Freshwater ecosystems and the species that reside therein are disproportionately imperiled compared to terrestrial systems. Over the past 150 years, the Columbia River basin in the western United States has gone from one of the most productive and abundant salmon watersheds in the world, to having just a small fraction of its former salmon abundance. The cause of declines in salmon productivity and abundance are related to overlapping and confounding stressors including changes in large-scale climatic patterns and anthropogenic alterations within and adjacent to the Columbia River. Four main anthropogenic stressors have been identified as the leading causes of salmonid declines: commercial harvest of adult salmon, hydroelectric power generation and associated reservoirs, habitat loss due to impassible dams and restricted access to historical habitat, and hatchery production. My dissertation broadly examined how salmon ecology and population dynamics have been influenced by anthropogenic alterations occurring within the Columbia River basin. This dissertation addresses three main questions: Do the hydroelectric dams on the Lower Columbia River represent a pulse- or press-type ecological disturbance to migrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) and what are the biotic and abiotic factors that most influence the survival of fish passing multiple dams? How do wild and hatchery fish differ in regards to the precocious life-history strategy, and which variables influence this strategy across environments (freshwater to marine) and life stages (egg to adult)? What are the morphological differences between wild and hatchery salmonids and how much of that variation is attributable to rearing-environment? I found that high outflow volumes led to involuntary spill in 2011 and created an environment of supersaturated dissolved gas concentrations. In this environment, migrating smolt survival was strongly influenced by barometric pressure, fish velocity and water temperature. The effect of these variables on survival was compounded by multiple dam passages compared to fish passing a single dam. Despite spatial isolation between dams in the Lower Columbia River hydrosystem, migrating smolt appear to experience cumulative effects akin to an ecological press disturbance. In general, Chinook salmon and steelhead respond similarly in terms of survival rates and responses to altered environmental conditions. Management actions that limit dissolved gas concentrations in years of high flow will benefit migrating salmonids during this life stage. Both biotic and environmental factors affect precociousness in hatchery and wild Chinook salmon, across freshwater and marine environments. Wild fish are influenced by density-dependent processes in freshwater, as well as marine conditions that promote growth. Wild Chinook have the highest probability of precocious maturation when large smolt (>150 mm) experience productive marine environments within the first several months of ocean residence. Precocious hatchery fish are broadly influenced by conditions experienced during freshwater residency, outmigration, and in marine habitats. There was no interaction between the size of hatchery fish and environmental variables, suggesting that these fish attained the size required to mature precociously prior to migration. These results indicate that hatchery Chinook salmon do not respond to the same environmental cues that determine life history transitions as wild Chinook salmon, likely as a result of different physiological conditions and environmental exposures during early life stages. There are ecological and economic consequences to the precocious life history strategy including reduced marine-derived nutrients entering freshwater ecosystems and a loss of investment for fish intended for the adult fishery. There are significant differences in body shape between wild and hatchery origin Chinook salmon and steelhead that can be partially explained by rearing environment and variables influenced by smoltification. Hatchery fish of both species are significantly larger (i.e. centroid size, length, weight) than wild fish but have comparable or lower condition factor. In general, hatchery fish have smaller heads and longer, thinner tails (i.e. fusiform) compared to wild fish. Allometric trajectories (i.e. shape change with size) indicate that the shape of wild and hatchery fish are significantly different at small and large sizes. Wild and hatchery Chinook salmon became more morphologically different as size increased, while steelhead became more similar. The overall amount of shape variation was not significantly different between wild and hatchery Chinook salmon. This finding suggests that regardless of significant differences in the way shapes vary, hatchery Chinook have not lost overall shape variation. Total amount of shape variation was significantly greater in wild compared to hatchery steelhead, indicating that hatcheries may have a homogenizing effect on steelhead shape. I recommend a coordinated effort between federal, state and tribal hatcheries to incorporate elements of the natural rearing environment into conventional hatcheries. These elements include in-water structure that promotes the burst swimming mode, increased water velocities to increase dorsal-ventral distance, under-water feeding apparatus that reduce surface feeding behavior, overhead cover and mimicked predators to teach escape behavior. Major advancements have been made in identifying and ameliorating negative effects of anthropogenic alterations within the Columbia Basin, however, many wild populations continue to decline. My research suggests that the physical (i.e. weirs and bypass structures) and operational alterations (i.e. voluntary spill) to the lower Columbia hydrosystem have substantially improved conditions for migrating smolt compared to past years, but involuntary spill during years of high flow continue to create deleterious conditions for migrating smolt. Riverscape-scale management strategies that recognize biotic and abiotic connectivity between dams (i.e. press disturbance) will benefit migrating smolt. My research indicates that hatchery fish are not currently equal or adequate replacements for wild fish. Hatcheries vary greatly in their stated goals and desired outcomes and several coordinated changes to general hatchery practices may help produce fish that are more similar to wild fish in morphology and life histories: 1) Change the goals of production away from producing as many, large individuals as possible, to producing fish that resemble the target wild populations they are intended to support; 2) Alter the hatchery environment to reflect the rearing environments in which salmon evolved and into which they will be released; and 3) Reduce the annual number of hatchery fish released into the Columbia Basin for the sole purpose of harvest. Recovering and rehabilitating critical and diverse habitats utilized by salmonids at each life stage (spawning, rearing, migration, estuary and marine) remains crucial for wild population success into the future.

Caspian terns (Hydroprogne caspia) and double-crested cormorants (Phalacrocorax auritus) nest in large colonies on East Sand Island in the Columbia River estuary, the largest known colonies for the two species in the world. Both species of piscivorous colonial waterbirds have been identified as predators with a significant impact on the survival of juvenile salmonids (Oncorhynchus spp.) listed under the U.S. Endangered Species Act. To better understand and address issues related to seabird-fisheries interactions in the Columbia River estuary, I conducted studies related to the ecology, conservation, and management of these two species of piscivorous waterbirds. I evaluated the demographics and inter-colony movements of Caspian terns belonging to the Pacific Coast metapopulation, with special emphasis on two breeding colonies, one on East Sand Island in the Columbia River estuary and the other on Crescent Island in the mid-Columbia River, based on re-sightings of color-banded individuals. Apparent annual adult survival at both colonies was high, and age at first reproduction was greater than previously reported for the species. Colony site philopatry of breeding adults at both colonies was high; however, some individuals prospected for breeding colonies over much of the Pacific Coast region and moved to other colonies over distances of up to 3,000 km. Some terns from the large colony in the Columbia River estuary responded quickly to the availability of new colony sites as distant as 550 km from the estuary, and established successful breeding colonies within less than a year of the new sites becoming available. The Caspian tern colony on East Sand Island appears to be an important source colony for a number of smaller, less productive colonies distributed over an extensive area from the Salton Sea, California to the Copper River Delta, Alaska, an area with limited and ephemeral nesting opportunities. Environmental contaminants have been a conservation concern for wildlife in the Columbia River estuary, especially species that consume fish and are therefore likely to bioaccumulate persistent organic pollutants. I measured and compared levels of polychlorinated biphenyls (PCBs) in eggs and chicks of Caspian terns and doublecrested cormorants, as well as their primary prey fish types, at colonies on East Sand Island and farther up-river. Based on differences in tern and cormorant diet composition at the various study colonies, higher PCB levels in eggs and chicks were associated with diets dominated by resident freshwater and estuarine fishes. PCB levels in prey fish were positively correlated with lipid content; however, PCB levels in the livers of chicks were negatively correlated with chick fat scores, suggesting that chick fat reserves are a sink for ingested PCBs. Lower PCB levels in terns and cormorants from East Sand Island compared to colonies farther up-river reflected diets with a higher proportion of marine forage fishes at East Sand Island; marine forage fishes had lower average levels of PCBs than their resident freshwater and estuarine counterparts. In order to explore non-destructive techniques for managing nesting colonies of double-crested cormorants, I evaluated habitat enhancement and social attraction, two techniques that have proven effective for relocating Caspian tern colonies to sites where impacts on fish stocks of conservation concern would be minimal. Cormorants were attracted to nest and successfully raised young at test plots on East Sand Island and on islands in the estuary with a previous history of cormorant nesting or unsuccessful nesting attempts. On an island with no history of cormorant nesting or prospecting, however, no cormorants were attracted to nest. My results suggest that attraction of nesting cormorants using these techniques is dependent on the previous history of cormorant nesting or nesting attempts, the frequency and intensity of disturbance by potential predators, and the presence of breeding cormorants nearby. While habitat enhancement and social attraction have potential as methods for redistributing nesting cormorants away from areas where fish stocks of concern are highly susceptible to predation, successful establishment of new colonies using these techniques will likely require a focus on sites with a history of cormorant nesting. Findings from this dissertation raise some concerns over the management of Caspian tern and double-crested cormorant colonies on East Sand Island in order to redistribute parts of these colonies to alternative sites and mitigate the impact of those piscivorous colonial waterbirds on ESA-listed salmonids. East Sand Island has supported source colonies of piscivorous colonial waterbirds for many smaller colonies throughout the region and is close to an abundant and relatively uncontaminated food supply. Also, alternative colony sites that can substitute for East Sand Island are not readily apparent, especially for double-crested cormorants. Therefore, management of Caspian tern and double-crested cormorant colonies on East Sand Island to benefit Columbia Basin salmonids needs to proceed cautiously and reversibly because of the implications for the region-wide populations of these piscivorous colonial waterbirds. / Graduation date: 2012

Galerucella pusilla and G. calmariensis have provided successful biological control of purple loosestrife (Lythrum salicaria L.) in non-tidal areas but only marginal control in areas of tidal influence. While a previous study identified mechanical scour by tidal waters as the main cause of establishment failure, purple loosestrife stem density explained more than 80% of the variability in presence and absence of Galerucella at my study sites in the Columbia River Estuary. A logistic regression model using purple loosestrife stem density, elevation, and their interaction as predictors accurately predicted 92.5% of Galerucella presence or absence observations of a test data set (n= 201). Field data also identified a critical threshold of approximately 32 purple loosestrife stems/m2 , above which Galerucella were present 100% of the time at the release sites.

Global Sensitivity Analysis (GSA) approach helps to identify the effectiveness of model parameters or inputs and thus provides essential information about the model performance. The effects of 14 parameters and one input (forcing data) of the Sacramento Soil Moisture Accounting (SAC-SMA) model are analyzed by using two GSA methods: Sobol' and Fourier Amplitude Sensitivity Test (FAST). The simulations are carried out over five sub-basins within the Columbia River Basin (CRB) for three different periods: one-year, four-year, and seven-year. The main parameter sensitivities (first-order) and the interactions sensitivities (second-order) are evaluated in this study. Our results show that some hydrological processes are highly affected by the simulation length. In other words, some parameters reveal importance during the short period simulation (e.g. one-year) while other parameters are effective in the long period simulations (e.g. four-year and seven-year). Moreover, the reliability of the sensitivity analysis results is compared based on 1) the agreement between the two sensitivity analysis methods (Sobol' and FAST) in terms of highlighting the same parameters or input as the most influential parameters or input and 2) how the methods are cohered in ranking these sensitive parameters under the same conditions (sub-basins and simulation length). The results show that the coherence between the Sobol' and FAST sensitivity analysis methods. Additionally, it is found that FAST method is sufficient to evaluate the main effects of the model parameters and inputs. This study confirms that the Sobol' and FAST methods are reliable GSA methods that can be applied in different scientific applications. Finally, as a future work, we suggest to study the uncertainty associated with the sensitivity analysis approach regarding the reliability of evaluating different sensitivity analysis methods.

The Early Miocene Eagle Creek Formation, a series of volcanic mudflows and debris flows, is exposed in the Columbia River Gorge about 64 kilometers east of Portland, Oregon. Eighty-seven samples were analyzed using instrumental neutron activation analysis for trace element concentrations. Eleven samples were analyzed by Dr. Peter Hooper at Washington State University using X-ray Fluorescence for major element chemistry. These data were used to determine that the Eagle Creek Formation compositionally ranges from andesite to dacite.

In transboundary water resources policy and management situations, such as the governance of the Columbia River Basin, complex social, ecological, and economic factors seem to be in irreconcilable competition with one another. However, cooperative negotiation provides an outlet for entities and stakeholders to "expand the pie" and develop creative alternatives for integrated, resilient management. To achieve these goals, it is critical that stakeholders have meaningful dialogue that goes beyond positions to identify the underlying values and interests in the basin. Furthermore, parties must develop a shared understanding of the substantive complexities of the social-ecological system. Collaborative learning allows participants to meet both of these objectives at once, and facilitators can spark collaboration through carefully planned interventions. The goal of this study was to test a carefully crafted "facilitative" documentary film as a facilitation tool to promote dialogue, understanding, and creative scenario development amongst parties. The study has three main components: 1) the resilience and learning analysis of the case study (the Columbia River Treaty) policy situation, 2) the creation of a facilitative film featuring interviews with diverse stakeholders in the basin, and 3) the qualitative and quantitative assessment of the effects of the film in the cooperative negotiation process. The film, A River Loved: A film about the Columbia River and the people invested in its future, premiered at the Universities Consortium Symposium on Columbia River Governance- an informal forum for dialogue held in Kimberley, British Columbia in October 2011. I measured participants' reactions to the film and found substantial support for my hypotheses, concluding that interventions such as facilitative documentary film have great potential to transform complex, multi-stakeholder social-ecological policy situations. / Graduation date: 2012

The Columbia Gorge Wine Region (CGWR) is an emerging wine producing area that extends for about 100km along the Columbia River in Oregon and Washington State in which the number of vineyards, wineries and physical terroir conditions have yet to be defined. To better understand the physical factors affecting Oregon and Washington wine, this project analyzes climate, topography, geology and soil at vineyards in the CGWR. This was accomplished using Geographic Information Systems, existing earth science databases and field work. The region, which includes the Columbia Gorge American Viticulture Area (AVA) and the southwest portion of the Columbia Valley AVA, is home to 82 vineyards, 513 hectares (1268 acres), 37 wineries and 41 different varieties of Vitus Vinifera. Vineyards range in elevation from 29 to 548 meters (95 to 1799 feet). Vintner responses to a grower's survey suggest that twenty-eight grape varieties account for 98% of the estimated grape variety acreage, with Pinot Noir being the most widely planted grape variety in both AVAs. The boundaries of each climatic regime were mapped based on 1981-2010 PRISM data, the Winkler Index (Amerine and Winkler, 1944) updated by Jones et al. (2010) and climatic maturity groupings designed for Oregon (Jones et al., 2002; Jones et al., 2010). Three Winkler climate regimes are represented within the CGWR, including regions Ia, Ib, and II from the Winkler Index (Jones et al., 2010). The diversity in regimes allows for a diversity of grape varieties to be planted within the regime. The average growing season temperatures and growing degree days, respectively, from 1981-2010 calculated for vineyards ranges from 13.7°C (55.7°F) to 17.7°C (63.9°F) and 871 for °C (1567 for °F) to 1664 for °C (2994 for °F) respectively. 58% of the vineyards are characterized in an intermediate climatic regime, 29% are within a cool climatic regime, 9% are within a warm climatic regime and 4% are on the boundaries between a cool, intermediate or warm regime. 80% of the vineyards are within Regions Ia and Ib characterized by the Winkler Index, and 20% are within Region II. The growing degrees days calculated for the CGWR are similar those measured in the Willamette Valley, Oregon, Burgundy, France, Umpqua Valley AVA in Oregon and Bordeaux wine region in France. All of the soils currently being used to grow grapes are well-drained and within a xeric moisture regime, which are favorable conditions for viticulture. 30 soil series are represented among the vineyard sites, with the Chemawa Series (Underwood Mountain) and Walla Walla Series (eastern portions) being the dominant soil series used to grow grapes. Majority of the soils contain a silt loam texture. Soil Survey data for Oregon and Washington suggest that loess is extensive in the CGWR, with 46.5% of the total vineyard acreage planted on soils formed in loess. The Missoula Floods also greatly influenced the texture and age of the soil in this region, with skeletal textures being close to the Columbia River. Other common geological deposits at vineyards in the CGWR include, Quaternary Basalt (19.6%), Missoula Flood deposits (9.1%), The Dalles Formation (8.0%), Columbia River Basalt Group (7.5%), Pliocene Basalt (3.0%), Quaternary Surficial deposits (3.0%), lahars (2.3%) and Quaternary Basaltic Andesite and Andesite (0.9%). Common geological deposits, soil series, and climate conditions at vineyard sites vary spatially in the region, and therefore it is suggested that future work focus on separating the region into separate climatic sub-AVA regimes to better reflect the diversity in terroir conditions.

The purpose of this study was to examine the characteristics of riparian plant communities along a succession gradient of livestock exclusion in the Lower Columbia River Basin (LCRB). Livestock exclusion is an example of a passive restoration practice throughout the region. However, few studies have focused on the effects of livestock or livestock exclusion on riparian wetland ecosystems in this area. Two passive restoration sites, 3 and 13 years since livestock exclusion, and a control site with a continued livestock grazing presence were examined. It was hypothesized that native plant species richness would be lower in the excluded wetlands than in the grazed wetland due to the competitive exclusion from an increase in non-native plant dominance in the absence of grazing. Data were collected along six (45-60m) randomly distributed transects which were aligned perpendicular to the wetland shoreline of each site, providing a total of 18 transects with an accumulative length of approximately 990 meters. Vegetation cover data were collected for 10 cm intervals along these transects using the line intercept method during low water periods in August and September of 2009. The Kruskal-Wallis one-way nonparametric analysis of variance by ranks and the Mann-Whitney U test were used to detect significant (p

Estuarine circulation and its associated transport processes drive the environmental integrity of many near-shore habitats (the coastal ocean, rivers, estuaries and emergent wetlands). A thorough understanding and consideration of this circulation is, therefore, vital in the proper management of these habitats. The aim of this study is to bring together theory and new satellite observations in the Columbia River Estuary to increase our understanding of estuarine circulation and transport. Surface reflectance measurements gathered by the Moderate Imaging Spectroradiometer (MODIS) are first compared to in situ observations to develop an empirical model for remotely derived surface turbidity. Results indicate that MODIS data significantly correlate with in situ measurements of turbidity throughout the CRE (R2 = 0.96). Remote estimates of turbidity are then used to explore the physical processes that drive their spatial distribution. Although the response to different hydrodynamic conditions varies throughout the system, global levels of turbidity are most sensitive to fluvial and tidal inputs and increase during spring tides and high river flow. As a result, the turbidity field has temporal cycles that are consistent with the frequency of these processes. The location of the estuarine turbidity maximum (ETM) is highly dynamic and typically migrates downstream as the tidal velocity or river flow increases. The ETM becomes trapped near the Megler Bridge (river kilometer 20), however, and the presence of strong topography in this region suggests there exists an interaction between bottom topography and sediment transport. A 2-D semi-analytical model, developed herein from the simplified Navier-Stokes equations, confirms that topographic features exhibit substantial influence on longitudinal turbidity distributions. The model considers the coupled, tidally-averaged velocity (composed of gravitational circulation, internal tidal asymmetry, and river flow) and salinity fields and assumes a condition of morphodynamic equilibrium to estimate the distribution of sediment for arbitrary channel configurations. Model simulations demonstrate that topographic highs tend to increase local seaward sediment fluxes, and that topographic lows increase local landward sediment fluxes. Sediment flux convergence near topographic highs compresses the local turbidity distribution, whereas flux divergence near topographic lows dilates the distribution and, under appropriate conditions, produces multiple ETMs. In summary a combination of the model and satellite data has given valuable new insights into the sediment dynamics of estuarine environments; in particular, both show that turbidity distribution and ETM location vary considerably with tidal and river flow conditions, fluctuating on a variety of timescales, and are heavily influenced by bottom topography.

Archaeological sites in the New World are the fragile and non-renewable remains of cultures which flourished for thousands of years prior to European contact and displacement. Sites which escape the effects of erosion and development often fall victim to vandalism. Cultural resources, including rock art and other archaeological sites, are protected by state and federal laws which prohibit the removal or disturbance of the sites, whether from development or from vandalism. Vandalism is frequently seen as a problem for law enforcement rather than a problem for cultural resource management. Management plans which include cultural resource protection provisions and guidelines often focus on threats to cultural resources from development, and omit planning which targets vandalism. The rock art sites of the Columbia River Gorge National Scenic Area ("Scenic Area") have been affected by developments such as The Dalles Dam and by the vandalism. In this study, the nature and degree of vandalism to the rock art sites in the Scenic Area is considered in the context of public awareness of, and access to, these sites. Rock art sites which are easily located and which have been the focus of public awareness are hypothesized to be the most severely vandalized. To test this hypothesis, fifteen of the 44 rock art sites in the Scenic Area were selected for study, and were assessed for kind and degree of vandalism, and means and ease of access. The results of analysis yielded two statistically significant associations of variables which support the hypothesis: an association between vandalism and public awareness of sites, and an association between vandalism and the primary means of access. The analysis suggests that public awareness is one of the most important issues which land managers must address when designing cultural resource protection plans.