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• 1. [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

• 2. [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

• 3. [Article] Sustainability from the Perspectives of Indigenous Leaders in the Bioregion Defined by the Pacific Salmon Runs of North America

  Extensive research suggests that the collective behavior of humanity is on an unsustainable path. As the evidence mounts and more people awaken to this reality, increased attention is being dedicated to ...

  Citation × Citation Citation Abstract Copy Title: Sustainability from the Perspectives of Indigenous Leaders in the Bioregion Defined by the Pacific Salmon Runs of North America Author: Hall, David Edward Year: 2008 Extensive research suggests that the collective behavior of humanity is on an unsustainable path. As the evidence mounts and more people awaken to this reality, increased attention is being dedicated to the pursuit of answers for a just and sustainable future. This dissertation grew from the premise that effectively moving towards sustainability requires change at all levels of the dominant Western culture, including deeply held worldviews. The worldviews of many indigenous cultures offer alternative values and beliefs that can contribute to addressing the root causes of problems related to sustainability. In the bioregion defined by the Pacific Salmon runs of North America there is a rich heritage and modern day presence of diverse indigenous cultures. In-depth semi-structured interviews were conducted with 13 indigenous leaders from within this bioregion to explore their mental models of sustainability. These interviews followed a general structure that covered: (a) the personal background and community affiliation of each interviewee; (b) the meaning of the concept of sustainability from their perspective; (c) visions of a sustainable future for their communities; and, (d) how to achieve such a future. A content analysis of the interviews was conducted and summarized into a narrative organized to correspond with the general interview structure. A process oftestimonial validity established that most participants found the narrative to be an accurate representation of their perspectives. Participant feedback led to several phrasing changes and other identified issues are discussed, including one participant's critique of the narrative's use of a first-person plural voice. Major themes from the interviews include the role of the human being as caretaker actively participating in the web of life, the importance of simultaneously restoring culture and ecology due to their interdependence, the need to educate and build awareness, and the importance of cooperation. Understanding who we are as a living species, including our profound connection with nature, along with a holistic and intergenerational perspective are suggested as prerequisite for balancing and aligning human modes of being with the larger patterns of life. The closing discussion addresses the importance of social action and going beyond a conceptual understanding to an embodiment of sustainability. Title: Sustainability from the Perspectives of Indigenous Leaders in the Bioregion Defined by the Pacific Salmon Runs of North America Author: Hall, David Edward Year: 2008 Extensive research suggests that the collective behavior of humanity is on an unsustainable path. As the evidence mounts and more people awaken to this reality, increased attention is being dedicated to the pursuit of answers for a just and sustainable future. This dissertation grew from the premise that effectively moving towards sustainability requires change at all levels of the dominant Western culture, including deeply held worldviews. The worldviews of many indigenous cultures offer alternative values and beliefs that can contribute to addressing the root causes of problems related to sustainability. In the bioregion defined by the Pacific Salmon runs of North America there is a rich heritage and modern day presence of diverse indigenous cultures. In-depth semi-structured interviews were conducted with 13 indigenous leaders from within this bioregion to explore their mental models of sustainability. These interviews followed a general structure that covered: (a) the personal background and community affiliation of each interviewee; (b) the meaning of the concept of sustainability from their perspective; (c) visions of a sustainable future for their communities; and, (d) how to achieve such a future. A content analysis of the interviews was conducted and summarized into a narrative organized to correspond with the general interview structure. A process oftestimonial validity established that most participants found the narrative to be an accurate representation of their perspectives. Participant feedback led to several phrasing changes and other identified issues are discussed, including one participant's critique of the narrative's use of a first-person plural voice. Major themes from the interviews include the role of the human being as caretaker actively participating in the web of life, the importance of simultaneously restoring culture and ecology due to their interdependence, the need to educate and build awareness, and the importance of cooperation. Understanding who we are as a living species, including our profound connection with nature, along with a holistic and intergenerational perspective are suggested as prerequisite for balancing and aligning human modes of being with the larger patterns of life. The closing discussion addresses the importance of social action and going beyond a conceptual understanding to an embodiment of sustainability. Close

• 4. [Article] The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations

  Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number ...

  Citation × Citation Citation Abstract Copy Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Close

• 5. [Article] Predator Exclosures, Predator Removal, and Habitat Improvement Increase Nest Success of Snowy Plovers in Oregon, USA

  Management to increase reproductive success is commonly used to aid recovery of threatened and endangered species. The Western Snowy Plover (Charadrius nivosus nivosus) breeds from coastal Washington, ...

  Citation × Citation Citation Abstract Copy Title: Predator Exclosures, Predator Removal, and Habitat Improvement Increase Nest Success of Snowy Plovers in Oregon, USA Author: Dinsmore, Stephen J., Lauten, David J., Castelein, Kathleen J., Gaines, Eleanor P., Stern, Mark A. Year: 2014 Management to increase reproductive success is commonly used to aid recovery of threatened and endangered species. The Western Snowy Plover (Charadrius nivosus nivosus) breeds from coastal Washington, USA, to Baja California, Mexico, and in disjunct interior sites. The Pacific coast population is federally listed as Threatened; habitat loss and nest loss to a suite of terrestrial and avian predators are thought to be primary factors limiting population growth in this species. In coastal Oregon, USA, a consortium of state and federal management agencies deployed nest exclosures on active Snowy Plover nests, initiated a lethal predator management program, and conducted local-scale habitat management in an effort to boost local productivity. During 1990–2009, we monitored 1,951 Snowy Plover nests at 9 sites with varying treatments. We examined the effectiveness of 3 types of nest exclosures (large, small, and outfitted with electric wire), predator removal, and habitat management on nest survival. Habitat management to remove invasive grasses and provide more suitable nesting substrate more than doubled nest survival. Predator management or use of any of the 3 types of exclosures also affected nest survival. There appeared to be no additional benefit to using both approaches, but the biological relevance of these findings is unclear because of site differences in treatments applied. Importantly, these management techniques only affected nesting success; their effect on other contributions to population viability (e.g., fledging success) was not correlated with nesting success. This long-term study illustrates the short-term benefits and tradeoffs of using nest exclosures, predator management, and habitat restoration to improve nesting success. Although we gained broader insight into the relative efficacy of common management techniques to improve avian nesting success, we cannot yet determine how improved nest success contributes to population growth. Title: Predator Exclosures, Predator Removal, and Habitat Improvement Increase Nest Success of Snowy Plovers in Oregon, USA Author: Dinsmore, Stephen J., Lauten, David J., Castelein, Kathleen J., Gaines, Eleanor P., Stern, Mark A. Year: 2014 Management to increase reproductive success is commonly used to aid recovery of threatened and endangered species. The Western Snowy Plover (Charadrius nivosus nivosus) breeds from coastal Washington, USA, to Baja California, Mexico, and in disjunct interior sites. The Pacific coast population is federally listed as Threatened; habitat loss and nest loss to a suite of terrestrial and avian predators are thought to be primary factors limiting population growth in this species. In coastal Oregon, USA, a consortium of state and federal management agencies deployed nest exclosures on active Snowy Plover nests, initiated a lethal predator management program, and conducted local-scale habitat management in an effort to boost local productivity. During 1990–2009, we monitored 1,951 Snowy Plover nests at 9 sites with varying treatments. We examined the effectiveness of 3 types of nest exclosures (large, small, and outfitted with electric wire), predator removal, and habitat management on nest survival. Habitat management to remove invasive grasses and provide more suitable nesting substrate more than doubled nest survival. Predator management or use of any of the 3 types of exclosures also affected nest survival. There appeared to be no additional benefit to using both approaches, but the biological relevance of these findings is unclear because of site differences in treatments applied. Importantly, these management techniques only affected nesting success; their effect on other contributions to population viability (e.g., fledging success) was not correlated with nesting success. This long-term study illustrates the short-term benefits and tradeoffs of using nest exclosures, predator management, and habitat restoration to improve nesting success. Although we gained broader insight into the relative efficacy of common management techniques to improve avian nesting success, we cannot yet determine how improved nest success contributes to population growth. Close

• 6. [Article] Impacts of Columbia River Discharge on Salmonid Habitat: 1. A Nonstationary Fluvial Tide Model

  This is the first part of a two-part investigation that applies nonstationary time series analysis methods and the St. Venant equations to the problem of understanding juvenile salmonid access to favorable ...

  Citation × Citation Citation Abstract Copy Title: Impacts of Columbia River Discharge on Salmonid Habitat: 1. A Nonstationary Fluvial Tide Model Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the first part of a two-part investigation that applies nonstationary time series analysis methods and the St. Venant equations to the problem of understanding juvenile salmonid access to favorable shallow-water habitat in a tidal river. Habitat access is a function of river stage, tidal range, and the distribution of bed elevation. Part 1 models nonstationary tidal properties: species amplitudes and phases and tidal range. Part 2 models low-frequency river stage in the Lower Columbia River and reconstructs historical water levels, using the tidal model from part 1. To incorporate the nonstationary frictional effects of variable river discharge into the tidal model, we decompose the tidal wave into tidal species and calculate daily tidal range. Our one-dimensional tidal model is based on analytic wave solutions to the linearized St. Venant equation and uses six coefficients per tidal species to represent the upstream evolution of the frictionally damped tidal wave. The form of the coefficients is derived from the St. Venant equations, but their values are determined objectively from the data. About 50 station-years of surface elevation data collected (1981-2000) below Bonneville Dam (235 km from the ocean) were processed with a wavelet filter bank to retrieve time series of tidal species properties. A min-max filter was used to estimate daily tidal range. Tidal range, diurnal, and semidiurnal amplitudes were predicted with mean root mean square errorsmm, which is significantly more accurate than predictions obtained from harmonic analysis. Thus despite the compact form of our solution, we model nonstationary fluvial tidal properties with a high level of accuracy. Title: Impacts of Columbia River Discharge on Salmonid Habitat: 1. A Nonstationary Fluvial Tide Model Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the first part of a two-part investigation that applies nonstationary time series analysis methods and the St. Venant equations to the problem of understanding juvenile salmonid access to favorable shallow-water habitat in a tidal river. Habitat access is a function of river stage, tidal range, and the distribution of bed elevation. Part 1 models nonstationary tidal properties: species amplitudes and phases and tidal range. Part 2 models low-frequency river stage in the Lower Columbia River and reconstructs historical water levels, using the tidal model from part 1. To incorporate the nonstationary frictional effects of variable river discharge into the tidal model, we decompose the tidal wave into tidal species and calculate daily tidal range. Our one-dimensional tidal model is based on analytic wave solutions to the linearized St. Venant equation and uses six coefficients per tidal species to represent the upstream evolution of the frictionally damped tidal wave. The form of the coefficients is derived from the St. Venant equations, but their values are determined objectively from the data. About 50 station-years of surface elevation data collected (1981-2000) below Bonneville Dam (235 km from the ocean) were processed with a wavelet filter bank to retrieve time series of tidal species properties. A min-max filter was used to estimate daily tidal range. Tidal range, diurnal, and semidiurnal amplitudes were predicted with mean root mean square errorsmm, which is significantly more accurate than predictions obtained from harmonic analysis. Thus despite the compact form of our solution, we model nonstationary fluvial tidal properties with a high level of accuracy. Close

• 7. [Article] Impacts of Columbia River Discharge on Salmonid Habitat: 2. Changes in Shallow-Water Habitat

  This is the second part of an investigation that analyzes human alteration of shallow-water habitat (SWH) available to juvenile salmonids in the tidal Lower Columbia River. Part 2 develops a one-dimensional, ...

  Citation × Citation Citation Abstract Copy Title: Impacts of Columbia River Discharge on Salmonid Habitat: 2. Changes in Shallow-Water Habitat Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the second part of an investigation that analyzes human alteration of shallow-water habitat (SWH) available to juvenile salmonids in the tidal Lower Columbia River. Part 2 develops a one-dimensional, subtidal river stage model that explains ~90% of the stage variance in the tidal river. This model and the tidal model developed in part 1 (Kukulka and Jay, 2003) uncouple the nonlinear interaction of river tides and river stage by referring both to external forcing by river discharge, ocean tides, and atmospheric pressure. Applying the two models, daily high-water levels were predicted for a reach from rkm-50 to rkm-90 during 1974 to 1998, the period of contemporary management. Predicted water levels were related to the bathymetry and topography to determine the changes in shallow-water habitat area (SWHA) caused by flood control dikes and altered flow management. Model results suggest that diking and a >40% reduction of peak flows have reduced SWHA by ~62% during the crucial spring freshet period during which juvenile salmon use of SWHA is maximal. Taken individually, diking and flow cycle alteration reduced spring freshet SWHA by 52% and 29%, respectively. SWHA has been both displaced to lower elevations and modified in its character because tidal range has increased. Our models of these processes are economical for the very long simulations (seasons to centuries) needed to understand historic changes and climate impacts on SWH. Through analysis of the nonlinear processes controlling surface elevation in a tidal river, we have identified some of the mechanisms that link freshwater discharge to SWH and salmonid survival. Title: Impacts of Columbia River Discharge on Salmonid Habitat: 2. Changes in Shallow-Water Habitat Author: Jay, David A., Kukulka, Tobias Year: 2003 This is the second part of an investigation that analyzes human alteration of shallow-water habitat (SWH) available to juvenile salmonids in the tidal Lower Columbia River. Part 2 develops a one-dimensional, subtidal river stage model that explains ~90% of the stage variance in the tidal river. This model and the tidal model developed in part 1 (Kukulka and Jay, 2003) uncouple the nonlinear interaction of river tides and river stage by referring both to external forcing by river discharge, ocean tides, and atmospheric pressure. Applying the two models, daily high-water levels were predicted for a reach from rkm-50 to rkm-90 during 1974 to 1998, the period of contemporary management. Predicted water levels were related to the bathymetry and topography to determine the changes in shallow-water habitat area (SWHA) caused by flood control dikes and altered flow management. Model results suggest that diking and a >40% reduction of peak flows have reduced SWHA by ~62% during the crucial spring freshet period during which juvenile salmon use of SWHA is maximal. Taken individually, diking and flow cycle alteration reduced spring freshet SWHA by 52% and 29%, respectively. SWHA has been both displaced to lower elevations and modified in its character because tidal range has increased. Our models of these processes are economical for the very long simulations (seasons to centuries) needed to understand historic changes and climate impacts on SWH. Through analysis of the nonlinear processes controlling surface elevation in a tidal river, we have identified some of the mechanisms that link freshwater discharge to SWH and salmonid survival. Close

• 8. [Article] Where Have All the Native Fish Gone? The Fate of Fish that Lewis and Clark Encountered on the Lower Columbia River

  As part of a special issue of the 'Oregon Historical Quarterly,' discusses the native species of fish in the lower Columbia River described by Meriwether Lewis and William Clark in 1805-06. They identified ...

  Citation × Citation Citation Abstract Copy Title: Where Have All the Native Fish Gone? The Fate of Fish that Lewis and Clark Encountered on the Lower Columbia River Author: Butler, Virginia L. Year: 2004 As part of a special issue of the 'Oregon Historical Quarterly,' discusses the native species of fish in the lower Columbia River described by Meriwether Lewis and William Clark in 1805-06. They identified red charr, salmon trout, sturgeon, anchovy, skeet, and other fish that Indians caught and used as trade items with the Corps of Discovery. However, editors of the Lewis and Clark journals have often erred in identifying the fish Lewis and Clark described; the challenge in identifying anadromous fish lies in changing coloration, markings, and examination of habitat. There has been a drastic decline of native fish since 1805 and a growing dominance of exotic species. Title: Where Have All the Native Fish Gone? The Fate of Fish that Lewis and Clark Encountered on the Lower Columbia River Author: Butler, Virginia L. Year: 2004 As part of a special issue of the 'Oregon Historical Quarterly,' discusses the native species of fish in the lower Columbia River described by Meriwether Lewis and William Clark in 1805-06. They identified red charr, salmon trout, sturgeon, anchovy, skeet, and other fish that Indians caught and used as trade items with the Corps of Discovery. However, editors of the Lewis and Clark journals have often erred in identifying the fish Lewis and Clark described; the challenge in identifying anadromous fish lies in changing coloration, markings, and examination of habitat. There has been a drastic decline of native fish since 1805 and a growing dominance of exotic species. Close

• 9. [Article] Archaeological Evidence for Resilience of Pacific Northwest Salmon Populations and the Socioecological System Over the Last ~7,500 Years

  Archaeological data on the long history of interaction between indigenous people and salmon have rarely been applied to conservation management. When joined with ethnohistoric records, archaeology provides ...

  Citation × Citation Citation Abstract Copy Title: Archaeological Evidence for Resilience of Pacific Northwest Salmon Populations and the Socioecological System Over the Last ~7,500 Years Author: Campbell, Sarah K., Butler, Virginia L. Year: 2010 Archaeological data on the long history of interaction between indigenous people and salmon have rarely been applied to conservation management. When joined with ethnohistoric records, archaeology provides an alternative conceptual view of the potential for sustainable harvests and can suggest possible social mechanisms for managing human behavior. Review of the ~7,500-year-long fish bone record from two subregions of the Pacific Northwest shows remarkable stability in salmon use. As major changes in the ecological and social system occurred over this lengthy period, persistence in the fishery is not due simply to a lack of perturbation, but rather indicates resilience in the ecological--human system. Of several factors possibly contributing to resilience, low human population size and harvesting pressure, habitat enhancement, and suppression of competing predators do not appear to be of major importance. Flexible resource use, including human use of a range of local resources, many of which are linked in a food web with salmon, likely contributed to resilience. Most important were the beliefs and social institutions (including ownership, regulation, rituals, and monitoring) that placed restraints on salmon use as a common pool resource. In contrast, only a small fraction of our modern society relies economically on or has direct interaction with the fish, which limits our concern and willingness to fundamentally change behaviors that contribute to habitat degradation and loss, the main challenges facing salmon populations today. Salmon recovery efforts may benefit substantially from investing more resources into establishing links between community groups and actual fish populations, which would create a sense of proprietorship, one of the keys to resilience in the indigenous salmon fishery. Title: Archaeological Evidence for Resilience of Pacific Northwest Salmon Populations and the Socioecological System Over the Last ~7,500 Years Author: Campbell, Sarah K., Butler, Virginia L. Year: 2010 Archaeological data on the long history of interaction between indigenous people and salmon have rarely been applied to conservation management. When joined with ethnohistoric records, archaeology provides an alternative conceptual view of the potential for sustainable harvests and can suggest possible social mechanisms for managing human behavior. Review of the ~7,500-year-long fish bone record from two subregions of the Pacific Northwest shows remarkable stability in salmon use. As major changes in the ecological and social system occurred over this lengthy period, persistence in the fishery is not due simply to a lack of perturbation, but rather indicates resilience in the ecological--human system. Of several factors possibly contributing to resilience, low human population size and harvesting pressure, habitat enhancement, and suppression of competing predators do not appear to be of major importance. Flexible resource use, including human use of a range of local resources, many of which are linked in a food web with salmon, likely contributed to resilience. Most important were the beliefs and social institutions (including ownership, regulation, rituals, and monitoring) that placed restraints on salmon use as a common pool resource. In contrast, only a small fraction of our modern society relies economically on or has direct interaction with the fish, which limits our concern and willingness to fundamentally change behaviors that contribute to habitat degradation and loss, the main challenges facing salmon populations today. Salmon recovery efforts may benefit substantially from investing more resources into establishing links between community groups and actual fish populations, which would create a sense of proprietorship, one of the keys to resilience in the indigenous salmon fishery. Close

• 10. [Article] Biological Erosion of Marine Habitats and Structures by Burrowing Crustaceans

  Marine bioeroders, borers, and burrowers can have drastic effects to marine habitats and facilities. By physically altering the structure of marine habitats, these organisms may elicit ecosystem-level ...

  Citation × Citation Citation Abstract Copy Title: Biological Erosion of Marine Habitats and Structures by Burrowing Crustaceans Author: Davidson, Timothy Mathias Year: 2011 Marine bioeroders, borers, and burrowers can have drastic effects to marine habitats and facilities. By physically altering the structure of marine habitats, these organisms may elicit ecosystem-level effects that cascade through the community. While borer damage is typically restricted to a few substratum types, burrowing isopods in the genus Sphaeroma attack a diversity of substrata in tropical and temperate systems. My dissertation examined how boring sphaeromatid isopods affect coastal habitats (saltmarshes, mangroves) and other estuarine substrata as well as marine structures. I used a combination of lab and mensurative field experiments to quantify the effects of boring by isopods and examine how select factors affect the colonization, hence burrowing damage by isopods. I explored these questions primarily using the temperate boring sphaeromatid, Sphaeroma quoianum, as a model organism. My initial lab experiments quantified the per capita erosion rates of S. quoianum in four commonly attacked estuarine substrata. I found marsh banks and Styrofoam substrata were the most affected per capita. I supplemented this lab experiment with a year-long mensurative field experiment examining how erosion rates differ between marshes infested and uninfested by boring isopods. Marshes infested with isopods eroded 300% faster than uninfested marshes. I further examined the boring effects on Styrofoam floats. I compiled surveys and observations and conducted a short experiment to describe how isopods affect Styrofoam floats used in floating docks. I observed dense colonies of isopods attacking floats and expelling millions of plastic particles in the ocean. The boring effects to simulated Styrofoam floats were also affected by seawater temperature. Burrowing effects in Styrofoam floats exhibited a curvilinear relationship with temperature and peaked around 18°C. These results suggest a 1-2°C increase in water temperature could increase boring effects 5-17% of populations of isopods in Oregon and California bays. To examine the small-scale factors that mediate colonization and boring, I conducted a series of binary choice experiments. I found the presence of conspecifics, biofilm, and shade were important factors influencing colonization. These small scale factors likely explain why isopod attack is focused in some substrata. Finally, to examine the boring effects of tropical isopods in mangroves, I examined the associations between burrowing by S. terebrans and mangrove performance and fecundity. I found negative relationships between boring effects and performance and fecundity in two mangrove species in a restored mangrove stand in Taiwan. Together, these studies elucidate the effects of bioerosive isopods on saltmarshes, mangroves, and marine structures. However, the similar mechanisms involved in bioerosion in other boring species suggest that these results can be used to infer similar effects of other borers. In addition, since many species of sphaeromatid isopods have been introduced, this research shows how the effects of a non-native bioeroder can damage marine facilities and degrade and alter marine habitats. Through biological erosion and thus changing the physical structure of a marine habitat these non-native species can have ecosystem-level effects that cascade throughout the local community. Title: Biological Erosion of Marine Habitats and Structures by Burrowing Crustaceans Author: Davidson, Timothy Mathias Year: 2011 Marine bioeroders, borers, and burrowers can have drastic effects to marine habitats and facilities. By physically altering the structure of marine habitats, these organisms may elicit ecosystem-level effects that cascade through the community. While borer damage is typically restricted to a few substratum types, burrowing isopods in the genus Sphaeroma attack a diversity of substrata in tropical and temperate systems. My dissertation examined how boring sphaeromatid isopods affect coastal habitats (saltmarshes, mangroves) and other estuarine substrata as well as marine structures. I used a combination of lab and mensurative field experiments to quantify the effects of boring by isopods and examine how select factors affect the colonization, hence burrowing damage by isopods. I explored these questions primarily using the temperate boring sphaeromatid, Sphaeroma quoianum, as a model organism. My initial lab experiments quantified the per capita erosion rates of S. quoianum in four commonly attacked estuarine substrata. I found marsh banks and Styrofoam substrata were the most affected per capita. I supplemented this lab experiment with a year-long mensurative field experiment examining how erosion rates differ between marshes infested and uninfested by boring isopods. Marshes infested with isopods eroded 300% faster than uninfested marshes. I further examined the boring effects on Styrofoam floats. I compiled surveys and observations and conducted a short experiment to describe how isopods affect Styrofoam floats used in floating docks. I observed dense colonies of isopods attacking floats and expelling millions of plastic particles in the ocean. The boring effects to simulated Styrofoam floats were also affected by seawater temperature. Burrowing effects in Styrofoam floats exhibited a curvilinear relationship with temperature and peaked around 18°C. These results suggest a 1-2°C increase in water temperature could increase boring effects 5-17% of populations of isopods in Oregon and California bays. To examine the small-scale factors that mediate colonization and boring, I conducted a series of binary choice experiments. I found the presence of conspecifics, biofilm, and shade were important factors influencing colonization. These small scale factors likely explain why isopod attack is focused in some substrata. Finally, to examine the boring effects of tropical isopods in mangroves, I examined the associations between burrowing by S. terebrans and mangrove performance and fecundity. I found negative relationships between boring effects and performance and fecundity in two mangrove species in a restored mangrove stand in Taiwan. Together, these studies elucidate the effects of bioerosive isopods on saltmarshes, mangroves, and marine structures. However, the similar mechanisms involved in bioerosion in other boring species suggest that these results can be used to infer similar effects of other borers. In addition, since many species of sphaeromatid isopods have been introduced, this research shows how the effects of a non-native bioeroder can damage marine facilities and degrade and alter marine habitats. Through biological erosion and thus changing the physical structure of a marine habitat these non-native species can have ecosystem-level effects that cascade throughout the local community. Close