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• 11. [Article] Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s central valley

  Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. ...

  Citation × Citation Citation Abstract Copy Title: Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s central valley Author: Brandes, Pat, Rashbrook, Vanessa K., Bernier-Latmani, Jeremiah, Banks, Michael A., Jacobson, David P., Greene, Sheila, O’Malley, Kathleen G., Greig, Carolyn A., Van Sickle, John, Meusnier, Isabelle, Ardren, William R., Smith, Christian T. Year: 2000 Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. Dataset. doi:10.7267/N9KW5CXX" Title: Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s central valley Author: Brandes, Pat, Rashbrook, Vanessa K., Bernier-Latmani, Jeremiah, Banks, Michael A., Jacobson, David P., Greene, Sheila, O’Malley, Kathleen G., Greig, Carolyn A., Van Sickle, John, Meusnier, Isabelle, Ardren, William R., Smith, Christian T. Year: 2000 Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. Dataset. doi:10.7267/N9KW5CXX" Close

• 12. [Article] An investigation into the genetic basis of migration timing in Chinook salmon (Oncorhynchus tshawytscha)

  The genetic basis of adaptation is complex as many fitness-related traits are quantitative and likely influenced by multiple genes with variable effects across different selective environments. One important ...

  Citation × Citation Citation Abstract Copy Title: An investigation into the genetic basis of migration timing in Chinook salmon (Oncorhynchus tshawytscha) Author: O'Malley, Kathleen Gallen, 1976- The genetic basis of adaptation is complex as many fitness-related traits are quantitative and likely influenced by multiple genes with variable effects across different selective environments. One important adaptation for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which individuals return to natal breeding sites within a reproductive season. Here, I tested for adaptive genetic differentiation among temporally divergent migratory runs using candidate loci. First, I isolated and characterized two copies of the circadian rhythm gene, Clock, from Chinook salmon (OtsClock1a and OtsClock1b). Phylogenetic analysis revealed that these copies likely arose subsequent to the salmonid genome-wide duplication event. Each copy contains a polyglutamine repeat motif (PolyQ), an essential binding domain of this transcription factor. However, a 1200bp non-coding segment, showing >90% sequence identity to the Salmo salar Transferrin gene, is located downstream of the OtsClock1a PolyQ, yet absent from OtsClock1b providing evidence for nonhomologous recombination. Another candidate, Ots515NWFSC, shows sequence identity to three salmonid genes central to reproductive development: Gonadotropin-releasing hormone, CYP19b-I, and Ghrelin. I employed OtsClock1b and Ots515NWFSC to test for differentiation in two unique systems: Feather River, California; and Waitaki and Poulter Rivers, New Zealand. Based on length variation in these candidate genes, Feather River fall and spring run Chinook salmon are genetically differentiated. In contrast, these seasonal runs are genetically indistinguishable based on neutral microsatellite loci. Correspondingly, temporally divergent Chinook salmon runs in the Waitaki and Poulter Rivers show greater differentiation based on variation in OtsClock1b and Ots515NWFSC than microsatellite loci. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC are likely under selection in both systems. In addition, I found evidence for a latitudinal cline in two OtsClock1b PolyQ alleles among 42 Chinook salmon runs which is likely maintained by selection and thus may reflect an adaptation to photoperiodic parameters. Lastly, a hierarchical gene diversity analysis of OtsClock1b PolyQ variation revealed that run timing explained 43.7% of the overall genetic variance which contrast sharply with the 8.1% calculated for microsatellite loci. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration timing of Chinook salmon. Title: An investigation into the genetic basis of migration timing in Chinook salmon (Oncorhynchus tshawytscha) Author: O'Malley, Kathleen Gallen, 1976- The genetic basis of adaptation is complex as many fitness-related traits are quantitative and likely influenced by multiple genes with variable effects across different selective environments. One important adaptation for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which individuals return to natal breeding sites within a reproductive season. Here, I tested for adaptive genetic differentiation among temporally divergent migratory runs using candidate loci. First, I isolated and characterized two copies of the circadian rhythm gene, Clock, from Chinook salmon (OtsClock1a and OtsClock1b). Phylogenetic analysis revealed that these copies likely arose subsequent to the salmonid genome-wide duplication event. Each copy contains a polyglutamine repeat motif (PolyQ), an essential binding domain of this transcription factor. However, a 1200bp non-coding segment, showing >90% sequence identity to the Salmo salar Transferrin gene, is located downstream of the OtsClock1a PolyQ, yet absent from OtsClock1b providing evidence for nonhomologous recombination. Another candidate, Ots515NWFSC, shows sequence identity to three salmonid genes central to reproductive development: Gonadotropin-releasing hormone, CYP19b-I, and Ghrelin. I employed OtsClock1b and Ots515NWFSC to test for differentiation in two unique systems: Feather River, California; and Waitaki and Poulter Rivers, New Zealand. Based on length variation in these candidate genes, Feather River fall and spring run Chinook salmon are genetically differentiated. In contrast, these seasonal runs are genetically indistinguishable based on neutral microsatellite loci. Correspondingly, temporally divergent Chinook salmon runs in the Waitaki and Poulter Rivers show greater differentiation based on variation in OtsClock1b and Ots515NWFSC than microsatellite loci. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC are likely under selection in both systems. In addition, I found evidence for a latitudinal cline in two OtsClock1b PolyQ alleles among 42 Chinook salmon runs which is likely maintained by selection and thus may reflect an adaptation to photoperiodic parameters. Lastly, a hierarchical gene diversity analysis of OtsClock1b PolyQ variation revealed that run timing explained 43.7% of the overall genetic variance which contrast sharply with the 8.1% calculated for microsatellite loci. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration timing of Chinook salmon. Close

• 13. [Article] A Review of Fishery Research in the Pacific Area

  It is impossible to place a date on the beginning of fishery research. It no doubt existed in a primitive way among the earliest civilizations. For practical reasons, the scope of this paper is limited ...

  Citation × Citation Citation Abstract Copy Title: A Review of Fishery Research in the Pacific Area Author: Atkinson, Clinton E. Year: 2001 It is impossible to place a date on the beginning of fishery research. It no doubt existed in a primitive way among the earliest civilizations. For practical reasons, the scope of this paper is limited to the four countries bordering the North Pacific--Japan, Canada, Russia and the United States--and to research directed towards a better understanding and management of the fishery resources of commercial value. It is interesting that development of fishery research in three of the four countries was prompted by a serious decline in their salmon runs and by the adoption of hatcheries as a means to restore or maintain the depleted runs. The only difference was in Russia where fishery research began with a decline in sturgeon in the Volga and the Caspian Sea. In the Russian Far East, however, it again was a decline in salmon in the Amur and Sakhalin rivers and all were linked primarily to loss or damage to their freshwater environment. Overfishing and destructive fishing practices were recognized almost from the beginning but it was not until 1917 that the work of Thompson on Pacific halibut led to the development of modern theory of population dynamics for the management of the fisheries. Following are notes on the development of fishery research in each of the four countries. Title: A Review of Fishery Research in the Pacific Area Author: Atkinson, Clinton E. Year: 2001 It is impossible to place a date on the beginning of fishery research. It no doubt existed in a primitive way among the earliest civilizations. For practical reasons, the scope of this paper is limited to the four countries bordering the North Pacific--Japan, Canada, Russia and the United States--and to research directed towards a better understanding and management of the fishery resources of commercial value. It is interesting that development of fishery research in three of the four countries was prompted by a serious decline in their salmon runs and by the adoption of hatcheries as a means to restore or maintain the depleted runs. The only difference was in Russia where fishery research began with a decline in sturgeon in the Volga and the Caspian Sea. In the Russian Far East, however, it again was a decline in salmon in the Amur and Sakhalin rivers and all were linked primarily to loss or damage to their freshwater environment. Overfishing and destructive fishing practices were recognized almost from the beginning but it was not until 1917 that the work of Thompson on Pacific halibut led to the development of modern theory of population dynamics for the management of the fisheries. Following are notes on the development of fishery research in each of the four countries. Close

• 14. [Article] Addressing Fish Uncertainty: The Quest for Rational Decisionmaking

  This paper explores the policy efforts dealing with the problem of declining Pacific Northwest fish runs. Results have been disappointing. Decades of expensive efforts costing billion of dollars have been ...

  Citation × Citation Citation Abstract Copy Title: Addressing Fish Uncertainty: The Quest for Rational Decisionmaking Author: Koss, Patricia, Katz, Mike, Shawcross, Jennifer Year: 2001 This paper explores the policy efforts dealing with the problem of declining Pacific Northwest fish runs. Results have been disappointing. Decades of expensive efforts costing billion of dollars have been relatively ineffective in increasing salmon runs. Many species of wild fish continue to decline or remain significantly below target levels of recovery. The issue of scientific and economic uncertainties is examined. Past and current policies have failed to adequately account for these uncertainties. One overall recommendation of this paper is that policymakers and their advisors should explicitly identify any decision criteria upon which they base their judgments or conclusions. A second recommendation is that policy analysis should be explicit about uncertainties. We offer the eighteen decision rules for fashioning fish recovery decisions in an environment of uncertainty. Title: Addressing Fish Uncertainty: The Quest for Rational Decisionmaking Author: Koss, Patricia, Katz, Mike, Shawcross, Jennifer Year: 2001 This paper explores the policy efforts dealing with the problem of declining Pacific Northwest fish runs. Results have been disappointing. Decades of expensive efforts costing billion of dollars have been relatively ineffective in increasing salmon runs. Many species of wild fish continue to decline or remain significantly below target levels of recovery. The issue of scientific and economic uncertainties is examined. Past and current policies have failed to adequately account for these uncertainties. One overall recommendation of this paper is that policymakers and their advisors should explicitly identify any decision criteria upon which they base their judgments or conclusions. A second recommendation is that policy analysis should be explicit about uncertainties. We offer the eighteen decision rules for fashioning fish recovery decisions in an environment of uncertainty. Close

• 15. [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

• 16. [Article] Economic Interactions of Farmed Salmon and North American Wild Salmon

  Research Paper

  Citation × Citation Citation Abstract Copy Title: Economic Interactions of Farmed Salmon and North American Wild Salmon Author: Knapp, Gunnar, Anderson, James, Roheim, Cathy A. Research Paper Title: Economic Interactions of Farmed Salmon and North American Wild Salmon Author: Knapp, Gunnar, Anderson, James, Roheim, Cathy A. Research Paper Close

• 17. [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

• 18. [Article] Market Interactions between Aquaculture and Common-Property Fisheries: Examining the Empirical Evidence from the Bristol Bay Sockeye Salmon Fishery in Alaska

  The impressive growth of world aquaculture has led to profound transformations in the economic structure of several capture fisheries. Evidence from the Alaska salmon fisheries supports this argument as ...

  Citation × Citation Citation Abstract Copy Title: Market Interactions between Aquaculture and Common-Property Fisheries: Examining the Empirical Evidence from the Bristol Bay Sockeye Salmon Fishery in Alaska Author: Valderrama, Diego, Anderson, James The impressive growth of world aquaculture has led to profound transformations in the economic structure of several capture fisheries. Evidence from the Alaska salmon fisheries supports this argument as a connection has been suggested between the recent trends of declining ex-vessel prices and the rapid development of salmon farming elsewhere in the world. In Bristol Bay, home of the largest sockeye salmon runs in the globe, participation in the limited-entry fishery has declined by approximately 20% since 2001. Likewise, permit market values have plummeted to historic low levels, with economic conditions not likely to improve significantly in the mid-term future. To examine this problem, we develop a formal analytical framework for the study of market interactions between a limited-entry fishery and an aquaculture sector. We adapt the model of regulated open-access developed by Homans and Wilen to examine the implications of aquaculture development on the actions of fishermen and the regulatory sector in a restricted-access setting. Results indicate that the emergence of a low-cost aquaculture sector brings about important structural changes in the restricted-access fishery, rendering limited-entry regulations irrelevant as participation rates decline due to the falling prices. An important implication is that, despite the limited-entry constraint, the fishery moves to an institutional arrangement closer to regulated open access, with resource rents drastically reduced. Model predictions are compared with the empirical evidence available from the Bristol Bay sockeye fishery. The advantages of cooperative management relative to the current competitive structure of the fishery are highlighted. Title: Market Interactions between Aquaculture and Common-Property Fisheries: Examining the Empirical Evidence from the Bristol Bay Sockeye Salmon Fishery in Alaska Author: Valderrama, Diego, Anderson, James The impressive growth of world aquaculture has led to profound transformations in the economic structure of several capture fisheries. Evidence from the Alaska salmon fisheries supports this argument as a connection has been suggested between the recent trends of declining ex-vessel prices and the rapid development of salmon farming elsewhere in the world. In Bristol Bay, home of the largest sockeye salmon runs in the globe, participation in the limited-entry fishery has declined by approximately 20% since 2001. Likewise, permit market values have plummeted to historic low levels, with economic conditions not likely to improve significantly in the mid-term future. To examine this problem, we develop a formal analytical framework for the study of market interactions between a limited-entry fishery and an aquaculture sector. We adapt the model of regulated open-access developed by Homans and Wilen to examine the implications of aquaculture development on the actions of fishermen and the regulatory sector in a restricted-access setting. Results indicate that the emergence of a low-cost aquaculture sector brings about important structural changes in the restricted-access fishery, rendering limited-entry regulations irrelevant as participation rates decline due to the falling prices. An important implication is that, despite the limited-entry constraint, the fishery moves to an institutional arrangement closer to regulated open access, with resource rents drastically reduced. Model predictions are compared with the empirical evidence available from the Bristol Bay sockeye fishery. The advantages of cooperative management relative to the current competitive structure of the fishery are highlighted. Close

• 19. [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

• 20. [Article] Oregon coastal community water supply assessment

  On the Oregon coast, however, the issue of water supply has become paramount, especially given the need to restore instream flows in order to restore coastal salmon runs and meet water quality standards. ...

  Citation × Citation Citation Abstract Copy Title: Oregon coastal community water supply assessment Author: Achterman, Gail, Rolston, Irene, Davis-Born, Renee, Institute for Natural Resources, Gaines, Lisa On the Oregon coast, however, the issue of water supply has become paramount, especially given the need to restore instream flows in order to restore coastal salmon runs and meet water quality standards. With the ebb and flow of population and the economic growth of Oregon coastal communities, three hypotheses have been generated about the ability of these communities to meet future water supply needs. The purpose of this project was to better understand the challenges and opportunities facing coastal community water suppliers as a whole and to ultimately improve the prospects for meeting future water needs. Findings show that contrary to the first hypothesis, most of those interviewed do not think that economic development is constrained by waters supply. However, it does appear that it would be difficult for state economic development officials to match businesses and industries interested in relocating to the Oregon coast with community water supply availability and reliability. Findings also show that the major problem facing community water suppliers in preparing water management and conservation plans cited by interviewees is financial. Though Oregon’s coastal communities face several planning, management, physical, economic, and regulatory challenges in preparing for future water supply needs, numerous partnership, conservation, and research and training opportunities exist. What is needed is an opportunity for a facilitated process of restructuring water supply systems. Title: Oregon coastal community water supply assessment Author: Achterman, Gail, Rolston, Irene, Davis-Born, Renee, Institute for Natural Resources, Gaines, Lisa On the Oregon coast, however, the issue of water supply has become paramount, especially given the need to restore instream flows in order to restore coastal salmon runs and meet water quality standards. With the ebb and flow of population and the economic growth of Oregon coastal communities, three hypotheses have been generated about the ability of these communities to meet future water supply needs. The purpose of this project was to better understand the challenges and opportunities facing coastal community water suppliers as a whole and to ultimately improve the prospects for meeting future water needs. Findings show that contrary to the first hypothesis, most of those interviewed do not think that economic development is constrained by waters supply. However, it does appear that it would be difficult for state economic development officials to match businesses and industries interested in relocating to the Oregon coast with community water supply availability and reliability. Findings also show that the major problem facing community water suppliers in preparing water management and conservation plans cited by interviewees is financial. Though Oregon’s coastal communities face several planning, management, physical, economic, and regulatory challenges in preparing for future water supply needs, numerous partnership, conservation, and research and training opportunities exist. What is needed is an opportunity for a facilitated process of restructuring water supply systems. Close