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• 1. [Article] Trophically transmitted parasites as ecosystem indicators : relationships among parasite community structure, juvenile salmon diet composition, and ocean conditions

  Recent research conducted throughout the Northern California Current (NCC) on the ecology of Pacific salmon (Oncorhynchus spp.) indicates that variable ocean conditions affect the community composition ...

  Citation × Citation Citation Abstract Copy Title: Trophically transmitted parasites as ecosystem indicators : relationships among parasite community structure, juvenile salmon diet composition, and ocean conditions Author: Losee, James P. Recent research conducted throughout the Northern California Current (NCC) on the ecology of Pacific salmon (Oncorhynchus spp.) indicates that variable ocean conditions affect the community composition of zooplankton in the nearshore environment which, in turn, can affect the quality of prey for fish, sea birds and mammals. Interannual variability in the quality and composition of the copepod community in the NCC during early marine residency of some Pacific salmon populations is related to survival to adulthood. However, copepods make up a small portion of the diet of coho and Chinook salmon, and the mechanistic linkages between ocean climate, zooplankton composition and salmon prey remain unclear. Parasite analysis provides a supplement to traditional diet analysis that can describe the foraging history of a host species. Coho salmon (O. kisutch) and Chinook salmon (O. tshawytscha) serve as hosts to an array of marine parasites acquired through consumption of infected intermediate hosts such as copepods, euphausiids, and planktivorous fishes. Causing little or no harm to their salmon host, the presence of trophically transmitted parasites provides information on the dietary history of their salmonid host beyond the 24 hours associated with traditional diet analysis. This study (1) examined differences in feeding behavior of coho and Chinook salmon during their early marine residency using both stomach and parasite community analyses and (2) tested the hypothesis that variability in ocean circulation patterns (measured through the Pacific Decadal Oscillation, sea surface temperature (SST) and Bakun's upwelling index) and copepod species composition are related to variability in the community structure of trophically transmitted marine parasites found in juvenile salmon. I compared the abundance and species composition of parasites recovered from juvenile Columbia River coho and upper Columbia River summer and fall Chinook salmon captured off the coast of Washington from 2002 to 2009. I also compared interannual variability in parasite assemblages to physical and biological indices of ocean conditions. Coho and Chinook salmon consumed similar prey taxa; however, the species richness and abundance of trophically transmitted parasites indicated that Chinook salmon consumed a greater diversity and abundance of infected prey. In addition, differences in the abundance of fish in the diet and Anisakis simplex, a parasitic nematode known to infect salmon through fish consumption, suggest that Chinook salmon consistently consumed more fish prey than coho. In contrast, coho appeared to consume more euphausiids as indicated by stomach content analysis and increased abundance of the euphausiid parasite, Rhadinorhynchus trachuri. Shifts in the parasite community composition of both coho and Chinook salmon were related to interannual variability in SST and the biomass of southern-origin copepods (r > 0.7, P < 0.05). The acanthocephalan R. trachuri and a tetraphyllid cestode were associated with "warm" SSTs and greater biomass of lipid-poor, subtropical copepods while the nematode A. simplex was more abundant in years of "cold" SST and a relatively low biomass of subtropical copepods. These results provide novel insight into differences in the diet of Columbia River coho and Chinook salmon and illustrate linkages between ocean climate, zooplankton community composition and salmon diet during early marine residency. Title: Trophically transmitted parasites as ecosystem indicators : relationships among parasite community structure, juvenile salmon diet composition, and ocean conditions Author: Losee, James P. Recent research conducted throughout the Northern California Current (NCC) on the ecology of Pacific salmon (Oncorhynchus spp.) indicates that variable ocean conditions affect the community composition of zooplankton in the nearshore environment which, in turn, can affect the quality of prey for fish, sea birds and mammals. Interannual variability in the quality and composition of the copepod community in the NCC during early marine residency of some Pacific salmon populations is related to survival to adulthood. However, copepods make up a small portion of the diet of coho and Chinook salmon, and the mechanistic linkages between ocean climate, zooplankton composition and salmon prey remain unclear. Parasite analysis provides a supplement to traditional diet analysis that can describe the foraging history of a host species. Coho salmon (O. kisutch) and Chinook salmon (O. tshawytscha) serve as hosts to an array of marine parasites acquired through consumption of infected intermediate hosts such as copepods, euphausiids, and planktivorous fishes. Causing little or no harm to their salmon host, the presence of trophically transmitted parasites provides information on the dietary history of their salmonid host beyond the 24 hours associated with traditional diet analysis. This study (1) examined differences in feeding behavior of coho and Chinook salmon during their early marine residency using both stomach and parasite community analyses and (2) tested the hypothesis that variability in ocean circulation patterns (measured through the Pacific Decadal Oscillation, sea surface temperature (SST) and Bakun's upwelling index) and copepod species composition are related to variability in the community structure of trophically transmitted marine parasites found in juvenile salmon. I compared the abundance and species composition of parasites recovered from juvenile Columbia River coho and upper Columbia River summer and fall Chinook salmon captured off the coast of Washington from 2002 to 2009. I also compared interannual variability in parasite assemblages to physical and biological indices of ocean conditions. Coho and Chinook salmon consumed similar prey taxa; however, the species richness and abundance of trophically transmitted parasites indicated that Chinook salmon consumed a greater diversity and abundance of infected prey. In addition, differences in the abundance of fish in the diet and Anisakis simplex, a parasitic nematode known to infect salmon through fish consumption, suggest that Chinook salmon consistently consumed more fish prey than coho. In contrast, coho appeared to consume more euphausiids as indicated by stomach content analysis and increased abundance of the euphausiid parasite, Rhadinorhynchus trachuri. Shifts in the parasite community composition of both coho and Chinook salmon were related to interannual variability in SST and the biomass of southern-origin copepods (r > 0.7, P < 0.05). The acanthocephalan R. trachuri and a tetraphyllid cestode were associated with "warm" SSTs and greater biomass of lipid-poor, subtropical copepods while the nematode A. simplex was more abundant in years of "cold" SST and a relatively low biomass of subtropical copepods. These results provide novel insight into differences in the diet of Columbia River coho and Chinook salmon and illustrate linkages between ocean climate, zooplankton community composition and salmon diet during early marine residency. Close

• 2. [Article] Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry

  Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing ...

  Citation × Citation Citation Abstract Copy Title: Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry Author: Campbell, Lance A. Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing hypotheses about the estuary’s importance as a salmon rearing environment. Many contemporary tagging studies indicate that salmon residency within the estuary is short (< 1 week) and that mortality of estuarine migrants is a significant impediment to recovery of depressed salmon stocks. On the other hand, life history interpretations from fish scales collected early in the twentieth century suggest that juvenile Chinook salmon reared extensively in the estuary, leading some to hypothesize that life history variation has been constrained by anthropogenic changes in the Columbia River basin. To test these hypotheses we first validated previous methods of life history interpretation by comparing the results of otolith chemistry, scale chemistry, and scale morphology from juvenile salmon collected during monthly beach seine surveys in 2003. Although scale and otolith chemistry were strongly correlated, and scale chemistry was an accurate indicator of salt-water entry, scale morphometric characteristics did not coincide consistently with the time of salmon entry into brackish water. We measured Strontium 86 and Calcium 43 in salmon otoliths collected in the lower Columbia River estuary in 2003-05 to quantify the period of salt-water residency of juvenile salmon and to back-calculate their size at salt-water entry. The estimated salt-water residency of juvenile Chinook ranged from 0-176 days with a mean residence time of 54, 67 and 30 days in 2003, 2004 and 2005, respectively. Chinook salmon that resided in salt water for more than 30 days comprised 55, 51 and 30% of the total estuary beach seine collections during each of these years. Forty to fifty percent of Chinook salmon had entered the saline portion of the estuary at a fork length < 60 mm. Furthermore we found a negative relationship between the size and time of entry with residency, where smaller earlier migrants on average resided for longer periods then larger late migrants. Peak migration times occurred in May, and 90% of the outmigration was completed by August 30 in all years. This pattern is substantially truncated relative to the results of a 1914-1916 salmon life-history survey, which showed that the historical outmigration period lasted well into the fall and was characterized by late pulses of new recruits into the lower estuary. Nonetheless, recent otolith results indicate that subyearling Chinook salmon use the saline portion of the estuary in a high proportion and for extended periods of time in contrast to short residency times reported by contemporary tagging and marking studies. Title: Life histories of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Columbia River estuary as inferred from scale and otolith microchemistry Author: Campbell, Lance A. Despite evidence that juvenile Chinook salmon (Oncorhynchus tshawytscha) utilize North Pacific estuaries for growth and salinity acclimation, research in the Columbia River estuary has lead to opposing hypotheses about the estuary’s importance as a salmon rearing environment. Many contemporary tagging studies indicate that salmon residency within the estuary is short (< 1 week) and that mortality of estuarine migrants is a significant impediment to recovery of depressed salmon stocks. On the other hand, life history interpretations from fish scales collected early in the twentieth century suggest that juvenile Chinook salmon reared extensively in the estuary, leading some to hypothesize that life history variation has been constrained by anthropogenic changes in the Columbia River basin. To test these hypotheses we first validated previous methods of life history interpretation by comparing the results of otolith chemistry, scale chemistry, and scale morphology from juvenile salmon collected during monthly beach seine surveys in 2003. Although scale and otolith chemistry were strongly correlated, and scale chemistry was an accurate indicator of salt-water entry, scale morphometric characteristics did not coincide consistently with the time of salmon entry into brackish water. We measured Strontium 86 and Calcium 43 in salmon otoliths collected in the lower Columbia River estuary in 2003-05 to quantify the period of salt-water residency of juvenile salmon and to back-calculate their size at salt-water entry. The estimated salt-water residency of juvenile Chinook ranged from 0-176 days with a mean residence time of 54, 67 and 30 days in 2003, 2004 and 2005, respectively. Chinook salmon that resided in salt water for more than 30 days comprised 55, 51 and 30% of the total estuary beach seine collections during each of these years. Forty to fifty percent of Chinook salmon had entered the saline portion of the estuary at a fork length < 60 mm. Furthermore we found a negative relationship between the size and time of entry with residency, where smaller earlier migrants on average resided for longer periods then larger late migrants. Peak migration times occurred in May, and 90% of the outmigration was completed by August 30 in all years. This pattern is substantially truncated relative to the results of a 1914-1916 salmon life-history survey, which showed that the historical outmigration period lasted well into the fall and was characterized by late pulses of new recruits into the lower estuary. Nonetheless, recent otolith results indicate that subyearling Chinook salmon use the saline portion of the estuary in a high proportion and for extended periods of time in contrast to short residency times reported by contemporary tagging and marking studies. Close

• 3. [Article] Multivariate Models of Adult Pacific Salmon Returns

  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 Public ...

  Citation × Citation Citation Abstract Copy Title: Multivariate Models of Adult Pacific Salmon Returns Author: Morgan, Cheryl, Litz, Marisa, Burke, Brian J., Peterson, William T., Daly, Elizabeth A., Beckman, Brian 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 published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action. Title: Multivariate Models of Adult Pacific Salmon Returns Author: Morgan, Cheryl, Litz, Marisa, Burke, Brian J., Peterson, William T., Daly, Elizabeth A., Beckman, Brian 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 published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action. Close

• 4. [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

• 5. [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

• 6. [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

• 7. [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

• 8. [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

• 9. [Article] Bioenergetics-based predator-prey relationships between piscivorous birds and juvenile salmonids in the Columbia River estuary

  This dissertation focuses on the predator-prey relationship between two species of avian predators, Caspian terns (Hydroprogne caspia) and double-crested cormorants (Phalacrocorax auritus), and one of ...

  Citation × Citation Citation Abstract Copy Title: Bioenergetics-based predator-prey relationships between piscivorous birds and juvenile salmonids in the Columbia River estuary Author: Lyons, Donald E. This dissertation focuses on the predator-prey relationship between two species of avian predators, Caspian terns (Hydroprogne caspia) and double-crested cormorants (Phalacrocorax auritus), and one of their important prey types, juvenile salmonids (Oncorhynchus spp.), in the Columbia River estuary of Oregon and Washington states during the period 1998 – 2007. I used a data-rich bioenergetics framework to estimate juvenile salmonid consumption by these two avian predators, assessed impacts to at-risk salmonid populations by estimating salmonid mortality rates due to avian predation, and estimated potential demographic benefits to salmonids if avian predation were reduced. The managed relocation of the Caspian tern colony from Rice Island to East Sand Island, lower in the Columbia River estuary, reduced tern predation on salmonids from over 11 million smolts consumed annually to 4 – 7 million, but those benefits accrued primarily to sub-yearling Chinook salmon (O. tshawytscha). Combined consumption of juvenile salmonids by Caspian terns and double-crested cormorants in the Columbia River estuary was ca. 7 – 15 million smolts per year during 2006-2007, causing an 8 – 17% mortality rate among smolts migrating through the estuary, with higher mortality rates for steelhead (O. mykiss) and coho salmon (O. kisutch). Under a potential management scenario to reduce avian predation by both species, improvements in the average annual population growth rate (λ) of salmonids ranged from 0.4% for sub-yearling Chinook to 3.1% for coho. These improvements are generally less than what is possible from altered hydropower system operation within the Columbia Basin for salmonid populations that are more severely affected by dams. For a few salmonid populations, reduced avian predation might contribute to stabilizing the population (λ = 1), but would need to be part of a broader recovery strategy to ensure population growth and recovery (λ > 1). Climate was an important factor modulating Caspian tern predation on salmonids, with greater consumption of smolts occurring in years of cooler ocean conditions and higher Columbia River flows. Climate did not contribute to variation in consumption of salmonids by cormorants, perhaps due to the larger effect of growth in the size of the cormorant colony during the study period. Due to current trends in colony size (terns: stable, cormorants: increasing) and the planned dispersal of a portion of the tern population, cormorant predation will likely be a more significant mortality factor for Columbia Basin salmonids in the future than will tern predation. A critical unknown factor remains; that is the degree to which reductions in avian predation on salmonids might be compensated for by other salmonid mortality factors. Title: Bioenergetics-based predator-prey relationships between piscivorous birds and juvenile salmonids in the Columbia River estuary Author: Lyons, Donald E. This dissertation focuses on the predator-prey relationship between two species of avian predators, Caspian terns (Hydroprogne caspia) and double-crested cormorants (Phalacrocorax auritus), and one of their important prey types, juvenile salmonids (Oncorhynchus spp.), in the Columbia River estuary of Oregon and Washington states during the period 1998 – 2007. I used a data-rich bioenergetics framework to estimate juvenile salmonid consumption by these two avian predators, assessed impacts to at-risk salmonid populations by estimating salmonid mortality rates due to avian predation, and estimated potential demographic benefits to salmonids if avian predation were reduced. The managed relocation of the Caspian tern colony from Rice Island to East Sand Island, lower in the Columbia River estuary, reduced tern predation on salmonids from over 11 million smolts consumed annually to 4 – 7 million, but those benefits accrued primarily to sub-yearling Chinook salmon (O. tshawytscha). Combined consumption of juvenile salmonids by Caspian terns and double-crested cormorants in the Columbia River estuary was ca. 7 – 15 million smolts per year during 2006-2007, causing an 8 – 17% mortality rate among smolts migrating through the estuary, with higher mortality rates for steelhead (O. mykiss) and coho salmon (O. kisutch). Under a potential management scenario to reduce avian predation by both species, improvements in the average annual population growth rate (λ) of salmonids ranged from 0.4% for sub-yearling Chinook to 3.1% for coho. These improvements are generally less than what is possible from altered hydropower system operation within the Columbia Basin for salmonid populations that are more severely affected by dams. For a few salmonid populations, reduced avian predation might contribute to stabilizing the population (λ = 1), but would need to be part of a broader recovery strategy to ensure population growth and recovery (λ > 1). Climate was an important factor modulating Caspian tern predation on salmonids, with greater consumption of smolts occurring in years of cooler ocean conditions and higher Columbia River flows. Climate did not contribute to variation in consumption of salmonids by cormorants, perhaps due to the larger effect of growth in the size of the cormorant colony during the study period. Due to current trends in colony size (terns: stable, cormorants: increasing) and the planned dispersal of a portion of the tern population, cormorant predation will likely be a more significant mortality factor for Columbia Basin salmonids in the future than will tern predation. A critical unknown factor remains; that is the degree to which reductions in avian predation on salmonids might be compensated for by other salmonid mortality factors. Close

• 10. [Article] Columbia Basin Heritage Fish Consumption Rates

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10745

  Citation × Citation Citation Abstract Copy Title: Columbia Basin Heritage Fish Consumption Rates Author: Harper, Barbara L., Walker, Deward E., Jr. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10745 Title: Columbia Basin Heritage Fish Consumption Rates Author: Harper, Barbara L., Walker, Deward E., Jr. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10745 Close