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• 101. [Article] Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary

  This is the publisher’s final pdf. The published article is copyrighted by National Marine Fisheries Service, NOAA, Scientific Publications Office and can be found at: http://fishbull.noaa.gov/. To the ...

  Citation × Citation Citation Abstract Copy Title: Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary Author: Litz, Marisa N. C., Weitkamp, Laurie A., Bentley, Paul J. This is the publisher’s final pdf. The published article is copyrighted by National Marine Fisheries Service, NOAA, Scientific Publications Office and can be found at: http://fishbull.noaa.gov/. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Title: Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary Author: Litz, Marisa N. C., Weitkamp, Laurie A., Bentley, Paul J. This is the publisher’s final pdf. The published article is copyrighted by National Marine Fisheries Service, NOAA, Scientific Publications Office and can be found at: http://fishbull.noaa.gov/. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Close

• 102. [Article] Viruses infecting salmonid fishes from Oregon : A. The occurrence and distribution of infectious pancreatic necrosis virus. B. The development of an attenuated strain of infectious hematopoietic necrosis virus (IHNV) for immunization of salmonids

  The occurrence and distribution of fish viruses in Oregon were determined by the examination of anadromous and fresh water salmonids. Infectious pancreatic necrosis virus (IPNV) was isolated and identified ...

  Citation × Citation Citation Abstract Copy Title: Viruses infecting salmonid fishes from Oregon : A. The occurrence and distribution of infectious pancreatic necrosis virus. B. The development of an attenuated strain of infectious hematopoietic necrosis virus (IHNV) for immunization of salmonids Author: Tebbit, Guy Lee The occurrence and distribution of fish viruses in Oregon were determined by the examination of anadromous and fresh water salmonids. Infectious pancreatic necrosis virus (IPNV) was isolated and identified from asymptomatic adult coho (Oncorhynchus kisutch) and chinook (0. tshawytscha) salmon returning to the Columbia River system. Infectious pancreatic necrosis virus was also identified as the causative agent of severe losses of eastern brook trout juveniles (Salvelinus fontinalis) at the Fall River trout hatchery in central Oregon. This was the first documented IPNV epizootic in fish from Oregon. A high incidence of IPNV was detected in eastern brook trout populations from central Oregon indicating that this virus poses a threat to the rearing of that species in Oregon. An attenuated strain of infectious hematopoietic necrosis virus (IHNV) was developed for use as a water-borne vaccine for the control of IHNV disease. This water-brone vaccine is easily administered as an immunizing agent by direct addition to the water containing fish. The attenuated IHNV water-borne vaccine strain was determined to be one hundred three times less virulent than the wild type strain from which it was derived. This vaccine was proven to be efficacious against high levels of both water route and injected challenges of virulent wild type virus in kokanee (0. nerka) and sockeye salmon (0. nerka). Other parameters for the development of an effective vaccine preparation were also tested. An optimal exposure period to the immunizing virus of 48 hours was determined as were the minimum immunizing dose for sockeye and chinook salmon. The attenuated IHNV water-borne vaccine produced immunity with a duration of at least 110 days and was shown to provide protection to sockeye salmon challenged with four isolates of virulent IHNV from different geographic locations. Another method of immunization, vacuum infiltration, was tested using a second strain of attenuated IHNV as an immunizing agent. Even though this method of immunization was effective in eliciting a protective immune response in chinook and kokanee salmon, it did not produce the level of protection provided by the attenuated IHNV water-borne vaccine. Title: Viruses infecting salmonid fishes from Oregon : A. The occurrence and distribution of infectious pancreatic necrosis virus. B. The development of an attenuated strain of infectious hematopoietic necrosis virus (IHNV) for immunization of salmonids Author: Tebbit, Guy Lee The occurrence and distribution of fish viruses in Oregon were determined by the examination of anadromous and fresh water salmonids. Infectious pancreatic necrosis virus (IPNV) was isolated and identified from asymptomatic adult coho (Oncorhynchus kisutch) and chinook (0. tshawytscha) salmon returning to the Columbia River system. Infectious pancreatic necrosis virus was also identified as the causative agent of severe losses of eastern brook trout juveniles (Salvelinus fontinalis) at the Fall River trout hatchery in central Oregon. This was the first documented IPNV epizootic in fish from Oregon. A high incidence of IPNV was detected in eastern brook trout populations from central Oregon indicating that this virus poses a threat to the rearing of that species in Oregon. An attenuated strain of infectious hematopoietic necrosis virus (IHNV) was developed for use as a water-borne vaccine for the control of IHNV disease. This water-brone vaccine is easily administered as an immunizing agent by direct addition to the water containing fish. The attenuated IHNV water-borne vaccine strain was determined to be one hundred three times less virulent than the wild type strain from which it was derived. This vaccine was proven to be efficacious against high levels of both water route and injected challenges of virulent wild type virus in kokanee (0. nerka) and sockeye salmon (0. nerka). Other parameters for the development of an effective vaccine preparation were also tested. An optimal exposure period to the immunizing virus of 48 hours was determined as were the minimum immunizing dose for sockeye and chinook salmon. The attenuated IHNV water-borne vaccine produced immunity with a duration of at least 110 days and was shown to provide protection to sockeye salmon challenged with four isolates of virulent IHNV from different geographic locations. Another method of immunization, vacuum infiltration, was tested using a second strain of attenuated IHNV as an immunizing agent. Even though this method of immunization was effective in eliciting a protective immune response in chinook and kokanee salmon, it did not produce the level of protection provided by the attenuated IHNV water-borne vaccine. Close

• 103. [Article] Steelhead Escapement Monitoring In the Upper Grande Ronde River - Annual Technical Report 2011

  Abstract -- The UGRR basin supports a population of summer steelhead that has been segregated from three other populations in the entire Grande Ronde River basin based on topographic, genetic, observational, ...

  Citation × Citation Citation Abstract Copy Title: Steelhead Escapement Monitoring In the Upper Grande Ronde River - Annual Technical Report 2011 Abstract -- The UGRR basin supports a population of summer steelhead that has been segregated from three other populations in the entire Grande Ronde River basin based on topographic, genetic, observational, and other evidence of interactions. Historically, the Grande Ronde River was one of the more significant anadromous fish producing rivers in the Columbia River Basin. Summer steelhead in the Grande Ronde River basin compose part of the Snake River Distinct Population Segment (DPS) and are listed as threatened under the Endangered Species Act (62 FR 43937; August 18,1997). Despite recovery efforts, these populations remain depressed relative to historic levels. This project annually evaluates summer steelhead population abundance for the UGRR by conducting surveys of redds and spawning activity. These surveys provide the data needed to estimate adult steelhead escapement, improve our understanding of habitat utilization, and contribute to productivity and survival estimates for this population. Steelhead were monitored using a probabilistic sampling approach that incorporates a sample-site selection procedure created for the Environmental Protection Agency’s environmental monitoring and assessment program (EMAP). We used this EMAP design to select sample sites for status and trend monitoring of steelhead redds within the UGRR watershed. This method allowed us to sample spatially balanced survey sites distributed within the basin, and followed the Oregon Plan for Salmon and Watersheds Monitoring Program approach (Stevens 2002). ODFW- Eastern Oregon Fish Research (EOFR). BPA contract # IGC 51891 Title: Steelhead Escapement Monitoring In the Upper Grande Ronde River - Annual Technical Report 2011 Abstract -- The UGRR basin supports a population of summer steelhead that has been segregated from three other populations in the entire Grande Ronde River basin based on topographic, genetic, observational, and other evidence of interactions. Historically, the Grande Ronde River was one of the more significant anadromous fish producing rivers in the Columbia River Basin. Summer steelhead in the Grande Ronde River basin compose part of the Snake River Distinct Population Segment (DPS) and are listed as threatened under the Endangered Species Act (62 FR 43937; August 18,1997). Despite recovery efforts, these populations remain depressed relative to historic levels. This project annually evaluates summer steelhead population abundance for the UGRR by conducting surveys of redds and spawning activity. These surveys provide the data needed to estimate adult steelhead escapement, improve our understanding of habitat utilization, and contribute to productivity and survival estimates for this population. Steelhead were monitored using a probabilistic sampling approach that incorporates a sample-site selection procedure created for the Environmental Protection Agency’s environmental monitoring and assessment program (EMAP). We used this EMAP design to select sample sites for status and trend monitoring of steelhead redds within the UGRR watershed. This method allowed us to sample spatially balanced survey sites distributed within the basin, and followed the Oregon Plan for Salmon and Watersheds Monitoring Program approach (Stevens 2002). ODFW- Eastern Oregon Fish Research (EOFR). BPA contract # IGC 51891 Close

• 104. [Article] Systematics, variation, distribution, and biology of lampreys of the genus Lampetra in Oregon

  Based on the number of velar tentacles and the form of longitudinal lingual laminae found in Lampetra (Entosphenus) t. tridentata and its closely related forms, the taxon Entosphenus should not be considered ...

  Citation × Citation Citation Abstract Copy Title: Systematics, variation, distribution, and biology of lampreys of the genus Lampetra in Oregon Author: Kan, Ting Tien Based on the number of velar tentacles and the form of longitudinal lingual laminae found in Lampetra (Entosphenus) t. tridentata and its closely related forms, the taxon Entosphenus should not be considered as a genus as commonly adopted, but, along with the taxa Lethenteron and Lampetra, should be regarded as a subgenus of the genus Lampetra. The genus Lampetra is distinct for various reasons, including particularly the character that no cusps are present in the area distal to the lateral circumorals. Six nominal species, belonging to the subgenera Entosphenus and Lampetra, have been known to occur in four of the seven major drainage systems of Oregon. The anadromous L. (E.) t.tridentata, is widespread in the Columbia River and Coastal drainage systems, occurring in most streams with access to the ocean regardless of distance to the ocean, as long as suitable spawning grounds and ammocoete habitats are present. Morphometrics and dentitional features vary little over its geographical range. The number of trunk myomeres and the adult body size vary appreciably so that two categories of regional forms, coastal and inland, may be recognized. The coastal forms are generally smaller and have fewer trunk myomeres compared to those of the larger inland forms. The spawning migration begins from the late spring to late summer for the coastal forms but may occur much earlier for the inland forms. The adult body size appears to be positively correlated with absolute fecundity, but is negatively correlated with relative fecundity. Duration of the larval period is from four to six years. Metamorphosis usually takes place in the fall. Macrophthalmia are known to enter the ocean over a long period, those descending coastal streams enter salt water in the late fall and early winter, whereas the peak of emigration from inland streams is in the early spring. Duration of its marine parasitic phase appears to be from 20 to 40 months. The small landlocked L. (E.) t. kawiaga n. subsp., found only in the Klamath and Goose Lake drainage systems in southern Oregon and northern California, differs from t. tridentata in body size and various meristic and morphometric characters. Its lacustrine parasitic phase is about 12 months long. L. (E.) lethophaga, the nonparasitic derivative of tridentata, occurs in the Klamath and probably also the Goose Lake drainage system. It is characterized by an extension of the larval phase and by a greatly reduced post-larval period. The presumably extinct L. (E. ) minima, a parasitic derivative of tridentata, found formerly only in Miller Lake, Oregon, possessed a number of characters that were concomitants of dwarfism, the distinctive feature of the species. Relationships and evolution among the subgenus Entosphenus were discussed. Distributional records of L. ayresii and L. richardsoni of the subgenus Lampetra in Oregon were given. Evidence indicates that a complex of clinal races, including L. pacifica Vladykov, 1973, may exist in the latter species. Title: Systematics, variation, distribution, and biology of lampreys of the genus Lampetra in Oregon Author: Kan, Ting Tien Based on the number of velar tentacles and the form of longitudinal lingual laminae found in Lampetra (Entosphenus) t. tridentata and its closely related forms, the taxon Entosphenus should not be considered as a genus as commonly adopted, but, along with the taxa Lethenteron and Lampetra, should be regarded as a subgenus of the genus Lampetra. The genus Lampetra is distinct for various reasons, including particularly the character that no cusps are present in the area distal to the lateral circumorals. Six nominal species, belonging to the subgenera Entosphenus and Lampetra, have been known to occur in four of the seven major drainage systems of Oregon. The anadromous L. (E.) t.tridentata, is widespread in the Columbia River and Coastal drainage systems, occurring in most streams with access to the ocean regardless of distance to the ocean, as long as suitable spawning grounds and ammocoete habitats are present. Morphometrics and dentitional features vary little over its geographical range. The number of trunk myomeres and the adult body size vary appreciably so that two categories of regional forms, coastal and inland, may be recognized. The coastal forms are generally smaller and have fewer trunk myomeres compared to those of the larger inland forms. The spawning migration begins from the late spring to late summer for the coastal forms but may occur much earlier for the inland forms. The adult body size appears to be positively correlated with absolute fecundity, but is negatively correlated with relative fecundity. Duration of the larval period is from four to six years. Metamorphosis usually takes place in the fall. Macrophthalmia are known to enter the ocean over a long period, those descending coastal streams enter salt water in the late fall and early winter, whereas the peak of emigration from inland streams is in the early spring. Duration of its marine parasitic phase appears to be from 20 to 40 months. The small landlocked L. (E.) t. kawiaga n. subsp., found only in the Klamath and Goose Lake drainage systems in southern Oregon and northern California, differs from t. tridentata in body size and various meristic and morphometric characters. Its lacustrine parasitic phase is about 12 months long. L. (E.) lethophaga, the nonparasitic derivative of tridentata, occurs in the Klamath and probably also the Goose Lake drainage system. It is characterized by an extension of the larval phase and by a greatly reduced post-larval period. The presumably extinct L. (E. ) minima, a parasitic derivative of tridentata, found formerly only in Miller Lake, Oregon, possessed a number of characters that were concomitants of dwarfism, the distinctive feature of the species. Relationships and evolution among the subgenus Entosphenus were discussed. Distributional records of L. ayresii and L. richardsoni of the subgenus Lampetra in Oregon were given. Evidence indicates that a complex of clinal races, including L. pacifica Vladykov, 1973, may exist in the latter species. Close

• 105. [Article] Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries

  The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, ...

  Citation × Citation Citation Abstract Copy Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Close

• 106. [Article] Potential for dispersal of the non-native parasite Myxobolus cerebralis : qualitative risk assessments for the state of Alaska and the Willamette River Basin, Oregon

  First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations ...

  Citation × Citation Citation Abstract Copy Title: Potential for dispersal of the non-native parasite Myxobolus cerebralis : qualitative risk assessments for the state of Alaska and the Willamette River Basin, Oregon Author: Arsan, E. Leyla First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations in the intermountain west. Recent development of risk assessment models used to assess the likelihood and consequences of exotic parasite introduction, have strengthened the process of science-based decision-making in aquatic animal health. In the case of M. cerebralis, it is necessary to use a risk assessment model with two unique segments that clearly address the distinct life stages and respective hosts of the parasite separately. The studies described examine the probability of M. cerebralis introduction and establishment for two regions: the state of Alaska, and the Willamette River basin, Oregon. The Alaska risk assessment was based on the assumption that the parasite did not already occur in the state. However, in the process of validating this assumption, we documented the first polymerase chain reaction (PCR) detection of the parasite in the state. The pathogen was identified in hatchery rainbow trout (Oncorhynchus mykiss) from the Anchorage area. Although this is the first detection of the parasite in Alaska, clinical whirling disease has never been documented in the state. To qualitatively assess the risk of further spread of M. cerebralis in Alaska, four potential routes of dissemination were examined: movement of fish by humans, natural dispersal (via migratory birds and stray anadromous salmon), recreational activities, and commercial seafood processing. This research indicates the most likely pathway for M. cerebralis transport in Alaska is human movement of fish. In the Willamette River basin, Oregon, introduction of M. cerebralis has already occurred, though establishment appears limited to a single private hatchery. Introduction in this region was considered the most likely to occur as a result of human movements of fish. Straying anadromous salmonids were also assessed and were present in higher numbers than predicted. However, they were not infected with the parasite, and thus the probability for introduction by this route is low. The probability of introduction of the parasite varies throughout the Willamette River basin. Areas with the highest probability for M. cerebralis introduction were identified as the Clackamas and Santiam River subbasins. The Clackamas River has already experienced an introduction of the parasite, has the largest concentration of hatcheries (state, federal, and private), has a popular sport fishery, and is the closest major tributary to the enormous piscivorous bird-populations in the Columbia River estuary. The Santiam subbasin has a popular sport fishery, received the highest number of stray fish in the Willamette River basin, and has the second largest concentration of hatcheries in the Willamette River basin. Unique from introduction, establishment of the parasite is dependent upon several environmental and biological factors including: water temperatures, spatial/temporal overlap of hosts, and the distribution and genetic composition of the parasite’s invertebrate host, Tubifex tubifex. The distribution, genetic composition and susceptibility of T. tubifex, were considered the most important factor in the ability of M. cerebralis to establish in both systems. Surveys of oligochaete populations were conducted in both study regions. In Alaska, T. tubifex was not detected from the southeast region and the apparent lack of appropriate tubificid hosts may prevent establishment in that part of the state. However, 4 lineages (I, III, IV, and VI) of the species were identified from southcentral Alaska. Lineage IV has not been previously been described in North America and its susceptibility to M. cerebralis was unknown. When lineage IV T. tubifex and 3 mixed-lineage (I, III, IV and VI) groups were exposed to M. cerebralis, only lineage III became infected under our experimental conditions. Thus, if the parasite were dispersed, conditions are appropriate for establishment and propagation of the parasite life cycle in southcentral Alaska, although detrimental effects on fish populations may be reduced as a result of the presence of non-susceptible lineages of T. tubifex. The probability of further establishment in this area is greatest in Ship Creek, where the abundance of susceptible T. tubifex, the presence of susceptible rainbow trout (Oncorhynchus mykiss), and the proximity to the known area of infection make conditions particularly appropriate. Similar to findings in Alaska, the Willamette River basin, Oregon also supports populations of susceptible T. tubifex. If the pathogen were introduced, probability of establishment is high in certain areas of the basin as all conditions are appropriate for propagation of the parasite life cycle. Tributaries to the mainstem Willamette River have the highest probability of establishment as these areas have the greatest numbers of susceptible T. tubifex. However, the abundance of resistant strains of T. tubifex could mitigate the effects of M. cerebralis if introduced. Management recommendations to reduce the likelihood of parasite dissemination are similar for Oregon and Alaska since human movement of fish and angler activities were considered the most likely routes of introduction for both regions. Based on this research, steps should also be taken to limit human movement of fish, whether by restricting carcass planting for stream enrichment in Oregon, or by prohibiting use of fish heads as bait in southcentral Alaska. The states should also allot resources to angler education and awareness of the effects of angler activity and recreation on dispersal of M. cerebralis. This could be done using a combination of brochures and signage at boat ramps describing how to prevent spread of aquatic nuisance species. Title: Potential for dispersal of the non-native parasite Myxobolus cerebralis : qualitative risk assessments for the state of Alaska and the Willamette River Basin, Oregon Author: Arsan, E. Leyla First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations in the intermountain west. Recent development of risk assessment models used to assess the likelihood and consequences of exotic parasite introduction, have strengthened the process of science-based decision-making in aquatic animal health. In the case of M. cerebralis, it is necessary to use a risk assessment model with two unique segments that clearly address the distinct life stages and respective hosts of the parasite separately. The studies described examine the probability of M. cerebralis introduction and establishment for two regions: the state of Alaska, and the Willamette River basin, Oregon. The Alaska risk assessment was based on the assumption that the parasite did not already occur in the state. However, in the process of validating this assumption, we documented the first polymerase chain reaction (PCR) detection of the parasite in the state. The pathogen was identified in hatchery rainbow trout (Oncorhynchus mykiss) from the Anchorage area. Although this is the first detection of the parasite in Alaska, clinical whirling disease has never been documented in the state. To qualitatively assess the risk of further spread of M. cerebralis in Alaska, four potential routes of dissemination were examined: movement of fish by humans, natural dispersal (via migratory birds and stray anadromous salmon), recreational activities, and commercial seafood processing. This research indicates the most likely pathway for M. cerebralis transport in Alaska is human movement of fish. In the Willamette River basin, Oregon, introduction of M. cerebralis has already occurred, though establishment appears limited to a single private hatchery. Introduction in this region was considered the most likely to occur as a result of human movements of fish. Straying anadromous salmonids were also assessed and were present in higher numbers than predicted. However, they were not infected with the parasite, and thus the probability for introduction by this route is low. The probability of introduction of the parasite varies throughout the Willamette River basin. Areas with the highest probability for M. cerebralis introduction were identified as the Clackamas and Santiam River subbasins. The Clackamas River has already experienced an introduction of the parasite, has the largest concentration of hatcheries (state, federal, and private), has a popular sport fishery, and is the closest major tributary to the enormous piscivorous bird-populations in the Columbia River estuary. The Santiam subbasin has a popular sport fishery, received the highest number of stray fish in the Willamette River basin, and has the second largest concentration of hatcheries in the Willamette River basin. Unique from introduction, establishment of the parasite is dependent upon several environmental and biological factors including: water temperatures, spatial/temporal overlap of hosts, and the distribution and genetic composition of the parasite’s invertebrate host, Tubifex tubifex. The distribution, genetic composition and susceptibility of T. tubifex, were considered the most important factor in the ability of M. cerebralis to establish in both systems. Surveys of oligochaete populations were conducted in both study regions. In Alaska, T. tubifex was not detected from the southeast region and the apparent lack of appropriate tubificid hosts may prevent establishment in that part of the state. However, 4 lineages (I, III, IV, and VI) of the species were identified from southcentral Alaska. Lineage IV has not been previously been described in North America and its susceptibility to M. cerebralis was unknown. When lineage IV T. tubifex and 3 mixed-lineage (I, III, IV and VI) groups were exposed to M. cerebralis, only lineage III became infected under our experimental conditions. Thus, if the parasite were dispersed, conditions are appropriate for establishment and propagation of the parasite life cycle in southcentral Alaska, although detrimental effects on fish populations may be reduced as a result of the presence of non-susceptible lineages of T. tubifex. The probability of further establishment in this area is greatest in Ship Creek, where the abundance of susceptible T. tubifex, the presence of susceptible rainbow trout (Oncorhynchus mykiss), and the proximity to the known area of infection make conditions particularly appropriate. Similar to findings in Alaska, the Willamette River basin, Oregon also supports populations of susceptible T. tubifex. If the pathogen were introduced, probability of establishment is high in certain areas of the basin as all conditions are appropriate for propagation of the parasite life cycle. Tributaries to the mainstem Willamette River have the highest probability of establishment as these areas have the greatest numbers of susceptible T. tubifex. However, the abundance of resistant strains of T. tubifex could mitigate the effects of M. cerebralis if introduced. Management recommendations to reduce the likelihood of parasite dissemination are similar for Oregon and Alaska since human movement of fish and angler activities were considered the most likely routes of introduction for both regions. Based on this research, steps should also be taken to limit human movement of fish, whether by restricting carcass planting for stream enrichment in Oregon, or by prohibiting use of fish heads as bait in southcentral Alaska. The states should also allot resources to angler education and awareness of the effects of angler activity and recreation on dispersal of M. cerebralis. This could be done using a combination of brochures and signage at boat ramps describing how to prevent spread of aquatic nuisance species. Close

• 107. [Article] Willamette BiOp - Genetic Stock Identification and Relative Natural Production of Willamette River Steelhead

  Abstract -- We used genotypic data from 15 microsatellite loci to characterize the stock structure of Oncorhynchus mykiss in the upper Willamette River basin. We then used two analytical approaches, implemented ...

  Citation × Citation Citation Abstract Copy Title: Willamette BiOp - Genetic Stock Identification and Relative Natural Production of Willamette River Steelhead Abstract -- We used genotypic data from 15 microsatellite loci to characterize the stock structure of Oncorhynchus mykiss in the upper Willamette River basin. We then used two analytical approaches, implemented in the programs ONCOR and STRUCTURE, to assign (presumably) natural-origin, unmarked fish to their most likely reporting group or hybrid class. We investigated sibling relationships among unknown samples with the program ML RELATE. In the upper Willamette River, O. mykiss genetic structure can be characterized by four principal groups: summer steelhead of Skamania stock ancestry, eastern tributaries winter steelhead, western tributaries winter steelhead and resident rainbow trout. We found that about 10% of unmarked juvenile O. mykiss sampled at Willamette Falls in 2009-2011 were summer steelhead and that an additional 10% of samples were summer x winter steelhead hybrids. Most O. mykiss sampled from the McKenzie River were either summer steelhead or summer x winter steelhead hybrids. Natural production of pure summer steelhead appeared to be very low in the North and South Santiam rivers, though summer steelhead hybrids represented 11.1% and 14.8% of samples. Results from ML RELATE analyses appeared unreliable and inconclusive, and may have been limited by low genetic diversity among summer steelhead samples. We provide several recommendations to better understand and reduce potentially negative interactions between hatchery summer steelhead and native upper Willamette River O. mykiss populations. These include reductions in adult steelhead on natural spawning grounds, improved reproductive isolation between hatchery and native populations and additional research to evaluate genetic integrity within and among O. mykiss populations. Title: Willamette BiOp - Genetic Stock Identification and Relative Natural Production of Willamette River Steelhead Abstract -- We used genotypic data from 15 microsatellite loci to characterize the stock structure of Oncorhynchus mykiss in the upper Willamette River basin. We then used two analytical approaches, implemented in the programs ONCOR and STRUCTURE, to assign (presumably) natural-origin, unmarked fish to their most likely reporting group or hybrid class. We investigated sibling relationships among unknown samples with the program ML RELATE. In the upper Willamette River, O. mykiss genetic structure can be characterized by four principal groups: summer steelhead of Skamania stock ancestry, eastern tributaries winter steelhead, western tributaries winter steelhead and resident rainbow trout. We found that about 10% of unmarked juvenile O. mykiss sampled at Willamette Falls in 2009-2011 were summer steelhead and that an additional 10% of samples were summer x winter steelhead hybrids. Most O. mykiss sampled from the McKenzie River were either summer steelhead or summer x winter steelhead hybrids. Natural production of pure summer steelhead appeared to be very low in the North and South Santiam rivers, though summer steelhead hybrids represented 11.1% and 14.8% of samples. Results from ML RELATE analyses appeared unreliable and inconclusive, and may have been limited by low genetic diversity among summer steelhead samples. We provide several recommendations to better understand and reduce potentially negative interactions between hatchery summer steelhead and native upper Willamette River O. mykiss populations. These include reductions in adult steelhead on natural spawning grounds, improved reproductive isolation between hatchery and native populations and additional research to evaluate genetic integrity within and among O. mykiss populations. Close

• 108. [Article] Distribution and characteristics of an isolated population of coastal cutthroat trout (Oncorhynchus clarki) in streams of Triangle Lake Basin, Oregon

  This research focused on features of a genetically isolated population of cutthroat trout (Oncorhynchus clarki) in the Triangle Lake basin of coastal Oregon. A falls at the outlet of Triangle Lake has ...

  Citation × Citation Citation Abstract Copy Title: Distribution and characteristics of an isolated population of coastal cutthroat trout (Oncorhynchus clarki) in streams of Triangle Lake Basin, Oregon Author: Hurley, Steven M. This research focused on features of a genetically isolated population of cutthroat trout (Oncorhynchus clarki) in the Triangle Lake basin of coastal Oregon. A falls at the outlet of Triangle Lake has blocked upstream migration of trout and anadromous salmonids into the basin. Cutthroat trout were found throughout the six study streams of the Triangle Lake basin in association with other native fishes and introduced warmwater fishes. Warmwater species (e.g. Centrarchidae) were restricted largely to the lakes of Triangle Lake basin, and did not comprise a significant part of the stream fish fauna. Salmonids and cottids dominated the upper forested reaches of the basin, whereas nonsalmonids dominated the lower reaches. The middle reaches contained a transitional fish community between the upper and lower reaches. Reach type was a major factor influencing cutthroat trout density and size distribution. Areal densities of cutthroat trout were highest in the upper reaches and lowest in the lower reaches with the exception of 0+ cutthroat trout, which occurred at similar densities in all reaches. The highest frequency of 1+ cutthroat trout occurred in the middle reaches, whereas the highest frequency of 0+ cutthroat occurred in the lower reaches. Within reaches, channel unit type influenced the density and age structure of cutthroat trout. Pools and rapids had the highest densities of cutthroat trout, whereas riffles, glides, and cascades had lower densities. Larger trout were found primarily in pools and rapids. Planted steelhead fry (Oncorhynchus mykiss) were found in two streams, Congdon Creek and Lake Creek. Although most steelhead fry leave the basin as smolts, some steelhead appear to become resident and may hybridize with native cutthroat trout. Cutthroat trout spawning was observed from late December 1987 through late May 1988. Differences in the time and place of spawning may serve to genetically isolate two populations of cutthroat trout in Triangle Lake basin. One population may be lake dwelling as adults and spawn lower in the basin in late spring. The other population may be stream dwelling and spawn in the winter during higher flows, which allows them to spawn in the upper reaches of the basin. Title: Distribution and characteristics of an isolated population of coastal cutthroat trout (Oncorhynchus clarki) in streams of Triangle Lake Basin, Oregon Author: Hurley, Steven M. This research focused on features of a genetically isolated population of cutthroat trout (Oncorhynchus clarki) in the Triangle Lake basin of coastal Oregon. A falls at the outlet of Triangle Lake has blocked upstream migration of trout and anadromous salmonids into the basin. Cutthroat trout were found throughout the six study streams of the Triangle Lake basin in association with other native fishes and introduced warmwater fishes. Warmwater species (e.g. Centrarchidae) were restricted largely to the lakes of Triangle Lake basin, and did not comprise a significant part of the stream fish fauna. Salmonids and cottids dominated the upper forested reaches of the basin, whereas nonsalmonids dominated the lower reaches. The middle reaches contained a transitional fish community between the upper and lower reaches. Reach type was a major factor influencing cutthroat trout density and size distribution. Areal densities of cutthroat trout were highest in the upper reaches and lowest in the lower reaches with the exception of 0+ cutthroat trout, which occurred at similar densities in all reaches. The highest frequency of 1+ cutthroat trout occurred in the middle reaches, whereas the highest frequency of 0+ cutthroat occurred in the lower reaches. Within reaches, channel unit type influenced the density and age structure of cutthroat trout. Pools and rapids had the highest densities of cutthroat trout, whereas riffles, glides, and cascades had lower densities. Larger trout were found primarily in pools and rapids. Planted steelhead fry (Oncorhynchus mykiss) were found in two streams, Congdon Creek and Lake Creek. Although most steelhead fry leave the basin as smolts, some steelhead appear to become resident and may hybridize with native cutthroat trout. Cutthroat trout spawning was observed from late December 1987 through late May 1988. Differences in the time and place of spawning may serve to genetically isolate two populations of cutthroat trout in Triangle Lake basin. One population may be lake dwelling as adults and spawn lower in the basin in late spring. The other population may be stream dwelling and spawn in the winter during higher flows, which allows them to spawn in the upper reaches of the basin. Close

• 109. [Article] Bull Trout (Salvelinus confluentus) population and habitat surveys in the McKenzie and Middle Fork Willamette Basins, 2000

  DOE/BP-00004093-1

  Citation × Citation Citation Abstract Copy Title: Bull Trout (Salvelinus confluentus) population and habitat surveys in the McKenzie and Middle Fork Willamette Basins, 2000 Author: Taylor, Greg DOE/BP-00004093-1 Title: Bull Trout (Salvelinus confluentus) population and habitat surveys in the McKenzie and Middle Fork Willamette Basins, 2000 Author: Taylor, Greg DOE/BP-00004093-1 Close

• 110. [Article] Lower Snake River Compensation Plan; Oregon Evaluation Studies - 1995 and 1996 Annual Progress Report

  Abstract -- This report summarizes fish culture monitoring data for Lower Snake River Compensation Plan (LSRCP) facilities for each species. These data should serve as the basis for the analysis of trends ...

  Citation × Citation Citation Abstract Copy Title: Lower Snake River Compensation Plan; Oregon Evaluation Studies - 1995 and 1996 Annual Progress Report Abstract -- This report summarizes fish culture monitoring data for Lower Snake River Compensation Plan (LSRCP) facilities for each species. These data should serve as the basis for the analysis of trends in culture performance. Generally speaking, the data in this report were derived from hatchery inventories and standard databases (i.e., PSMFC, Coded-wire tag) or through standard measuring techniques. As such, specific protocols are usually not described. In cases where expansions of data or unique methodologies were used, protocols are described in more detail. Additional descriptions of protocols can be found in the 1995 and 1996 work statements (Carmichael 1995, 1996). Coded-wire tag (CWT) data that were collected from 1995-1996 adult returns is used to evaluate smolt-to-adult survival rates in experimental rearing and release groups. In 1995-1996, experimental treatments from which fish returned included acclimated vs. direct stream for steelhead and size-at-release for both steelhead and Chinook. In 1995-1996, experimental treatments for which fish were released included size-at-release, exercise, acclimation, and low density treatments for Chinook, acclimated vs. direct stream for both steelhead and Chinook, and forced vs. volitional release for steelhead. Analysis of specific survival studies will be completed once all brood years have returned and CWT data are complete for a given experiment. In addition, much of the data that we discuss in this report will be used in separate and specific evaluations of ongoing supplementation programs for both steelhead and Chinook in the Imnaha River basin. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Title: Lower Snake River Compensation Plan; Oregon Evaluation Studies - 1995 and 1996 Annual Progress Report Abstract -- This report summarizes fish culture monitoring data for Lower Snake River Compensation Plan (LSRCP) facilities for each species. These data should serve as the basis for the analysis of trends in culture performance. Generally speaking, the data in this report were derived from hatchery inventories and standard databases (i.e., PSMFC, Coded-wire tag) or through standard measuring techniques. As such, specific protocols are usually not described. In cases where expansions of data or unique methodologies were used, protocols are described in more detail. Additional descriptions of protocols can be found in the 1995 and 1996 work statements (Carmichael 1995, 1996). Coded-wire tag (CWT) data that were collected from 1995-1996 adult returns is used to evaluate smolt-to-adult survival rates in experimental rearing and release groups. In 1995-1996, experimental treatments from which fish returned included acclimated vs. direct stream for steelhead and size-at-release for both steelhead and Chinook. In 1995-1996, experimental treatments for which fish were released included size-at-release, exercise, acclimation, and low density treatments for Chinook, acclimated vs. direct stream for both steelhead and Chinook, and forced vs. volitional release for steelhead. Analysis of specific survival studies will be completed once all brood years have returned and CWT data are complete for a given experiment. In addition, much of the data that we discuss in this report will be used in separate and specific evaluations of ongoing supplementation programs for both steelhead and Chinook in the Imnaha River basin. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Close