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.

The restoration of rivers and streams should be based on a strong conceptual framework. Streams are developing systems. As such, streams exhibit temporal behaviors that change with changing stream environments. Underlying the dynamic development of streams is potential capacity. Streams express this capacity as an array of habitats over time and across the landscape. Human land uses in the western United States have rapidly altered aquatic habitats as well as the processes that shape habitat. As a result, the diversity of native fishes and their habitats has been suppressed. Restoration is fundamentally about allowing stream systems to re-express their capacities. Four steps are provided to guide stream restoration activities. Key tasks include: identification of the historic patterns of habitat development; protection of the developmental diversity that remains; local application of specific knowledge about suppressive factors; classification of sensitive, critical or refugium habitats; release of anthropogenic suppression; and monitoring of biotic response to habitat change. Applying these concepts, I describe potential habitat refugia for aquatic organisms in the Joseph Creek basin in the Blue Mountains of northeast Oregon. Five valley segment classes, differing in valley corridor landforms, are described. Of these, low-gradient wide alluvial valleys have been most altered by human land use. Riparian vegetation has been extensively removed or altered in alluvial valleys. Currently, stream habitats are structurally depauperate, and warm to temperatures well above thermal tolerances of native salmonids. Potential refugia for native coldwater fishes in these valleys include patches of complex habitat within stream reaches. Reaches fenced to exclude domestic livestock exhibit narrower channels, more pools, and higher frequencies of stable vegetated banks than nearby unfenced reaches. During summer low flow periods, cold groundwater seeping into and accumulating in stream channels forms "cold pools". Cold pools provide potential seasonal refuge for coldwater fish at microhabitat scales. Cold pools are associated with channel complexity, and are more frequent in reaches with vigorous riparian vegetation. Seven classes of cold pools are described. Cold pool classes differ in minimum temperature, maximum depth and volume. Distributions of cold pool classes between valley segment classes suggest that valley geomorphology in addition to local channel form may influence development of certain cold pool types. Although refugia at the microhabitat to reach scales are important, the context within which remnant or refugium habitats and associated relict populations are maintained may ultimately determine the persistence of those species and habitats. In managed landscapes, protection and restoration of habitats at many scales may be necessary if we are to best insure the persistence of native species. / Graduation date: 1995

BC Hydro’s Water Use Planning (WUP) process is one of the world’s most comprehensive hydroelectric dam operational reviews and has served as a model to revise hydropower operating plans with the participation of an inclusive range of stakeholders, rights holders, and the use of up-to-date scientific information, that meets social and environmental goals alongside economic targets. In 2000, BC Hydro initiated a WUP process in the Jordan River watershed. This watershed hosts a wide diversity of water users, including active resource industry stakeholders (mining, forestry, and hydropower), Indigenous rights holders, and rural community citizens; which is representative of watersheds in British Columbia with established WUPs. BC Hydro finalized the Jordan River WUP in 2003, which focuses on establishing critical freshwater flows for fish habitat and achieving specific recreational values of the local community. However, numerous other issues still remain that were beyond the scope of the WUP process, including water quality concerns that were continually brought up by citizens during the consultative process of the WUP. In addition to these concerns, biological monitoring following the implementation of the WUP suggests that contamination from an inactive copper mine has affected and altered sensitive water quality parameters for a healthy Pacific salmon habitat in Jordan River. Yet, there has not been an extensive water quality study conducted that examines the spatial or seasonal water quality extents of the mining contamination in Jordan River, specifically copper. Consequently, fourteen years after the creation of the WUP, local advocates are still struggling to have their concerns heard by the entity responsible for freshwater flow, BC Hydro, alongside federal and provincial government agencies. Advocates are calling for the creation of a watershed-based group as a mechanism for having greater influence in water planning and governance processes. This study explores the research question: if and how has the WUP process contributed to creating watershed governance capacity? This social science thesis project employs a mixed-methods approach using both quantitative and qualitative data. The study includes a document review of relevant water governance literature and focuses on examining the freshwater quality of the Jordan River. Water quality samples were collected over a five-week period from five sites on the Jordan River beginning in September and concluding in October of 2015 during the most sensitive periods of salmon spawning activity in the lower reaches of the Jordan River. Spatial and seasonal water quality trends were identified, and analysis concluded that copper is the primary contaminate affecting the productivity of a healthy salmon habitat in the Jordan River. Acid mine drainage (AMD) processes were identified throughout the water quality data and are strongly influenced by the proximity of existing mine waste piles sourced from an abandoned copper mine, and unnatural anthropogenic flows from the three BC Hydro dams present in the Jordan River system. The final stage of the research project focuses on assessing the adaptive capacity in the watershed to address the issues of concern outlined in the WUP. There is a current movement to create watershed organizations that are formally supported through new legislation in British Columbia, but questions remain about the capacities of these watershed communities to sustain such a formal institution and if these watershed communities are ready to successfully implement a local watershed governance model. The Gupta et al. (2010) six adaptive capacity dimensions provide a logical framework to explore if these capacities are present such that it could be expected that local watershed organizations would be effective as society adapts to more watershed-based governance approaches. Thirteen semi-structured interviews were conducted from October 2016 to February 2017. Interviews and observational data focused on the WUP process and prospective and current members of the Jordan Watershed Round Table (JWRT). The research evaluated whether these six adaptive capacity dimensions are present in watershed communities that have been subjected to water management processes, specifically the WUP program. Overall, the research concluded that the WUP has contributed to some adaptive capacity for watershed governance in the Jordan River, specifically on building the adaptive capacity dimensions: variety, learning capacity, room for autonomous change, leadership, and resources within the JWRT. / Graduate