This Ph.D. project aims to aquire a better understanding of sedimentological and ecological processes within the immediate vicinity of Large Igneous Province (LIP) activity and of the effects that LIP volcanism may have on the environment. The Miocene Columbia River Flood Basalt Province (CRBP) comprises an up to 4500 m thick succession of basaltic lavas intercalated with fluvio-lacustrine siliciclastic and volcaniclastic sediments. Detailed field-based studies (logging of 47 interbed sites) and the generation of geochemical (XRF, SEM, and microprobe) and palynological data provide an integrative study of characterising and modeling sedimentological and ecological processes within the lava field. The generation of a sedimentary facies scheme allowed a reconstruction of the intra-lava drainage system through time. Drainage system evolution is largely controlled by CRBP volcanism which is capable of forcing fluvial systems to the margin of the lava field during the phases of high volcanic activity, while phases of waning effusion frequencies and volumes allow the fluvial environment to migrate back into the central part of the lava field. The composition of the siliciclastic sediments suggests external source areas mainly located in the Cascade Range west and north of the CRBP. High plant diversity and late successions occurred during the early stage of CRBP evolution, and were affected by the increased deposition of ash derived from Cascade Range volcanoes and the Yellowstone hot spot during the late stage of CRBP evolution. Interbed sites distal to the volcanic source are generally colonized by late-successional plants and suggest a relationship between nutrient flux, sedimentary environment and volcanism. Palaeoclimate reconstructions based on soil chemistry and floral composition suggest that climatic changes within the CRBP reflect the global trend of the Mid-Miocene Climate Optimum. The present work allows to model sedimentological and ecological processes within the CRBP and considers the various effects that volcanic activity has on the environment. The complexity and differences in the geology and igenous evolution of individual LIPs need to be considered when applying this model to other LIPs.

River systems, such as the Columbia River in the Pacific Northwest, USA have been influenced by human activities, resulting in changes to the physical processes that drive landform evolution. This work describes an inventory of landforms along the Columbia River estuary between the Pacific Ocean and Bonneville Dam in Oregon and Washington. Groupings of landforms are assigned to formative process regimes that are used to assess historical changes to floodplain features. The estuary was historically a complex system of channels with a floodplain dominated by extensive tidal wetlands in the lower reaches and backswamp lakes and wetlands in upper reaches. Natural levees flank most channels in the upper reaches, locally including areas of ridge and swale topography and crevasse splays that intrude into backswamps. Other Holocene process regimes affecting floodplain morphology have included volcanogenic deltas, tributary fans, dunes, and landslides. Pre-Holocene landforms are locally prominent and include ancient fluvial deposits and bedrock. Historical changes to streamflow regimes, floodplain isolation by flood-control systems, and direct anthropogenic disturbance have resulted in channel narrowing and limited the amount of floodplain that can be shaped by flowing water. Floodplain isolation has caused relative subsidence of tidal floodplains along much of the lower estuary. Most extant landforms are on trajectories controlled by humans and new landforms are mostly created by humans.

Graduation date: 1995

Pacific lamprey (Entosphenus tridentatus), an endemic species to the Columbia River Basin, U.S.A, has experienced staggering decreases in returns to spawning territories in recent decades. As lamprey are threatened severely by a lack of passage at mainstem dams, lamprey specific passage structures have been designed and constructed to address the problem. The Cascades Island Lamprey Passage Structure (LPS) at Bonneville Dam is the longest and steepest structure of its type, following the addition of an exit pipe which allows lampreys to travel from the tailrace of the dam to the forebay. The intent of this study was to assess lamprey use of the structure and whether the structure hinders lamprey migration to subsequent dams. The study was carried out during the 2013 migration season. The study used three different treatment groups of lampreys released on five dates spanning the migration season (n=75 lamprey). Two of these groups (n=50), with different tagging methods, were released directly into the LPS to assess passage success, travel time, and tagging effect. The third group (n=25) was released into the forebay to test whether the structure impedes migration upstream. Fish were monitored via receiver arrays on the LPS and at dams on the river system. Overall passage efficiency was 74% (37 of 50 used the CI LPS successfully). Mean travel time to navigate the structure was 12 h. Fish size had no significant effect on travel time in the LPS. Water temperature had a significant effect on travel time in the LPS. There was no statistically significant effect of tagging on passage efficiency or travel time. The groups that used the LPS performed slightly better migrating upstream to the next dam than the group that bypassed the structure, but the difference was not significant. The groups that used the LPS traveled to more subsequent dams upstream than did the group that bypassed the LPS. It can be concluded that lamprey passed the structure successfully. Temperature (proxy for seasonality) had an effect on travel time in the LPS; however fish size and tagging had no effect. The LPS does not affect the ability of migrating lampreys to continue migration to subsequent dams. Such findings have important implications for management of lamprey in the region.

The multi downscaled-scenario products allow us to better assess the uncertainty of the variations of precipitation and temperature in the current and future periods. Joint Probability distribution functions (PDFs), of both the climatic variables, might help better understand the interdependence of the two, and thus in-turn help in accessing the future with confidence. In the present study, we have used multi-modelled statistically downscaled ensemble of precipitation and temperature variables. The dataset used is multi-model ensemble of 10 Global Climate Models (GCMs) downscaled product from CMIP5 daily dataset, using the Bias Correction and Spatial Downscaling (BCSD) technique, generated at Portland State University. The multi-model ensemble PDFs of both precipitation and temperature is evaluated for summer (dry) and winter (wet) periods for 10 sub-basins across Columbia River Basin (CRB). Eventually, Copula is applied to establish the joint distribution of two variables on multi-model ensemble data. Results have indicated that the probabilistic distribution helps remove the limitations on marginal distributions of variables in question and helps in better prediction. The joint distribution is then used to estimate the change in trends of said variables in future, along with estimation of the probabilities of the given change. The joint distribution trends are varied, but certainly positive, for summer and winter time scales based on sub-basins. Dry season, generally, is indicating towards higher positive changes in precipitation than temperature (as compared to historical) across sub-basins with wet season inferring otherwise. Probabilities of changes in future, as estimated by the joint precipitation and temperature, also indicates varied degree and forms during dry season whereas the wet season is rather constant across all the sub-basins.

The spawning habitat associated with fall chinook salmon (Oncorhynchus tshawytscha) redd clusters was investigated in the Hanford Reach of the Columbia River. A conceptual spawning habitat model is proposed that describes how geomorphic features of river channels create hydraulic processes, including hyporheic flows, that influence where salmon spawn in unconstrained reaches of large mainstem alluvial rivers. Spatial point pattern analysis of redds showed that redd clusters averaged approximately 10 hectares in area and their locations were consistent from year to year. The tendency to spawn in clusters suggests fall chinook salmon's use of spawning habitat is highly selective. Hydraulic characteristics of the redd clusters were significantly different than the habitat surrounding them. Velocity and lateral slope of the river bottom were the most important habitat variables in predicting redd site selection. While these variables explained a large proportion of the variance in redd site selection (86 to 96%), some unmeasured factors still accounted for a small percentage of actual spawning site selection. Further investigation showed that the magnitude and chemical characteristics of hyporheic discharge were different between and within two spawning areas. Apparently, fall chinook salmon used chemical and physical cues from the discharge to locate spawning areas. Traditional spawning habitat models could be improved if they: used spawning area-specific, rather than river-specific; spawning characteristics; incorporated hyporheic discharge measurements; and gave further consideration to the geomorphic features that are present in the unconstrained segments of large alluvial rivers. Ultimately the recovery of endangered fall chinook salmon will depend on how well we are able to recreate the characteristics once common in alluvial floodplains of large rivers. The results from this research can be used to better define the relationship between these physical habitat characteristics and fall chinook salmon spawning site selection, and provide more efficient use of limited recovery resources. / Graduation date: 1999

The role of fish in the Native American economy of the lower Columbia River has never been considered in detail. My study focused on the Columbia River from its mouth to the Cascades and the Willamette River from its confluence with the Columbia to Willamette Falls. For this study I asked: How was salmon used? What other fish were important? Where and how were these fish taken and used? To address these questions, I evaluated historical documents, including explorer's accounts and the administrative records of fur companies dating from the late 1700's through the 1850's. I used fishery data, physical descriptions, migratory and spawning habits, and foraging patterns to identify fish in historic accounts. I annotated historic information and provided a synthesis of the historic fisheries. White sturgeon (Acipenser transmontanus), eulachon (Thaleichthys pacificus) and chinook salmon (Oncorhynchus tshawytscha) dominated the trade. Chum (O.keta) and lamprey (Lampetra sp.) were available, although not traded in large numbers. White sturgeon, eulachon, fall chinook, chum and lamprey were smoke cured. Steel head (0. mykiss) , coho (O.kisutch), perch (Embiotocidae), and resident trout were traded in small numbers indicating that other fish were part of the economy. Sockeye. salmon (O.nerka) was not traded. f "~{.' Indians captured white sturgeon with: multiple hooks on set-lines and funnel nets to take white sturgeon during the winter; scoop nets and the eulachon rake took eulachon; spring and summer chinook were taken with hoop nets and platforms in the Cascades rapids and at Willamette Falls; gaffs were used to take chinook and sturgeon during the summer in Baker Bay; and hoop nets took fall chinook in streams. Seine nets were noted but not were not discussed except for the chinook fishery of Baker Bay. Historic information on fishes used and methods of capture contrasts with the archaeological record of the Portland Basin. Resident freshwater fish, minnows (Cyprinidae) and suckers (Catostomus sp.), are abundant in the archaeological faunal record, but are rarely mentioned in historic accounts. Artifacts such as net weights are common in archaeological contexts in contrast with the limited discussions in the historic record. Possible explanations for these discrepancies are reviewed.

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.

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 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