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• 1. [Article] Salmon Abundances and Effects of Harvest: Implications for Rebuilding Stocks of Wild Coho Salmon in Oregon

  This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds.

  Citation × Citation Citation Abstract Copy Title: Salmon Abundances and Effects of Harvest: Implications for Rebuilding Stocks of Wild Coho Salmon in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Title: Salmon Abundances and Effects of Harvest: Implications for Rebuilding Stocks of Wild Coho Salmon in Oregon Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Close

• 2. [Article] Defining and evaluating recovery of OCN coho salmon stocks: implications for rebuilding stocks under the Oregon Plan : summary of a workshop organized by the Independent Multidisciplinary Science Team, August 4-5, 1999

  This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds.

  Citation × Citation Citation Abstract Copy Title: Defining and evaluating recovery of OCN coho salmon stocks: implications for rebuilding stocks under the Oregon Plan : summary of a workshop organized by the Independent Multidisciplinary Science Team, August 4-5, 1999 Author: Independent Multidisciplinary Science Team (Or.) This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Title: Defining and evaluating recovery of OCN coho salmon stocks: implications for rebuilding stocks under the Oregon Plan : summary of a workshop organized by the Independent Multidisciplinary Science Team, August 4-5, 1999 Author: Independent Multidisciplinary Science Team (Or.) This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Close

• 3. [Article] Evidence that summer jellyfish blooms impact Pacific Northwest salmon production

  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: Evidence that summer jellyfish blooms impact Pacific Northwest salmon production Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. 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 Ecological Society of America. The published article can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Title: Evidence that summer jellyfish blooms impact Pacific Northwest salmon production Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. 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 Ecological Society of America. The published article can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Close

• 4. [Article] RuzickaEvidencethatSummerJellyfish.pdf

  Citation × Citation Citation Abstract Copy Title: RuzickaEvidencethatSummerJellyfish.pdf Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. Title: RuzickaEvidencethatSummerJellyfish.pdf Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. Close

• 5. [Article] RuzickaEvidencethatSummerJellyfishSupplementalTables.pdf

  Citation × Citation Citation Abstract Copy Title: RuzickaEvidencethatSummerJellyfishSupplementalTables.pdf Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. Title: RuzickaEvidencethatSummerJellyfishSupplementalTables.pdf Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. Close

• 6. [Article] RuzickaEvidencethatSummerJellyfishSupplementS1.zip

  Citation × Citation Citation Abstract Copy Title: RuzickaEvidencethatSummerJellyfishSupplementS1.zip Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. Title: RuzickaEvidencethatSummerJellyfishSupplementS1.zip Author: Daly, Elizabeth A., Ruzicka, James J., Brodeur, Richard D. Close

• 7. [Article] Patterns of natural selection and demography in coastal Oregon coho salmon (Oncorhynchus kisutch) populations : evidence from neutral and olfactory receptor gene-linked markers

  For Pacific salmon, the evolution of local adaptations depends upon the species' propensity to return, or "home", to natal streams at time of reproduction. Pacific salmon use olfactory cues to guide homing ...

  Citation × Citation Citation Abstract Copy Title: Patterns of natural selection and demography in coastal Oregon coho salmon (Oncorhynchus kisutch) populations : evidence from neutral and olfactory receptor gene-linked markers Author: Johnson, Marc Aaron For Pacific salmon, the evolution of local adaptations depends upon the species' propensity to return, or "home", to natal streams at time of reproduction. Pacific salmon use olfactory cues to guide homing behavior, yet little is known about the genetics of olfaction in salmon. In this study, I use putatively neutral microsatellite markers to estimate demographic parameters and describe the population genetic structure of Oregon Coastal coho salmon (Oncorhynchus kisutch). Microsatellite analyses indicated weak population structure among coho populations (overall θ = 0.021), modulated by moderate levels of migration (straying). Allelic richness was higher in wild populations than both hatchery populations and wild populations from lake dominated systems. The Coos and Nehalem river populations appeared to be primary migrant sources, possibly elevating allelic richness for central coast populations. I then used genomic sequence data from nine species of salmon and trout to infer the evolutionary history for eight olfactory receptor genes, representing two major gene classes (main olfactory receptors and ORAs). Through a maximum likelihood based analysis of site-specific, non-synonymous to synonymous nucleotide substitution rates, I found strong evidence for positive selection having influenced the diversification of four paralogous main olfactory receptor genes. Main olfactory receptor orthologues appeared highly conserved among species, yet site-specific positive selection may be affecting interspecific divergence of an ORA gene in salmonids. Finally, I used molecular markers linked to olfactory receptor genes to test for a signal of selection among coho salmon populations from different rivers. By examining interlocus variance of F[subscript]ST, I found evidence for directional selection on an olfactory receptor gene-linked marker in coho salmon populations. Pairwise θ values calculated from gene-linked markers were nearly an order of magnitude greater than observed for putatively neutral microsatellites. Title: Patterns of natural selection and demography in coastal Oregon coho salmon (Oncorhynchus kisutch) populations : evidence from neutral and olfactory receptor gene-linked markers Author: Johnson, Marc Aaron For Pacific salmon, the evolution of local adaptations depends upon the species' propensity to return, or "home", to natal streams at time of reproduction. Pacific salmon use olfactory cues to guide homing behavior, yet little is known about the genetics of olfaction in salmon. In this study, I use putatively neutral microsatellite markers to estimate demographic parameters and describe the population genetic structure of Oregon Coastal coho salmon (Oncorhynchus kisutch). Microsatellite analyses indicated weak population structure among coho populations (overall θ = 0.021), modulated by moderate levels of migration (straying). Allelic richness was higher in wild populations than both hatchery populations and wild populations from lake dominated systems. The Coos and Nehalem river populations appeared to be primary migrant sources, possibly elevating allelic richness for central coast populations. I then used genomic sequence data from nine species of salmon and trout to infer the evolutionary history for eight olfactory receptor genes, representing two major gene classes (main olfactory receptors and ORAs). Through a maximum likelihood based analysis of site-specific, non-synonymous to synonymous nucleotide substitution rates, I found strong evidence for positive selection having influenced the diversification of four paralogous main olfactory receptor genes. Main olfactory receptor orthologues appeared highly conserved among species, yet site-specific positive selection may be affecting interspecific divergence of an ORA gene in salmonids. Finally, I used molecular markers linked to olfactory receptor genes to test for a signal of selection among coho salmon populations from different rivers. By examining interlocus variance of F[subscript]ST, I found evidence for directional selection on an olfactory receptor gene-linked marker in coho salmon populations. Pairwise θ values calculated from gene-linked markers were nearly an order of magnitude greater than observed for putatively neutral microsatellites. Close

• 8. [Article] IMST Review of the USFWS and NMFS 2001 Biological Opinions on Management of the Klamath Reclamation Project and Related Reports

  This report was prepared by the Independent Multidisciplinary Science Team to the Oregon Plan for Salmon and Watersheds.

  Citation × Citation Citation Abstract Copy Title: IMST Review of the USFWS and NMFS 2001 Biological Opinions on Management of the Klamath Reclamation Project and Related Reports Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team to the Oregon Plan for Salmon and Watersheds. Title: IMST Review of the USFWS and NMFS 2001 Biological Opinions on Management of the Klamath Reclamation Project and Related Reports Author: Independent Multidisciplinary Science Team (Or.) This report was prepared by the Independent Multidisciplinary Science Team to the Oregon Plan for Salmon and Watersheds. Close

• 9. [Article] Policy Patterns across Riverscapes : Riparian Land Standards in the Oregon Coast Range

  Land management policies are ideas about nature projected onto the landscape. Culminations of social, economic, and scientific influences, these policies create standards affecting the function of ecological ...

  Citation × Citation Citation Abstract Copy Title: Policy Patterns across Riverscapes : Riparian Land Standards in the Oregon Coast Range Author: Boisjolie, Brett A. Land management policies are ideas about nature projected onto the landscape. Culminations of social, economic, and scientific influences, these policies create standards affecting the function of ecological systems. In the case of riparian lands in the Oregon Coast Range, policy requirements vary considerably across federal, state, and private land ownerships. Protective measures, such as the adoption of fixed buffer widths for maintaining vegetation, are intended to preserve natural processes important to instream habitat and water quality. However, the "policy landscape" of variable management standards can result in a fragmented approach to policy protection. This fragmentation complicates recovery efforts for threatened anadromous fish species such as coho salmon (Oncorhynchus kisutch), which require connectivity in suitable habitat segments throughout the river network. Taking a riverscape perspective, this study evaluates how aquatic protections vary across the river and its valley. To explore the patterns created from variable standard, the study first delineates categories of riparian management standards in the Oregon Coast Range. Using a geographic information system (GIS), these standards are mapped across the river networks of this region. The extent of each policy category is quantified in stream kilometers in order to evaluate policy efforts within and across the riverscapes of the Oregon Coast Range. A model of intrinsic potential for coho salmon habitat is used to identify the policy standards in stream reaches where flow, valley constraint, and channel gradient are appropriate for coho salmon habitat. A second model of the stream network (hydrography) is developed to evaluate how differences in stream delineation can influence policy patterns. Results indicate that riparian lands of the Oregon Coast Range are protected by variable standards for land management, including buffer widths that range from 0 to ~152m. In streams important to coho salmon, a lower proportion of the stream network was found to be protected by policy standards compared to the watershed and ESU scale. A lack of stream data central to policy application (fish use, stream flow duration, mean annual flow, water use) complicated our ability to attribute stream segments with specific land management requirements. The choice of hydrographic data was also found to influence the proportional extent of policies within riverscapes. This framework for assessing the spatial distribution of policies can provide insights for future studies of riverscape systems. Title: Policy Patterns across Riverscapes : Riparian Land Standards in the Oregon Coast Range Author: Boisjolie, Brett A. Land management policies are ideas about nature projected onto the landscape. Culminations of social, economic, and scientific influences, these policies create standards affecting the function of ecological systems. In the case of riparian lands in the Oregon Coast Range, policy requirements vary considerably across federal, state, and private land ownerships. Protective measures, such as the adoption of fixed buffer widths for maintaining vegetation, are intended to preserve natural processes important to instream habitat and water quality. However, the "policy landscape" of variable management standards can result in a fragmented approach to policy protection. This fragmentation complicates recovery efforts for threatened anadromous fish species such as coho salmon (Oncorhynchus kisutch), which require connectivity in suitable habitat segments throughout the river network. Taking a riverscape perspective, this study evaluates how aquatic protections vary across the river and its valley. To explore the patterns created from variable standard, the study first delineates categories of riparian management standards in the Oregon Coast Range. Using a geographic information system (GIS), these standards are mapped across the river networks of this region. The extent of each policy category is quantified in stream kilometers in order to evaluate policy efforts within and across the riverscapes of the Oregon Coast Range. A model of intrinsic potential for coho salmon habitat is used to identify the policy standards in stream reaches where flow, valley constraint, and channel gradient are appropriate for coho salmon habitat. A second model of the stream network (hydrography) is developed to evaluate how differences in stream delineation can influence policy patterns. Results indicate that riparian lands of the Oregon Coast Range are protected by variable standards for land management, including buffer widths that range from 0 to ~152m. In streams important to coho salmon, a lower proportion of the stream network was found to be protected by policy standards compared to the watershed and ESU scale. A lack of stream data central to policy application (fish use, stream flow duration, mean annual flow, water use) complicated our ability to attribute stream segments with specific land management requirements. The choice of hydrographic data was also found to influence the proportional extent of policies within riverscapes. This framework for assessing the spatial distribution of policies can provide insights for future studies of riverscape systems. Close

• 10. [Article] Irrigated agriculture, energy, and endangered species in the Upper Klamath Basin : evaluating trade-offs and interconnections

  In 2001, an extreme drought tightened water supply in the Upper Klamath Basin (basin) while earlier increases in Endangered Species Act (ESA) water requirements for basin fish species that same year elevated ...

  Citation × Citation Citation Abstract Copy Title: Irrigated agriculture, energy, and endangered species in the Upper Klamath Basin : evaluating trade-offs and interconnections Author: Boehlert, Brent B. In 2001, an extreme drought tightened water supply in the Upper Klamath Basin (basin) while earlier increases in Endangered Species Act (ESA) water requirements for basin fish species that same year elevated demands. The Bureau of Reclamation (Reclamation), which manages irrigation water in parts of the basin located near the Oregon-California border, responded to ESA Section 7 obligations by severely curtailing water allocations to Reclamation Project irrigators for the 2001 growing season, costing irrigators an estimated $35 million in farm income. This event has directed attention to several important factors that may further undermine effective water management in the basin. These include higher ESA flow requirements due to a recent Ninth Circuit Court ruling and a ten-fold energy rate increase to irrigators resulting from a mid-2006 contract expiration with the regional energy provider. The overall objective of this research is to assess the impact of changes in ESA flow requirements and energy prices on the Upper Klamath Basin farm economy given variable levels of water trading flexibility and groundwater availability. A mathematical programming and Geographic Information System (GIS) framework is used in which farm decisions are assumed to maximize net revenue subject to hydrological, institutional, economic, and agronomic constraints. The results suggest that greater development of basin groundwater resources and the institution of a flexible water bank may be sufficient to mitigate the majority of costs related to increased ESA flow requirements in future years. Title: Irrigated agriculture, energy, and endangered species in the Upper Klamath Basin : evaluating trade-offs and interconnections Author: Boehlert, Brent B. In 2001, an extreme drought tightened water supply in the Upper Klamath Basin (basin) while earlier increases in Endangered Species Act (ESA) water requirements for basin fish species that same year elevated demands. The Bureau of Reclamation (Reclamation), which manages irrigation water in parts of the basin located near the Oregon-California border, responded to ESA Section 7 obligations by severely curtailing water allocations to Reclamation Project irrigators for the 2001 growing season, costing irrigators an estimated $35 million in farm income. This event has directed attention to several important factors that may further undermine effective water management in the basin. These include higher ESA flow requirements due to a recent Ninth Circuit Court ruling and a ten-fold energy rate increase to irrigators resulting from a mid-2006 contract expiration with the regional energy provider. The overall objective of this research is to assess the impact of changes in ESA flow requirements and energy prices on the Upper Klamath Basin farm economy given variable levels of water trading flexibility and groundwater availability. A mathematical programming and Geographic Information System (GIS) framework is used in which farm decisions are assumed to maximize net revenue subject to hydrological, institutional, economic, and agronomic constraints. The results suggest that greater development of basin groundwater resources and the institution of a flexible water bank may be sufficient to mitigate the majority of costs related to increased ESA flow requirements in future years. Close