intensive, and localized population reductions, are unlikely to negatively affect the short-term viability of cougar populations in northeast Oregon. However, at this time, it is not known if intensive lethal control efforts funded by state agencies will be cost-effective (i.e., increased sales of tags to hunt deer and elk will offset the costs of control efforts). Further research is needed to investigate the cost-effectiveness of cougar control efforts in Oregon. I developed a Leslie matrix population model, parameterized with empirically-derived vital rates for elk in northeast Oregon, to investigate the relative influence on elk population growth rates of (1) survival and pregnancy, and (2) top-down, bottom-up, and climatic variables. I then estimated the effect of varying the strength of top-down factors on growth rates of elk populations. Growth rates of the model elk population were most sensitive to changes in adult female survival, but due to the inherent empirical variation in juvenile survival rates explained the overwhelming majority of variation in model population growth rates (r² = 0.92). Harvest of female elk had a strong negative effect on model population growth rates of elk (r² = 0.63). An index of cougar density was inversely related to population growth rates of elk in my model (r² = 0.38). A delay in mean date of birth was associated with reduced juvenile survival, but this had a minimal effect on population growth rates in my model (r² = 0.06). Climatic variables, which were used as surrogates for nutritional condition of females, had minimal effects on population growth rates. Likewise, elk density had almost no effect on population growth rates (r² = 0.002). The results of my model provided a novel finding that cougars can be a strong limiting factor on elk populations. Wildlife managers should consider the potential top-down effects of cougars and other predators as a limiting factor on elk populations. Close

• 8465. [Article] The influence of climate change and restoration on stream temperature

  Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, ...

  Citation × Citation Citation Abstract Copy Title: The influence of climate change and restoration on stream temperature Author: Diabat, Mousa Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, and channel structure directly influence stream temperature. Numerous studies indicate that increased average air temperature during the past century has led to stream warming across the world. The trend of stream warming was also present in spring-fed watersheds, where summer flow has decreased. In addition, anthropogenic practices that alter the natural landscape and channel structure, such as forest management, agriculture, and mining contributed to stream warming. For example, deforested and unshaded stream reaches or dredged channels were warmer than shaded reaches and meandering streams. Stream temperatures in North American lotic habitats are of a specific concern due to their significant economic, cultural, and ecological value. With climate projections indicating that air temperature will only continue to rise throughout the 21st century, cold- or cool-water organisms, especially fishes, will be affected. Therefore, there is a strong need to better understand the impacts of changing climate, riparian landscape, and channel structure on a stream's heat budget. This may assist in restoring the historic thermal regime in impacted sites and mitigating the impacts of future climate change. This study looks into the relative influences of the different factors on a stream's heat budget with three manuscripts: one on stream temperature response to diel timing of air warming, one on stream temperature response to changes in air temperature, flow, and riparian vegetation, and one on stream temperature response to air warming and channel reconstruction. I used the software Heat Source version 8.05 to simulate stream temperature for all three analyses along the Middle Fork John Day River, Oregon USA. Two of the manuscripts were applied to an upper 37 km section of the Middle Fork John Day River (presented in chapter 2 and 3), where the third manuscript was applied to a 1.5-km section. The sensitivity analysis of stream temperature response to diel timing of air warming (Chapter 2: Diel Timing of Warmer Air under Climate Change Affects Magnitude, Timing, and Duration of Stream Temperature Change) was based on scenarios representing uniform air warming over the diel period, daytime warming, and nighttime warming. Uniform warming of air temperature is a simple representation of increases in the average daily or monthly temperatures generated by the 'delta method'. The delta method relies on adding a constant value to the air temperature time-series data. This constant value is the difference (delta) between base case average air temperatures and the projected one. Scenarios of daytime or nighttime warming represent conditions under which most of the warming of the air occurs during the daytime or the nighttime, respectively. I simulated the stream temperature response to warmer air conditions of +2 °C and +4 °C in daily average for all three cases of air warming conditions. The three cases of different diel distributions of air warming generated 7-day average daily maximum stream temperature (7DADM) increases of approximately +1.8 °C ± 0.1 °C at the downstream end of the study section relative to the base case. In most parts of the reach, the three distributions of air warming generated different ranges of stream temperatures, different 7DADM values, different durations of stream temperature changes, and different average daily temperatures. Changes of stream temperature were out of phase with imposed changes of air temperature. Therefore, nighttime warming of air temperatures would cause the greatest increase in maximum daily stream temperature, which typically occurs during the daytime. The sensitivity analysis of the relative influences of changes in air temperature, stream flow, and riparian vegetation on stream temperature (Chapter 3: Assessing Stream Temperature Response to Cumulative Influence of Changing Air Temperature, Flow, and Riparian Vegetation). This study summarized stream temperature simulation in 36 scenarios representing possible manifestations of 21st century climate conditions and land management strategies. In addition to existing conditions (base case) of flow, air temperature, and riparian vegetation, scenarios consisted of: two air temperature increases of 2 °C and 4 °C, two stream flow variations of +30% and -30%, three spatially uniform riparian vegetation conditions that create averages of effective shade 7%, 34%, and 79%, in addition to 14% for base case conditions. Results suggest that variation in riparian vegetation was the dominant factor influencing stream temperature because it regulates incoming shortwave radiation, the largest heat input to the stream, while variation in stream flow has a negligible influence. Results indicated that increasing the effective shade along the study section, particularly in the currently unshaded sections, could mitigate the influence of increasing air temperature, and would reduce stream temperature maxima below current values even under future climate conditions of warmer air. With the small influence it had, increasing stream flow reduced the 7DADM under low shade conditions. However, increasing stream flow showed counterintuitive results as it contributed to increasing stream temperature maxima when the stream was heavily shaded. The applied study examined the stream temperature response to restoration practices and their potential to mitigate the influence of warmer air conditions (Chapter 4: Estimating Stream Temperature Response to Restoring Channel and Riparian Vegetation and the Potential to Mitigate Warmer Air Conditions). This study focused on a 1.5 km section along the upper part of the Middle Fork John Day River that was modified due to past anthropogenic activities of mining for gold and timber harvest. Currently, the riparian vegetation of the study site is mostly shrubs and stands of short trees. Restoration designs call for the restoration of both the channel structure and replanting the riparian vegetation. Simulation results showed that the 7DADM was higher in the restored channel than the existing channel with both conditions of low and high effective shade conditions. However, a combined restoration practice of channel reconstruction and medium effective shade conditions reduced stream temperature maxima more than restoring riparian vegetation alone. In addition, results showed that restoring riparian vegetation was sufficient to mitigate the influence of warmer air on stream temperature, while restoring the channel alone is not. Heat budget analysis showed that heat accumulation during the daytime increased in the restored channel, which was longer, narrower, and deeper than the existing channel. It is important to emphasize that stream temperature is one of many goals that restoration activities aim to improve. Furthermore, differences in 7DADM among the different scenarios of restoration are negligible. Such small differences could hardly be measure. While this study examined a short section of 1.5 km, longer stream sections may increase the differences in 7DADM. Primary conclusions of this study are: 1) daily maxima of stream temperature will increase in response to increased air temperature regardless of the distribution of air warming during the diel cycle; 2) nighttime air warming caused a greater increase in stream temperature maximum than daytime warming; 3) riparian vegetation was the dominant factor on stream's heat budget, more than air temperature or stream flow; 4) restoring riparian vegetation mitigated the influence of warmer air; 5) restoring channel structure alone was not sufficient to lower temperature maxima; and 6) restoration project was most successful in improving degraded stream temperature when combined with channel reconstruction and improved riparian shade. Title: The influence of climate change and restoration on stream temperature Author: Diabat, Mousa Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, and channel structure directly influence stream temperature. Numerous studies indicate that increased average air temperature during the past century has led to stream warming across the world. The trend of stream warming was also present in spring-fed watersheds, where summer flow has decreased. In addition, anthropogenic practices that alter the natural landscape and channel structure, such as forest management, agriculture, and mining contributed to stream warming. For example, deforested and unshaded stream reaches or dredged channels were warmer than shaded reaches and meandering streams. Stream temperatures in North American lotic habitats are of a specific concern due to their significant economic, cultural, and ecological value. With climate projections indicating that air temperature will only continue to rise throughout the 21st century, cold- or cool-water organisms, especially fishes, will be affected. Therefore, there is a strong need to better understand the impacts of changing climate, riparian landscape, and channel structure on a stream's heat budget. This may assist in restoring the historic thermal regime in impacted sites and mitigating the impacts of future climate change. This study looks into the relative influences of the different factors on a stream's heat budget with three manuscripts: one on stream temperature response to diel timing of air warming, one on stream temperature response to changes in air temperature, flow, and riparian vegetation, and one on stream temperature response to air warming and channel reconstruction. I used the software Heat Source version 8.05 to simulate stream temperature for all three analyses along the Middle Fork John Day River, Oregon USA. Two of the manuscripts were applied to an upper 37 km section of the Middle Fork John Day River (presented in chapter 2 and 3), where the third manuscript was applied to a 1.5-km section. The sensitivity analysis of stream temperature response to diel timing of air warming (Chapter 2: Diel Timing of Warmer Air under Climate Change Affects Magnitude, Timing, and Duration of Stream Temperature Change) was based on scenarios representing uniform air warming over the diel period, daytime warming, and nighttime warming. Uniform warming of air temperature is a simple representation of increases in the average daily or monthly temperatures generated by the 'delta method'. The delta method relies on adding a constant value to the air temperature time-series data. This constant value is the difference (delta) between base case average air temperatures and the projected one. Scenarios of daytime or nighttime warming represent conditions under which most of the warming of the air occurs during the daytime or the nighttime, respectively. I simulated the stream temperature response to warmer air conditions of +2 °C and +4 °C in daily average for all three cases of air warming conditions. The three cases of different diel distributions of air warming generated 7-day average daily maximum stream temperature (7DADM) increases of approximately +1.8 °C ± 0.1 °C at the downstream end of the study section relative to the base case. In most parts of the reach, the three distributions of air warming generated different ranges of stream temperatures, different 7DADM values, different durations of stream temperature changes, and different average daily temperatures. Changes of stream temperature were out of phase with imposed changes of air temperature. Therefore, nighttime warming of air temperatures would cause the greatest increase in maximum daily stream temperature, which typically occurs during the daytime. The sensitivity analysis of the relative influences of changes in air temperature, stream flow, and riparian vegetation on stream temperature (Chapter 3: Assessing Stream Temperature Response to Cumulative Influence of Changing Air Temperature, Flow, and Riparian Vegetation). This study summarized stream temperature simulation in 36 scenarios representing possible manifestations of 21st century climate conditions and land management strategies. In addition to existing conditions (base case) of flow, air temperature, and riparian vegetation, scenarios consisted of: two air temperature increases of 2 °C and 4 °C, two stream flow variations of +30% and -30%, three spatially uniform riparian vegetation conditions that create averages of effective shade 7%, 34%, and 79%, in addition to 14% for base case conditions. Results suggest that variation in riparian vegetation was the dominant factor influencing stream temperature because it regulates incoming shortwave radiation, the largest heat input to the stream, while variation in stream flow has a negligible influence. Results indicated that increasing the effective shade along the study section, particularly in the currently unshaded sections, could mitigate the influence of increasing air temperature, and would reduce stream temperature maxima below current values even under future climate conditions of warmer air. With the small influence it had, increasing stream flow reduced the 7DADM under low shade conditions. However, increasing stream flow showed counterintuitive results as it contributed to increasing stream temperature maxima when the stream was heavily shaded. The applied study examined the stream temperature response to restoration practices and their potential to mitigate the influence of warmer air conditions (Chapter 4: Estimating Stream Temperature Response to Restoring Channel and Riparian Vegetation and the Potential to Mitigate Warmer Air Conditions). This study focused on a 1.5 km section along the upper part of the Middle Fork John Day River that was modified due to past anthropogenic activities of mining for gold and timber harvest. Currently, the riparian vegetation of the study site is mostly shrubs and stands of short trees. Restoration designs call for the restoration of both the channel structure and replanting the riparian vegetation. Simulation results showed that the 7DADM was higher in the restored channel than the existing channel with both conditions of low and high effective shade conditions. However, a combined restoration practice of channel reconstruction and medium effective shade conditions reduced stream temperature maxima more than restoring riparian vegetation alone. In addition, results showed that restoring riparian vegetation was sufficient to mitigate the influence of warmer air on stream temperature, while restoring the channel alone is not. Heat budget analysis showed that heat accumulation during the daytime increased in the restored channel, which was longer, narrower, and deeper than the existing channel. It is important to emphasize that stream temperature is one of many goals that restoration activities aim to improve. Furthermore, differences in 7DADM among the different scenarios of restoration are negligible. Such small differences could hardly be measure. While this study examined a short section of 1.5 km, longer stream sections may increase the differences in 7DADM. Primary conclusions of this study are: 1) daily maxima of stream temperature will increase in response to increased air temperature regardless of the distribution of air warming during the diel cycle; 2) nighttime air warming caused a greater increase in stream temperature maximum than daytime warming; 3) riparian vegetation was the dominant factor on stream's heat budget, more than air temperature or stream flow; 4) restoring riparian vegetation mitigated the influence of warmer air; 5) restoring channel structure alone was not sufficient to lower temperature maxima; and 6) restoration project was most successful in improving degraded stream temperature when combined with channel reconstruction and improved riparian shade. Close