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• 21. [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

• 22. [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

• 23. [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

• 24. [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

• 25. [Image] "Iron chink" in operation

  	This slide represents a catch of salmon on the floor of the cannery. In the larger and more modern plants very specialized machinery is used. The first machine through which the salmon are run is the "iron ...
  	Citation × Citation Citation Abstract Copy Title: "Iron chink" in operation Year: 1925 This slide represents a catch of salmon on the floor of the cannery. In the larger and more modern plants very specialized machinery is used. The first machine through which the salmon are run is the "iron chink". This removes the head and the fins and opens and cleans the fish. The work is done very rapidly and quite completely. The cleaning, however, must usually be completed by hand, which process removes clotted blood and other waste material. Title: "Iron chink" in operation Year: 1925 This slide represents a catch of salmon on the floor of the cannery. In the larger and more modern plants very specialized machinery is used. The first machine through which the salmon are run is the "iron chink". This removes the head and the fins and opens and cleans the fish. The work is done very rapidly and quite completely. The cleaning, however, must usually be completed by hand, which process removes clotted blood and other waste material. Close

• 26. [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

• 27. [Article] Coos River Basin Master Plan for Angler Access and Associated Recreational Uses 1967

  Abstract -- The Coos River system is composed of the Coos River and the Millicoma River. The Coos drains the southeast portion of the basin and the Millicoma the northeast. The two rivers fork at river ...

  Citation × Citation Citation Abstract Copy Title: Coos River Basin Master Plan for Angler Access and Associated Recreational Uses 1967 Abstract -- The Coos River system is composed of the Coos River and the Millicoma River. The Coos drains the southeast portion of the basin and the Millicoma the northeast. The two rivers fork at river mile 5.5 above its confluence with Coos Bay at Eastside. The principle fisheries in the Coos system are winter steelhead, striped bass, shad, coho salmon, sea-run cutthroat trout and rainbow trout. Title: Coos River Basin Master Plan for Angler Access and Associated Recreational Uses 1967 Abstract -- The Coos River system is composed of the Coos River and the Millicoma River. The Coos drains the southeast portion of the basin and the Millicoma the northeast. The two rivers fork at river mile 5.5 above its confluence with Coos Bay at Eastside. The principle fisheries in the Coos system are winter steelhead, striped bass, shad, coho salmon, sea-run cutthroat trout and rainbow trout. Close

• 28. [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

• 29. [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

• 30. [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