Thesis (M.S.)--Humboldt State University, 2008. / Includes bibliographical references (leaves 50-54). Also available via Humboldt Digital Scholar.

Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental cues. Two major methods are utilized for the study of transcriptomes, high-throughput sequencing and microarray analysis. High-throughput sequencing technologies such as the Illumina platform are relatively new and protocols must be developed for the analyses of transcriptomes (RNA-sequencing). A RNA-seq protocol was developed and refined for the Illumina sequencing platform. This protocol was then utilized for the de novo sequencing of the steelhead salmon transcriptome. Hatchery steelhead exhibit a reduced fitness compared to wild steelhead that has been shown to be genetically based. Consequently, the steelhead transcriptome was assembled, annotated, and used to identify gene expression differences between hatchery and wild fish. We uncovered many differentially expressed genes involved in metabolic processes and growth and development. This work has created a better understanding of the genetic differences between hatchery and wild steelhead salmon. Brachypodium distachyon is a monocot grass important as a model for cereal crops and potential biofuels feedstocks. To better understand the genetic response of this plant to different environmental cues, a comprehensive assessment of the transcriptomic response was conducted under a variety of conditions including diurnal/circadian light/dark/temperature environments and different abiotic stress conditions. Using a whole-genome tiling DNA microarray, we identified that the majority of transcripts in Brachypodium exhibit a daily rhythm in their abundance that is conserved between rice and Brachypodium. We also identified numerous cis-regulatory elements dictating these rhythmic expression patterns. We also identified the genetic response to abiotic stresses such as salinity, drought, cold, heat, and high light. We uncovered a core set of genes which responds to all stresses, indicating a core stress response. A large number of transcription factors were uncovered as potential nodes for regulating the abiotic stress response in Brachypodium. Moreover, promoter elements that drive specific responses to discrete abiotic stresses were uncovered. Altogether, the transcriptome analyses in this work furthers our understandings of how particular organisms respond to environmental cues and better elucidates the relationship between genes and the environment. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Oct. 5, 2011 - April 5, 2012.

The growing demand for water in the arid regions of the West increases the need for optimal allocation of water among competing uses. An efficient allocation of water between instream and out-of-stream uses has been impeded by institutional constraints and the scarcity of information regarding instream flow benefits. The objectives of this thesis were to provide preliminary economic data on the value of instream water in "producing" recreational fishing and to examine the effect of forestry, agriculture, and livestock practices on temporal streamflow patterns and anadromous fish production. The steelhead trout (Salmo gairdneri) sport fishery within the John Day River basin in north-central Oregon provided the setting for this research. The interdisciplinary methodology employed in estimating the marginal value of water with respect to steelhead production consisted of two tasks. The first task involved valuing a marginal change in the quality of the steelhead recreational fishery. The contingent valuation method (CVM) was selected for this purpose. Both open- and closed-ended willingness-to-pay (WTP) questions were included in a questionnaire administered to John Day River steelhead anglers during the 1986/87 steelhead fishing season. Survey data were analyzed to arrive at individual and aggregate bid functions relating WTP to expected angling success rates. Results indicate that, under current conditions, the average angler is willing to pay approximately $7.20 to catch an additional steelhead. The second task of the instream water valuation methodology was directed at deriving a streamflow/steelhead production relationship. By including variables influencing steelhead production in a Ricker stock-recruitment model, it was possible to develop a model which could be estimated using linear regression techniques. Some difficulty arose, however, with interpretation of the model due to the unavailability of cohort escapement data and the subsequent use of standing crop data. While possibly masking the true magnitude of streamflow's effect on fish production, this drawback was not deemed limiting within the general context of the interdisciplinary methodology. Results of the biological model conformed to a priori expectations. Increases in summer and winter streamflows led to increased steelhead survival, whereas higher spring flows increased mortality levels. Other results indicate that the John Day Dam was responsible for a 31.5 percent decline in the population index for the 1969-1983 period. Combining the economic and biological results into one equation yielded an estimate of the marginal value of summer instream water in "producing" recreational steelhead angling. Similar equations were developed for winter and spring flows. The marginal value of water in producing recreational steelhead fishing within the John Day basin was estimated at $0.56 per acre-foot for summer flows, $0.046 for winter flows, and -$0.075 for spring flows. By including out-of-basin benefits, these values increased to $2.26, $0.19, and -$0.30, respectively. In comparison, water's value in irrigation within the John Day basin has been estimated at between $10 to $24 per acre-foot. However, nonuse values of steelhead, as well as the increased production of other fish species (such as spring chinook salmon) were not included in the instream water values. In addition, no attempt was made at valuing instream water's contribution to boating, camping, or other benefit-producing activities. A secondary objective of this thesis was to briefly examine the possible benefits accruing to other instream and out-of-stream users due to an alteration in streamflow patterns. In addition, the impact of activities by other resource users -- namely forestry, agriculture, and livestock production --on anadromous fish production was reviewed. Improper management practices by these activities can negatively impact the aquatic and riparian ecosystems. While no firm conclusions were drawn, it appears the quality of these ecosystems, as opposed to the amount of streamflow, has the largest marginal impact on anadromous fish populations. / Graduation date: 1988

The Bonneville Power Administration (BPA) Fish and Wildlife Program mitigates for impacts of hydroelectric dams on ESA-listed salmon and steelhead populations in the Columbia River Basin (CRB). Considering the sizable investments in mitigation and the diversity of stream habitats within the CRB, there has been a pointed effort to develop and identify meaningful metrics relating to fish populations and trends in their habitat across the CRB. The Integrated Status and Effectiveness Monitoring Program (ISEMP) was developed in 2003 specifically for this purpose, and is tasked with developing and testing strategies for determining the status and trend of salmonid populations and their habitats in the CRB. This thesis was funded by the BPA, ISEMP, Eco Logical Research Inc., the Snake River Salmon Recovery Board, and the Intensively Monitored Watershed project in the Asotin Creek basin with the purpose of investigating the efficacy of foraging modeling as part of a large fish habitat monitoring program. The primary objectives were i) to assess a foraging model's ability to predict fish density in study sites involved in long-term monitoring and ii) to evaluate energetic implications of restoration design and progress after implementation using a foraging model. To assess the foraging model's ability to predict fish density (objective i), we collected topography, drift, temperature, discharge, and fish population information to support foraging modeling, and we simulated flow patterns, drift, foraging, swimming costs, carrying capacity, and density. We then compared observed and predicted densities in 22 study sites from the John Day and Asotin Creek watersheds: Linear regression between observed and predicted fish densities was significant (R2 = 0.61, p < 0.001). When assuming spatially uniform drift densities and small fish territories, carrying capacity predictions were related to the number of foraging locations simulated, suggesting the model is highly sensitive to territory size assumptions. To evaluate restoration design and monitor restoration progress (objective ii), we simulated foraging before restoration, after a virtual restoration (carried out using the restoration designs in a GIS environment), and again followinfg restoration implementation. We used raster differencing to compare the "before" results to the virtual restoration results and then the "before" results to the "after" results. Hydraulic and foraging models suggested: Mean net energy intake increased following both simulated and actual restoration. Restoration structures generally slowed water's progress through the study site or caused pooling, both resulting in an increase in energetically favorable areas. Generally, more areas shifted from another state to having an acceptable energy balance than to an unacceptable energy balance.

Life history within a single species can vary significantly. Many of these differences are associated with varying environmental conditions. Understanding what environmental conditions cue alternate life histories within a single species has been researched extensively. In salmonid fishes, more than almost any other group, varying environmental conditions give rise to individuals within species that take markedly different life history trajectories. Oncorhynchus mykissis a species of salmonid native to the Pacific Northwest region of North America. This species has two life history forms, anadromous and resident. The anadromous form spends a portion of its life in ocean while the resident life history form completes its entire life history in freshwater. Until the decision to migrate and morphological changes associated with smoltification occur, the two life history variants of this species are indistinguishable from each other. This ambiguity in juvenile O. mykiss morphology presents challenges for conservation managers charged with protecting and increasing threatened O. mykiss populations around the Pacific Northwest because conservation efforts cannot be evaluated until juvenile fish make the decision to migrate. Microarray gene expression analysis was used to profile gene expression in juvenile populations of wild and hatchery O. mykiss to identify gene expression variation associated with alternate life history variants. This analysis identified 8 DNA sequences present in both brain and gill tissues that differ in expression in rainbow trout and steelhead hatchery stocks. Differential expression as quantified by microarrays was validated with quantitative real-time PCR. Lastly, the expression of these putative life history markers was preliminarily evaluated in a wild population of O. mykiss at sample locations in the South Fork John Day River Basin, Oregon with known ratios of juvenile anadromous and resident fish.

In late Spring of 1969, shortly before the Oregon Legislative Session adjourned, House Bill No. 1302 as amended passed the last legislative hurdle and was signed by the Governor. The new statute recognized steelhead trout as a game fish and provided for an incidental catch of these fish by the commercial fishery. HB 1302 was a turning point in a century of conflict over anadromous fish of the Columbia River. The bill served as an armistice in a long sports-commercial steelhead conflict by providing some protection for these fish from commercial fishing. However the bill held off a major shift in the sports-commercial balance of power for only five years. The "final" victory went to the sports fishermen in 1974--the voters approved Ballot Measure No. 15 which banned steelhead from sale. Although the sportsmen finally won the steelhead battle, they may have lost the war. Unless the erosion of fish runs caused primarily by dams is checked the fishery may disappear. Chapter I gives an overview of HB 130 and discusses the significance of the Columbia River anadromous fishery to Oregon. Chapter II is a history of the Columbia River fishery and traces the conflict between the various fishing interest groups. Chapter III details the causes of the conflict and describes the relationship between dams and declining runs of fish. Chapter IV discusses the Legislative passage of HB 1302. Chapter V discusses lobbying and pressure group activities concerning HB 1302. Chapter VI chronicles events subsequent to passage of HB 1302. Chapter VII contains summary and concluding remarks.

Graduation date: 1981

Thesis (M.S.)--Humboldt State University, 2008. / Includes bibliographical references (leaves 58-66). Also available via Humboldt Digital Scholar.

The feasibility of using freshwater and first marine year scale patterns to identify component stocks of steelhead trout (Salmo gairdneri) in the Skeena River was investigated. Scale samples and sex and size data were attained from adult steelhead originating from five Skeena River tributaries (Zymoetz, Kispiox, Morice-Bulkley, Babine, Sustut) over a series of different years. Adult scale samples were also collected from the 1984 incidental steelhead catch in the Area 4 commercial salmon fishery for potential stock classification purposes. Significant differences in scale pattern growth, age composition, and sizes at age were found between the five Skeena River steelhead stocks. Linear discriminant function analysis indicated that the five stocks could be classified to correct river of origin with between 45% and 62% average classification accuracy (range Zymoetz 29%-60%, Kispiox 35%-60%, Morice-Bulkley 44%-76%, Babine 54%-64%, Sustut 56%-72%) depending upon the classification model used. Juvenile morphometric analysis for three of the stocks (Kispiox, Morice-Bulkley, Zymoetz) indicated the presence of significant between stock differences in standardized body form. These results support the notion that Skeena River steelhead exist as quantifiably discrete stocks. Classifying the 1984 mixed stock commercial fishery catches to probable stock of origin indicated that distinct peaks of stock abundance and run-timing occur through the fishery. In general, Morice-Bulkley and Sustut River steelhead were predicted to be most abundant with run-timings during the earlier portions of the fishery. Kispiox, Babine, and Zymoetz River steelhead were predicted to be less abundant with later run-timings through the fishery. Potential commercial fishery impacts to steelhead are briefly discussed. These observations suggest that the technique of scale patterns is a feasible method for stock separation in Skeena River steelhead. Further study is required to clarify yearly variance in the technique and to better establish stock specific differences. / Science, Faculty of / Zoology, Department of / Graduate

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