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• 1. [Article] A geophysical study of the North Scappoose Creek, Alder Creek, Clatskanie River lineament, along the trend of the Portland Hills fault, Columbia County, Oregon

  The Portland Hills fault forms a strong northwest trending lineament along the east side of the Tualatin Mountains. An en echelon lineament follows North Scappoose Creek, Alder Creek, and the Clatskanie ...

  Citation × Citation Citation Abstract Copy Title: A geophysical study of the North Scappoose Creek, Alder Creek, Clatskanie River lineament, along the trend of the Portland Hills fault, Columbia County, Oregon Author: Haas, Nina Year: 1982 The Portland Hills fault forms a strong northwest trending lineament along the east side of the Tualatin Mountains. An en echelon lineament follows North Scappoose Creek, Alder Creek, and the Clatskanie River along the same trend, through Columbia County, Oregon. The possibility that this lineament follows a fault or fault zone was investigated in this study. Geophysical methods were used, with seismic refraction, magnetic and gravity lines run perpendicular to the lineament. The seismic refraction models indicate the near surface basalt is broken in many places, with 15 - 30 meters (50 - 100 feet) vertical displacement, down to the west, at Bunker Hill along the Alder Creek fault. Gravity models required a faulted zone approximately two kilometers wide across the lineament. The proposed fault zone is more clearly defined in the south, becoming more diffuse and branching in the northern part of the study area. The Bouguer gravity values from this study distort the -40 milligal contour farther to the northwest than is shown on the Complete Bouguer Gravity Anomaly Map of Oregon {Berg and Thiruvathukal, 1967b). The existence of sharp topographic features and the geophysical evidence indicate fault activity along the zone. Title: A geophysical study of the North Scappoose Creek, Alder Creek, Clatskanie River lineament, along the trend of the Portland Hills fault, Columbia County, Oregon Author: Haas, Nina Year: 1982 The Portland Hills fault forms a strong northwest trending lineament along the east side of the Tualatin Mountains. An en echelon lineament follows North Scappoose Creek, Alder Creek, and the Clatskanie River along the same trend, through Columbia County, Oregon. The possibility that this lineament follows a fault or fault zone was investigated in this study. Geophysical methods were used, with seismic refraction, magnetic and gravity lines run perpendicular to the lineament. The seismic refraction models indicate the near surface basalt is broken in many places, with 15 - 30 meters (50 - 100 feet) vertical displacement, down to the west, at Bunker Hill along the Alder Creek fault. Gravity models required a faulted zone approximately two kilometers wide across the lineament. The proposed fault zone is more clearly defined in the south, becoming more diffuse and branching in the northern part of the study area. The Bouguer gravity values from this study distort the -40 milligal contour farther to the northwest than is shown on the Complete Bouguer Gravity Anomaly Map of Oregon {Berg and Thiruvathukal, 1967b). The existence of sharp topographic features and the geophysical evidence indicate fault activity along the zone. Close

• 2. [Article] Evaluating the Effects of Road Crossing Structures on Stream-Associated Amphibians in the Wilson River Watershed, Tillamook State Forest, Oregon

  As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits ...

  Citation × Citation Citation Abstract Copy Title: Evaluating the Effects of Road Crossing Structures on Stream-Associated Amphibians in the Wilson River Watershed, Tillamook State Forest, Oregon Author: Twitchell, Sara Erin Year: 2013 As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits of these efforts on the in-stream and adjacent riparian habitat for other species of potential concern. This study compares stream-associated amphibian (SAA) occurrence in streams adjacent to different road crossing structures on unpaved forest roads in the Wilson River watershed located within the Tillamook State Forest, Oregon. Surveys were conducted at road crossing structures for three taxa of SAA; Pacific giant salamander (Dicamptodon tenebrosus), coastal tailed frog (Ascaphus truei), and Columbia torrent salamander (Rhyacotriton kezeri). Statistical models were created to analyze the effect of habitat variables on SAA occupancy, and determine whether those variables changed relative to road crossing structures. Results showed that coastal tailed frog occupancy was positively associated with dissolved oxygen and crayfish presence, negatively associated with longitude, and had a slight quadratic relationship to channel confinement. Because all sites were highly saturated with oxygen, percent dissolved oxygen was likely a surrogate for one or more other covariates, such as in-stream habitat or substrate size. Detection rates of Pacific giant salamander were too high and detection rates of Columbia torrent salamander were too low to provide reliable models, but they did provide some insight into the factors affecting occupancy in the study area, including information about their interactions with road crossing structures. Occupancy rates of Pacific giant salamanders in the study area appear to be unaffected by road crossings, fish passable or otherwise. Conversely, torrent salamanders seemed to be mostly absent from the study sites altogether, but based on the one stream where they were detected, they are not excluded from occupying fish barrier culvert sites. Top weighted habitat covariates, including dissolved oxygen, channel confinement, crayfish and fish presence, and flow constriction are all indicators of disturbance that can be linked to road crossings. Although the size and structure of road crossings did not prove to significantly influence SAA occupancy, indicators of stream disturbance that can be related to road crossings were included in the best models for predicting occupancy, demonstrating the importance of reducing disturbance related to road crossings on streams. Title: Evaluating the Effects of Road Crossing Structures on Stream-Associated Amphibians in the Wilson River Watershed, Tillamook State Forest, Oregon Author: Twitchell, Sara Erin Year: 2013 As replacement and removal of undersized culverts gains momentum as an effective technique for restoring natural stream flows and removing fish passage barriers, it is important to evaluate the benefits of these efforts on the in-stream and adjacent riparian habitat for other species of potential concern. This study compares stream-associated amphibian (SAA) occurrence in streams adjacent to different road crossing structures on unpaved forest roads in the Wilson River watershed located within the Tillamook State Forest, Oregon. Surveys were conducted at road crossing structures for three taxa of SAA; Pacific giant salamander (Dicamptodon tenebrosus), coastal tailed frog (Ascaphus truei), and Columbia torrent salamander (Rhyacotriton kezeri). Statistical models were created to analyze the effect of habitat variables on SAA occupancy, and determine whether those variables changed relative to road crossing structures. Results showed that coastal tailed frog occupancy was positively associated with dissolved oxygen and crayfish presence, negatively associated with longitude, and had a slight quadratic relationship to channel confinement. Because all sites were highly saturated with oxygen, percent dissolved oxygen was likely a surrogate for one or more other covariates, such as in-stream habitat or substrate size. Detection rates of Pacific giant salamander were too high and detection rates of Columbia torrent salamander were too low to provide reliable models, but they did provide some insight into the factors affecting occupancy in the study area, including information about their interactions with road crossing structures. Occupancy rates of Pacific giant salamanders in the study area appear to be unaffected by road crossings, fish passable or otherwise. Conversely, torrent salamanders seemed to be mostly absent from the study sites altogether, but based on the one stream where they were detected, they are not excluded from occupying fish barrier culvert sites. Top weighted habitat covariates, including dissolved oxygen, channel confinement, crayfish and fish presence, and flow constriction are all indicators of disturbance that can be linked to road crossings. Although the size and structure of road crossings did not prove to significantly influence SAA occupancy, indicators of stream disturbance that can be related to road crossings were included in the best models for predicting occupancy, demonstrating the importance of reducing disturbance related to road crossings on streams. Close

• 3. [Article] Assessing Hydrologic and Water Quality Sensitivities to Precipitation Changes, Urban Growth and Land Management Using SWAT

  Precipitation changes and urban growth are two factors altering the state of water quality. Changes in precipitation will alter the amount and timing of flows, and the corresponding sediment and nutrient ...

  Citation × Citation Citation Abstract Copy Title: Assessing Hydrologic and Water Quality Sensitivities to Precipitation Changes, Urban Growth and Land Management Using SWAT Author: Psaris, Alexander Michael Year: 2014 Precipitation changes and urban growth are two factors altering the state of water quality. Changes in precipitation will alter the amount and timing of flows, and the corresponding sediment and nutrient dynamics. Meanwhile, densification associated with urban growth will create more impervious surfaces which will alter sediment and nutrient loadings. Land and water managers often rely on models to develop possible future scenarios and devise management responses to these projected changes. We use the Soil and Water Assessment Tool (SWAT) to assess the sensitivities of stream flow, sediment, and nutrient loads in two urbanizing watersheds in Northwest Oregon, USA to various climate and urbanization scenarios. We evaluate the spatial patterns climate change and urban growth will have on water, sediment and nutrient yields. We also identify critical source areas (CSAs) and investigate how implementation of vegetative filter strips (VFS) could ameliorate the effects of these changes. Our findings suggest that: 1) Water yield is tightly coupled to precipitation. 2) Large increases in winter and spring precipitation provide enough sub-surface storage to increase summertime water yields despite a moderate decrease in summer precipitation. 3) Expansion of urban areas increases surface runoff and has mixed effects on sediment and nutrients. 4) Implementation of VFS reduces pollutant loads helping overall watershed health. This research demonstrates the usefulness of SWAT in facilitating informed land and water management decisions. Title: Assessing Hydrologic and Water Quality Sensitivities to Precipitation Changes, Urban Growth and Land Management Using SWAT Author: Psaris, Alexander Michael Year: 2014 Precipitation changes and urban growth are two factors altering the state of water quality. Changes in precipitation will alter the amount and timing of flows, and the corresponding sediment and nutrient dynamics. Meanwhile, densification associated with urban growth will create more impervious surfaces which will alter sediment and nutrient loadings. Land and water managers often rely on models to develop possible future scenarios and devise management responses to these projected changes. We use the Soil and Water Assessment Tool (SWAT) to assess the sensitivities of stream flow, sediment, and nutrient loads in two urbanizing watersheds in Northwest Oregon, USA to various climate and urbanization scenarios. We evaluate the spatial patterns climate change and urban growth will have on water, sediment and nutrient yields. We also identify critical source areas (CSAs) and investigate how implementation of vegetative filter strips (VFS) could ameliorate the effects of these changes. Our findings suggest that: 1) Water yield is tightly coupled to precipitation. 2) Large increases in winter and spring precipitation provide enough sub-surface storage to increase summertime water yields despite a moderate decrease in summer precipitation. 3) Expansion of urban areas increases surface runoff and has mixed effects on sediment and nutrients. 4) Implementation of VFS reduces pollutant loads helping overall watershed health. This research demonstrates the usefulness of SWAT in facilitating informed land and water management decisions. Close

• 4. [Article] A Study of the Adsorption of Some Atmospheric Gases on Soils of the Willamette Valley River Basin

  Recent work indicates that microorganisms present in soils can remove carbon monoxide from the atmosphere and as such constitutes a major sink. B.E.T. adsorption studies were carried out on representative ...

  Citation × Citation Citation Abstract Copy Title: A Study of the Adsorption of Some Atmospheric Gases on Soils of the Willamette Valley River Basin Author: Quale, Thomas R. Year: 1973 Recent work indicates that microorganisms present in soils can remove carbon monoxide from the atmosphere and as such constitutes a major sink. B.E.T. adsorption studies were carried out on representative soils from the Willamette Valley River Basin in order to determine their adsorptive characteristics for carbon monoxide and other gases. Attempts were made to isolate, through a non-soildestructive sterilization, the adsorptive characteristics of the soil microorganisms as well as of the test soil. The carbon monoxide studies show physical adsorption equivalent to the coverage of a few per cent of the surface area at 25.0° and 76 cm-Hg. Adsorption studies also shows that the soil rather then the microorganisms adsorbs most of the carbon monoxide. On sterilized soil, chemical sorption of oxygen was present and was probably caused by the oxidation of dead or damaged soil microorganisms. Hysteresis effects were present in all adsorption studies at 25.0° and appears to be a characteristic of the constituents of the soil and represents a new and as yet unexplained phenomenon. Title: A Study of the Adsorption of Some Atmospheric Gases on Soils of the Willamette Valley River Basin Author: Quale, Thomas R. Year: 1973 Recent work indicates that microorganisms present in soils can remove carbon monoxide from the atmosphere and as such constitutes a major sink. B.E.T. adsorption studies were carried out on representative soils from the Willamette Valley River Basin in order to determine their adsorptive characteristics for carbon monoxide and other gases. Attempts were made to isolate, through a non-soildestructive sterilization, the adsorptive characteristics of the soil microorganisms as well as of the test soil. The carbon monoxide studies show physical adsorption equivalent to the coverage of a few per cent of the surface area at 25.0° and 76 cm-Hg. Adsorption studies also shows that the soil rather then the microorganisms adsorbs most of the carbon monoxide. On sterilized soil, chemical sorption of oxygen was present and was probably caused by the oxidation of dead or damaged soil microorganisms. Hysteresis effects were present in all adsorption studies at 25.0° and appears to be a characteristic of the constituents of the soil and represents a new and as yet unexplained phenomenon. Close

• 5. [Article] Evaluating Global Sensitivity Analysis Methods for Hydrologic Modeling over the Columbia River Basin

  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 ...

  Citation × Citation Citation Abstract Copy Title: Evaluating Global Sensitivity Analysis Methods for Hydrologic Modeling over the Columbia River Basin Author: Hameed, Maysoun Ayad Year: 2015 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. Title: Evaluating Global Sensitivity Analysis Methods for Hydrologic Modeling over the Columbia River Basin Author: Hameed, Maysoun Ayad Year: 2015 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. Close

• 6. [Article] Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications

  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 ...

  Citation × Citation Citation Abstract Copy Title: Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications Author: Lopez-Johnston, Siena Marie Year: 2014 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. Title: Cascades Island Lamprey Passage Structure: Evaluating Passage and Migration Following Structure Modifications Author: Lopez-Johnston, Siena Marie Year: 2014 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. Close

• 7. [Article] Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis

  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 ...

  Citation × Citation Citation Abstract Copy Title: Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis Author: Stevenson, Alexander E. Year: 2011 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. Title: Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis Author: Stevenson, Alexander E. Year: 2011 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. Close

• 8. [Article] Quantifying the Impacts of Initial Condition and Model Uncertainty on Hydrological Forecasts

  Forecasts of hydrological information are vital for many of society's functions. Availability of water is a requirement for any civilization, and this necessitates quantitative estimates of water for effective ...

  Citation × Citation Citation Abstract Copy Title: Quantifying the Impacts of Initial Condition and Model Uncertainty on Hydrological Forecasts Author: DeChant, Caleb Matthew Year: 2014 Forecasts of hydrological information are vital for many of society's functions. Availability of water is a requirement for any civilization, and this necessitates quantitative estimates of water for effective resource management. The research in this dissertation will focus on the forecasting of hydrological quantities, with emphasis on times of anomalously low water availability, commonly referred to as droughts. Of particular focus is the quantification of uncertainty in hydrological forecasts, and the factors that affect that uncertainty. With this focus, Bayesian methods, including ensemble data assimilation and multi-model combinations, are utilized to develop a probabilistic forecasting system. This system is applied to the upper Colorado River Basin for water supply and drought forecast analysis. This dissertation examines further advancements related to the identification of drought intensity. Due to the reliance of drought forecasting on measures of the magnitude of a drought event, it is imperative that these measures be highly accurate. In order to quantify drought intensity, hydrologists typically use statistical indices, which place observed hydrological deficiencies within the context of historical climate. Although such indices are a convenient framework for understanding the intensity of a drought event, they have obstacles related to non-stationary climate, and non-uniformly distributed input variables. This dissertation discusses these shortcomings, demonstrates some errors that conventional indices may lead to, and then proposes a movement towards physically-based indices to overcome these issues. A final advancement in this dissertation is an examination of the sensitivity of hydrological forecasts to initial conditions. Although this has been performed in many recent studies, the experiment here takes a more detailed approach. Rather than determining the lead time at which meteorological forcing becomes dominant with respect to initial conditions, this study quantifies the lead time at which the forecast becomes entirely insensitive to initial conditions, and estimating the rate at which the forecast loses sensitivity to initial conditions. A primary goal with this study is to examine the recovery of drought, which is related to the loss of sensitivity to below average initial moisture conditions over time. Through this analysis, it is found that forecasts are sensitive to initial conditions at greater lead times than previously thought, which has repercussions for development of forecast systems. Title: Quantifying the Impacts of Initial Condition and Model Uncertainty on Hydrological Forecasts Author: DeChant, Caleb Matthew Year: 2014 Forecasts of hydrological information are vital for many of society's functions. Availability of water is a requirement for any civilization, and this necessitates quantitative estimates of water for effective resource management. The research in this dissertation will focus on the forecasting of hydrological quantities, with emphasis on times of anomalously low water availability, commonly referred to as droughts. Of particular focus is the quantification of uncertainty in hydrological forecasts, and the factors that affect that uncertainty. With this focus, Bayesian methods, including ensemble data assimilation and multi-model combinations, are utilized to develop a probabilistic forecasting system. This system is applied to the upper Colorado River Basin for water supply and drought forecast analysis. This dissertation examines further advancements related to the identification of drought intensity. Due to the reliance of drought forecasting on measures of the magnitude of a drought event, it is imperative that these measures be highly accurate. In order to quantify drought intensity, hydrologists typically use statistical indices, which place observed hydrological deficiencies within the context of historical climate. Although such indices are a convenient framework for understanding the intensity of a drought event, they have obstacles related to non-stationary climate, and non-uniformly distributed input variables. This dissertation discusses these shortcomings, demonstrates some errors that conventional indices may lead to, and then proposes a movement towards physically-based indices to overcome these issues. A final advancement in this dissertation is an examination of the sensitivity of hydrological forecasts to initial conditions. Although this has been performed in many recent studies, the experiment here takes a more detailed approach. Rather than determining the lead time at which meteorological forcing becomes dominant with respect to initial conditions, this study quantifies the lead time at which the forecast becomes entirely insensitive to initial conditions, and estimating the rate at which the forecast loses sensitivity to initial conditions. A primary goal with this study is to examine the recovery of drought, which is related to the loss of sensitivity to below average initial moisture conditions over time. Through this analysis, it is found that forecasts are sensitive to initial conditions at greater lead times than previously thought, which has repercussions for development of forecast systems. Close

• 9. [Article] Agricultural Management Decisions Impact Isoprene Emission and Physiology of Arundo donax, an Emerging Bioenergy Crop

  Arundo donax (Giant Reed) is quickly being developed as a rapidly-growing, robust, and highly productive bioenergy crop, with large scale cultivation of this species planned for the Columbia River basin ...

  Citation × Citation Citation Abstract Copy Title: Agricultural Management Decisions Impact Isoprene Emission and Physiology of Arundo donax, an Emerging Bioenergy Crop Author: Maxfield, Jason Charles Year: 2014 Arundo donax (Giant Reed) is quickly being developed as a rapidly-growing, robust, and highly productive bioenergy crop, with large scale cultivation of this species planned for the Columbia River basin of the Pacific Northwest (USA). Despite its potential as a next generation biomass crop, relatively few studies have examined the physiological performance of A. donax under agricultural conditions. Unlike traditional crops, A. donax is known to be a high-emitter of the volatile compound isoprene, which may significantly impact regional air quality, but it has not been widely cultivated in North America and little is known about how this species will perform in the Pacific Northwest. Over two field seasons, we measured isoprene fluxes from A. donax plants in both greenhouse conditions and in an agricultural field setting under a variety of conditions and fertilizer treatments. We also measured several other attributes of A. donax productivity and leaf physiology including chlorophyll content, photosynthesis rate, stomatal conductance, specific leaf mass, water use efficiency and gas exchange. We found that A. donax physiologically performs well under cultivation in the Columbia River basin, but that it also emits isoprene at significantly higher rates than previous reports indicate. We also found that both isoprene emission and leaf physiology were highly affected by agricultural management decisions, including nitrogen and irrigation management. Our findings indicate that crop management strategies can be developed that simultaneously seek to minimize isoprene emission while maximizing biomass production in this newly emerging bioenergy crop. Title: Agricultural Management Decisions Impact Isoprene Emission and Physiology of Arundo donax, an Emerging Bioenergy Crop Author: Maxfield, Jason Charles Year: 2014 Arundo donax (Giant Reed) is quickly being developed as a rapidly-growing, robust, and highly productive bioenergy crop, with large scale cultivation of this species planned for the Columbia River basin of the Pacific Northwest (USA). Despite its potential as a next generation biomass crop, relatively few studies have examined the physiological performance of A. donax under agricultural conditions. Unlike traditional crops, A. donax is known to be a high-emitter of the volatile compound isoprene, which may significantly impact regional air quality, but it has not been widely cultivated in North America and little is known about how this species will perform in the Pacific Northwest. Over two field seasons, we measured isoprene fluxes from A. donax plants in both greenhouse conditions and in an agricultural field setting under a variety of conditions and fertilizer treatments. We also measured several other attributes of A. donax productivity and leaf physiology including chlorophyll content, photosynthesis rate, stomatal conductance, specific leaf mass, water use efficiency and gas exchange. We found that A. donax physiologically performs well under cultivation in the Columbia River basin, but that it also emits isoprene at significantly higher rates than previous reports indicate. We also found that both isoprene emission and leaf physiology were highly affected by agricultural management decisions, including nitrogen and irrigation management. Our findings indicate that crop management strategies can be developed that simultaneously seek to minimize isoprene emission while maximizing biomass production in this newly emerging bioenergy crop. Close

• 10. [Article] The effect of human activity on the middle course of the Tualatin River, Oregon

  A diurnal study of biological, chemical, and physical parameters was made on the middle course of the, Tualatin River, which drains a 1840 km2 (711 mi2) basin adjacent to metropolitan Portland, Oregon. ...

  Citation × Citation Citation Abstract Copy Title: The effect of human activity on the middle course of the Tualatin River, Oregon Author: Carter, Lolita M. Year: 1975 A diurnal study of biological, chemical, and physical parameters was made on the middle course of the, Tualatin River, which drains a 1840 km2 (711 mi2) basin adjacent to metropolitan Portland, Oregon. This portion of the river lies along land in transition of use from rural agriculture to highly urbanized development. There is no nutrient loading of the river from farming practices because there was no return of water from summer, sprinkler irrigation of commercial crops. However, irrigation significantly reduces the volume of water in the river in the summers. Effluents from sewage treatment plants flowing into the tributaries that drain the highly urbanized eastern areas of the river basin are the main cause of degraded water quality and algal biomass in the lower reaches of the river. The Tualatin River above the mouth of Rock Creek is relatively unpolluted, but downstream from Rock Creek the river is highly eutrophic and during the periods of low flow in the summer serves as a sewage oxidation channel. In this same portion of the river there is also evidence that nitrification occurs. Winter floods leach nitrate-nitrogen from the basin, but in the summer the possibility exists. that nitrate-nitrogen may be a limiting nutrient for algal productivity in the river above Hillsboro. The principal source of poly-phosphates is from sewage treatment plant effluents, but concentrations of poly-phosphates in the middle reaches of the river indicate that there is a natural source of poly- and/or ortho-phosphates in the watershed. Removal of phosphorous compounds from the effluents probably would not affect the large algal blooms occurring in the river below Hillsboro. Trace metal analyses indicated that iron, potassium, nickel, zinc, lead, copper, cobalt, and chromium concentrations were higher during flooding. Turbidity readings suggest that these trace elements are deposited on the floodplain. Melted snow water, which caused one of the winter floods, contained concentrations of zinc, ·copper, and lead greater than those found in the river during the flood. Greater concentrations of arsenic and zinc came from farmland than from urban areas. Diversities of the net plankton as measured by the Shannon-Weaver Index did not change from season to season, nor with downstream flow. Species in the net plankton were benthic forms at the upper stations and planktonic forms downstream from Hillsboro, especially in the summer when the reduced flow caused the river to pond. The enriched effluents from Rock Creek did not affect the diversity of the organisms downstream, but supported a larger biomass. By rating the diversities with other studies it was found that the middle course of the Tualatin River is eutrophic but not heavily polluted. A diurnal study was especially valuable from April to September, inclusive, when insolation and temperatures favored biological activities such as photosynthesis and decomposition. From November to January little diurnal change in the water quality was found. Farming had its greatest impact in the quantity of water and municipalities had a more serious impact on the water quality in the middle course of the Tualatin River. Even with the reduced flow from agricultural irrigation, the river can maintain relatively good water quality, except when effluents from sewage plants caused highly eutrophic conditions. Title: The effect of human activity on the middle course of the Tualatin River, Oregon Author: Carter, Lolita M. Year: 1975 A diurnal study of biological, chemical, and physical parameters was made on the middle course of the, Tualatin River, which drains a 1840 km2 (711 mi2) basin adjacent to metropolitan Portland, Oregon. This portion of the river lies along land in transition of use from rural agriculture to highly urbanized development. There is no nutrient loading of the river from farming practices because there was no return of water from summer, sprinkler irrigation of commercial crops. However, irrigation significantly reduces the volume of water in the river in the summers. Effluents from sewage treatment plants flowing into the tributaries that drain the highly urbanized eastern areas of the river basin are the main cause of degraded water quality and algal biomass in the lower reaches of the river. The Tualatin River above the mouth of Rock Creek is relatively unpolluted, but downstream from Rock Creek the river is highly eutrophic and during the periods of low flow in the summer serves as a sewage oxidation channel. In this same portion of the river there is also evidence that nitrification occurs. Winter floods leach nitrate-nitrogen from the basin, but in the summer the possibility exists. that nitrate-nitrogen may be a limiting nutrient for algal productivity in the river above Hillsboro. The principal source of poly-phosphates is from sewage treatment plant effluents, but concentrations of poly-phosphates in the middle reaches of the river indicate that there is a natural source of poly- and/or ortho-phosphates in the watershed. Removal of phosphorous compounds from the effluents probably would not affect the large algal blooms occurring in the river below Hillsboro. Trace metal analyses indicated that iron, potassium, nickel, zinc, lead, copper, cobalt, and chromium concentrations were higher during flooding. Turbidity readings suggest that these trace elements are deposited on the floodplain. Melted snow water, which caused one of the winter floods, contained concentrations of zinc, ·copper, and lead greater than those found in the river during the flood. Greater concentrations of arsenic and zinc came from farmland than from urban areas. Diversities of the net plankton as measured by the Shannon-Weaver Index did not change from season to season, nor with downstream flow. Species in the net plankton were benthic forms at the upper stations and planktonic forms downstream from Hillsboro, especially in the summer when the reduced flow caused the river to pond. The enriched effluents from Rock Creek did not affect the diversity of the organisms downstream, but supported a larger biomass. By rating the diversities with other studies it was found that the middle course of the Tualatin River is eutrophic but not heavily polluted. A diurnal study was especially valuable from April to September, inclusive, when insolation and temperatures favored biological activities such as photosynthesis and decomposition. From November to January little diurnal change in the water quality was found. Farming had its greatest impact in the quantity of water and municipalities had a more serious impact on the water quality in the middle course of the Tualatin River. Even with the reduced flow from agricultural irrigation, the river can maintain relatively good water quality, except when effluents from sewage plants caused highly eutrophic conditions. Close