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• 1. [Article] Clear and Foster Creek Watershed Assessment

  Abstract -- A watershed assessment was completed in the Clear and Foster Creek watersheds to evaluate existing conditions and make recommendations to protect or enhance watershed natural resources. Clear ...

  Citation × Citation Citation Abstract Copy Title: Clear and Foster Creek Watershed Assessment Abstract -- A watershed assessment was completed in the Clear and Foster Creek watersheds to evaluate existing conditions and make recommendations to protect or enhance watershed natural resources. Clear and Foster Creek are tributaries to the Clackamas River below any major dams on the system; consequently these tributaries are positioned favorably to contribute to recovery of important anadromous fish populations. Anadromous fish species in the Clackamas basin include spring and fall chinook, coho salmon, winter steelhead, summer steelhead (non-native), migratory cutthroat trout and lamprey. Clear and Foster Creeks are utilized by fall chinook, winter steelhead and coho salmon. The assessment generally followed the framework described in the Oregon Watershed Enhancement Board’s Watershed Assessment Manual (WPN, 1999). The assessment focused on the following components: Channel habitat classification and modification; hydrology and water use; riparian/wetlands; sediment sources; water quality; fisheries; and wildlife and upland vegetation. Generally the approach builds on existing information, and enhances this information with aerial photo interpretation and limited field checking. Additional fieldwork was used to verify channel habitat types and to characterize fish habitat condition. GIS was used as a critical assessment tool and method of displaying results. Title: Clear and Foster Creek Watershed Assessment Abstract -- A watershed assessment was completed in the Clear and Foster Creek watersheds to evaluate existing conditions and make recommendations to protect or enhance watershed natural resources. Clear and Foster Creek are tributaries to the Clackamas River below any major dams on the system; consequently these tributaries are positioned favorably to contribute to recovery of important anadromous fish populations. Anadromous fish species in the Clackamas basin include spring and fall chinook, coho salmon, winter steelhead, summer steelhead (non-native), migratory cutthroat trout and lamprey. Clear and Foster Creeks are utilized by fall chinook, winter steelhead and coho salmon. The assessment generally followed the framework described in the Oregon Watershed Enhancement Board’s Watershed Assessment Manual (WPN, 1999). The assessment focused on the following components: Channel habitat classification and modification; hydrology and water use; riparian/wetlands; sediment sources; water quality; fisheries; and wildlife and upland vegetation. Generally the approach builds on existing information, and enhances this information with aerial photo interpretation and limited field checking. Additional fieldwork was used to verify channel habitat types and to characterize fish habitat condition. GIS was used as a critical assessment tool and method of displaying results. Close

• 2. [Article] Alsea Watershed Report

  Abstract -- This report explains how forested lands provided historically for native salmon; presents information on salmon habitat and land ownership in the Alsea watershed; and recommends changes in ...

  Citation × Citation Citation Abstract Copy Title: Alsea Watershed Report Abstract -- This report explains how forested lands provided historically for native salmon; presents information on salmon habitat and land ownership in the Alsea watershed; and recommends changes in forest practices to restore salmon runs in the watershed. Title: Alsea Watershed Report Abstract -- This report explains how forested lands provided historically for native salmon; presents information on salmon habitat and land ownership in the Alsea watershed; and recommends changes in forest practices to restore salmon runs in the watershed. Close

• 3. [Article] Nehalem Watershed Report

  Abstract -- This report explains how forested lands provided historically for native salmon; presents information on salmon habitat and land ownership in the Nehalem watershed; and recommends changes in ...

  Citation × Citation Citation Abstract Copy Title: Nehalem Watershed Report Abstract -- This report explains how forested lands provided historically for native salmon; presents information on salmon habitat and land ownership in the Nehalem watershed; and recommends changes in forest practices to restore salmon runs in the watershed. Title: Nehalem Watershed Report Abstract -- This report explains how forested lands provided historically for native salmon; presents information on salmon habitat and land ownership in the Nehalem watershed; and recommends changes in forest practices to restore salmon runs in the watershed. Close

• 4. [Article] Lower Pony Creek Watershed Assessment and Potential Action Plan

  Abstract -- The Lower Pony Creek Watershed has been undergoing significant change in recent decades, as the area has transitioned from a forested coastal valley to urban and suburban in character. This ...

  Citation × Citation Citation Abstract Copy Title: Lower Pony Creek Watershed Assessment and Potential Action Plan Abstract -- The Lower Pony Creek Watershed has been undergoing significant change in recent decades, as the area has transitioned from a forested coastal valley to urban and suburban in character. This transition has . ~I presented significant issues for the Cities of North Bend and Coos Bay and these issues are the focus of this project. Flooding in the Creek system has become an increasingly regular occurrence in specific areas. Water quality has deteriorated to the point that, in 1998, the Oregon Department of Water Quality listed Pony Creek and Pony Slough as being water quality limited for high bacterial counts. The Creek system supports or has supported salmon runs (now protected under the Endangered Species Act) and is o designated Essential Salmonid Habitat by the Oregon Department of State Lands and the Oregon Department ofFish and Wildlife. Citizens and agency staff have come together to better understand the current condition of the Lower Pony Creek, and to chart a course toward an ecologically healthier future for the watershed. Title: Lower Pony Creek Watershed Assessment and Potential Action Plan Abstract -- The Lower Pony Creek Watershed has been undergoing significant change in recent decades, as the area has transitioned from a forested coastal valley to urban and suburban in character. This transition has . ~I presented significant issues for the Cities of North Bend and Coos Bay and these issues are the focus of this project. Flooding in the Creek system has become an increasingly regular occurrence in specific areas. Water quality has deteriorated to the point that, in 1998, the Oregon Department of Water Quality listed Pony Creek and Pony Slough as being water quality limited for high bacterial counts. The Creek system supports or has supported salmon runs (now protected under the Endangered Species Act) and is o designated Essential Salmonid Habitat by the Oregon Department of State Lands and the Oregon Department ofFish and Wildlife. Citizens and agency staff have come together to better understand the current condition of the Lower Pony Creek, and to chart a course toward an ecologically healthier future for the watershed. Close

• 5. [Article] OASIS - Calibration of Estimates of Coho Spawner Abundance in Smith River Basin, 2001

  Abstract -- Estimates of coho spawner abundance derived from spawning surveys are a fundamental component of the Oregon Department of Fish and Wildlife’s (ODFW) Oregon Plan Monitoring (Jacobs et al. 2001). ...

  Citation × Citation Citation Abstract Copy Title: OASIS - Calibration of Estimates of Coho Spawner Abundance in Smith River Basin, 2001 Abstract -- Estimates of coho spawner abundance derived from spawning surveys are a fundamental component of the Oregon Department of Fish and Wildlife’s (ODFW) Oregon Plan Monitoring (Jacobs et al. 2001). The basis of these estimates are visual counts of adult spawners in randomly selected stream reaches. To date, survey-derived estimates have not been validated against known spawner abundances. Beginning in 1999, we initiated a study at Smith River (Umpqua Basin) to calibrate survey-based spawner estimates. Smith River provides an ideal location for this type of study because it is typical of many other coastal streams that support coho salmon, contains large quantities of habitat and spawners, and provides the ability to efficiently trap and tag adequate portions of the coho run. Title: OASIS - Calibration of Estimates of Coho Spawner Abundance in Smith River Basin, 2001 Abstract -- Estimates of coho spawner abundance derived from spawning surveys are a fundamental component of the Oregon Department of Fish and Wildlife’s (ODFW) Oregon Plan Monitoring (Jacobs et al. 2001). The basis of these estimates are visual counts of adult spawners in randomly selected stream reaches. To date, survey-derived estimates have not been validated against known spawner abundances. Beginning in 1999, we initiated a study at Smith River (Umpqua Basin) to calibrate survey-based spawner estimates. Smith River provides an ideal location for this type of study because it is typical of many other coastal streams that support coho salmon, contains large quantities of habitat and spawners, and provides the ability to efficiently trap and tag adequate portions of the coho run. Close

• 6. [Article] OASIS - Lower Columbia River Coho Status Report 2002 – 2004: Population abundance, distribution, run timing, and hatchery influence.

  Abstract -- This report provides an assessment of abundance, distribution, spawn timing, and hatchery:wild ratios of spawning adult coho salmon (Oncorhynchus kisutch) based on EMAP spawning surveys in ...

  Citation × Citation Citation Abstract Copy Title: OASIS - Lower Columbia River Coho Status Report 2002 – 2004: Population abundance, distribution, run timing, and hatchery influence. Abstract -- This report provides an assessment of abundance, distribution, spawn timing, and hatchery:wild ratios of spawning adult coho salmon (Oncorhynchus kisutch) based on EMAP spawning surveys in the Oregon portion of the Lower Columbia River in the 2002, 2003, and 2004 spawning seasons. The Oregon portion of the Lower Columbia River Evolutionarily Significant Unit (ESU) extends from the mouth of the Columbia River to the Hood River, excluding areas above Willamette Falls. Analysis is conducted at the population complex level, six subsets of the ESU defined during Oregon Department of Fish and Wildlife Status Review (Chilcote 1999). Population characteristics, most notably the proportion of wild spawners and spawn timing, vary among complexes. Interannual variation within complexes over the last three years is linked to streamflow variation. Most hatchery straying occurred within complex, though the Bonneville complex received strays from further upriver. Abundance increased in areas without evidence of hatchery inputs. Abundance goals established by the ODFW endangered species management plan (Chilcote 2001) in the Clackamas (>1900 adults) and Sandy (>670 adults) have been met the last two years; however, spawner densities and the proportion of wild spawners are lower than on the Oregon Coast. Title: OASIS - Lower Columbia River Coho Status Report 2002 – 2004: Population abundance, distribution, run timing, and hatchery influence. Abstract -- This report provides an assessment of abundance, distribution, spawn timing, and hatchery:wild ratios of spawning adult coho salmon (Oncorhynchus kisutch) based on EMAP spawning surveys in the Oregon portion of the Lower Columbia River in the 2002, 2003, and 2004 spawning seasons. The Oregon portion of the Lower Columbia River Evolutionarily Significant Unit (ESU) extends from the mouth of the Columbia River to the Hood River, excluding areas above Willamette Falls. Analysis is conducted at the population complex level, six subsets of the ESU defined during Oregon Department of Fish and Wildlife Status Review (Chilcote 1999). Population characteristics, most notably the proportion of wild spawners and spawn timing, vary among complexes. Interannual variation within complexes over the last three years is linked to streamflow variation. Most hatchery straying occurred within complex, though the Bonneville complex received strays from further upriver. Abundance increased in areas without evidence of hatchery inputs. Abundance goals established by the ODFW endangered species management plan (Chilcote 2001) in the Clackamas (>1900 adults) and Sandy (>670 adults) have been met the last two years; however, spawner densities and the proportion of wild spawners are lower than on the Oregon Coast. Close

• 7. [Article] Salmon Run Golf Course Hole 3_Design Report

  Abstract -- The design report summarizes the investigations that have been completed to-date for a restoration project on Hole 3 of Salmon Run Golf Course, including the development of a preliminary project ...

  Citation × Citation Citation Abstract Copy Title: Salmon Run Golf Course Hole 3_Design Report Abstract -- The design report summarizes the investigations that have been completed to-date for a restoration project on Hole 3 of Salmon Run Golf Course, including the development of a preliminary project design. Title: Salmon Run Golf Course Hole 3_Design Report Abstract -- The design report summarizes the investigations that have been completed to-date for a restoration project on Hole 3 of Salmon Run Golf Course, including the development of a preliminary project design. Close

• 8. [Article] Salmon Run Golf Course Hole 4_Design Report

  Abstract -- The design report summarizes the investigations completed to-date for a restoration project on Hole 4 of Salmon Run Golf Course, and includes a preliminary project design.

  Citation × Citation Citation Abstract Copy Title: Salmon Run Golf Course Hole 4_Design Report Abstract -- The design report summarizes the investigations completed to-date for a restoration project on Hole 4 of Salmon Run Golf Course, and includes a preliminary project design. Title: Salmon Run Golf Course Hole 4_Design Report Abstract -- The design report summarizes the investigations completed to-date for a restoration project on Hole 4 of Salmon Run Golf Course, and includes a preliminary project design. Close

• 9. [Article] Oregon Fish Habitat Distribution - Pacific Lamprey

  Abstract -- The Pacific lamprey has inhabited the rivers, streams and coastal waters of the west for 350 million years (BPA, 2005). These data describe areas of suitable habitat currently and historically ...

  Citation × Citation Citation Abstract Copy Title: Oregon Fish Habitat Distribution - Pacific Lamprey Abstract -- The Pacific lamprey has inhabited the rivers, streams and coastal waters of the west for 350 million years (BPA, 2005). These data describe areas of suitable habitat currently and historically used by Pacific lamprey populations. Pacific lamprey, Lampetra tridentata, (more recently identified as Entosphenus tridentatus), are native to the Pacific coast from Baja California to the Bering Sea. They are anadromous, migrating from their natal stream to the ocean and back, but unlike salmon, Pacific lamprey spend well over half of their total life cycle in freshwater. The Pacific lamprey was listed as an Oregon State sensitive species in 1993 and in 1996 was protected through restriction of harvest (ODFW 2006). These data now comply with the Oregon Fish Habitat Distribution Data Standard that was adopted by the Oregon Geographic Information Council in February 2011. The Standard document can be found at: http://gis.oregon.gov/DAS/EISPD/GEO/standards/docs/OregonFishHabitatDistributionDataStandardv2.pdf The term "currently" is defined as within the past five reproductive cycles. This information is based on sampling (see the fhdBasis field). Due to natural variations in run size, water conditions, or other environmental factors, some habitats identified may not be used annually.Habitat distribution data are mapped at a 1:24,000 scale statewide and are based on the Pacific Northwest Framework Hydrography dataset. The data are made available as GIS files in both shapefile and ESRI geodatabase format. The data were developed over an extensive time period ranging from 1990 to 2011. Data were migrated to the NHD in Spring of 2014. Title: Oregon Fish Habitat Distribution - Pacific Lamprey Abstract -- The Pacific lamprey has inhabited the rivers, streams and coastal waters of the west for 350 million years (BPA, 2005). These data describe areas of suitable habitat currently and historically used by Pacific lamprey populations. Pacific lamprey, Lampetra tridentata, (more recently identified as Entosphenus tridentatus), are native to the Pacific coast from Baja California to the Bering Sea. They are anadromous, migrating from their natal stream to the ocean and back, but unlike salmon, Pacific lamprey spend well over half of their total life cycle in freshwater. The Pacific lamprey was listed as an Oregon State sensitive species in 1993 and in 1996 was protected through restriction of harvest (ODFW 2006). These data now comply with the Oregon Fish Habitat Distribution Data Standard that was adopted by the Oregon Geographic Information Council in February 2011. The Standard document can be found at: http://gis.oregon.gov/DAS/EISPD/GEO/standards/docs/OregonFishHabitatDistributionDataStandardv2.pdf The term "currently" is defined as within the past five reproductive cycles. This information is based on sampling (see the fhdBasis field). Due to natural variations in run size, water conditions, or other environmental factors, some habitats identified may not be used annually.Habitat distribution data are mapped at a 1:24,000 scale statewide and are based on the Pacific Northwest Framework Hydrography dataset. The data are made available as GIS files in both shapefile and ESRI geodatabase format. The data were developed over an extensive time period ranging from 1990 to 2011. Data were migrated to the NHD in Spring of 2014. Close

• 10. [Article] West Fork Smith River Catch Summary Data

  Abstract -- The Salmonid Life Cycle Monitoring Project of the Oregon Department of Fish and Wildlife (ODFW) has guided monitoring of juvenile and adult salmonid fishes (Oncorhynchus spp.) in the West Fork ...

  Citation × Citation Citation Abstract Copy Title: West Fork Smith River Catch Summary Data Abstract -- The Salmonid Life Cycle Monitoring Project of the Oregon Department of Fish and Wildlife (ODFW) has guided monitoring of juvenile and adult salmonid fishes (Oncorhynchus spp.) in the West Fork Smith River (Umpqua basin) since 1998. These activities are coordinated under the Oregon Plan for Salmon and Watersheds and are part of a broader effort to monitor populations of salmonids in select Oregon coastal streams. Two objectives of this program are to estimate the abundance of returning adult salmonids and downstream-migrating juvenile salmonids, and estimate the marine and freshwater survival rates for coho salmon. This record provided catch summary reports from monitoring activities for the 2005-2006 run-year of returning adult fish and year 2006 out-migration of juvenile fish in the West Fork Smith River. Title: West Fork Smith River Catch Summary Data Abstract -- The Salmonid Life Cycle Monitoring Project of the Oregon Department of Fish and Wildlife (ODFW) has guided monitoring of juvenile and adult salmonid fishes (Oncorhynchus spp.) in the West Fork Smith River (Umpqua basin) since 1998. These activities are coordinated under the Oregon Plan for Salmon and Watersheds and are part of a broader effort to monitor populations of salmonids in select Oregon coastal streams. Two objectives of this program are to estimate the abundance of returning adult salmonids and downstream-migrating juvenile salmonids, and estimate the marine and freshwater survival rates for coho salmon. This record provided catch summary reports from monitoring activities for the 2005-2006 run-year of returning adult fish and year 2006 out-migration of juvenile fish in the West Fork Smith River. Close

• 11. [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

• 12. [Article] Irrigation, Power, and Salmon: The Case for Voluntary Water Transfers in the Columbia Basin

  This paper begins with a brief history of water law in the west, illustrating the roots of conflict over water allocation. A more detailed examination of activities in the Columbia Basin follows, describing ...

  Citation × Citation Citation Abstract Copy Title: Irrigation, Power, and Salmon: The Case for Voluntary Water Transfers in the Columbia Basin Author: Kuhner, Eric Year: 1996 This paper begins with a brief history of water law in the west, illustrating the roots of conflict over water allocation. A more detailed examination of activities in the Columbia Basin follows, describing the many parties affected by issues of water use and the overlapping institutional structures that govern the river and its water. Sources of pressure to change the current pattern of water use are then considered. These include requirements to protect endangered salmon runs and the change over time in the relative values of water for power production and irrigation. This section demonstrates how changes in the value of resources can create conflict when resource allocations are inflexible. Alternative approaches to water allocation are then detailed. An argument is made that water use on the Columbia should be flexible, and that the ability to transfer water more easily from one use to another would be beneficial. The potential economic, social, and environmental benefits and costs of water transfers are also considered. The final section of the paper looks at barriers to water transfers and recommendations for institutional change. The section offers examples of market structures and policy options that might overcome some of the obstacles to water transfers. The argument for a more flexible system of water allocation is then summarized. Title: Irrigation, Power, and Salmon: The Case for Voluntary Water Transfers in the Columbia Basin Author: Kuhner, Eric Year: 1996 This paper begins with a brief history of water law in the west, illustrating the roots of conflict over water allocation. A more detailed examination of activities in the Columbia Basin follows, describing the many parties affected by issues of water use and the overlapping institutional structures that govern the river and its water. Sources of pressure to change the current pattern of water use are then considered. These include requirements to protect endangered salmon runs and the change over time in the relative values of water for power production and irrigation. This section demonstrates how changes in the value of resources can create conflict when resource allocations are inflexible. Alternative approaches to water allocation are then detailed. An argument is made that water use on the Columbia should be flexible, and that the ability to transfer water more easily from one use to another would be beneficial. The potential economic, social, and environmental benefits and costs of water transfers are also considered. The final section of the paper looks at barriers to water transfers and recommendations for institutional change. The section offers examples of market structures and policy options that might overcome some of the obstacles to water transfers. The argument for a more flexible system of water allocation is then summarized. Close

• 13. [Article] The Columbia River's fate in the twentieth century

  Discusses the history of the Columbia River during the 20th century, emphasizing the image of the river as both a source of industry and an example of wild natural beauty. In 1933 the river was dammed ...

  Citation × Citation Citation Abstract Copy Title: The Columbia River's fate in the twentieth century Author: Lang, William L. Year: 2000 Discusses the history of the Columbia River during the 20th century, emphasizing the image of the river as both a source of industry and an example of wild natural beauty. In 1933 the river was dammed to harness its power for hydroelectricity and control its unpredictable flooding. With the completion of the dams in the 1970's, however, came problems with the edenic vision of the river, especially with the annual salmon run. By the late 20th century, the salmon had all but disappeared, leading to an ongoing conflict between supporters of the dams and conservationists. Title: The Columbia River's fate in the twentieth century Author: Lang, William L. Year: 2000 Discusses the history of the Columbia River during the 20th century, emphasizing the image of the river as both a source of industry and an example of wild natural beauty. In 1933 the river was dammed to harness its power for hydroelectricity and control its unpredictable flooding. With the completion of the dams in the 1970's, however, came problems with the edenic vision of the river, especially with the annual salmon run. By the late 20th century, the salmon had all but disappeared, leading to an ongoing conflict between supporters of the dams and conservationists. Close

• 14. [Article] Assessing the feasibility of policy prescriptions in the Salmon 2100 Project

  Wild salmon populations are in decline in the Pacific Northwest. In the region populations and runs of Chinook (Oncorhynchus tshawytsha), Chum (Oncorhynchus keta), Coho (Oncorhynchus kisutch), Sockey (Oncorhynchus ...

  Citation × Citation Citation Abstract Copy Title: Assessing the feasibility of policy prescriptions in the Salmon 2100 Project Author: Whitehead, Katharine S. Wild salmon populations are in decline in the Pacific Northwest. In the region populations and runs of Chinook (Oncorhynchus tshawytsha), Chum (Oncorhynchus keta), Coho (Oncorhynchus kisutch), Sockey (Oncorhynchus nerka), and Steelhead (Oncorhynchus mykiss) have been listed as threatened and/or endangered under the Endangered Species Act (ESA) in the U.S. and/or the Species at Risk Act (SARA) in Canada in the years 1991-2007. Considerable time, money and brainpower has been put into salmon recovery with mixed results. The future for wild salmon in the Pacific Northwest remains uncertain. In 2006 Salmon 2100: The Future of Wild Pacific Salmon was published. The book is made up of 23 essays by 33 authors who were challenged to each develop a comprehensive policy prescription in response to the question: “What specific policies must be implemented in order to have a high probability of sustaining significant runs of wild salmon through 2100 in California, Oregon, Washington, Idaho, and southern British Columbia?” A qualitative study was designed to assess whether any of the policy prescriptions presented in Salmon 2100: The Future of Wild Pacific Salmon are feasible or viable in the real world. A thorough document analysis was conducted of Salmon 2100: The Future of Wild Pacific Salmon. The Social Construction Framework was used to categorize the target populations, code the policy prescriptions, and identify the benefits and burdens of each policy prescription for each target population. This information was then used to assess the feasibility of each policy prescription, based on the Social Construction Framework. The findings suggest that some of the policy prescriptions are feasible and could be developed for successful implementation in the real world. There is evidence that projects similar to the Salmon 2100 project could provide useful information and potential solutions to other natural resource policy challenges. Title: Assessing the feasibility of policy prescriptions in the Salmon 2100 Project Author: Whitehead, Katharine S. Wild salmon populations are in decline in the Pacific Northwest. In the region populations and runs of Chinook (Oncorhynchus tshawytsha), Chum (Oncorhynchus keta), Coho (Oncorhynchus kisutch), Sockey (Oncorhynchus nerka), and Steelhead (Oncorhynchus mykiss) have been listed as threatened and/or endangered under the Endangered Species Act (ESA) in the U.S. and/or the Species at Risk Act (SARA) in Canada in the years 1991-2007. Considerable time, money and brainpower has been put into salmon recovery with mixed results. The future for wild salmon in the Pacific Northwest remains uncertain. In 2006 Salmon 2100: The Future of Wild Pacific Salmon was published. The book is made up of 23 essays by 33 authors who were challenged to each develop a comprehensive policy prescription in response to the question: “What specific policies must be implemented in order to have a high probability of sustaining significant runs of wild salmon through 2100 in California, Oregon, Washington, Idaho, and southern British Columbia?” A qualitative study was designed to assess whether any of the policy prescriptions presented in Salmon 2100: The Future of Wild Pacific Salmon are feasible or viable in the real world. A thorough document analysis was conducted of Salmon 2100: The Future of Wild Pacific Salmon. The Social Construction Framework was used to categorize the target populations, code the policy prescriptions, and identify the benefits and burdens of each policy prescription for each target population. This information was then used to assess the feasibility of each policy prescription, based on the Social Construction Framework. The findings suggest that some of the policy prescriptions are feasible and could be developed for successful implementation in the real world. There is evidence that projects similar to the Salmon 2100 project could provide useful information and potential solutions to other natural resource policy challenges. Close

• 15. [Article] Migratory Patterns of Wild Chinook Salmon Oncorhynchus tshawytscha Returning to a Large, Free-Flowing River Basin

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library ...

  Citation × Citation Citation Abstract Copy Title: Migratory Patterns of Wild Chinook Salmon Oncorhynchus tshawytscha Returning to a Large, Free-Flowing River Basin Author: Schreck, Carl B., Evans, Allison N., Eiler, John H. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library of Science and is in the public domain. The published article can be found at: http://www.plosone.org/. Title: Migratory Patterns of Wild Chinook Salmon Oncorhynchus tshawytscha Returning to a Large, Free-Flowing River Basin Author: Schreck, Carl B., Evans, Allison N., Eiler, John H. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library of Science and is in the public domain. The published article can be found at: http://www.plosone.org/. Close

• 16. [Article] Differential use of salmon by vertebrate consumers: implications for conservation

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/

  Citation × Citation Citation Abstract Copy Title: Differential use of salmon by vertebrate consumers: implications for conservation Author: Allen, Jennifer M., Wilmers, Christopher C., Wheat, Rachel E., Levi, Taal This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/ Title: Differential use of salmon by vertebrate consumers: implications for conservation Author: Allen, Jennifer M., Wilmers, Christopher C., Wheat, Rachel E., Levi, Taal This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by PeerJ. The published article can be found at: https://peerj.com/ Close

• 17. [Article] Designing a Monitoring Program to Estimate Estuarine Survival of Anadromous Salmon Smolts: Simulating the Effect of Sample Design on Inference

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library ...

  Citation × Citation Citation Abstract Copy Title: Designing a Monitoring Program to Estimate Estuarine Survival of Anadromous Salmon Smolts: Simulating the Effect of Sample Design on Inference Author: Schreck, Carl B., Gitelman, Alix I., Romer, Jeremy D., Clements, Shaun To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library of Science and is in the public domain. The published article can be found at: http://www.plosone.org/. Title: Designing a Monitoring Program to Estimate Estuarine Survival of Anadromous Salmon Smolts: Simulating the Effect of Sample Design on Inference Author: Schreck, Carl B., Gitelman, Alix I., Romer, Jeremy D., Clements, Shaun To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the Public Library of Science and is in the public domain. The published article can be found at: http://www.plosone.org/. Close

• 18. [Article] Production of Ceratonova shasta Myxospores from Salmon Carcasses: Carcass Removal Is Not a Viable Management Option

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries ...

  Citation × Citation Citation Abstract Copy Title: Production of Ceratonova shasta Myxospores from Salmon Carcasses: Carcass Removal Is Not a Viable Management Option Author: Bartholomew, J. L., Fogerty, R., True, K., Buckles, G. R., Alexander, J. D., Foott, J. S., Hallett, S. L., Bolick, A., Stone, R. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/uahh20/current Title: Production of Ceratonova shasta Myxospores from Salmon Carcasses: Carcass Removal Is Not a Viable Management Option Author: Bartholomew, J. L., Fogerty, R., True, K., Buckles, G. R., Alexander, J. D., Foott, J. S., Hallett, S. L., Bolick, A., Stone, R. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/uahh20/current Close

• 19. [Article] Effective size of a wild salmonid population is greatly reduced by hatchery supplementation

  This is the publisher’s final pdf. The published article is copyrighted by Macmillan Publishers Limited and the Nature Publishing Group and can be found at: http://www.nature.com/hdy/index.html. To the ...

  Citation × Citation Citation Abstract Copy Title: Effective size of a wild salmonid population is greatly reduced by hatchery supplementation Author: Blouin, M. S., French, R. A., Marine, M. L., Christie, M. R., Waples, R. S. This is the publisher’s final pdf. The published article is copyrighted by Macmillan Publishers Limited and the Nature Publishing Group and can be found at: http://www.nature.com/hdy/index.html. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Title: Effective size of a wild salmonid population is greatly reduced by hatchery supplementation Author: Blouin, M. S., French, R. A., Marine, M. L., Christie, M. R., Waples, R. S. This is the publisher’s final pdf. The published article is copyrighted by Macmillan Publishers Limited and the Nature Publishing Group and can be found at: http://www.nature.com/hdy/index.html. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Close

• 20. [Article] Expansion and Consolidation in The British Columbia Salmon Processing Industry

  Research Paper

  Citation × Citation Citation Abstract Copy Title: Expansion and Consolidation in The British Columbia Salmon Processing Industry Author: Millerd, Frank Research Paper Title: Expansion and Consolidation in The British Columbia Salmon Processing Industry Author: Millerd, Frank Research Paper Close

• 21. [Article] The US salmon market : demand characteristics and price linkage

  Research Paper

  Citation × Citation Citation Abstract Copy Title: The US salmon market : demand characteristics and price linkage Author: Gordon, Daniel V., Clay, Patty L. Research Paper Title: The US salmon market : demand characteristics and price linkage Author: Gordon, Daniel V., Clay, Patty L. Research Paper Close

• 22. [Article] Cormorant harassment to protect juvenile salmonids in Tillamook County, Oregon

  The goal of the Oregon Plan is to restore wild coho and wild steelhead runs. Under the federal Endangered Species Act, wild coho salmon along the Oregon Coast are listed as Threatened and wild Oregon Coast ...

  Citation × Citation Citation Abstract Copy Title: Cormorant harassment to protect juvenile salmonids in Tillamook County, Oregon Author: Bayer, Range D., 1947- The goal of the Oregon Plan is to restore wild coho and wild steelhead runs. Under the federal Endangered Species Act, wild coho salmon along the Oregon Coast are listed as Threatened and wild Oregon Coast steelhead are a candidate for listing. Although cormorants have been hazed at the Nehalem Estuary for at least 10 years and at the Tillamook and Nestucca Estuaries for at least three years, spawning ground counts of wild coho salmon, winter steelhead, and fall chinook have averaged less since hazing began. Thus, hazing does not appear to be useful in recovering wild salmonids. Hazing is not correlated with consistently improved hatchery returns. The survival of Coded Wire Tag marked coho smolts at the Nehalem was about the same whether hazing occurred or not, the percent return for coho smolts was not significantly greater at the hazed Nehalem than at the nonhazed Salmon River, and the number of returning adult coho salmon was significantly greater with hazing at the Nehalem hatchery but not at the Trask hatchery in the Tillamook Basin. For winter steelhead, the number of returning adults to the Nehalem and jacks to the Cedar Creek hatchery in the Nestucca Basin did not increase significantly with hazing, but the number of jacks returning to the Nehalem did. Changes in fisheries subsequent to hazing are mixed. Coho catches increased with hazing at the Nehalem but not at the Tillamook Basin. Nehalem steelhead catches averaged less with hazing, but chinook fisheries have grown. However, the increase in chinook catches occurred as the number of wild chinook at spawning areas declined, so the larger catch may be a consequence of a greater harvest of wild chinook rather than hazing. Returns may not have increased with hazing because it was ineffective in substantially reducing predation, because smolts saved by hazing died anyway, or because other factors such as unfavorable ocean conditions may have been much more important in affecting smolt survival than hazing. In any case, hazing does not appear to be a panacea for salmonid recovery, and it has costs. During 1996-1999, the Oregon Legislature spent $100,000 for cormorant hazing, and a biological cost of hazing is the disturbance of wildlife other than cormorants. Title: Cormorant harassment to protect juvenile salmonids in Tillamook County, Oregon Author: Bayer, Range D., 1947- The goal of the Oregon Plan is to restore wild coho and wild steelhead runs. Under the federal Endangered Species Act, wild coho salmon along the Oregon Coast are listed as Threatened and wild Oregon Coast steelhead are a candidate for listing. Although cormorants have been hazed at the Nehalem Estuary for at least 10 years and at the Tillamook and Nestucca Estuaries for at least three years, spawning ground counts of wild coho salmon, winter steelhead, and fall chinook have averaged less since hazing began. Thus, hazing does not appear to be useful in recovering wild salmonids. Hazing is not correlated with consistently improved hatchery returns. The survival of Coded Wire Tag marked coho smolts at the Nehalem was about the same whether hazing occurred or not, the percent return for coho smolts was not significantly greater at the hazed Nehalem than at the nonhazed Salmon River, and the number of returning adult coho salmon was significantly greater with hazing at the Nehalem hatchery but not at the Trask hatchery in the Tillamook Basin. For winter steelhead, the number of returning adults to the Nehalem and jacks to the Cedar Creek hatchery in the Nestucca Basin did not increase significantly with hazing, but the number of jacks returning to the Nehalem did. Changes in fisheries subsequent to hazing are mixed. Coho catches increased with hazing at the Nehalem but not at the Tillamook Basin. Nehalem steelhead catches averaged less with hazing, but chinook fisheries have grown. However, the increase in chinook catches occurred as the number of wild chinook at spawning areas declined, so the larger catch may be a consequence of a greater harvest of wild chinook rather than hazing. Returns may not have increased with hazing because it was ineffective in substantially reducing predation, because smolts saved by hazing died anyway, or because other factors such as unfavorable ocean conditions may have been much more important in affecting smolt survival than hazing. In any case, hazing does not appear to be a panacea for salmonid recovery, and it has costs. During 1996-1999, the Oregon Legislature spent $100,000 for cormorant hazing, and a biological cost of hazing is the disturbance of wildlife other than cormorants. Close

• 23. [Article] Integrating Ecosystem Services, River Restoration and Community: A Case Study at Fisher's Bend

  Natural areas and ecosystem services at the edge of urban areas are threatened by increasing development. This paper examines how community based restoration partnerships can work to identify, protect ...

  Citation × Citation Citation Abstract Copy Title: Integrating Ecosystem Services, River Restoration and Community: A Case Study at Fisher's Bend Author: Carlson, Michael Year: 2011 Natural areas and ecosystem services at the edge of urban areas are threatened by increasing development. This paper examines how community based restoration partnerships can work to identify, protect and restore ecosystem services provided by salmon and our local rivers. Floodplains provide a wide range of ecosystem services to urban and rural communities and we should work collaboratively to protect and restore them. Floodplains are especially valuable and important for salmon recovery. By using a case study, we explore the process and feasibility of restoring off-channel salmon habitat at Fisher's Bend in the lower Clackamas river. A feasibility study was conducted to identify costs, benefits and risks of different design alternatives for the side channel. Hydrology of the river and hydraulics of the site were determined by estimating peak and low flow hydrology then running a HEC-RAS hydraulic model. Results indicate that the river overflows into the side channel near the 2 year recurrence interval. On average there is currently about a 50 % chance each year that the river will enter the side channel. These current flows do not provide much opportunity for juvenile salmon to access the side channel where they can grow and thrive in a protected habitat before their journey to the ocean. Further investigation produced results that indicate 95% of the time from 1959-2009 the river discharge was above 726 cfs from October to June. These results highlight that we will need to excavate about 9 feet from current elevations at the side-channel outlet to gain reasonable assurance of a one foot water depth for good salmon access. This depth will provide access from the river during critical periods when adult and juvenile salmon are seeking refuge from predators and high flood flows in the main channel. Although more design is needed for the inlet and outlet it appears the project is feasible and will meet the objective of providing salmonid access to critical habitat. In closing, I recommend investment in natural area protection and restoration at the edges of the urban growth boundary to maintain valuable ecosystem services provided by river floodplains and salmon. Title: Integrating Ecosystem Services, River Restoration and Community: A Case Study at Fisher's Bend Author: Carlson, Michael Year: 2011 Natural areas and ecosystem services at the edge of urban areas are threatened by increasing development. This paper examines how community based restoration partnerships can work to identify, protect and restore ecosystem services provided by salmon and our local rivers. Floodplains provide a wide range of ecosystem services to urban and rural communities and we should work collaboratively to protect and restore them. Floodplains are especially valuable and important for salmon recovery. By using a case study, we explore the process and feasibility of restoring off-channel salmon habitat at Fisher's Bend in the lower Clackamas river. A feasibility study was conducted to identify costs, benefits and risks of different design alternatives for the side channel. Hydrology of the river and hydraulics of the site were determined by estimating peak and low flow hydrology then running a HEC-RAS hydraulic model. Results indicate that the river overflows into the side channel near the 2 year recurrence interval. On average there is currently about a 50 % chance each year that the river will enter the side channel. These current flows do not provide much opportunity for juvenile salmon to access the side channel where they can grow and thrive in a protected habitat before their journey to the ocean. Further investigation produced results that indicate 95% of the time from 1959-2009 the river discharge was above 726 cfs from October to June. These results highlight that we will need to excavate about 9 feet from current elevations at the side-channel outlet to gain reasonable assurance of a one foot water depth for good salmon access. This depth will provide access from the river during critical periods when adult and juvenile salmon are seeking refuge from predators and high flood flows in the main channel. Although more design is needed for the inlet and outlet it appears the project is feasible and will meet the objective of providing salmonid access to critical habitat. In closing, I recommend investment in natural area protection and restoration at the edges of the urban growth boundary to maintain valuable ecosystem services provided by river floodplains and salmon. Close

• 24. [Article] Report on "Yaquina River" : Investigation sponsored by Oregon State Fish Commission, July, 1936

  Reports on potential sites for a salmon hatchery on the Yaquina River. "Each tributary has been carefully studied and special attention given to those creeks on which possible hatchery sites were found. ...

  Citation × Citation Citation Abstract Copy Title: Report on "Yaquina River" : Investigation sponsored by Oregon State Fish Commission, July, 1936 Author: Reynolds, John, Ledgerwood, Edgar, Oregon. Fish Commission Reports on potential sites for a salmon hatchery on the Yaquina River. "Each tributary has been carefully studied and special attention given to those creeks on which possible hatchery sites were found. Items given consideration on each stream were: pond site locations, flow of water, drop of stream bed, nature of creek bottom, temperature of water, flow of water, flood water levels, salmon run, obstructions to salmon run, stranded fingerlings, ownership of land, water rights, irrigation projects, etc." (From the Introduction) Includes hand-drawn maps. Title: Report on "Yaquina River" : Investigation sponsored by Oregon State Fish Commission, July, 1936 Author: Reynolds, John, Ledgerwood, Edgar, Oregon. Fish Commission Reports on potential sites for a salmon hatchery on the Yaquina River. "Each tributary has been carefully studied and special attention given to those creeks on which possible hatchery sites were found. Items given consideration on each stream were: pond site locations, flow of water, drop of stream bed, nature of creek bottom, temperature of water, flow of water, flood water levels, salmon run, obstructions to salmon run, stranded fingerlings, ownership of land, water rights, irrigation projects, etc." (From the Introduction) Includes hand-drawn maps. Close

• 25. [Article] Administrative Design for Yakima-Klickitat Production Project: Final Report

  This report provides the administrative design to implement the Yakima/Klickitat Production Project. This project is a scientifically designed salmon fishery restoration project funded by the Bonneville ...

  Citation × Citation Citation Abstract Copy Title: Administrative Design for Yakima-Klickitat Production Project: Final Report Author: Churchill, Jack, Shissler, Lee, Edner, Sheldon, Smith, Randy Year: 1990 This report provides the administrative design to implement the Yakima/Klickitat Production Project. This project is a scientifically designed salmon fishery restoration project funded by the Bonneville Power Administration in compliance with the .fishery policies established by the Northwest Power Planning Council under the authority of the Northwest Power Planning Act. This project breaks new ground in the field of fishery management. It is the first full scale application of supplementation technology directed toward maintaining and rebuilding native fish stocks and sub stocks with hatchery rearing methods. The work of the organization is an inherently more complex production function than traditional fish hatchery operations. This is in part because the project requires a high level of continuing quality control. It is also due in part because the fisheries management takes place over an extended geographical space of the watershed. The pre-design work for this project has been underway since 1987 by an ad hoc planning group composed of representative of the Yakima Indian Nation, the Washington Department of Fisheries and the Washington Department of Wildlife, and private consultants under funding of the Bonneville Power Administration. The project experimental design has been developed by the Experimental Design Work Group. The Bonneville Power Administration is contracting for design and construction of the fish rearing facilities. The research challenge was to design an organization to .implement the adaptive management concept of biological systems management. The management of complex biological systems such as salmon fish runs is character:ized by a high degree of uncertainty. Management for uncertain outcomes requires an organizational process that will induce a continuing learning atmosphere. Over time, most bureaucratic organizations suffer from inertia and are not conducive to a learning environment. Research methods involved the review of literature and related administrative experience, an interview process, a modified Delphi questionnaire, a series of group dynamic exercises, and observation of the work teams during the last six months of the planing process. The results of our research suggest that a new non-profit corporation be formed to implement the program under the direction of the three primary fish management basin agencies. The corporation should have flexibility and the organization will be phased in during the five year planning and construction cycle. A primary result of our research is the conclusion that the team management concept be the dominant organizational unit for both management of field operations and for management of scientific design and evaluation. Title: Administrative Design for Yakima-Klickitat Production Project: Final Report Author: Churchill, Jack, Shissler, Lee, Edner, Sheldon, Smith, Randy Year: 1990 This report provides the administrative design to implement the Yakima/Klickitat Production Project. This project is a scientifically designed salmon fishery restoration project funded by the Bonneville Power Administration in compliance with the .fishery policies established by the Northwest Power Planning Council under the authority of the Northwest Power Planning Act. This project breaks new ground in the field of fishery management. It is the first full scale application of supplementation technology directed toward maintaining and rebuilding native fish stocks and sub stocks with hatchery rearing methods. The work of the organization is an inherently more complex production function than traditional fish hatchery operations. This is in part because the project requires a high level of continuing quality control. It is also due in part because the fisheries management takes place over an extended geographical space of the watershed. The pre-design work for this project has been underway since 1987 by an ad hoc planning group composed of representative of the Yakima Indian Nation, the Washington Department of Fisheries and the Washington Department of Wildlife, and private consultants under funding of the Bonneville Power Administration. The project experimental design has been developed by the Experimental Design Work Group. The Bonneville Power Administration is contracting for design and construction of the fish rearing facilities. The research challenge was to design an organization to .implement the adaptive management concept of biological systems management. The management of complex biological systems such as salmon fish runs is character:ized by a high degree of uncertainty. Management for uncertain outcomes requires an organizational process that will induce a continuing learning atmosphere. Over time, most bureaucratic organizations suffer from inertia and are not conducive to a learning environment. Research methods involved the review of literature and related administrative experience, an interview process, a modified Delphi questionnaire, a series of group dynamic exercises, and observation of the work teams during the last six months of the planing process. The results of our research suggest that a new non-profit corporation be formed to implement the program under the direction of the three primary fish management basin agencies. The corporation should have flexibility and the organization will be phased in during the five year planning and construction cycle. A primary result of our research is the conclusion that the team management concept be the dominant organizational unit for both management of field operations and for management of scientific design and evaluation. Close

• 26. [Article] Effects of juvenile steelhead on juvenile chinook salmon behavior and physiology

  Experiments were designed to determine whether and how steelhead Oncorhynchus mykiss affect chinook salmon O. tshawytscha when the two species are confined together. In a behavioral experiment, we observed ...

  Citation × Citation Citation Abstract Copy Title: Effects of juvenile steelhead on juvenile chinook salmon behavior and physiology Author: Schreck, Carl B., Congleton, J. L., Kelsey, D. A., Davis, L. E. Experiments were designed to determine whether and how steelhead Oncorhynchus mykiss affect chinook salmon O. tshawytscha when the two species are confined together. In a behavioral experiment, we observed groups of juvenile chinook salmon and steelhead together and groups of chinook salmon alone to determine whether the steelhead were aggressive and their presence changed the behavior of chinook salmon. We also performed two runs of a physiological experiment to determine whether the addition of steelhead to tanks containing chinook salmon would stress the chinook salmon, as determined by a change in their plasma cortisol levels. Behavioral changes were observed in the chinook salmon when they were held with steelhead; they reduced their movements, darted less, were attacked up to 16 times as often, and were found less frequently in the shade than chinook salmon held without steelhead. Steelhead were found to establish territories and defend them with chases, charges, and nips. In their attempts to establish and defend territories, the steelhead attacked the chinook salmon as often as they attacked other steelhead, but the chinook salmon showed little aggression toward the steelhead. Cortisol concentrations were significantly higher for chinook salmon in tanks receiving steelhead than in tanks receiving additional chinook salmon or no additional fish after 2 h (in one of the two experimental runs) and after 32 h (in both experimental runs; combined data). These results suggest that confining steelhead and chinook salmon together, such as in raceways and barges in the Columbia River system and in other situations, is stressful to the chinook salmon. Title: Effects of juvenile steelhead on juvenile chinook salmon behavior and physiology Author: Schreck, Carl B., Congleton, J. L., Kelsey, D. A., Davis, L. E. Experiments were designed to determine whether and how steelhead Oncorhynchus mykiss affect chinook salmon O. tshawytscha when the two species are confined together. In a behavioral experiment, we observed groups of juvenile chinook salmon and steelhead together and groups of chinook salmon alone to determine whether the steelhead were aggressive and their presence changed the behavior of chinook salmon. We also performed two runs of a physiological experiment to determine whether the addition of steelhead to tanks containing chinook salmon would stress the chinook salmon, as determined by a change in their plasma cortisol levels. Behavioral changes were observed in the chinook salmon when they were held with steelhead; they reduced their movements, darted less, were attacked up to 16 times as often, and were found less frequently in the shade than chinook salmon held without steelhead. Steelhead were found to establish territories and defend them with chases, charges, and nips. In their attempts to establish and defend territories, the steelhead attacked the chinook salmon as often as they attacked other steelhead, but the chinook salmon showed little aggression toward the steelhead. Cortisol concentrations were significantly higher for chinook salmon in tanks receiving steelhead than in tanks receiving additional chinook salmon or no additional fish after 2 h (in one of the two experimental runs) and after 32 h (in both experimental runs; combined data). These results suggest that confining steelhead and chinook salmon together, such as in raceways and barges in the Columbia River system and in other situations, is stressful to the chinook salmon. Close

• 27. [Article] Spatial and Temporal Variability of Macroinvertebrates in Spawning and Non-Spawning Habitats during a Salmon Run in Southeast Alaska

  This is the publisher’s final pdf. The published article is copyrighted by PLoS ONE and can be found at: http://www.plosone.org/home.action.

  Citation × Citation Citation Abstract Copy Title: Spatial and Temporal Variability of Macroinvertebrates in Spawning and Non-Spawning Habitats during a Salmon Run in Southeast Alaska Author: Merritt, Richard W., Campbell, Emily Y., Benbow, M. Eric, Cummins, Kenneth W. This is the publisher’s final pdf. The published article is copyrighted by PLoS ONE and can be found at: http://www.plosone.org/home.action. Title: Spatial and Temporal Variability of Macroinvertebrates in Spawning and Non-Spawning Habitats during a Salmon Run in Southeast Alaska Author: Merritt, Richard W., Campbell, Emily Y., Benbow, M. Eric, Cummins, Kenneth W. This is the publisher’s final pdf. The published article is copyrighted by PLoS ONE and can be found at: http://www.plosone.org/home.action. Close

• 28. [Article] When is bigger better? Early marine residence of middle and upper Columbia River spring Chinook salmon

  This is the publisher’s final pdf. The published article is copyrighted by Inter-Research and can be found at: http://www.int-res.com/journals/meps/meps-home/. To the best of our knowledge, one or more ...

  Citation × Citation Citation Abstract Copy Title: When is bigger better? Early marine residence of middle and upper Columbia River spring Chinook salmon Author: Teel, David J., Miller, Jessica A., Tomaro, Londi M., Peterson, William T. This is the publisher’s final pdf. The published article is copyrighted by Inter-Research and can be found at: http://www.int-res.com/journals/meps/meps-home/. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Title: When is bigger better? Early marine residence of middle and upper Columbia River spring Chinook salmon Author: Teel, David J., Miller, Jessica A., Tomaro, Londi M., Peterson, William T. This is the publisher’s final pdf. The published article is copyrighted by Inter-Research and can be found at: http://www.int-res.com/journals/meps/meps-home/. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Close

• 29. [Article] Potential Effects of Management on Caspian Tern Hydroprogne caspia Predation on Juvenile Salmonids at a Colony in San Francisco Bay, California

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is published by Taylor & ...

  Citation × Citation Citation Abstract Copy Title: Potential Effects of Management on Caspian Tern Hydroprogne caspia Predation on Juvenile Salmonids at a Colony in San Francisco Bay, California Author: Evans, Allen F., Adrean, Lindsay J., Roby, Daniel D., Lyons, Donald E., Collis, Ken To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is published by Taylor & Francis and can be found at: http://www.taylorandfrancis.com. Copyrighted by American Fisheries Society (http://afsjournals.org/). Title: Potential Effects of Management on Caspian Tern Hydroprogne caspia Predation on Juvenile Salmonids at a Colony in San Francisco Bay, California Author: Evans, Allen F., Adrean, Lindsay J., Roby, Daniel D., Lyons, Donald E., Collis, Ken To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is published by Taylor & Francis and can be found at: http://www.taylorandfrancis.com. Copyrighted by American Fisheries Society (http://afsjournals.org/). Close

• 30. [Article] Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths

  Published March 1989. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog...

  Citation × Citation Citation Abstract Copy Title: Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths Author: Hankin, David G., Oregon State University. Extension Service, Oregon. Fish Division, Nicholas, Jay W., Oregon. Dept. of Fish and Wildlife. Research and Development Section Published March 1989. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog Title: Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths Author: Hankin, David G., Oregon State University. Extension Service, Oregon. Fish Division, Nicholas, Jay W., Oregon. Dept. of Fish and Wildlife. Research and Development Section Published March 1989. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog Close

• 31. [Article] Marine distributions of chinook salmon from the West Coast of North America determined by coded wire tag recoveries

  The coded wire tag (CWT) database contains detailed information on millions of Pacific salmon Oncorhynchus spp. released from hatcheries or smolt traps and recovered in the north Pacific Ocean and its ...

  Citation × Citation Citation Abstract Copy Title: Marine distributions of chinook salmon from the West Coast of North America determined by coded wire tag recoveries Author: Weitkamp, Laurie A. The coded wire tag (CWT) database contains detailed information on millions of Pacific salmon Oncorhynchus spp. released from hatcheries or smolt traps and recovered in the north Pacific Ocean and its tributaries. I used this data set to examine the spatial and temporal variation in the marine distributions of 77 hatchery and 16 wild populations of Chinook salmon O. tshawytscha based on recoveries of an estimated 632,000 tagged salmon in coastal waters from southern California to the Bering Sea during 1979–1994 (and 1995–2004 for select hatcheries). Chinook salmon showed 12 distinct region-specific recovery patterns. Chinook salmon originating in a common freshwater region had similar marine distributions, which were distinct from those of adjacent regions. Different run types (e.g., spring, summer, and fall runs) originating in the same region exhibited variation in their marine distributions consistent with recovery at different stages of their ocean residence period. Recovery patterns were surprisingly stable across years, despite high interannual variation in ocean conditions. By contrast, ocean age influenced recovery patterns, as older fish were recovered further from their natal stream than younger fish. Although most of the CWT data used in the analysis came from hatchery fish, recoveries of tagged wild populations indicate patterns similar to those of fish from nearby hatcheries. The consistency in these findings across broad geographic areas suggests that they apply to Chinook salmon across the entire Pacific Rim. Similar findings for tagged coho salmon O. kisutch indicate that the observed patterns may apply to Pacific salmon as a whole and provide a model for other highly migratory fishes that have not benefited from such intensive tagging programs. The results also have implications for the genetic control of migration and salmon’s ability to respond to climate change. Title: Marine distributions of chinook salmon from the West Coast of North America determined by coded wire tag recoveries Author: Weitkamp, Laurie A. The coded wire tag (CWT) database contains detailed information on millions of Pacific salmon Oncorhynchus spp. released from hatcheries or smolt traps and recovered in the north Pacific Ocean and its tributaries. I used this data set to examine the spatial and temporal variation in the marine distributions of 77 hatchery and 16 wild populations of Chinook salmon O. tshawytscha based on recoveries of an estimated 632,000 tagged salmon in coastal waters from southern California to the Bering Sea during 1979–1994 (and 1995–2004 for select hatcheries). Chinook salmon showed 12 distinct region-specific recovery patterns. Chinook salmon originating in a common freshwater region had similar marine distributions, which were distinct from those of adjacent regions. Different run types (e.g., spring, summer, and fall runs) originating in the same region exhibited variation in their marine distributions consistent with recovery at different stages of their ocean residence period. Recovery patterns were surprisingly stable across years, despite high interannual variation in ocean conditions. By contrast, ocean age influenced recovery patterns, as older fish were recovered further from their natal stream than younger fish. Although most of the CWT data used in the analysis came from hatchery fish, recoveries of tagged wild populations indicate patterns similar to those of fish from nearby hatcheries. The consistency in these findings across broad geographic areas suggests that they apply to Chinook salmon across the entire Pacific Rim. Similar findings for tagged coho salmon O. kisutch indicate that the observed patterns may apply to Pacific salmon as a whole and provide a model for other highly migratory fishes that have not benefited from such intensive tagging programs. The results also have implications for the genetic control of migration and salmon’s ability to respond to climate change. Close

• 32. [Article] Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression

  Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been ...

  Citation × Citation Citation Abstract Copy Title: Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression Author: Banks, Michael A., McArthur, Andrew G., Birkeland, Shanda R., Bernier, Jeremiah C., Cipriano, Michael J. Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data. Title: Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression Author: Banks, Michael A., McArthur, Andrew G., Birkeland, Shanda R., Bernier, Jeremiah C., Cipriano, Michael J. Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data. Close

• 33. [Article] The value of short run in-stream temperature forecasts : an application to salmonids in the Klamath and John Day Rivers

  Water temperature is an important measure of water quality, as well as a dominant factor affecting aquatic life within the stream environment. Elevated water temperatures can decrease the survival rate ...

  Citation × Citation Citation Abstract Copy Title: The value of short run in-stream temperature forecasts : an application to salmonids in the Klamath and John Day Rivers Author: Huang, Biao Water temperature is an important measure of water quality, as well as a dominant factor affecting aquatic life within the stream environment. Elevated water temperatures can decrease the survival rate of fish in each life stage. Cold water species, such as salmonids, are particularly susceptible to elevated water temperatures. For example, increased water temperatures are believed to have been the major cause of the large fish kill observed in the Klamath River in September 2002. This thesis examines the economic value of short-term water temperature forecasts for salmonid management. Forecasts may have value if they allow the water resource manager to make more cost-effective water allocation decisions. Specifically, this study considers two applications. One is the case of adult Chinook salmon (O. tshawytscha) returning to the Lower Klamath River in California, where cold water could be released upstream from the Lewiston Dam into the Trinity River to lower The Klamath River water temperature. Water releases create opportunity costs because of foregone hydropower production and crop irrigation. The second application is to juvenile summer steelhead (Oncorhynchus mykiss) in the North Fork John Day River, where water could be purchased from agricultural uses to prevent excessive water temperature increases. This generates opportunity costs in the form of lower crop yields. This thesis incorporates bio-physical models and water temperature distribution data into a Bayesian framework to simulate the potential fish populations after ten generations and the corresponding opportunity cost of water under different forecast accuracies. Simulation results indicate that the marginal cost in the Klamath River decreases from about $80 per fish saved when the forecast standard deviation is 6 to about $40 when the forecast standard deviation is 0(perfect forecast). In the John Day River the marginal cost per fish decreases from $34 for a standard deviation of 6 to $29 for a standard deviation of 0. A key result of the thesis is the pattern of decreasing marginal costs as the forecast accuracy increases, suggesting that provision and use of such stream temperature forecasts would have value to society. Title: The value of short run in-stream temperature forecasts : an application to salmonids in the Klamath and John Day Rivers Author: Huang, Biao Water temperature is an important measure of water quality, as well as a dominant factor affecting aquatic life within the stream environment. Elevated water temperatures can decrease the survival rate of fish in each life stage. Cold water species, such as salmonids, are particularly susceptible to elevated water temperatures. For example, increased water temperatures are believed to have been the major cause of the large fish kill observed in the Klamath River in September 2002. This thesis examines the economic value of short-term water temperature forecasts for salmonid management. Forecasts may have value if they allow the water resource manager to make more cost-effective water allocation decisions. Specifically, this study considers two applications. One is the case of adult Chinook salmon (O. tshawytscha) returning to the Lower Klamath River in California, where cold water could be released upstream from the Lewiston Dam into the Trinity River to lower The Klamath River water temperature. Water releases create opportunity costs because of foregone hydropower production and crop irrigation. The second application is to juvenile summer steelhead (Oncorhynchus mykiss) in the North Fork John Day River, where water could be purchased from agricultural uses to prevent excessive water temperature increases. This generates opportunity costs in the form of lower crop yields. This thesis incorporates bio-physical models and water temperature distribution data into a Bayesian framework to simulate the potential fish populations after ten generations and the corresponding opportunity cost of water under different forecast accuracies. Simulation results indicate that the marginal cost in the Klamath River decreases from about $80 per fish saved when the forecast standard deviation is 6 to about $40 when the forecast standard deviation is 0(perfect forecast). In the John Day River the marginal cost per fish decreases from $34 for a standard deviation of 6 to $29 for a standard deviation of 0. A key result of the thesis is the pattern of decreasing marginal costs as the forecast accuracy increases, suggesting that provision and use of such stream temperature forecasts would have value to society. Close

• 34. [Article] Arctic Char Fish Farming in Iceland: Is it a Success?

  Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, ...

  Citation × Citation Citation Abstract Copy Title: Arctic Char Fish Farming in Iceland: Is it a Success? Author: Arnason, Ragnar, Olafsdottir, Gudrun, Heimisson, Asgeir Fridrik Year: 2016 Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, July 11-15, 2016. Compiled by Stefani J. Evers and Ann L. Shriver. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Title: Arctic Char Fish Farming in Iceland: Is it a Success? Author: Arnason, Ragnar, Olafsdottir, Gudrun, Heimisson, Asgeir Fridrik Year: 2016 Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, July 11-15, 2016. Compiled by Stefani J. Evers and Ann L. Shriver. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Close

• 35. [Article] Riverscape Patterns among Years of Juvenile Coho Salmon in Midcoastal Oregon: Implications for Conservation

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Taylor ...

  Citation × Citation Citation Abstract Copy Title: Riverscape Patterns among Years of Juvenile Coho Salmon in Midcoastal Oregon: Implications for Conservation Author: Reeves, G., Flitcroft, R., Snyder, J., Burnett, K., Ganio, L. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Taylor & Francis Inc. on behalf of the American Fisheries Society and can be found at: http://www.tandfonline.com/toc/utaf20/current#.Uxn53fPTmHs. Title: Riverscape Patterns among Years of Juvenile Coho Salmon in Midcoastal Oregon: Implications for Conservation Author: Reeves, G., Flitcroft, R., Snyder, J., Burnett, K., Ganio, L. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Taylor & Francis Inc. on behalf of the American Fisheries Society and can be found at: http://www.tandfonline.com/toc/utaf20/current#.Uxn53fPTmHs. Close

• 36. [Article] Early Ocean Dispersal Patterns of Columbia River Chinook and Coho Salmon

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Taylor ...

  Citation × Citation Citation Abstract Copy Title: Early Ocean Dispersal Patterns of Columbia River Chinook and Coho Salmon Author: Orsi, J. A., Morris, J. F. T., Teel, D. J., Farley, E. V., Jr., Weitkamp, L. A., Trudel, M., Fisher, J. P., Sweeting, R. M., Hinton, S. A., Thiess, M. E. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Taylor & Francis and can be found at: http://www.tandfonline.com/toc/utaf20/current#.Uz8B2_Pn-Hs. Title: Early Ocean Dispersal Patterns of Columbia River Chinook and Coho Salmon Author: Orsi, J. A., Morris, J. F. T., Teel, D. J., Farley, E. V., Jr., Weitkamp, L. A., Trudel, M., Fisher, J. P., Sweeting, R. M., Hinton, S. A., Thiess, M. E. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Taylor & Francis and can be found at: http://www.tandfonline.com/toc/utaf20/current#.Uz8B2_Pn-Hs. Close

• 37. [Article] Innate and adaptive immune responses in migrating spring-run adult chinook salmon, Oncorhynchus tshawytscha

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier ...

  Citation × Citation Citation Abstract Copy Title: Innate and adaptive immune responses in migrating spring-run adult chinook salmon, Oncorhynchus tshawytscha Author: Schreck, Carl B., Kent, Michael L., Dolan, Brian P., Colvin, Michael E., Fisher, Kathleen M., Benda, Susan E., Peterson, James T. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/fish-and-shellfish-immunology/ Title: Innate and adaptive immune responses in migrating spring-run adult chinook salmon, Oncorhynchus tshawytscha Author: Schreck, Carl B., Kent, Michael L., Dolan, Brian P., Colvin, Michael E., Fisher, Kathleen M., Benda, Susan E., Peterson, James T. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/fish-and-shellfish-immunology/ Close

• 38. [Article] Relationships among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics over multiple years and spatial scales in the Elk River, Oregon

  Research on the distribution of juvenile salmonids in streams has been dominated by studies examining small areas over short periods. However, information relevant to freshwater influences on population ...

  Citation × Citation Citation Abstract Copy Title: Relationships among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics over multiple years and spatial scales in the Elk River, Oregon Author: Burnett, Kelly M. Research on the distribution of juvenile salmonids in streams has been dominated by studies examining small areas over short periods. However, information relevant to freshwater influences on population persistence is likely to derive from longer-term, multi-scale studies. Relationships were examined among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics throughout the Elk River, Oregon over 7 years at multiple spatial scales. Ocean-type chinook salmon (Oncorhynchus tshawytscha), coho salmon (0. kisutch), coastal cutthroat trout (0. clarki) and winter-run steelhead (0. mykiss) comprised the salmonid assemblage. Habitat selection was quantified at stream system, valley segment, and channel unit scales by selection ratios estimated with bootstrapping methods. Unconstrained valleys in tributaries and pools in the mainstem were typically selected by each species except steelhead, which often avoided these. Valley segment types generally did not differ for characteristics routinely assessed in stream surveys. Thus, fish probably perceived other biotic or abiotic differences among valley segment types. Evidence suggested competition may have influenced selection by coho and chinook salmon. Discriminant analysis indicated that level of use by juvenile chinook salmon appeared related to valley segment type and spatial position. Unconstrained valleys, nearby valley segments, and valley segments with larger, deeper pools, containing more wood were most highly used by chinook salmon. Mean volume and maximum depth of pools were each directly related to catchment area, which explained more variation than landscape characteristics summarized at any of five spatial scales. At each scale except the most spatially extensive, wood density in valley segments was negatively related to the percent area in resistant rock types and positively related to the percent area in mature to old forests. The most variation was explained with these landscape variables summarized at an intermediate spatial scale (i.e., sub-catchment). Although spatial scales appeared similar in processes affecting wood density, finer scales omitted key source areas for wood delivery, and coarser scales included source areas less tightly coupled to wood dynamics in surveyed channels. If only 1 or 2 years of data or one spatial scale had been examined, as commonly occurs, conclusions may have differed substantially from those in this study. Title: Relationships among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics over multiple years and spatial scales in the Elk River, Oregon Author: Burnett, Kelly M. Research on the distribution of juvenile salmonids in streams has been dominated by studies examining small areas over short periods. However, information relevant to freshwater influences on population persistence is likely to derive from longer-term, multi-scale studies. Relationships were examined among juvenile anadromous salmonids, their freshwater habitat, and landscape characteristics throughout the Elk River, Oregon over 7 years at multiple spatial scales. Ocean-type chinook salmon (Oncorhynchus tshawytscha), coho salmon (0. kisutch), coastal cutthroat trout (0. clarki) and winter-run steelhead (0. mykiss) comprised the salmonid assemblage. Habitat selection was quantified at stream system, valley segment, and channel unit scales by selection ratios estimated with bootstrapping methods. Unconstrained valleys in tributaries and pools in the mainstem were typically selected by each species except steelhead, which often avoided these. Valley segment types generally did not differ for characteristics routinely assessed in stream surveys. Thus, fish probably perceived other biotic or abiotic differences among valley segment types. Evidence suggested competition may have influenced selection by coho and chinook salmon. Discriminant analysis indicated that level of use by juvenile chinook salmon appeared related to valley segment type and spatial position. Unconstrained valleys, nearby valley segments, and valley segments with larger, deeper pools, containing more wood were most highly used by chinook salmon. Mean volume and maximum depth of pools were each directly related to catchment area, which explained more variation than landscape characteristics summarized at any of five spatial scales. At each scale except the most spatially extensive, wood density in valley segments was negatively related to the percent area in resistant rock types and positively related to the percent area in mature to old forests. The most variation was explained with these landscape variables summarized at an intermediate spatial scale (i.e., sub-catchment). Although spatial scales appeared similar in processes affecting wood density, finer scales omitted key source areas for wood delivery, and coarser scales included source areas less tightly coupled to wood dynamics in surveyed channels. If only 1 or 2 years of data or one spatial scale had been examined, as commonly occurs, conclusions may have differed substantially from those in this study. Close

• 39. [Article] Regions to streams : spatial and temporal variation in stream occupancy patterns of coho salmon (Oncorhynchus kisutch) on the Oregon coast

  Aquatic ecological investigation is expanding to encompass considerations of multiple scales across large landscapes. Much of the analysis included in this work focuses specifically on coho salmon (Oncorhynchus ...

  Citation × Citation Citation Abstract Copy Title: Regions to streams : spatial and temporal variation in stream occupancy patterns of coho salmon (Oncorhynchus kisutch) on the Oregon coast Author: Flitcroft, Rebecca L. Aquatic ecological investigation is expanding to encompass considerations of multiple scales across large landscapes. Much of the analysis included in this work focuses specifically on coho salmon (Oncorhynchus kisutch) in multiple subbasins on the Oregon coast. Coho salmon were chosen for an investigation of spatial scales, network connections, and life history stages due to their broad distribution on the Oregon coast, and abundant data describing their distribution, habitat needs, behavior, and survival. Chapter 2 introduces dynamic network topology (DNT) as a framework for analysis and interpretation of aquatic obligate species. DNT is based on the premise that in-stream habitats change in form and organization over time, and native aquatic species are adapted to those changes through movement and life history diversity. Chapter 3 analyzes juvenile coho salmon density and stream network occupancy at three spatial scales (site, patch, and subbasin). The site scale analysis indicated that combining network and traditional in-stream habitat metrics (i.e., substrate and habitat juxtaposition variables) are most effective at describing juvenile coho salmon density. Patch sizes of juvenile coho salmon were defined using variograms. Variogram shape indicated that a nested spatial structure may be present in larger subbasins, indicating overlapping patterns of juvenile stream use. At the subbasin scale, stream network occupancy by juvenile coho salmon was shown to vary over time within subbasins, and appeared to increase or decrease similarly to the size of the adult spawning run. In chapter 3, two-tier Bayesian hierarchical models were applied to adult (subbasin and basin scales) and juvenile (site and subbasin scales) coho salmon in an attempt to combine spatial scales that might be influential at each life history stage. The best fitting adult model included the percent of large trees in the riparian zone at the subbasin scale with mean annual precipitation at the basin scale. The best fitting juvenile model included three variables, percent sand, stream order, and network distance to spawning habitat which mirrors the result of modeling efforts in Chapter 3. Multiple spatial scales and the framework of a stream network were informative at detecting patterns and interactions among scales and life history stages of coho salmon. Title: Regions to streams : spatial and temporal variation in stream occupancy patterns of coho salmon (Oncorhynchus kisutch) on the Oregon coast Author: Flitcroft, Rebecca L. Aquatic ecological investigation is expanding to encompass considerations of multiple scales across large landscapes. Much of the analysis included in this work focuses specifically on coho salmon (Oncorhynchus kisutch) in multiple subbasins on the Oregon coast. Coho salmon were chosen for an investigation of spatial scales, network connections, and life history stages due to their broad distribution on the Oregon coast, and abundant data describing their distribution, habitat needs, behavior, and survival. Chapter 2 introduces dynamic network topology (DNT) as a framework for analysis and interpretation of aquatic obligate species. DNT is based on the premise that in-stream habitats change in form and organization over time, and native aquatic species are adapted to those changes through movement and life history diversity. Chapter 3 analyzes juvenile coho salmon density and stream network occupancy at three spatial scales (site, patch, and subbasin). The site scale analysis indicated that combining network and traditional in-stream habitat metrics (i.e., substrate and habitat juxtaposition variables) are most effective at describing juvenile coho salmon density. Patch sizes of juvenile coho salmon were defined using variograms. Variogram shape indicated that a nested spatial structure may be present in larger subbasins, indicating overlapping patterns of juvenile stream use. At the subbasin scale, stream network occupancy by juvenile coho salmon was shown to vary over time within subbasins, and appeared to increase or decrease similarly to the size of the adult spawning run. In chapter 3, two-tier Bayesian hierarchical models were applied to adult (subbasin and basin scales) and juvenile (site and subbasin scales) coho salmon in an attempt to combine spatial scales that might be influential at each life history stage. The best fitting adult model included the percent of large trees in the riparian zone at the subbasin scale with mean annual precipitation at the basin scale. The best fitting juvenile model included three variables, percent sand, stream order, and network distance to spawning habitat which mirrors the result of modeling efforts in Chapter 3. Multiple spatial scales and the framework of a stream network were informative at detecting patterns and interactions among scales and life history stages of coho salmon. Close

• 40. [Article] Distribution, Stock Composition and Timing, and Tagging Response of Wild Chinook Salmon Returning to a Large, Free-Flowing River Basin

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries ...

  Citation × Citation Citation Abstract Copy Title: Distribution, Stock Composition and Timing, and Tagging Response of Wild Chinook Salmon Returning to a Large, Free-Flowing River Basin Author: Schreck, Carl B., Spencer, Ted R., Eiler, John H., Driscoll, Richard J., Masuda, Michele M. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/loi/utaf20#.VLRgimN_t8E. Title: Distribution, Stock Composition and Timing, and Tagging Response of Wild Chinook Salmon Returning to a Large, Free-Flowing River Basin Author: Schreck, Carl B., Spencer, Ted R., Eiler, John H., Driscoll, Richard J., Masuda, Michele M. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/loi/utaf20#.VLRgimN_t8E. Close

• 41. [Article] An economic analysis of alternative water allocations and habitat investments for anadromous fish production, John Day Basin, Oregon

  This thesis focuses on the economic efficiency of alternative habitat, streamfiow, and land use allocations within a major drainage of the Pacific Northwest. Specifically, productivity of present habitat and ...

  Citation × Citation Citation Abstract Copy Title: An economic analysis of alternative water allocations and habitat investments for anadromous fish production, John Day Basin, Oregon Author: Cerda, Arcadio Alberto This thesis focuses on the economic efficiency of alternative habitat, streamfiow, and land use allocations within a major drainage of the Pacific Northwest. Specifically, productivity of present habitat and streamfiow conditions is evaluated with respect to anadromous fish species (chinook salmon and steelhead trout) in the John Day River Basin, a high-desert system in the Pacific Northwest. Alternative water allocations and fish habitat enhancements to improve anadromous fish productivity are also examined. This biophysical information is combined with economics concepts to evaluate comparative benefits and economic efficiency of selected technically feasible habitat/streamflow alternatives. The John Day River Basin is used as a case study because it provides one of the most significant runs of wild summer steelhead trout and spring chinook salmon in the Columbia River Basin. Specific categories of alternative enhancements included water transfers to instream flow, habitat vegetation improvements, and habitat structural measures. The benefits of changes in fish numbers are valued through the travel cost method. Costs of habitat investments are derived from a synthesis of cost data for similar investments for the region. For most lower-reach stream sections, benefits of habitat investments/streamflow alternatives do not equal costs. However, changes in water allocations and habitat do appear economically efficient to some upper reaches. The main results suggest that economic efficiency varies greatly within the system, indicating the need for site-specific proposals for streamfiow or habitat alterations within this or similar high desert streams. In addition to providing preliminary estimates of the economic efficency of streamfiow and habitat investments, this thesis serves as a methodological template for future integrated bioeconomic evaluations of water and fishery management issues. Title: An economic analysis of alternative water allocations and habitat investments for anadromous fish production, John Day Basin, Oregon Author: Cerda, Arcadio Alberto This thesis focuses on the economic efficiency of alternative habitat, streamfiow, and land use allocations within a major drainage of the Pacific Northwest. Specifically, productivity of present habitat and streamfiow conditions is evaluated with respect to anadromous fish species (chinook salmon and steelhead trout) in the John Day River Basin, a high-desert system in the Pacific Northwest. Alternative water allocations and fish habitat enhancements to improve anadromous fish productivity are also examined. This biophysical information is combined with economics concepts to evaluate comparative benefits and economic efficiency of selected technically feasible habitat/streamflow alternatives. The John Day River Basin is used as a case study because it provides one of the most significant runs of wild summer steelhead trout and spring chinook salmon in the Columbia River Basin. Specific categories of alternative enhancements included water transfers to instream flow, habitat vegetation improvements, and habitat structural measures. The benefits of changes in fish numbers are valued through the travel cost method. Costs of habitat investments are derived from a synthesis of cost data for similar investments for the region. For most lower-reach stream sections, benefits of habitat investments/streamflow alternatives do not equal costs. However, changes in water allocations and habitat do appear economically efficient to some upper reaches. The main results suggest that economic efficiency varies greatly within the system, indicating the need for site-specific proposals for streamfiow or habitat alterations within this or similar high desert streams. In addition to providing preliminary estimates of the economic efficency of streamfiow and habitat investments, this thesis serves as a methodological template for future integrated bioeconomic evaluations of water and fishery management issues. Close

• 42. [Article] The size of the Oregon coastal salmon runs in the mid-1800s

  Abstract.- Increasing the abundance of salmon in coastal Oregon rivers and streams is a high priority public policy objective. Salmon runs have been reduced from pre-development conditions (typically defined ...

  Citation × Citation Citation Abstract Copy Title: The size of the Oregon coastal salmon runs in the mid-1800s Author: Meengs, Chad C. Abstract.- Increasing the abundance of salmon in coastal Oregon rivers and streams is a high priority public policy objective. Salmon runs have been reduced from pre-development conditions (typically defined as the 1 850s), but it is unclear by how much. Considerable resources have been allocated to restoring salmon runs, but it is uncertain what the current recovery potential is because much of the freshwater and estuarine habitat for salmon has been altered. The goals of all recovery efforts are based on assumptions, often unstated, for what the size if the runs were prior to significant habitat alteration, coupled with an estimate of the amount and quality of freshwater and estuarine habitat currently available. At one extreme, it may be that current run sizes reflect the recovery potential of the existing salmon habitat. At the other extreme, the recovery potential may be as high as the mid 1800 levels. Historical salmon runs sizes on the Oregon coast were estimated using two methods: (1) Converting aboriginal population levels and their salmon consumption rate into numbers of salmon; (2) Extrapolating cannery pack into numbers of salmon. Annual aboriginal harvest of all salmon species is estimated to have been approximately 10 million pounds/year or between 1.75 million and 5.36 million salmonids, a harvest level similar to that occurring during the height of commercial fishing on Oregon's coastal rivers in the late 1 800s and early 1 900s. Extrapolating cannery pack data, the estimated size of the late 1 800s aggregate runs of coho (Oncorhynchus kisutch) was 1.5-2.5 million. The estimated size of aggregate runs of chinook (Oncorhynchus tshawytscha) runs was 290,000-517,000. Compared to mid 1 800s coho estimates, current runs (during favorable ocean conditions), are 11-19%. During poor ocean conditions, current coho runs are 3-6% of the historical size. Title: The size of the Oregon coastal salmon runs in the mid-1800s Author: Meengs, Chad C. Abstract.- Increasing the abundance of salmon in coastal Oregon rivers and streams is a high priority public policy objective. Salmon runs have been reduced from pre-development conditions (typically defined as the 1 850s), but it is unclear by how much. Considerable resources have been allocated to restoring salmon runs, but it is uncertain what the current recovery potential is because much of the freshwater and estuarine habitat for salmon has been altered. The goals of all recovery efforts are based on assumptions, often unstated, for what the size if the runs were prior to significant habitat alteration, coupled with an estimate of the amount and quality of freshwater and estuarine habitat currently available. At one extreme, it may be that current run sizes reflect the recovery potential of the existing salmon habitat. At the other extreme, the recovery potential may be as high as the mid 1800 levels. Historical salmon runs sizes on the Oregon coast were estimated using two methods: (1) Converting aboriginal population levels and their salmon consumption rate into numbers of salmon; (2) Extrapolating cannery pack into numbers of salmon. Annual aboriginal harvest of all salmon species is estimated to have been approximately 10 million pounds/year or between 1.75 million and 5.36 million salmonids, a harvest level similar to that occurring during the height of commercial fishing on Oregon's coastal rivers in the late 1 800s and early 1 900s. Extrapolating cannery pack data, the estimated size of the late 1 800s aggregate runs of coho (Oncorhynchus kisutch) was 1.5-2.5 million. The estimated size of aggregate runs of chinook (Oncorhynchus tshawytscha) runs was 290,000-517,000. Compared to mid 1 800s coho estimates, current runs (during favorable ocean conditions), are 11-19%. During poor ocean conditions, current coho runs are 3-6% of the historical size. Close

• 43. [Article] The intrusion of logging debris into artificial gravel streambeds

  The objective of this study was to quantitatively describe the intrusion of logging debris into artificial gravel streambeds during conditions of low stream flow with a stable streambed, and begin an analysis ...

  Citation × Citation Citation Abstract Copy Title: The intrusion of logging debris into artificial gravel streambeds Author: Garvin, William Fredrick The objective of this study was to quantitatively describe the intrusion of logging debris into artificial gravel streambeds during conditions of low stream flow with a stable streambed, and begin an analysis of the effect of high flow and unstable streambeds. This study was initiated because prior studies indicated that logging debris was responsible for dissolved oxygen reduction within the gravel bed of spawning streams. Low flow -- stable streambed studies were run for eighteen to twenty days in a flume. Two control samples of the gravel were taken. Logging slash was then placed on the gravel in volumes approximating those of logged streams. A sample was taken every other day for eighteen to twenty days using a device which froze a core of the streambed gravel. Since there were many problems with vandalism and weather, only two low flow replications were completed. shows the large random error which occurs even in the deeper sections. The range of debris concentrations of the two deeper sections for low flow studies one and two were .07 gm/l and .15 gm/l respectively. The average concentration values for low flow studies one and two were .03 gm/l and .02 gm/l respectively. No variables in the high flow study were found to be good predictors of intrusion. Natural random error and the extreme variability of this dynamic system were too great to draw even general conclusions. The range of concentrations of high flow studies one and two were .14 gm/l and .04 gm/l respectively. The average concentration values for high flow studies one and two were .01 gm/l and .02 gm/l respectively. Beneath the armour layer, the streambed exhibits less variability, but the large random error is sufficient to make prediction of intrusion difficult. During high flow periods where the streambed is moving, no predictive equation could be developed to estimate organic material release or incorporation owing to the large variability existing in the system. Title: The intrusion of logging debris into artificial gravel streambeds Author: Garvin, William Fredrick The objective of this study was to quantitatively describe the intrusion of logging debris into artificial gravel streambeds during conditions of low stream flow with a stable streambed, and begin an analysis of the effect of high flow and unstable streambeds. This study was initiated because prior studies indicated that logging debris was responsible for dissolved oxygen reduction within the gravel bed of spawning streams. Low flow -- stable streambed studies were run for eighteen to twenty days in a flume. Two control samples of the gravel were taken. Logging slash was then placed on the gravel in volumes approximating those of logged streams. A sample was taken every other day for eighteen to twenty days using a device which froze a core of the streambed gravel. Since there were many problems with vandalism and weather, only two low flow replications were completed. shows the large random error which occurs even in the deeper sections. The range of debris concentrations of the two deeper sections for low flow studies one and two were .07 gm/l and .15 gm/l respectively. The average concentration values for low flow studies one and two were .03 gm/l and .02 gm/l respectively. No variables in the high flow study were found to be good predictors of intrusion. Natural random error and the extreme variability of this dynamic system were too great to draw even general conclusions. The range of concentrations of high flow studies one and two were .14 gm/l and .04 gm/l respectively. The average concentration values for high flow studies one and two were .01 gm/l and .02 gm/l respectively. Beneath the armour layer, the streambed exhibits less variability, but the large random error is sufficient to make prediction of intrusion difficult. During high flow periods where the streambed is moving, no predictive equation could be developed to estimate organic material release or incorporation owing to the large variability existing in the system. Close

• 44. [Article] In the midst of a revolution : science, fish culture, and the Oregon Game Commission, 1935-1949

  This thesis will address the transformation of biological sciences during the 1930s and 1940s and it effects on fisheries science. It will focus on Oregon State College and specifically the Department ...

  Citation × Citation Citation Abstract Copy Title: In the midst of a revolution : science, fish culture, and the Oregon Game Commission, 1935-1949 Author: Hahn, Linda This thesis will address the transformation of biological sciences during the 1930s and 1940s and it effects on fisheries science. It will focus on Oregon State College and specifically the Department of Fish and Game Management and the interaction with the Oregon Game Commission. Support for mutation theory and neo- Lamarckism lasted throughout this study's time frame. The resulting belief that the environment can directly affect species fitness could have been a factor in fisheries managers' support for fish hatcheries. Throughout this time frame the science of ecology was emerging, but the dominant science of agricultural breeding science within wildlife management took precedence over ecology. Two case studies show changing ideas about agricultural breeding science as applied to wildlife management. In the first case study, the debate concerning fishways over Bonneville Dam shows that fish hatcheries were counted on to mitigate the loss of salmon habitat due to construction, and to act as a failsafe should the fishways fail. When the 1934 Oregon Game Commission members failed to enthusiastically support the construction of the dam and the fishway plans, this thesis argues that the commission members were dismissed in 1935. The second case study addresses the actions of the Oregon Game Commission in placing some high dams on tributaries of the Willamette River, the Willamette Valley project. This thesis shows that the inclusion of ecological principles in the evaluation of fish hatcheries led the commission to oppose this project. For their opposition, this thesis argues that the 1949 Oregon Game Commission members were dismissed. In both cases, this thesis concludes that the federal funding of water development projects played an important role in the dismissals of both Oregon Game Commissions. In addition, the evolving nature of biological science during the 1 930s and 1940s shows that lingering beliefs in mutation theory and neo-Lamarckism would have supported the use of fish hatcheries as a scientifically acceptable solution to declines in fish runs within the scientific tradition of agricultural methods of breeding wildlife. Title: In the midst of a revolution : science, fish culture, and the Oregon Game Commission, 1935-1949 Author: Hahn, Linda This thesis will address the transformation of biological sciences during the 1930s and 1940s and it effects on fisheries science. It will focus on Oregon State College and specifically the Department of Fish and Game Management and the interaction with the Oregon Game Commission. Support for mutation theory and neo- Lamarckism lasted throughout this study's time frame. The resulting belief that the environment can directly affect species fitness could have been a factor in fisheries managers' support for fish hatcheries. Throughout this time frame the science of ecology was emerging, but the dominant science of agricultural breeding science within wildlife management took precedence over ecology. Two case studies show changing ideas about agricultural breeding science as applied to wildlife management. In the first case study, the debate concerning fishways over Bonneville Dam shows that fish hatcheries were counted on to mitigate the loss of salmon habitat due to construction, and to act as a failsafe should the fishways fail. When the 1934 Oregon Game Commission members failed to enthusiastically support the construction of the dam and the fishway plans, this thesis argues that the commission members were dismissed in 1935. The second case study addresses the actions of the Oregon Game Commission in placing some high dams on tributaries of the Willamette River, the Willamette Valley project. This thesis shows that the inclusion of ecological principles in the evaluation of fish hatcheries led the commission to oppose this project. For their opposition, this thesis argues that the 1949 Oregon Game Commission members were dismissed. In both cases, this thesis concludes that the federal funding of water development projects played an important role in the dismissals of both Oregon Game Commissions. In addition, the evolving nature of biological science during the 1 930s and 1940s shows that lingering beliefs in mutation theory and neo-Lamarckism would have supported the use of fish hatcheries as a scientifically acceptable solution to declines in fish runs within the scientific tradition of agricultural methods of breeding wildlife. Close

• 45. [Article] Caspian tern (Hydroprogne caspia) foraging ecology and predation on juvenile salmonids in San Francisco Bay, California

  Brooks Island, located in central San Francisco Bay, California, currently supports the largest breeding colony of Caspian terns (Hydroprogne caspia) in the Bay Area, and is one of several proposed relocation ...

  Citation × Citation Citation Abstract Copy Title: Caspian tern (Hydroprogne caspia) foraging ecology and predation on juvenile salmonids in San Francisco Bay, California Author: Adrean, Lindsay J. Brooks Island, located in central San Francisco Bay, California, currently supports the largest breeding colony of Caspian terns (Hydroprogne caspia) in the Bay Area, and is one of several proposed relocation sites for some Caspian terns from the world's largest colony in the Columbia River estuary of Oregon. Juvenile salmonids have been identified in the diet of Caspian terns nesting at Brooks Island, so I investigated whether the colony, at its current or an enhanced size, poses a threat to the recovery of several runs of salmonids (Oncorhynchus spp.) in San Francisco Bay that are listed under the U.S. Endangered Species Act (ESA). I also examined the foraging ecology of Brooks Island Caspian terns to 1) determine whether the colony is suitable for expansion based on availability of forage fish resources, a factor potentially limiting the size and productivity of the colony, and 2) investigate how Caspian terns nesting at this colony exploit forage fish resources. I used a bioenergetics modeling approach, employing estimates of tern energy requirements and proportions of energy supplied by various prey types, to estimate consumption of juvenile salmonids by Caspian terns nesting on Brooks Island during 2008 and 2009. Estimated salmonid consumption was 205,000 smolts (95% CI: 175,000 – 245,000 smolts) in 2008 and 167,000 smolts (95% CI: 144,000 – 191,000 smolts) in 2009. Predation rates on ESA-listed Central Valley spring-run Chinook salmon (O. tshawytscha; 0.08%) were lower than those on unlisted fall-run Chinook salmon (1.0%). Average per capita predation rates on juvenile salmonids by Brooks Island Caspian terns (2008: 126 fish; 2009: 123 fish) were less than half those of Caspian terns nesting in the Columbia River estuary. If the current downward trend in the number of Caspian terns nesting on Brooks Island continues until the colony is no longer extant, the resulting declines in predation on salmonids would lead to increases in annual population growth rates (Δλ) of salmonid runs of just small fractions of one percentage point. The proposed enhancement of the Brooks Island Caspian tern colony to 3,000 individuals would at most cause declines in annual population growth rates of 0.3% for fall-run Chinook salmon and 0.02% for threatened spring-run Chinook salmon, assuming that smolt mortality from tern predation is 100% additive. This level of impact to the ESA-listed spring-run Chinook salmon stock is less than the level considered acceptable by the National Marine Fisheries Service (Δλ = 0.05%). Radio-tracking of Caspian terns nesting on Brooks Island revealed that the maximum foraging distance from the colony was 80 km. The median foraging distance from the colony was greater in 2009 compared to 2008 (20.6 km vs. 14.0 km), average number of foraging trips per day was higher (4.4 vs. 3.4 foraging trips), and average adult colony attendance was lower (43% vs. 52% of daylight hours). These results indicate that the colony was more food-limited during the 2009 breeding season, concurrent with anomalous downwelling along the coast of northern California and reduced availability and size of marine forage fishes, such as herring, sardines, and anchovies. Caspian terns used a number of core foraging areas within 30 km of the Brooks Island colony, both inside and just outside the Bay. Two large core foraging areas were close to or overlapped with the release site for juvenile salmonids in eastern San Pablo Bay, where > 10 million hatchery-raised smolts were released from net pens during both the 2008 and 2009 tern nesting seasons. This finding supports the hypothesis that most juvenile salmonids consumed by terns nesting at the Brooks Island colony were captured at or near the release site. Individual Caspian terns displayed foraging site fidelity, suggesting that foraging at the release site for hatchery-raised salmonids was a learned behavior by some terns. The Brooks Island colony site is within foraging distance of adequate marine forage fish resources in most years, and Caspian terns nesting there are not dependent on juvenile salmonids as a food resource. Consumption of juvenile salmonids by Brooks Island terns would be largely curtailed by modification of hatchery release practices. Title: Caspian tern (Hydroprogne caspia) foraging ecology and predation on juvenile salmonids in San Francisco Bay, California Author: Adrean, Lindsay J. Brooks Island, located in central San Francisco Bay, California, currently supports the largest breeding colony of Caspian terns (Hydroprogne caspia) in the Bay Area, and is one of several proposed relocation sites for some Caspian terns from the world's largest colony in the Columbia River estuary of Oregon. Juvenile salmonids have been identified in the diet of Caspian terns nesting at Brooks Island, so I investigated whether the colony, at its current or an enhanced size, poses a threat to the recovery of several runs of salmonids (Oncorhynchus spp.) in San Francisco Bay that are listed under the U.S. Endangered Species Act (ESA). I also examined the foraging ecology of Brooks Island Caspian terns to 1) determine whether the colony is suitable for expansion based on availability of forage fish resources, a factor potentially limiting the size and productivity of the colony, and 2) investigate how Caspian terns nesting at this colony exploit forage fish resources. I used a bioenergetics modeling approach, employing estimates of tern energy requirements and proportions of energy supplied by various prey types, to estimate consumption of juvenile salmonids by Caspian terns nesting on Brooks Island during 2008 and 2009. Estimated salmonid consumption was 205,000 smolts (95% CI: 175,000 – 245,000 smolts) in 2008 and 167,000 smolts (95% CI: 144,000 – 191,000 smolts) in 2009. Predation rates on ESA-listed Central Valley spring-run Chinook salmon (O. tshawytscha; 0.08%) were lower than those on unlisted fall-run Chinook salmon (1.0%). Average per capita predation rates on juvenile salmonids by Brooks Island Caspian terns (2008: 126 fish; 2009: 123 fish) were less than half those of Caspian terns nesting in the Columbia River estuary. If the current downward trend in the number of Caspian terns nesting on Brooks Island continues until the colony is no longer extant, the resulting declines in predation on salmonids would lead to increases in annual population growth rates (Δλ) of salmonid runs of just small fractions of one percentage point. The proposed enhancement of the Brooks Island Caspian tern colony to 3,000 individuals would at most cause declines in annual population growth rates of 0.3% for fall-run Chinook salmon and 0.02% for threatened spring-run Chinook salmon, assuming that smolt mortality from tern predation is 100% additive. This level of impact to the ESA-listed spring-run Chinook salmon stock is less than the level considered acceptable by the National Marine Fisheries Service (Δλ = 0.05%). Radio-tracking of Caspian terns nesting on Brooks Island revealed that the maximum foraging distance from the colony was 80 km. The median foraging distance from the colony was greater in 2009 compared to 2008 (20.6 km vs. 14.0 km), average number of foraging trips per day was higher (4.4 vs. 3.4 foraging trips), and average adult colony attendance was lower (43% vs. 52% of daylight hours). These results indicate that the colony was more food-limited during the 2009 breeding season, concurrent with anomalous downwelling along the coast of northern California and reduced availability and size of marine forage fishes, such as herring, sardines, and anchovies. Caspian terns used a number of core foraging areas within 30 km of the Brooks Island colony, both inside and just outside the Bay. Two large core foraging areas were close to or overlapped with the release site for juvenile salmonids in eastern San Pablo Bay, where > 10 million hatchery-raised smolts were released from net pens during both the 2008 and 2009 tern nesting seasons. This finding supports the hypothesis that most juvenile salmonids consumed by terns nesting at the Brooks Island colony were captured at or near the release site. Individual Caspian terns displayed foraging site fidelity, suggesting that foraging at the release site for hatchery-raised salmonids was a learned behavior by some terns. The Brooks Island colony site is within foraging distance of adequate marine forage fish resources in most years, and Caspian terns nesting there are not dependent on juvenile salmonids as a food resource. Consumption of juvenile salmonids by Brooks Island terns would be largely curtailed by modification of hatchery release practices. Close

• 46. [Article] Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/jo...

  Citation × Citation Citation Abstract Copy Title: Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow Author: Jacobson, Dave P., Banks, Michael A., Dill, Allen J., Kurth, Ryon, O'Malley, Kathleen G. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1752-4571. Title: Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow Author: Jacobson, Dave P., Banks, Michael A., Dill, Allen J., Kurth, Ryon, O'Malley, Kathleen G. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1752-4571. Close

• 47. [Article] Use of Genetic Stock Identification Data for Comparison of the Ocean Spatial Distribution, Size at Age, and Fishery Exposure of an Untagged Stock and Its Indicator: California Coastal versus Klamath River Chinook Salmon

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries ...

  Citation × Citation Citation Abstract Copy Title: Use of Genetic Stock Identification Data for Comparison of the Ocean Spatial Distribution, Size at Age, and Fishery Exposure of an Untagged Stock and Its Indicator: California Coastal versus Klamath River Chinook Salmon Author: Mohr, Michael S., Banks, Michael A., Borgerson, Lisa A., Lawson, Peter W., Anderson, Eric C., Garza, John Carlos, Crandall, Eric D., Satterthwaite, William H., O'Farrell, Michael R., Bellinger, M. Renee, Palmer-Zwahlen, Melodie L., Bates, Sarah J., Kormos, Brett J. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/utaf20/current#.UzNNkfPn-Hs. Title: Use of Genetic Stock Identification Data for Comparison of the Ocean Spatial Distribution, Size at Age, and Fishery Exposure of an Untagged Stock and Its Indicator: California Coastal versus Klamath River Chinook Salmon Author: Mohr, Michael S., Banks, Michael A., Borgerson, Lisa A., Lawson, Peter W., Anderson, Eric C., Garza, John Carlos, Crandall, Eric D., Satterthwaite, William H., O'Farrell, Michael R., Bellinger, M. Renee, Palmer-Zwahlen, Melodie L., Bates, Sarah J., Kormos, Brett J. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the American Fisheries Society and published by Taylor & Francis. It can be found at: http://www.tandfonline.com/toc/utaf20/current#.UzNNkfPn-Hs. Close

• 48. [Article] Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) ...

  Citation × Citation Citation Abstract Copy Title: Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test Author: Banks, Michael A., Ardren, William R., Bernier-Latmani, Jeremiah, Meusnier, Isabelle, Van Sickle, John, Rashbrook, Vanessa K., Jacobson, David P., Smith, Christian T., O'Malley, Kathleen G., Greig, Carolyn A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2052. Title: Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test Author: Banks, Michael A., Ardren, William R., Bernier-Latmani, Jeremiah, Meusnier, Isabelle, Van Sickle, John, Rashbrook, Vanessa K., Jacobson, David P., Smith, Christian T., O'Malley, Kathleen G., Greig, Carolyn A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2052. Close

• 49. [Article] Neural gene expression profiling in chinook salmon (Oncorhynchus tshawytscha) of alternate run times

  Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Differential return times to freshwater have segregated populations of ...

  Citation × Citation Citation Abstract Copy Title: Neural gene expression profiling in chinook salmon (Oncorhynchus tshawytscha) of alternate run times Author: Bernier, Jeremiah C. Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Differential return times to freshwater have segregated populations of Chinook into two broad types or runs, fall and spring, named for the time of year in which they migrate to freshwater. Migration time in Chinook has a strong genetic component, and historically, fall and spring runs were spatially and temporally isolated in watersheds. Using a population of Chinook from California’s Central Valley, I sought to examine gene regulation that results in differential run-timing. Functional genomics has proven to be powerful in distinguishing genes differentially expressed between alternate behaviors in other systems and I used the technique LongSAGE to examine genes differentially regulated between fall and spring run Chinook during freshwater migration. I constructed three LongSAGE libraries from the brains of a spring, fall and ocean sample and observed 221 differentially expressed tags. Using expressed sequence tag (EST) libraries from Atlantic salmon (Salmo salar) and rainbow trout (O. mykiss), I was able to assign putative functions to 59% of differentially expressed tags. Additionally, I tested the expression levels of seven genes in the brains of 8 additional individuals from both runs and found none significantly differentially expressed between fall and spring runs. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future gene expression research into reproduction and migration times, as well as physiology of migrating salmon. Title: Neural gene expression profiling in chinook salmon (Oncorhynchus tshawytscha) of alternate run times Author: Bernier, Jeremiah C. Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Differential return times to freshwater have segregated populations of Chinook into two broad types or runs, fall and spring, named for the time of year in which they migrate to freshwater. Migration time in Chinook has a strong genetic component, and historically, fall and spring runs were spatially and temporally isolated in watersheds. Using a population of Chinook from California’s Central Valley, I sought to examine gene regulation that results in differential run-timing. Functional genomics has proven to be powerful in distinguishing genes differentially expressed between alternate behaviors in other systems and I used the technique LongSAGE to examine genes differentially regulated between fall and spring run Chinook during freshwater migration. I constructed three LongSAGE libraries from the brains of a spring, fall and ocean sample and observed 221 differentially expressed tags. Using expressed sequence tag (EST) libraries from Atlantic salmon (Salmo salar) and rainbow trout (O. mykiss), I was able to assign putative functions to 59% of differentially expressed tags. Additionally, I tested the expression levels of seven genes in the brains of 8 additional individuals from both runs and found none significantly differentially expressed between fall and spring runs. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future gene expression research into reproduction and migration times, as well as physiology of migrating salmon. Close

• 50. [Article] The relationships between fluctuations in oceanographic conditions, forage fishes, predatory fishes, predator food habits, and juvenile salmonid marine survival off the Columbia River

  Salmonid run sizes are strongly affected by their early marine stage. Fully understanding the life history of salmonids means understanding how they interact with their marine environment and with other ...

  Citation × Citation Citation Abstract Copy Title: The relationships between fluctuations in oceanographic conditions, forage fishes, predatory fishes, predator food habits, and juvenile salmonid marine survival off the Columbia River Author: Emmett, Robert L. Salmonid run sizes are strongly affected by their early marine stage. Fully understanding the life history of salmonids means understanding how they interact with their marine environment and with other fishes. Changes in the biological and physical environment off the Columbia River region affects the distribution and abundance of predatory fishes and their feeding, forage fishes, and juvenile salmonid marine survival. From 1998-2004, forage fish and predatory fish distribution and abundance off the Columbia River was quantified by surface trawling at night during spring/summer. The effect of predation on salmonids was measured by stomach analysis of predatory fishes. During the study period (1998-2004), forage fishes increased in abundance by orders of magnitude and were strongly related to the abundance of cold-water copepods the previous year. Higher forage fish populations were also linked to cooler ocean conditions and perhaps fewer predatory Pacific hake (Merluccius productus). Most forage fishes were distributed nearshore while predators had a more offshore distribution. Pacific hake was most abundant in 1998, 2003, and 2004; warm ocean years. Jack mackerel (Trachurus symmetricus) was most abundant during 1999-2002; relatively cool ocean years. Deep (50-m) ocean temperatures and the date of the spring transition, when nearshore currents switched from northward to southward, were good predictors of Pacific hake abundance in the study area. Forage fish or salmonid occurrence in a haul was negatively related to the occurrence of predators. Pacific hake and jack mackerel ate primarily euphausiids and small fishes. Salmonids were rarely eaten by either predator. However, because the Pacific hake population can be very large, hake predation can be a significant source of juvenile salmon mortality off the Columbia River during some years. A trophic model showed that marine mortality of Columbia River juvenile salmonids may be related to the abundance of Pacific hake and forage fishes. A multiple regression using the predictions from the trophic model of annual numbers of juvenile salmonids eaten by hake and Columbia River spring flows as independent variables, accounted for much of the variation observed in the annual marine survival of Columbia River coho (Oncorhynchus kisutch) and Chinook salmon (O. tshawytscha), the dependent variable. Future research should identify the physical and biological forces that alter the feeding habits, migration and movements of Pacific hake and jack mackerel off the Northwest, and how Columbia River flows affect trophic interactions. Title: The relationships between fluctuations in oceanographic conditions, forage fishes, predatory fishes, predator food habits, and juvenile salmonid marine survival off the Columbia River Author: Emmett, Robert L. Salmonid run sizes are strongly affected by their early marine stage. Fully understanding the life history of salmonids means understanding how they interact with their marine environment and with other fishes. Changes in the biological and physical environment off the Columbia River region affects the distribution and abundance of predatory fishes and their feeding, forage fishes, and juvenile salmonid marine survival. From 1998-2004, forage fish and predatory fish distribution and abundance off the Columbia River was quantified by surface trawling at night during spring/summer. The effect of predation on salmonids was measured by stomach analysis of predatory fishes. During the study period (1998-2004), forage fishes increased in abundance by orders of magnitude and were strongly related to the abundance of cold-water copepods the previous year. Higher forage fish populations were also linked to cooler ocean conditions and perhaps fewer predatory Pacific hake (Merluccius productus). Most forage fishes were distributed nearshore while predators had a more offshore distribution. Pacific hake was most abundant in 1998, 2003, and 2004; warm ocean years. Jack mackerel (Trachurus symmetricus) was most abundant during 1999-2002; relatively cool ocean years. Deep (50-m) ocean temperatures and the date of the spring transition, when nearshore currents switched from northward to southward, were good predictors of Pacific hake abundance in the study area. Forage fish or salmonid occurrence in a haul was negatively related to the occurrence of predators. Pacific hake and jack mackerel ate primarily euphausiids and small fishes. Salmonids were rarely eaten by either predator. However, because the Pacific hake population can be very large, hake predation can be a significant source of juvenile salmon mortality off the Columbia River during some years. A trophic model showed that marine mortality of Columbia River juvenile salmonids may be related to the abundance of Pacific hake and forage fishes. A multiple regression using the predictions from the trophic model of annual numbers of juvenile salmonids eaten by hake and Columbia River spring flows as independent variables, accounted for much of the variation observed in the annual marine survival of Columbia River coho (Oncorhynchus kisutch) and Chinook salmon (O. tshawytscha), the dependent variable. Future research should identify the physical and biological forces that alter the feeding habits, migration and movements of Pacific hake and jack mackerel off the Northwest, and how Columbia River flows affect trophic interactions. Close