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• 41. [Article] Banks_etal_2013_Dataset.zip

  Citation × Citation Citation Abstract Copy Title: Banks_etal_2013_Dataset.zip Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Title: Banks_etal_2013_Dataset.zip Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Close

• 42. [Article] FieldNames_Metadata.pdf

  Citation × Citation Citation Abstract Copy Title: FieldNames_Metadata.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Title: FieldNames_Metadata.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Close

• 43. [Article] CompletionReport_Banks.pdf

  Citation × Citation Citation Abstract Copy Title: CompletionReport_Banks.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Title: CompletionReport_Banks.pdf Author: Moyer, Gregory R., Banks, Michael A., Whitcomb, Amelia, Loomis, David, Jackson, Laura S., Theriault, Veronique, Blouin, Michael S. Close

• 44. [Article] Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers

  I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical ...

  Citation × Citation Citation Abstract Copy Title: Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers Author: Lewis, Sierra Koch I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical salmonid-bearing rivers, little documentation exists for anadromous fish presence above potential natural obstacles upstream of Soda Springs Dam. My prediction was that if migratory salmonids are allowed to move upstream of the dam using a new fish ladder they would utilize available upstream spawning habitat. I captured, radio-tagged, and transplanted wild adult summer steelhead, O. mykiss, above Soda Springs Dam and tracked daily movements for 1 year to observe habitat preferences. I also investigated evidence of historical anadromy throughout the North Umpqua River basin using stable isotope analysis of salmon-derived nitrogen (¹⁵N) in foliar samples from Douglas fir trees, P. menziesii, (>100 years old). I tested the hypothesis that I could identify undocumented, historical salmon spawning reaches above natural and anthropogenic obstacles based solely upon δ¹⁵N foliar deposition patterns. While tracking radio-tagged steelhead, I documented holding locations, the timing of spawning activities, and the outmigration of kelts. Tagged fish did not show any extensive movement in the river or tributaries above the dam. Most of the tagged adults showed incremental daily movements near the release site or downstream into the hydropower reservoir but did not travel further than 1 kilometer upstream in the main river channel. I recorded movements and localized activities that suggested some of the fish spawned and subsequently moved downstream towards the Pacific Ocean. My observations indicated that spawning behavior of tagged fish above Soda Springs Dam was delayed several weeks relative to fish spawning below the dam. There was no evidence from telemetry that any fish moved upstream in Fish Creek, the newly accessible habitat of interest in this project. My data suggest that steelhead will use restored habitat above dams, but that re-colonization activities are variable and may be affected by altered flow regimes within the restored habitat upstream of the dam and intra-specific density dependence. My stable isotope data indicated that the foliar δ¹⁵N deposition patterns were confounded with elevation. I documented potential "salmon-derived" false positives on the Umpqua National Forest above impassable waterfalls. Overall I found that foliar δ¹⁵N deposition patterns were highly variable and unexpectedly indicated a statistically significant negative correlation of foliar δ¹⁵N values with historical salmon presence. My linear mixed-effects modeling suggests that the presence of salmon is the most important indicator of foliar δ¹⁵N values, rather than the proximity of a sampled tree to stream flow above or below migratory barriers. I was not able to use the mixed effects model to identify previously undocumented salmon spawning habitat. My results from the foliar technique suggest that the method may not be universally applicable as has been previously suggested in the literature. Title: Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers Author: Lewis, Sierra Koch I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical salmonid-bearing rivers, little documentation exists for anadromous fish presence above potential natural obstacles upstream of Soda Springs Dam. My prediction was that if migratory salmonids are allowed to move upstream of the dam using a new fish ladder they would utilize available upstream spawning habitat. I captured, radio-tagged, and transplanted wild adult summer steelhead, O. mykiss, above Soda Springs Dam and tracked daily movements for 1 year to observe habitat preferences. I also investigated evidence of historical anadromy throughout the North Umpqua River basin using stable isotope analysis of salmon-derived nitrogen (¹⁵N) in foliar samples from Douglas fir trees, P. menziesii, (>100 years old). I tested the hypothesis that I could identify undocumented, historical salmon spawning reaches above natural and anthropogenic obstacles based solely upon δ¹⁵N foliar deposition patterns. While tracking radio-tagged steelhead, I documented holding locations, the timing of spawning activities, and the outmigration of kelts. Tagged fish did not show any extensive movement in the river or tributaries above the dam. Most of the tagged adults showed incremental daily movements near the release site or downstream into the hydropower reservoir but did not travel further than 1 kilometer upstream in the main river channel. I recorded movements and localized activities that suggested some of the fish spawned and subsequently moved downstream towards the Pacific Ocean. My observations indicated that spawning behavior of tagged fish above Soda Springs Dam was delayed several weeks relative to fish spawning below the dam. There was no evidence from telemetry that any fish moved upstream in Fish Creek, the newly accessible habitat of interest in this project. My data suggest that steelhead will use restored habitat above dams, but that re-colonization activities are variable and may be affected by altered flow regimes within the restored habitat upstream of the dam and intra-specific density dependence. My stable isotope data indicated that the foliar δ¹⁵N deposition patterns were confounded with elevation. I documented potential "salmon-derived" false positives on the Umpqua National Forest above impassable waterfalls. Overall I found that foliar δ¹⁵N deposition patterns were highly variable and unexpectedly indicated a statistically significant negative correlation of foliar δ¹⁵N values with historical salmon presence. My linear mixed-effects modeling suggests that the presence of salmon is the most important indicator of foliar δ¹⁵N values, rather than the proximity of a sampled tree to stream flow above or below migratory barriers. I was not able to use the mixed effects model to identify previously undocumented salmon spawning habitat. My results from the foliar technique suggest that the method may not be universally applicable as has been previously suggested in the literature. Close

• 45. [Article] Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing

  Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental ...

  Citation × Citation Citation Abstract Copy Title: Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing Author: Bellinger, M. Renee Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental gaps in our knowledge remain. In my dissertation, I applied emerging genetic technologies to conduct a top-down and bottom-up investigation of animal movement and cue perception. First, in partnership with Project CROOS and the California Salmon Genetic Stock Identification project, stock-specific, marine migratory distributions of Chinook salmon (Oncorhynchus tshawytscha) were characterized for five consecutive months (2010) over 1000 km of coastline. A statistical model was developed to provide measures of relative stockspecific abundance, insights into broad factors that influence migratory distribution, and for fisheries management applications. For the second component of my dissertation, I studied specialized olfactory cells of salmonids that are proposed to contain nanometer-sized magnetite crystals that interact with earth strength magnetic fields to transduce them into neural signals. The transcriptome profiles of candidate magnetoreceptor and non-magnetic cells isolated from olfactory rosette tissue, whole olfactory rosettes, and blood and muscle tissue were characterized from ~661 million Illumina RNA-seq reads. A total of 1,006 differentially expressed genes were identified in the magnetic cell sample type. Results, consistent with having identified genes involved in magnetite crystal formation in fish, were used to develop a genetic model of magnetic sensory perception. Finally, to provide insights into olfaction-based homing that takes place in freshwater, the olfactory repertoire of salmonids was inferred from the Rainbow trout (O. mykiss) genome and compared to that of 15 other teleosts and the jawless fish, sea lamprey (Petromyzon marinus), an ancient species. The abundance and diversity of trace amine-associated and V2R-like genes suggests that these classes of chemoreceptors have biological importance. These findings have relevance for resolving if salmon and other marine organisms imprint on magnetic fields, and contribute to our understanding of how magnetic sense, olfaction, and genetic programming are involved in migratory distributions. Title: Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing Author: Bellinger, M. Renee Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental gaps in our knowledge remain. In my dissertation, I applied emerging genetic technologies to conduct a top-down and bottom-up investigation of animal movement and cue perception. First, in partnership with Project CROOS and the California Salmon Genetic Stock Identification project, stock-specific, marine migratory distributions of Chinook salmon (Oncorhynchus tshawytscha) were characterized for five consecutive months (2010) over 1000 km of coastline. A statistical model was developed to provide measures of relative stockspecific abundance, insights into broad factors that influence migratory distribution, and for fisheries management applications. For the second component of my dissertation, I studied specialized olfactory cells of salmonids that are proposed to contain nanometer-sized magnetite crystals that interact with earth strength magnetic fields to transduce them into neural signals. The transcriptome profiles of candidate magnetoreceptor and non-magnetic cells isolated from olfactory rosette tissue, whole olfactory rosettes, and blood and muscle tissue were characterized from ~661 million Illumina RNA-seq reads. A total of 1,006 differentially expressed genes were identified in the magnetic cell sample type. Results, consistent with having identified genes involved in magnetite crystal formation in fish, were used to develop a genetic model of magnetic sensory perception. Finally, to provide insights into olfaction-based homing that takes place in freshwater, the olfactory repertoire of salmonids was inferred from the Rainbow trout (O. mykiss) genome and compared to that of 15 other teleosts and the jawless fish, sea lamprey (Petromyzon marinus), an ancient species. The abundance and diversity of trace amine-associated and V2R-like genes suggests that these classes of chemoreceptors have biological importance. These findings have relevance for resolving if salmon and other marine organisms imprint on magnetic fields, and contribute to our understanding of how magnetic sense, olfaction, and genetic programming are involved in migratory distributions. Close

• 46. [Article] Long-distance migration of prey synchronizes demographic rates of top predators across broad spatial scales

  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 author(s) and ...

  Citation × Citation Citation Abstract Copy Title: Long-distance migration of prey synchronizes demographic rates of top predators across broad spatial scales Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. 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 author(s) and published by John Wiley & Sons, Inc. on behalf of Ecological Society of America. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Title: Long-distance migration of prey synchronizes demographic rates of top predators across broad spatial scales Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. 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 author(s) and published by John Wiley & Sons, Inc. on behalf of Ecological Society of America. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Close

• 47. [Article] Urban and rural-residential land uses : their role in watershed health and the rehabilitation of Oregon's wild salmonids

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

  Citation × Citation Citation Abstract Copy Title: Urban and rural-residential land uses : their role in watershed health and the rehabilitation of Oregon's wild salmonids Author: Independent Multidisciplinary Science Team This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Title: Urban and rural-residential land uses : their role in watershed health and the rehabilitation of Oregon's wild salmonids Author: Independent Multidisciplinary Science Team This report was prepared by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Close

• 48. [Article] On the reproductive success of early-generation hatchery fish in the wild

  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: On the reproductive success of early-generation hatchery fish in the wild Author: Christie, Mark R., Ford, Michael J., Blouin, Michael S. 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%291752-4571. Title: On the reproductive success of early-generation hatchery fish in the wild Author: Christie, Mark R., Ford, Michael J., Blouin, Michael S. 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%291752-4571. Close

• 49. [Article] WardLongDistanceMigration.pdf

  Citation × Citation Citation Abstract Copy Title: WardLongDistanceMigration.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Title: WardLongDistanceMigration.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Close

• 50. [Article] WardLongDistanceMigrationAppendixS1.pdf

  Citation × Citation Citation Abstract Copy Title: WardLongDistanceMigrationAppendixS1.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Title: WardLongDistanceMigrationAppendixS1.pdf Author: Marshall, K. N., Balcomb, K. C. III, Dahlheim, M. E., Emmons, C. K., Waite, J. M., Chasco, B. E., Ward, E. J. Close