Thesis (M.S.)--Oregon State University, 1989. / Typescript (photocopy). Includes bibliographical references. Also available on the World Wide Web.

The freshwater polychaete Manayunkia speciosa was identified as an obligate host of the salmonid parasite Ceratomyxa shasta in 1997, prompting increased research on the small benthic invertebrate. Ceratomyxa shasta infection in fish can cause mortality, and presents a disease risk for both hatchery and wild salmon and trout. Ceratomyxa shasta is endemic to rivers of the Pacific Northwest, and its effects have been particularly well documented in the Klamath River, Oregon and California. One option for managing C. shasta impacts is by decreasing densities of M. speciosa through habitat manipulation, thus decreasing amplification of the parasite. The Klamath River is regulated by irrigation and hydropower dams, thus manipulating the hydrograph to destabilize habitat is a possibility. Decreasing habitat through flow manipulation requires a thorough understanding of the hydraulic environment of polychaete habitat, and how that environment changes with discharge. This thesis proposes an influence diagram of physical variables driving M. speciosa density, and investigates several of them. Samples were collected for enumerating M. speciosa density from nine sites in the Klamath River over 15 months, and seasonal density changes were examined, as were the relationships between density and hydraulic variables (depth, average velocity, substrate size, Reynolds number, Froude number). Density increased directly with depth and inversely with velocity, and was greater on small (silt, sand) and large (boulder, bedrock) substrate relative to medium substrate (gravel, cobble). Density was highest in the summer (July, August, September), and there was evidence that summer densities were influenced by spring discharges through the mechanism of substrate mobilization. Differences in infection prevalence among seasons and habitats were also investigated; however, very low overall incidence of infection limited any conclusions. Based on these results, it is recommended that habitat modeling for management of M. speciosa populations include a habitat stability component that incorporates s whether peak discharge the previous year surpassed a stability threshold. / Graduation date: 2013

Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region prior to the construction of the Copco I Dam on the Klamath River (c.1917) have relied on sparse, contradictory and sometimes unreliable historic documentation and informant testimony. Current restoration projects with very high financial and social costs necessitate accurate and reliable data on salmonid species which once called the region home. Often, archaeolofaunal remains present a novel way to determine species present in an area prior to major habitat losses. This project analyzed fish remains from five previously excavated archaeological sites within the Upper Klamath Basin to determine which salmonid species were present prior to dam construction. A total of 5,859 fish remains were identified to at least taxonomic order using morphological distinctions. Site collections were dominated by those of catostomids (suckers) and cyprinids (minnows). Archaeological deposits at these sites dated as far back as approximately 7,500 BP but were primarily from the last 2,000 years. Only eighty-one salmonid remains were observed within the sites included in this project. The low frequency of salmonid remains in these sites may be the result of cultural and/or natural processes such as density mediated attrition and archaeological sampling. Of these 81 specimens, 38 were subjected to mtDNA analysis for species identification. Seven specimens did not yield DNA sufficient for species identification, six specimens were identified as O. tshawytscha (Chinook) and the remaining 25 specimens were identified as O. mykiss (steelhead or redband trout). Geochemical analysis was used to determine the life history of the fish represented by the remains within these collections. Strontium Calcium (Sr:Ca) ratios were measured on twenty-eight specimens. Three specimens were determined to be from freshwater resident fish and 25 were determined to be from anadromous fish. The specimens which were genetically identified as O. tshawytscha were all determined to be anadromous. Of the 18 specimens which were identified as O. mykiss and were subjected to geochemical analysis two were from freshwater resident fish and sixteen were from anadromous fish. Four samples were not characterized genetically but were subjected to geochemical analysis; three of these were determined to be from anadromous fish and one from a freshwater resident fish. Thus, the remains of anadromous O. mykiss and O. tshawytscha were identified in archaeological deposits predating construction of the Copco I dam in the Upper Klamath Basin While the genetic and geochemical analyses confirm the presence of skeletal remains from anadromous salmonids in the Upper Klamath Basin archaeological sites prior to dam construction these remains may, represent fish caught elsewhere and traded in. Two hypotheses address the introduction of these fish remains into pre-dam archaeological deposits, either they were traded/transported in from elsewhere (Trade/Transport Hypothesis) or they were caught locally (Local Catch Hypothesis). Expectations linked to each of these hypotheses were generated using ethnographic information from across the Pacific Northwest, including modern testimony from the Klamath Basin. Fish heads were often removed soon after capture in order to reduce spoilage of the rest of the fish. Thus, assemblages with many head parts are probably the result of local catch while those without head parts are probably the result of trade and/or transport. Two approaches were used to estimate the extent to which fish heads were deposited in sites. Basic proportions of cranial to post cranial remains from two sites provided a varied picture and did not readily support either the Local Catch or Trade/Transport hypotheses. Evaluation using scaled proportions based on frequency of skeletal elements within the body (Minimum Animal Units) show that four of the five assemblages were dominated by cranial remains and therefore suggest these fish were locally caught. Small samples sizes make it difficult to rigorously evaluate the hypotheses, though the dominance of cranial remains suggests salmonids were taken locally. Together these data indicate that anadromous O. tshawytscha and O. mykiss were taken from waters within the Upper Klamath Basin prior to the construction of Copco I. This study has provided accurate and reliable data, using a novel approach, on which restoration efforts in the region can rely for proper species reintroduction and habitat restoration efforts.

Thesis/Project (M.S.)--Humboldt State University, 2005. / Includes bibliographical references (leaves 63-66). Also available via the Internet from the Humboldt Digital Scholar web site.

Availability of suitable nesting habitat that is free of nest predators and provides access to adequate prey resources within commuting distance is a major factor limiting seabird populations. Caspian terns (Hydroprogne caspia) in western North America have shifted their breeding habitat from naturally occurring habitats in interior wetlands, lakes, and rivers to primarily human-created habitats in coastal bays and estuaries. This shift has brought Caspian terns into conflict with fisheries of conservation concern, in particular anadromous salmonids. Prior to the 2010 breeding season, three artificial islands were built in the Klamath Basin National Wildlife Refuge (NWR) Complex as alternative nesting habitat for Caspian terns currently nesting at the world's largest colony for the species, near the mouth of the Columbia River, Oregon. I investigated the efficacy of habitat creation (island building) and social attraction (decoys and recorded vocalizations) for establishing new breeding colonies in the Upper Klamath Basin, California. In 2010, approximately 258 pairs of Caspian terns attempted to nest on the new islands and raised an average of 0.65 fledglings/breeding pair; in 2011, 222 pairs attempted to nest and raised an average of 0.11 fledglings/breeding pair. Competition with California and ring-billed gulls (Larus californicus and L. delawarensis) for nesting space, gull predation on Caspian tern eggs and chicks, low water levels, and depredation by great horned owls (Bubo virginianus) were the primary factors limiting colony development and productivity, especially in 2011. The immediate response by Caspian terns to habitat creation and social attraction in the Upper Klamath Basin demonstrates that these can be effective restoration techniques to establish new breeding colonies where nesting habitat is a major limiting factor; however, continued management of other limiting factors (e.g., control of on-colony predators and competitors) will likely be necessary to promote the development of established, self-sustaining breeding colonies on these artificial islands. Efforts to conserve and restore seabird colonies can be compromised by low prey availability within foraging distance of the breeding colony. I used GPS telemetry to study the fine-scale foraging behavior of Caspian terns nesting at two newly established colonies and cluster analysis to discriminate behavioral states based on movement characteristics. Terns breeding at the Sheepy Lake colony spent less time at the colony (52% of the day) than terns breeding at the Tule Lake colony (74%). Caspian terns breeding at Sheepy Lake foraged more extensively than terns breeding at Tule Lake; the foraging trips of Sheepy Lake terns lasted longer (median = 186 min) and were longer-distance (27 km) compared to those of Tule Lake terns (55 min and 6 km, respectively). Between-colony differences in foraging behavior corresponded to 5% lower average body mass of breeding adults and significantly lower size-adjusted body mass of chicks at the Sheepy Lake colony compared to the Tule Lake colony. Proximity to high-quality foraging areas influenced the foraging behavior and parental care of breeding Caspian terns, which in turn had effects on nesting success. The successful use of GPS telemetry to study the fine-scale foraging behavior of Caspian terns represents a significant advance in our ability to investigate the foraging ecology of this species and other moderate-sized seabirds. / Graduation date: 2013

Drought is a recurrent extreme climate event with tremendous hazard for every specter of natural environment and human lives. Drought analysis usually involves characterizing drought severity, duration and intensity. Similar to most of the hydrological problems, such characteristic variables are usually not independent. Copula, as a model of multivariate distribution, widely used in finance, actuarial analysis, has won increasingly popularity in hydrological study. Here, the study has two major focuses: (1) fit drought characteristics from Streamflow Drought Index (SDI) or Standardized Runoff Index (SRI) to appropriate copulas, then using fitted copulas to estimate conditional drought severity distribution and joint return periods for both historical time period 1920-2009 and future time period 2020-2090. SDI is calculated based on long term observed streamflow while SRI is based on simulated future runoff. Parameters estimation of marginal distribution and copulas are provided, with goodness fit measures as well; (2) investigate the effects of climate change on the frequency and severity of droughts. In order to quantify the impact, three drought indices have been proposed for this study to characterize the drought duration, severity and intensity changes under the climate change in Upper Klamath River Basin. Since drought can be defined as different types, such as meteorological drought, agricultural drought, hydrological drought and social economical drought, this study chooses Standardized Precipitation Index (SPI), Palmer Drought Severity Index (PDSI) and Surface Water Supply Index (SWSI) to estimate the meteorological, agricultural and hydrological drought, respectively. Climate change effects come from three sources: the inherent reason, the human activity and the GCMs uncertainties. Therefore, the results show the long term drought condition by calculating yearly drought indices, and compared in three ways: First, compare drought characteristics of future time periods with base period; second, show the uncertainties of three greenhouse gas emission scenarios; third, present the uncertainties of six General Circulation Models (GCMs).

Water allocation in the upper Klamath Basin of Oregon and California has been challenging. Irrigators have increasingly turned to groundwater to make up for surface water shortages because of shifts in allocation toward in-stream flows for Endangered Species Act listed fishes. The largest increase in groundwater pumping has been in and around the Bureau of Reclamation's Klamath Irrigation Project, which includes the Tule Lake subbasin in the southern part of the upper Klamath Basin. Previous groundwater flow model simulations indicate that water level declines from pumping may result in decreased flow to agricultural drains in the Tule Lake subbasin. Agricultural drains on the Klamath Project are an important source of water for downstream irrigators and for the Tule Lake and Lower Klamath Lake National Wildlife Refuges. To better assess the impact of increased pumping on drain flow and on the water balance of the groundwater system, flow data from agricultural drains were evaluated to investigate the changes that have taken place in groundwater discharge to drains since pumping volumes increased. Additionally, a fine-grid groundwater model of the Tule Lake subbasin was developed based on the existing regional flow model. The fine-grid model has sufficient vertical and horizontal resolution to simulate vertical head gradients, takes advantage of time-series data from 38 observation wells for model calibration, and allows agricultural drains to be more explicitly represented. Results of the drain flow analysis show that the groundwater discharge to agricultural drains has decreased by approximately 4000 hectare-meters from the 1997-2000 average discharge. Most of this decrease takes place in the northern and southeastern portions of the subbasin. Results of the groundwater model show that the initial source of water to wells is groundwater storage. By 2006, approximately 56% of the water from wells is sourced from agricultural drains.

A study was conducted in the Upper Klamath Basin, south-central Oregon, to test Luther s. Cressman' s hypothesis characterizing prehistoric Klamath Basin culture as having, from an early date, a marsh/riverine subsistence focus with long-term stability and a slow rate of internal change emphasizing intensification of the existing marsh/riverine utilization pattern. A subsistence/ settlement pattern model was developed to predict aboriginal site occurrence in the upper Klamath Basin.

Aquatic ecosystems continue to be increasingly affected by climate warming. For salmonids in the Pacific Northwest of North America, increasing temperatures pose tighter thermal constraints on their habitat use as well as aspects of their individual performance, such as disease resistance. This thesis examines the effect of temperature on the phenology of the Ceratomyxa shasta life cycle, the effect of thermal refugia on disease risk in juvenile salmonids in the Klamath River, CA, and the spatial and temporal distribution of C. shasta in the Willamette River, OR. We developed a biological model that predicts an acceleration of the C. shasta life cycle development due to climate shifts in the Klamath River, resulting in more generations per year and earlier seasonal parasite occurrence. We showed that in early summer the Beaver Creek-Klamath River confluence provides juvenile Chinook and coho salmon an area of lower parasite doses and cooler temperatures than the main stem, thus lessening disease risk. By accelerating the development of C. shasta in its hosts, increasing temperatures will result in earlier parasite transmission to juvenile salmonids and a longer season of infectivity. These fish may find disease refuge at cold tributary inflows to the main stem of the Klamath River in early summer, further adding to the benefit of these important thermal habitats. To determine if similar disease patterns occur in other rivers with the parasite, we described spatial and temporal occurrence of C. shasta in the Willamette River. By collecting weekly water sampling at four sites over 28 months we characterize seasonal and annual differences of parasite abundance, which varies with weekly temperature. We also collected samples along the length of the main stem and its tributaries and identified spatial differences in C. shasta spore densities. Identification of spatial and temporal variation of C. shasta in the Willamette River provides a foundation for understanding future patterns of disease occurrence in this river where conservation of anadromous fisheries is also of concern. This thesis identifies likely responses of C. shasta to climate warming in the Klamath River, with useful application to other rivers in the Pacific Northwest. / Graduation date: 2013

The uses and management of water resources play an important role in the development of a culture and the health of its environment and population. Humans throughout history have consistently exploited rivers, which degrades water quality and leads to water scarcity. This thesis is an examination of two river restoration projects, one on the Oder River in Germany and the other on the Klamath River in the United States, that represent each country's efforts to reverse river exploitation. These cases in Germany and the United States demonstrate the importance of achieving a better understanding of the political instruments and strategies for mitigating environmental issues on a global scale.