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• 941. [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

• 942. [Article] Performance of Progeny From Steelhead and Rainbow Trout Crosses - Final Report 2009

  Abstract -- Many salmonids exhibit partial migration: the phenomenon of populations partitioned into migratory and non-migratory individuals (Jonsson and Jonsson 1993). Oncorhynchus mykiss exhibit a complex ...

  Citation × Citation Citation Abstract Copy Title: Performance of Progeny From Steelhead and Rainbow Trout Crosses - Final Report 2009 Abstract -- Many salmonids exhibit partial migration: the phenomenon of populations partitioned into migratory and non-migratory individuals (Jonsson and Jonsson 1993). Oncorhynchus mykiss exhibit a complex of life-history strategies ranging from residency in small headwater streams to anadromy involving migrations of hundreds of kilometers. In the Grande Ronde River basin of northeast Oregon, both resident and anadromous life-history forms coexist, and thus populations found there likely exhibit partial migration. Partial migration may have important consequences for anadromous species listed under the Endangered Species Act (ESA). The recent decline of summer steelhead (Oncorhynchus mykiss) populations in the lower Snake River has prompted their listing under the ESA. Declines in steelhead are potentially due to elevated mortality rates associated with anadromous migrations. If resident and anadromous life-history characteristics result from a phenotypically plastic trait (i.e. a genetic trait that is highly variable due to influences from environmental factors), then elevated mortality associated with the anadromous type may be shifting the populations towards residency. Further, although the anadromous expression of the trait may be declining, the trait would not necessarily be lost. Identification of the plasticity of these traits would then be important for the management of these populations. We investigated life history traits of O. mykiss with studies in both the hatchery and natural environment. We anticipated that these complimentary approaches would allow us to evaluate the relationship between the two life-history forms. They should further allow us to explore the feasibility of using hatcheries to produce anadromous progeny from resident parents if the number of anadromous life-history forms becomes severely depressed. The overall goal of this study was to determine the plasticity of life history forms, specifically the ability of resident adults to produce anadromous progeny. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Title: Performance of Progeny From Steelhead and Rainbow Trout Crosses - Final Report 2009 Abstract -- Many salmonids exhibit partial migration: the phenomenon of populations partitioned into migratory and non-migratory individuals (Jonsson and Jonsson 1993). Oncorhynchus mykiss exhibit a complex of life-history strategies ranging from residency in small headwater streams to anadromy involving migrations of hundreds of kilometers. In the Grande Ronde River basin of northeast Oregon, both resident and anadromous life-history forms coexist, and thus populations found there likely exhibit partial migration. Partial migration may have important consequences for anadromous species listed under the Endangered Species Act (ESA). The recent decline of summer steelhead (Oncorhynchus mykiss) populations in the lower Snake River has prompted their listing under the ESA. Declines in steelhead are potentially due to elevated mortality rates associated with anadromous migrations. If resident and anadromous life-history characteristics result from a phenotypically plastic trait (i.e. a genetic trait that is highly variable due to influences from environmental factors), then elevated mortality associated with the anadromous type may be shifting the populations towards residency. Further, although the anadromous expression of the trait may be declining, the trait would not necessarily be lost. Identification of the plasticity of these traits would then be important for the management of these populations. We investigated life history traits of O. mykiss with studies in both the hatchery and natural environment. We anticipated that these complimentary approaches would allow us to evaluate the relationship between the two life-history forms. They should further allow us to explore the feasibility of using hatcheries to produce anadromous progeny from resident parents if the number of anadromous life-history forms becomes severely depressed. The overall goal of this study was to determine the plasticity of life history forms, specifically the ability of resident adults to produce anadromous progeny. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Close

• 943. [Article] Stream Habitat Conditions in Western Oregon 2005 Monitoring Report Report Number: OPSW-ODFW-2007-5

  Abstract -- Monitoring programs under the Oregon Plan for Salmon and Watersheds were designed to assess the status and trend in fish populations and aquatic habitat in Oregon’s coastal basins. Although ...

  Citation × Citation Citation Abstract Copy Title: Stream Habitat Conditions in Western Oregon 2005 Monitoring Report Report Number: OPSW-ODFW-2007-5 Abstract -- Monitoring programs under the Oregon Plan for Salmon and Watersheds were designed to assess the status and trend in fish populations and aquatic habitat in Oregon’s coastal basins. Although the Oregon Plan for Salmon and Watersheds was initiated in response to the petition to list Oregon coastal coho salmon (Oncorhynchus kisutch) as threatened under the Endangered Species Act (ESA), monitoring was subsequently expanded to include other salmonids. Through coordinated surveys we are able to evaluate freshwater habitat, fish distribution, and abundance of juvenile and adult coho salmon and steelhead trout. The habitat survey project has the broadest geographic scope of inference and ties to other program components as well – basin surveys, surveys at habitat restoration sites, adult and juvenile coho surveys, and life cycle watersheds (Flitcroft et al. 2002). The Oregon Plan facilitated cooperation and partnerships to study the contemporary life history dynamics of coho salmon in the Oregon coastal ESU (Evolutionary Significant Unit). A viability and status assessment of Oregon coastal Coho (Chilcote 2005) and the Conservation Plan for the Oregon Coast Coho Evolutionary Significant Unit (Nicholas 2006) evaluated the relationship of aquatic habitat to the productivity of coho salmon populations and recommended actions to promote recovery. The habitat portion of the viability assessment was based on a review of aquatic and riparian habitat collected by the Aquatic Inventories Project (ODFW) from 1990 to 2004 (Rodgers et al. 2005). The authors of the habitat assessment (Rodgers et al 2005) and viability assessment (Chilcote 2005) concluded that coho productivity in 22 coastal coho populations was limited by the complexity of stream habitat used by juvenile coho during their first winter of freshwater residence. The term “stream complexity” integrates geomorphic and structural characteristics of streams and associated aquatic habitat. Complex geomorphic features may be observed in low gradient streams flowing through wide valley floors with multiple channels and off-channel habitats. Structural complexity refers to the size and configuration of pools, large wood pieces and jams, substrate, and undercut banks. The combination of geomorphic and structural features provides cover and refugia during high winter flows for juvenile coho. Stream reaches that can or have the potential to create these conditions are commonly located in lower reaches of moderate size streams in areas with wide valley floors and are considered to contain high quality habitat for juvenile coho. Burnett et al. (2007) developed spatial models to estimate high-quality habitat rearing potential, termed intrinsic potential, in coastal streams. A stream’s intrinsic potential was modeled using valley width, gradient, and stream flow. Historically, streams identified as having high intrinsic potential may have been the most productive for juvenile coho salmon; restoration of these reaches may be the key to recovery of coho salmon. The viability assessment and Coho Plan recommend that we monitor the trends in total amount and spatial distribution of these habitats in coastal drainages. This report discusses the findings from aquatic habitat surveys conducted in summer 2005 in coastal drainages. Our objectives are to describe and compare channel morphology, instream habitat and complexity, and riparian conditions in all wadeable streams in five monitoring areas. The sample design permitted us to post stratify the sample sites into three additional frames: sites within coho and steelhead distribution, sites outside coho distribution, and sites within high intrinsic potential for coho. We also used two habitat models to integrate habitat attributes to describe the habitat quality and capacity for different life stages of juvenile coho and steelhead. Title: Stream Habitat Conditions in Western Oregon 2005 Monitoring Report Report Number: OPSW-ODFW-2007-5 Abstract -- Monitoring programs under the Oregon Plan for Salmon and Watersheds were designed to assess the status and trend in fish populations and aquatic habitat in Oregon’s coastal basins. Although the Oregon Plan for Salmon and Watersheds was initiated in response to the petition to list Oregon coastal coho salmon (Oncorhynchus kisutch) as threatened under the Endangered Species Act (ESA), monitoring was subsequently expanded to include other salmonids. Through coordinated surveys we are able to evaluate freshwater habitat, fish distribution, and abundance of juvenile and adult coho salmon and steelhead trout. The habitat survey project has the broadest geographic scope of inference and ties to other program components as well – basin surveys, surveys at habitat restoration sites, adult and juvenile coho surveys, and life cycle watersheds (Flitcroft et al. 2002). The Oregon Plan facilitated cooperation and partnerships to study the contemporary life history dynamics of coho salmon in the Oregon coastal ESU (Evolutionary Significant Unit). A viability and status assessment of Oregon coastal Coho (Chilcote 2005) and the Conservation Plan for the Oregon Coast Coho Evolutionary Significant Unit (Nicholas 2006) evaluated the relationship of aquatic habitat to the productivity of coho salmon populations and recommended actions to promote recovery. The habitat portion of the viability assessment was based on a review of aquatic and riparian habitat collected by the Aquatic Inventories Project (ODFW) from 1990 to 2004 (Rodgers et al. 2005). The authors of the habitat assessment (Rodgers et al 2005) and viability assessment (Chilcote 2005) concluded that coho productivity in 22 coastal coho populations was limited by the complexity of stream habitat used by juvenile coho during their first winter of freshwater residence. The term “stream complexity” integrates geomorphic and structural characteristics of streams and associated aquatic habitat. Complex geomorphic features may be observed in low gradient streams flowing through wide valley floors with multiple channels and off-channel habitats. Structural complexity refers to the size and configuration of pools, large wood pieces and jams, substrate, and undercut banks. The combination of geomorphic and structural features provides cover and refugia during high winter flows for juvenile coho. Stream reaches that can or have the potential to create these conditions are commonly located in lower reaches of moderate size streams in areas with wide valley floors and are considered to contain high quality habitat for juvenile coho. Burnett et al. (2007) developed spatial models to estimate high-quality habitat rearing potential, termed intrinsic potential, in coastal streams. A stream’s intrinsic potential was modeled using valley width, gradient, and stream flow. Historically, streams identified as having high intrinsic potential may have been the most productive for juvenile coho salmon; restoration of these reaches may be the key to recovery of coho salmon. The viability assessment and Coho Plan recommend that we monitor the trends in total amount and spatial distribution of these habitats in coastal drainages. This report discusses the findings from aquatic habitat surveys conducted in summer 2005 in coastal drainages. Our objectives are to describe and compare channel morphology, instream habitat and complexity, and riparian conditions in all wadeable streams in five monitoring areas. The sample design permitted us to post stratify the sample sites into three additional frames: sites within coho and steelhead distribution, sites outside coho distribution, and sites within high intrinsic potential for coho. We also used two habitat models to integrate habitat attributes to describe the habitat quality and capacity for different life stages of juvenile coho and steelhead. Close

• 944. [Article] Abundance Monitoring of Juvenile Salmonids In Coastal Oregon and Lower Columbia Streams, 2008 Report Number: OPSW-ODFW-2009-1

  Abstract -- As part of the Oregon Plan for Salmon and Watersheds, the Oregon Department of Fish and Wildlife (ODFW) initiated this project in 1998 to monitor the status and trend in abundance and distribution ...

  Citation × Citation Citation Abstract Copy Title: Abundance Monitoring of Juvenile Salmonids In Coastal Oregon and Lower Columbia Streams, 2008 Report Number: OPSW-ODFW-2009-1 Abstract -- As part of the Oregon Plan for Salmon and Watersheds, the Oregon Department of Fish and Wildlife (ODFW) initiated this project in 1998 to monitor the status and trend in abundance and distribution of juvenile coho salmon (Oncorhynchus kisutch) in coastal Oregon streams. This report summarizes the data collected during the summer of 2008 and, for coho salmon, compares it to data previously collected. The project originally surveyed only 1st-3rd order (tributary) streams but was expanded in 2002 to include juvenile steelhead (Oncorhynchus mykiss) and 4th-6th order (mainstem) rearing areas and in 2006 to the Oregon portion of the Lower Columbia River coho evolutionarily significant unit (ESU) (Figure 1). The sampling frame is intended to encompass all non-tidal coho and steelhead rearing habitat. The original 100k stream layer frame was replaced by a 24k frame in 2007. A Generalized Random Tessellation Stratified design (GRTS) (Stevens 2002) was used to create a spatially balanced, random point distribution. Sites were stratified by Monitoring Area (MA) and stream order (Table 1). A detailed description of the sampling frames and survey designs are found in Jepsen and Rodgers (2004) and Jepsen and Leader (2007). Field crews snorkeled all pools meeting the size criteria (6 m2 in surface area and 40 cm in maximum depth) in one kilometer of stream encompassing the GRTS point. Snorkeling was conducted during the minimum flow period from July to September using a single pass of one to four snorkelers, depending on stream width. In each pool counts were made of juvenile coho, Chinook, steelhead 90 mm, and cutthroat 90 mm. Presence was noted for dace, shiners, and trout < 90 mm. Sites with poor water clarity or quality were electrofished using a single pass without block nets to determine presence for coho, steelhead and cutthroat in each pool. To assess repeatability and quality control supervisory staff resurveyed 10% of tributary sites in each MA. Data were summarized by MA and stream order for analyses. Average pool density and percent pool occupancy for each site was averaged by MA. The percent of sites with at least one fish and with >0.7 coho/m2 are reported for each MA. 0.7 coho/m2 is regarded as full seeding after Nickelson et al. (1992) who reported full seeding based on electrofishing as 1.0 coho/m2 and Rodgers et al. (1992) who found that snorkelers observed 70% of the coho counted by electrofishing. CDFs, variances, and confidence intervals were created using tools developed by the EMAP Design and Analysis Team (EPA 2009). Title: Abundance Monitoring of Juvenile Salmonids In Coastal Oregon and Lower Columbia Streams, 2008 Report Number: OPSW-ODFW-2009-1 Abstract -- As part of the Oregon Plan for Salmon and Watersheds, the Oregon Department of Fish and Wildlife (ODFW) initiated this project in 1998 to monitor the status and trend in abundance and distribution of juvenile coho salmon (Oncorhynchus kisutch) in coastal Oregon streams. This report summarizes the data collected during the summer of 2008 and, for coho salmon, compares it to data previously collected. The project originally surveyed only 1st-3rd order (tributary) streams but was expanded in 2002 to include juvenile steelhead (Oncorhynchus mykiss) and 4th-6th order (mainstem) rearing areas and in 2006 to the Oregon portion of the Lower Columbia River coho evolutionarily significant unit (ESU) (Figure 1). The sampling frame is intended to encompass all non-tidal coho and steelhead rearing habitat. The original 100k stream layer frame was replaced by a 24k frame in 2007. A Generalized Random Tessellation Stratified design (GRTS) (Stevens 2002) was used to create a spatially balanced, random point distribution. Sites were stratified by Monitoring Area (MA) and stream order (Table 1). A detailed description of the sampling frames and survey designs are found in Jepsen and Rodgers (2004) and Jepsen and Leader (2007). Field crews snorkeled all pools meeting the size criteria (6 m2 in surface area and 40 cm in maximum depth) in one kilometer of stream encompassing the GRTS point. Snorkeling was conducted during the minimum flow period from July to September using a single pass of one to four snorkelers, depending on stream width. In each pool counts were made of juvenile coho, Chinook, steelhead 90 mm, and cutthroat 90 mm. Presence was noted for dace, shiners, and trout < 90 mm. Sites with poor water clarity or quality were electrofished using a single pass without block nets to determine presence for coho, steelhead and cutthroat in each pool. To assess repeatability and quality control supervisory staff resurveyed 10% of tributary sites in each MA. Data were summarized by MA and stream order for analyses. Average pool density and percent pool occupancy for each site was averaged by MA. The percent of sites with at least one fish and with >0.7 coho/m2 are reported for each MA. 0.7 coho/m2 is regarded as full seeding after Nickelson et al. (1992) who reported full seeding based on electrofishing as 1.0 coho/m2 and Rodgers et al. (1992) who found that snorkelers observed 70% of the coho counted by electrofishing. CDFs, variances, and confidence intervals were created using tools developed by the EMAP Design and Analysis Team (EPA 2009). Close

• 945. [Article] Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis

  Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region ...

  Citation × Citation Citation Abstract Copy Title: Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis Author: Stevenson, Alexander E. Year: 2011 Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region prior to the construction of the Copco I Dam on the Klamath River (c.1917) have relied on sparse, contradictory and sometimes unreliable historic documentation and informant testimony. Current restoration projects with very high financial and social costs necessitate accurate and reliable data on salmonid species which once called the region home. Often, archaeolofaunal remains present a novel way to determine species present in an area prior to major habitat losses. This project analyzed fish remains from five previously excavated archaeological sites within the Upper Klamath Basin to determine which salmonid species were present prior to dam construction. A total of 5,859 fish remains were identified to at least taxonomic order using morphological distinctions. Site collections were dominated by those of catostomids (suckers) and cyprinids (minnows). Archaeological deposits at these sites dated as far back as approximately 7,500 BP but were primarily from the last 2,000 years. Only eighty-one salmonid remains were observed within the sites included in this project. The low frequency of salmonid remains in these sites may be the result of cultural and/or natural processes such as density mediated attrition and archaeological sampling. Of these 81 specimens, 38 were subjected to mtDNA analysis for species identification. Seven specimens did not yield DNA sufficient for species identification, six specimens were identified as O. tshawytscha (Chinook) and the remaining 25 specimens were identified as O. mykiss (steelhead or redband trout). Geochemical analysis was used to determine the life history of the fish represented by the remains within these collections. Strontium Calcium (Sr:Ca) ratios were measured on twenty-eight specimens. Three specimens were determined to be from freshwater resident fish and 25 were determined to be from anadromous fish. The specimens which were genetically identified as O. tshawytscha were all determined to be anadromous. Of the 18 specimens which were identified as O. mykiss and were subjected to geochemical analysis two were from freshwater resident fish and sixteen were from anadromous fish. Four samples were not characterized genetically but were subjected to geochemical analysis; three of these were determined to be from anadromous fish and one from a freshwater resident fish. Thus, the remains of anadromous O. mykiss and O. tshawytscha were identified in archaeological deposits predating construction of the Copco I dam in the Upper Klamath Basin While the genetic and geochemical analyses confirm the presence of skeletal remains from anadromous salmonids in the Upper Klamath Basin archaeological sites prior to dam construction these remains may, represent fish caught elsewhere and traded in. Two hypotheses address the introduction of these fish remains into pre-dam archaeological deposits, either they were traded/transported in from elsewhere (Trade/Transport Hypothesis) or they were caught locally (Local Catch Hypothesis). Expectations linked to each of these hypotheses were generated using ethnographic information from across the Pacific Northwest, including modern testimony from the Klamath Basin. Fish heads were often removed soon after capture in order to reduce spoilage of the rest of the fish. Thus, assemblages with many head parts are probably the result of local catch while those without head parts are probably the result of trade and/or transport. Two approaches were used to estimate the extent to which fish heads were deposited in sites. Basic proportions of cranial to post cranial remains from two sites provided a varied picture and did not readily support either the Local Catch or Trade/Transport hypotheses. Evaluation using scaled proportions based on frequency of skeletal elements within the body (Minimum Animal Units) show that four of the five assemblages were dominated by cranial remains and therefore suggest these fish were locally caught. Small samples sizes make it difficult to rigorously evaluate the hypotheses, though the dominance of cranial remains suggests salmonids were taken locally. Together these data indicate that anadromous O. tshawytscha and O. mykiss were taken from waters within the Upper Klamath Basin prior to the construction of Copco I. This study has provided accurate and reliable data, using a novel approach, on which restoration efforts in the region can rely for proper species reintroduction and habitat restoration efforts. Title: Using Archaeological Fish Remains to Determine the Native Status of Anadromous Salmonids in the Upper Klamath Basin (Oregon, USA) Through mtDNA and Geochemical Analysis Author: Stevenson, Alexander E. Year: 2011 Within the Upper Klamath Basin, Oregon, the native status of anadromous salmonids (Oncorhynchus spp.) has been a long standing question. Ongoing efforts to establish if these fish were native to the region prior to the construction of the Copco I Dam on the Klamath River (c.1917) have relied on sparse, contradictory and sometimes unreliable historic documentation and informant testimony. Current restoration projects with very high financial and social costs necessitate accurate and reliable data on salmonid species which once called the region home. Often, archaeolofaunal remains present a novel way to determine species present in an area prior to major habitat losses. This project analyzed fish remains from five previously excavated archaeological sites within the Upper Klamath Basin to determine which salmonid species were present prior to dam construction. A total of 5,859 fish remains were identified to at least taxonomic order using morphological distinctions. Site collections were dominated by those of catostomids (suckers) and cyprinids (minnows). Archaeological deposits at these sites dated as far back as approximately 7,500 BP but were primarily from the last 2,000 years. Only eighty-one salmonid remains were observed within the sites included in this project. The low frequency of salmonid remains in these sites may be the result of cultural and/or natural processes such as density mediated attrition and archaeological sampling. Of these 81 specimens, 38 were subjected to mtDNA analysis for species identification. Seven specimens did not yield DNA sufficient for species identification, six specimens were identified as O. tshawytscha (Chinook) and the remaining 25 specimens were identified as O. mykiss (steelhead or redband trout). Geochemical analysis was used to determine the life history of the fish represented by the remains within these collections. Strontium Calcium (Sr:Ca) ratios were measured on twenty-eight specimens. Three specimens were determined to be from freshwater resident fish and 25 were determined to be from anadromous fish. The specimens which were genetically identified as O. tshawytscha were all determined to be anadromous. Of the 18 specimens which were identified as O. mykiss and were subjected to geochemical analysis two were from freshwater resident fish and sixteen were from anadromous fish. Four samples were not characterized genetically but were subjected to geochemical analysis; three of these were determined to be from anadromous fish and one from a freshwater resident fish. Thus, the remains of anadromous O. mykiss and O. tshawytscha were identified in archaeological deposits predating construction of the Copco I dam in the Upper Klamath Basin While the genetic and geochemical analyses confirm the presence of skeletal remains from anadromous salmonids in the Upper Klamath Basin archaeological sites prior to dam construction these remains may, represent fish caught elsewhere and traded in. Two hypotheses address the introduction of these fish remains into pre-dam archaeological deposits, either they were traded/transported in from elsewhere (Trade/Transport Hypothesis) or they were caught locally (Local Catch Hypothesis). Expectations linked to each of these hypotheses were generated using ethnographic information from across the Pacific Northwest, including modern testimony from the Klamath Basin. Fish heads were often removed soon after capture in order to reduce spoilage of the rest of the fish. Thus, assemblages with many head parts are probably the result of local catch while those without head parts are probably the result of trade and/or transport. Two approaches were used to estimate the extent to which fish heads were deposited in sites. Basic proportions of cranial to post cranial remains from two sites provided a varied picture and did not readily support either the Local Catch or Trade/Transport hypotheses. Evaluation using scaled proportions based on frequency of skeletal elements within the body (Minimum Animal Units) show that four of the five assemblages were dominated by cranial remains and therefore suggest these fish were locally caught. Small samples sizes make it difficult to rigorously evaluate the hypotheses, though the dominance of cranial remains suggests salmonids were taken locally. Together these data indicate that anadromous O. tshawytscha and O. mykiss were taken from waters within the Upper Klamath Basin prior to the construction of Copco I. This study has provided accurate and reliable data, using a novel approach, on which restoration efforts in the region can rely for proper species reintroduction and habitat restoration efforts. Close

• 946. [Article] Distribution of Clostridium botulinum type E in fish, shellfish and the marine environment of the Pacific Northwest, and protein patterns of the toxigenic and non-toxigenic stains

  Interest in the distribution of Clostridium botulinum type E was heightened by the sudden outbreak of human botulism from smoked whitefish chubs and canned tuna fish in 1963. The question arose as to how ...

  Citation × Citation Citation Abstract Copy Title: Distribution of Clostridium botulinum type E in fish, shellfish and the marine environment of the Pacific Northwest, and protein patterns of the toxigenic and non-toxigenic stains Author: Craig, James Morrison Interest in the distribution of Clostridium botulinum type E was heightened by the sudden outbreak of human botulism from smoked whitefish chubs and canned tuna fish in 1963. The question arose as to how widely the organism is distributed among fish and shellfish in the Northwest and what potential hazard exists for the consumer of fish products. This sporeforming anaerobic orgnism is heat sensitive and had eluded detection in other surveys where heat shock had been used to eliminate non sporeforming contaminants. More recent study using other techniques than heat to facilitate recovery has shown this organism to be widespread, especially in the marine environment. This study was undertaken to find the incidence and distribution of C. botulinum in the marine organisms and environment of the Pacific Northwest and the food products derived therefrom. All species of fish were examined by incubating the gills and viscera individually in tryptone-peptone-glucose medium anaerobically at 28 C for four days and testing the culture filtrate for mouse toxicity by intraperitoneal injection. Toxic filtrates were typed by retesting them in mice protected by specific botulinal antitoxin of type A, B, E, or F. Among salmonid fish the proportions of specimens of each species yielding toxic filtrates were as follows. Sockeye salmon from the Columbia River, 14 of 59 (23.7%); Chinook salmon from the Columbia River, 19 of 106 (18.0%); Chinook salmon from the Pacific Ocean, 1 of 18 (5,6%); Coho salmon from the Columbia River, 10 of 19 (34.4%); Coho salmon from the Pacific Ocean, 13 of 186 (7.0%); Steelhead trout from the Alsea River, 7 of 37 (19.0%). About one-third of the toxic cultural filtrates were successfully typed and proven to contain botulinal toxin. Most of them proved to be type E toxin but 3 were type A, 3 were type B and one, a comparatively new type, type F, was isolated from a Sockeye salmon in the Columbia River. Pure cultures of Clostridium botulinum type E were isolated from 18 specimens and one specimen yielded a pure culture of type F from a sockeye salmon. This was the second time this type had been isolated. In all of the experimental groups the proportion of fish producing toxigenic cultures was significantly higher in those taken in the two rivers than those of the same species taken from the ocean waters. "Bottom fish" represented by Cod, Sole, Grouper and members of the Sebastodes group were also tested in the manner described above. The number of specimens yielding toxic filtrates were 28 of 157 (17.8%). When grouped according to location at which the fish were caught, those near the mouth of the Columbia River produced a greater percentage of toxic filtrates than did those caught off the open shore line. The results were as follows: Bottom fish from Astoria, 23 of 70 (32.8%), Botton fish from Coos Bay, 5 of 87 (5.6%). Sturgeon specimens produced 3 of 24 (12.5%) toxic filtrates. Most of the species contained type E; however, one type A and one type B were found on typing, with about one-third of the toxic filtrates being successfully typed. Environmental swab samples from the "deep sea" fillet processing plants produced 3 of 39 (7.7%) toxic filtrates. None of the 53 samples taken in the salmon processing plants produced toxic filtrates. Shellfish were collected along the ocean beach and in the estuaries. Three to five shellfish were combined into a single specimen and treated as described. All shellfish obtained from the estuaries demonstrated a higher percentage of toxic filtrates than those obtained from the ocean beach. The results were as follows: Razor clams, 11 of 75 (14.6%), Cockle clams, 12 of 15 (80.0%); Softshell clams, 8 of 12 (66.4%); Littleneck clams, 4 of 11(36.2%); Horseneck clams, 1 of 3 (33.3%); Oysters, 6 of 19 (31.6%); Dungeness crabs, 17 of 24 (71%). Only the razor clams were collected exclusively from the ocean beach. Loss of toxicity on holding mixed cultures at -15 C while awaiting typing was a continual problem. This accounts for only one-third of toxic filtrates being successfully typed. Electrophoretic analysis of the total bacterial proteins was carried out on cell sonicates and cell free culture filtrates by first growing cells for four days at 28 C anaerobically. The cells were separated, washed and disrupted with ultrasonic energy. The cell free culture filtrate was concentrated 10 fold by dialysis against polyethylene glycol 4000. Both the toxigenic organisms and the toxic filtrate demonstrated an extra common protein band in the upper third of the electrophoretic pattern not present in the nontoxic spectra. This band might represent the type E toxin. Differences could also be noted in the number of protein bands in the lower third of the patterns in different nontoxigenic strains and also when the toxigenic and nontoxigenic strains were compared. This could suggest an association with a phage in the toxigenic cultures. Title: Distribution of Clostridium botulinum type E in fish, shellfish and the marine environment of the Pacific Northwest, and protein patterns of the toxigenic and non-toxigenic stains Author: Craig, James Morrison Interest in the distribution of Clostridium botulinum type E was heightened by the sudden outbreak of human botulism from smoked whitefish chubs and canned tuna fish in 1963. The question arose as to how widely the organism is distributed among fish and shellfish in the Northwest and what potential hazard exists for the consumer of fish products. This sporeforming anaerobic orgnism is heat sensitive and had eluded detection in other surveys where heat shock had been used to eliminate non sporeforming contaminants. More recent study using other techniques than heat to facilitate recovery has shown this organism to be widespread, especially in the marine environment. This study was undertaken to find the incidence and distribution of C. botulinum in the marine organisms and environment of the Pacific Northwest and the food products derived therefrom. All species of fish were examined by incubating the gills and viscera individually in tryptone-peptone-glucose medium anaerobically at 28 C for four days and testing the culture filtrate for mouse toxicity by intraperitoneal injection. Toxic filtrates were typed by retesting them in mice protected by specific botulinal antitoxin of type A, B, E, or F. Among salmonid fish the proportions of specimens of each species yielding toxic filtrates were as follows. Sockeye salmon from the Columbia River, 14 of 59 (23.7%); Chinook salmon from the Columbia River, 19 of 106 (18.0%); Chinook salmon from the Pacific Ocean, 1 of 18 (5,6%); Coho salmon from the Columbia River, 10 of 19 (34.4%); Coho salmon from the Pacific Ocean, 13 of 186 (7.0%); Steelhead trout from the Alsea River, 7 of 37 (19.0%). About one-third of the toxic cultural filtrates were successfully typed and proven to contain botulinal toxin. Most of them proved to be type E toxin but 3 were type A, 3 were type B and one, a comparatively new type, type F, was isolated from a Sockeye salmon in the Columbia River. Pure cultures of Clostridium botulinum type E were isolated from 18 specimens and one specimen yielded a pure culture of type F from a sockeye salmon. This was the second time this type had been isolated. In all of the experimental groups the proportion of fish producing toxigenic cultures was significantly higher in those taken in the two rivers than those of the same species taken from the ocean waters. "Bottom fish" represented by Cod, Sole, Grouper and members of the Sebastodes group were also tested in the manner described above. The number of specimens yielding toxic filtrates were 28 of 157 (17.8%). When grouped according to location at which the fish were caught, those near the mouth of the Columbia River produced a greater percentage of toxic filtrates than did those caught off the open shore line. The results were as follows: Bottom fish from Astoria, 23 of 70 (32.8%), Botton fish from Coos Bay, 5 of 87 (5.6%). Sturgeon specimens produced 3 of 24 (12.5%) toxic filtrates. Most of the species contained type E; however, one type A and one type B were found on typing, with about one-third of the toxic filtrates being successfully typed. Environmental swab samples from the "deep sea" fillet processing plants produced 3 of 39 (7.7%) toxic filtrates. None of the 53 samples taken in the salmon processing plants produced toxic filtrates. Shellfish were collected along the ocean beach and in the estuaries. Three to five shellfish were combined into a single specimen and treated as described. All shellfish obtained from the estuaries demonstrated a higher percentage of toxic filtrates than those obtained from the ocean beach. The results were as follows: Razor clams, 11 of 75 (14.6%), Cockle clams, 12 of 15 (80.0%); Softshell clams, 8 of 12 (66.4%); Littleneck clams, 4 of 11(36.2%); Horseneck clams, 1 of 3 (33.3%); Oysters, 6 of 19 (31.6%); Dungeness crabs, 17 of 24 (71%). Only the razor clams were collected exclusively from the ocean beach. Loss of toxicity on holding mixed cultures at -15 C while awaiting typing was a continual problem. This accounts for only one-third of toxic filtrates being successfully typed. Electrophoretic analysis of the total bacterial proteins was carried out on cell sonicates and cell free culture filtrates by first growing cells for four days at 28 C anaerobically. The cells were separated, washed and disrupted with ultrasonic energy. The cell free culture filtrate was concentrated 10 fold by dialysis against polyethylene glycol 4000. Both the toxigenic organisms and the toxic filtrate demonstrated an extra common protein band in the upper third of the electrophoretic pattern not present in the nontoxic spectra. This band might represent the type E toxin. Differences could also be noted in the number of protein bands in the lower third of the patterns in different nontoxigenic strains and also when the toxigenic and nontoxigenic strains were compared. This could suggest an association with a phage in the toxigenic cultures. Close

• 947. [Article] A bioeconomic analysis of altering instream flows anadromous fish production and competing demands for water in the John Day River basin, Oregon

  The growing demand for water in the arid regions of the West increases the need for optimal allocation of water among competing uses. An efficient allocation of water between instream and out-of-stream uses ...

  Citation × Citation Citation Abstract Copy Title: A bioeconomic analysis of altering instream flows anadromous fish production and competing demands for water in the John Day River basin, Oregon Author: Johnson, Neal S. The growing demand for water in the arid regions of the West increases the need for optimal allocation of water among competing uses. An efficient allocation of water between instream and out-of-stream uses has been impeded by institutional constraints and the scarcity of information regarding instream flow benefits. The objectives of this thesis were to provide preliminary economic data on the value of instream water in "producing" recreational fishing and to examine the effect of forestry, agriculture, and livestock practices on temporal streamflow patterns and anadromous fish production. The steelhead trout (Salmo gairdneri) sport fishery within the John Day River basin in north-central Oregon provided the setting for this research. The interdisciplinary methodology employed in estimating the marginal value of water with respect to steelhead production consisted of two tasks. The first task involved valuing a marginal change in the quality of the steelhead recreational fishery. The contingent valuation method (CVM) was selected for this purpose. Both open- and closed-ended willingness-to-pay (WTP) questions were included in a questionnaire administered to John Day River steelhead anglers during the 1986/87 steelhead fishing season. Survey data were analyzed to arrive at individual and aggregate bid functions relating WTP to expected angling success rates. Results indicate that, under current conditions, the average angler is willing to pay approximately $7.20 to catch an additional steelhead. The second task of the instream water valuation methodology was directed at deriving a streamflow/steelhead production relationship. By including variables influencing steelhead production in a Ricker stock-recruitment model, it was possible to develop a model which could be estimated using linear regression techniques. Some difficulty arose, however, with interpretation of the model due to the unavailability of cohort escapement data and the subsequent use of standing crop data. While possibly masking the true magnitude of streamflow's effect on fish production, this drawback was not deemed limiting within the general context of the interdisciplinary methodology. Results of the biological model conformed to a priori expectations. Increases in summer and winter streamflows led to increased steelhead survival, whereas higher spring flows increased mortality levels. Other results indicate that the John Day Dam was responsible for a 31.5 percent decline in the population index for the 1969-1983 period. Combining the economic and biological results into one equation yielded an estimate of the marginal value of summer instream water in "producing" recreational steelhead angling. Similar equations were developed for winter and spring flows. The marginal value of water in producing recreational steelhead fishing within the John Day basin was estimated at $0.56 per acre-foot for summer flows, $0.046 for winter flows, and -$0.075 for spring flows. By including out-of-basin benefits, these values increased to $2.26, $0.19, and -$0.30, respectively. In comparison, water's value in irrigation within the John Day basin has been estimated at between $10 to $24 per acre-foot. However, nonuse values of steelhead, as well as the increased production of other fish species (such as spring chinook salmon) were not included in the instream water values. In addition, no attempt was made at valuing instream water's contribution to boating, camping, or other benefit-producing activities. A secondary objective of this thesis was to briefly examine the possible benefits accruing to other instream and out-of-stream users due to an alteration in streamflow patterns. In addition, the impact of activities by other resource users -- namely forestry, agriculture, and livestock production --on anadromous fish production was reviewed. Improper management practices by these activities can negatively impact the aquatic and riparian ecosystems. While no firm conclusions were drawn, it appears the quality of these ecosystems, as opposed to the amount of streamflow, has the largest marginal impact on anadromous fish populations. Title: A bioeconomic analysis of altering instream flows anadromous fish production and competing demands for water in the John Day River basin, Oregon Author: Johnson, Neal S. The growing demand for water in the arid regions of the West increases the need for optimal allocation of water among competing uses. An efficient allocation of water between instream and out-of-stream uses has been impeded by institutional constraints and the scarcity of information regarding instream flow benefits. The objectives of this thesis were to provide preliminary economic data on the value of instream water in "producing" recreational fishing and to examine the effect of forestry, agriculture, and livestock practices on temporal streamflow patterns and anadromous fish production. The steelhead trout (Salmo gairdneri) sport fishery within the John Day River basin in north-central Oregon provided the setting for this research. The interdisciplinary methodology employed in estimating the marginal value of water with respect to steelhead production consisted of two tasks. The first task involved valuing a marginal change in the quality of the steelhead recreational fishery. The contingent valuation method (CVM) was selected for this purpose. Both open- and closed-ended willingness-to-pay (WTP) questions were included in a questionnaire administered to John Day River steelhead anglers during the 1986/87 steelhead fishing season. Survey data were analyzed to arrive at individual and aggregate bid functions relating WTP to expected angling success rates. Results indicate that, under current conditions, the average angler is willing to pay approximately $7.20 to catch an additional steelhead. The second task of the instream water valuation methodology was directed at deriving a streamflow/steelhead production relationship. By including variables influencing steelhead production in a Ricker stock-recruitment model, it was possible to develop a model which could be estimated using linear regression techniques. Some difficulty arose, however, with interpretation of the model due to the unavailability of cohort escapement data and the subsequent use of standing crop data. While possibly masking the true magnitude of streamflow's effect on fish production, this drawback was not deemed limiting within the general context of the interdisciplinary methodology. Results of the biological model conformed to a priori expectations. Increases in summer and winter streamflows led to increased steelhead survival, whereas higher spring flows increased mortality levels. Other results indicate that the John Day Dam was responsible for a 31.5 percent decline in the population index for the 1969-1983 period. Combining the economic and biological results into one equation yielded an estimate of the marginal value of summer instream water in "producing" recreational steelhead angling. Similar equations were developed for winter and spring flows. The marginal value of water in producing recreational steelhead fishing within the John Day basin was estimated at $0.56 per acre-foot for summer flows, $0.046 for winter flows, and -$0.075 for spring flows. By including out-of-basin benefits, these values increased to $2.26, $0.19, and -$0.30, respectively. In comparison, water's value in irrigation within the John Day basin has been estimated at between $10 to $24 per acre-foot. However, nonuse values of steelhead, as well as the increased production of other fish species (such as spring chinook salmon) were not included in the instream water values. In addition, no attempt was made at valuing instream water's contribution to boating, camping, or other benefit-producing activities. A secondary objective of this thesis was to briefly examine the possible benefits accruing to other instream and out-of-stream users due to an alteration in streamflow patterns. In addition, the impact of activities by other resource users -- namely forestry, agriculture, and livestock production --on anadromous fish production was reviewed. Improper management practices by these activities can negatively impact the aquatic and riparian ecosystems. While no firm conclusions were drawn, it appears the quality of these ecosystems, as opposed to the amount of streamflow, has the largest marginal impact on anadromous fish populations. Close

• 948. [Article] Characteristics of two salmonid fish cell lines : glycolytic rates, CO₂ requirements and susceptibility to Reovirus and Reovirus-like agents

  The research presented in this thesis is concerned with the characterization of two salmonid cell lines, CSE 119 derived from embryos of coho salmon (Oncorhynchus kisutch) and STE 137 derived from embryos ...

  Citation × Citation Citation Abstract Copy Title: Characteristics of two salmonid fish cell lines : glycolytic rates, CO₂ requirements and susceptibility to Reovirus and Reovirus-like agents Author: Kleeman, Karl Terrence The research presented in this thesis is concerned with the characterization of two salmonid cell lines, CSE 119 derived from embryos of coho salmon (Oncorhynchus kisutch) and STE 137 derived from embryos of steelhead trout (Salmo gairdneri). The rates of glucose utilization and lactic acid production during the most active growth phase of each cell line were determined and the results were compared to data from parallel experiments using a human embryonic cell line. The salmonid cells were grown at 23° C and the human cells at 35° C. All cells were grown in Eagle's minimal essential medium supplemented with 20% dialyzed newborn agamma calf The Q[superscript]O₂[subscript]CO₂ serum. values (equivalent microliters CO₂ produced per mg dry weight of cells per hour) were calculated for each cell type, and values of 7.97 and 4.50 were obtained for CSE 119 and STE 137, respectively. These values were somewhat lower than the value of 13.19 calculated for the human cells. In all three cell lines studied, the rates of glucose utilized and lactic acid produced per cell decreased over the growth periods observed. The decreases in the salmonid cells were most likely related to a concomitant increase in population density. In addition, it was shown that the very gradual fall in pH observed during the growth of the salmonid cells is apparently due in part, at least, to the smaller amount of lactic acid produced by these cells. During the course of the studies with the salmonid cell lines, an investigation of the CO₂ requirements of these cells was undertaken. For these experiments, Tris buffer was used to replace the bicarbonate in the medium and 20% dialyzed serum was again used. Results from the salmonid cells grown at 18° C were compared to parallel experiments using He La cells grown at 35° C. It was shown that growth under 2% (salmonid) and 3% (He La) atmospheric CO₂ was comparable to growth in stoppered cultures for CSE 119, STE 137 and the He La cells. The salmonid cells showed good growth in cul- tures that were open to the air (0.03% CO₂), but little or no growth occurred in the He La cells under the same conditions. To determine if CO₂ was actually required for growth of the salmonid cells, CO₂ free cultures were prepared using Conway microdiffusion dishes in which the cells were grown in the center well and a 10% solution of KOH was added to the outer well. The cultures were sealed with high vacuum grease. Under these conditions, both salmonid cell lines demonstrated a growth requirement for CO₂ comparable to that shown by the He La cells. Attempts were made to use oxalacetate to substitute for CO₂ in these cultures. Oxalacetate partially substituted for CO₂ in the He La cell cultures, but little or no growth occurred in the salmonid cell cultures under the same conditions. As part of a continuing effort to determine the viral susceptibility of salmonid cell lines, the coho cells (CSE 119) and the steelhead cells (STE 137) were tested for their susceptibility to Reovirus types 1 and 3, Infectious Pancreatic Necrosis (IPN) virus and Wound Tumor virus (WTV). Neither salmonid cell line nor He La cells were shown to produce infectious virus when inoculated with either reovirus type at 26° C. The salmonid cells would not tolerate 30° C for even short periods of time. Good replication of both reovirus types occurred in He La cells at 35° C. IPN virus replicated well in both salmonid cell lines at 18° C. Phase contrast studies of IPN infected salmonid cells showed an early webbing of the cytoplasm, followed by a rounding up of the cells, shrinkage of the nuclei and a heavy margination of nuclear chromatin. Because of its similarity to the reoviruses and its ability to replicate in an insect cell line, attempts were made to infect the salmonid cells with WTV at 23° C. No indications of WTV inclusion bodies or of a cytopathic effect were found in either salmonid cell line. Title: Characteristics of two salmonid fish cell lines : glycolytic rates, CO₂ requirements and susceptibility to Reovirus and Reovirus-like agents Author: Kleeman, Karl Terrence The research presented in this thesis is concerned with the characterization of two salmonid cell lines, CSE 119 derived from embryos of coho salmon (Oncorhynchus kisutch) and STE 137 derived from embryos of steelhead trout (Salmo gairdneri). The rates of glucose utilization and lactic acid production during the most active growth phase of each cell line were determined and the results were compared to data from parallel experiments using a human embryonic cell line. The salmonid cells were grown at 23° C and the human cells at 35° C. All cells were grown in Eagle's minimal essential medium supplemented with 20% dialyzed newborn agamma calf The Q[superscript]O₂[subscript]CO₂ serum. values (equivalent microliters CO₂ produced per mg dry weight of cells per hour) were calculated for each cell type, and values of 7.97 and 4.50 were obtained for CSE 119 and STE 137, respectively. These values were somewhat lower than the value of 13.19 calculated for the human cells. In all three cell lines studied, the rates of glucose utilized and lactic acid produced per cell decreased over the growth periods observed. The decreases in the salmonid cells were most likely related to a concomitant increase in population density. In addition, it was shown that the very gradual fall in pH observed during the growth of the salmonid cells is apparently due in part, at least, to the smaller amount of lactic acid produced by these cells. During the course of the studies with the salmonid cell lines, an investigation of the CO₂ requirements of these cells was undertaken. For these experiments, Tris buffer was used to replace the bicarbonate in the medium and 20% dialyzed serum was again used. Results from the salmonid cells grown at 18° C were compared to parallel experiments using He La cells grown at 35° C. It was shown that growth under 2% (salmonid) and 3% (He La) atmospheric CO₂ was comparable to growth in stoppered cultures for CSE 119, STE 137 and the He La cells. The salmonid cells showed good growth in cul- tures that were open to the air (0.03% CO₂), but little or no growth occurred in the He La cells under the same conditions. To determine if CO₂ was actually required for growth of the salmonid cells, CO₂ free cultures were prepared using Conway microdiffusion dishes in which the cells were grown in the center well and a 10% solution of KOH was added to the outer well. The cultures were sealed with high vacuum grease. Under these conditions, both salmonid cell lines demonstrated a growth requirement for CO₂ comparable to that shown by the He La cells. Attempts were made to use oxalacetate to substitute for CO₂ in these cultures. Oxalacetate partially substituted for CO₂ in the He La cell cultures, but little or no growth occurred in the salmonid cell cultures under the same conditions. As part of a continuing effort to determine the viral susceptibility of salmonid cell lines, the coho cells (CSE 119) and the steelhead cells (STE 137) were tested for their susceptibility to Reovirus types 1 and 3, Infectious Pancreatic Necrosis (IPN) virus and Wound Tumor virus (WTV). Neither salmonid cell line nor He La cells were shown to produce infectious virus when inoculated with either reovirus type at 26° C. The salmonid cells would not tolerate 30° C for even short periods of time. Good replication of both reovirus types occurred in He La cells at 35° C. IPN virus replicated well in both salmonid cell lines at 18° C. Phase contrast studies of IPN infected salmonid cells showed an early webbing of the cytoplasm, followed by a rounding up of the cells, shrinkage of the nuclei and a heavy margination of nuclear chromatin. Because of its similarity to the reoviruses and its ability to replicate in an insect cell line, attempts were made to infect the salmonid cells with WTV at 23° C. No indications of WTV inclusion bodies or of a cytopathic effect were found in either salmonid cell line. Close

• 949. [Article] 2008 Amphibian Distribution Surveys in Wadeable Streams and Ponds in Western and Southeast Oregon, Information Reports Number 2010-05

  Abstract -- The ODFW Oregon Conservation Strategy identified monitoring needs for 17 amphibian species native to the state of Oregon that are designated as “Strategy species”, or Species of Greatest Conservation ...

  Citation × Citation Citation Abstract Copy Title: 2008 Amphibian Distribution Surveys in Wadeable Streams and Ponds in Western and Southeast Oregon, Information Reports Number 2010-05 Abstract -- The ODFW Oregon Conservation Strategy identified monitoring needs for 17 amphibian species native to the state of Oregon that are designated as “Strategy species”, or Species of Greatest Conservation Need (per USFWS requirements for State Wildlife Action Plans). The distribution of many species of amphibians in western Oregon is sparsely documented (Oregon Conservation Strategy, page 27). Although a broad-scale survey for amphibian presence would provide important baseline information about amphibian species composition and distribution, most studies have focused on limited areas. The majority of Oregon’s amphibians rely on aquatic habitats at some point of their life, either for breeding and juvenile development or to inhabit as adults. Most aquatic amphibians breed from late winter to early summer, and adults frequently remain in or near their breeding sites into the summer. Most tadpoles and juvenile amphibians are also active in and occupy aquatic habitats during the summer. Ongoing aquatic habitat and fish surveys are opportunities to observe species and life stages (breeding adults, tadpoles and juveniles) that occupy aquatic or riparian habitats during the summer. One cost-effective approach is to combine amphibian surveys with existing aquatic habitat and fish surveys such as those conducted as part of the Oregon Plan for Salmon and Watersheds (OCSRI 1997). The Oregon Plan has been in place since 1997 and the monitoring component provides a survey framework for streams in the lower Columbia River and Oregon coast drainages. The sampling framework is also compatible with implementation of the aquatic components of the Conservation Strategy, as demonstrated by this study. This study describes the presence of amphibians in and along wadeable streams in coast and lower Columbia River drainages of Oregon, ponds and sloughs in the Willamette Valley, and selected streams in the Great Basin of southeast and central Oregon. As a component of monitoring under the Oregon Plan, the Aquatic Inventories Project (AIP) conducts aquatic habitat surveys at randomly selected and spatially balanced sites across all 1st through 4th order streams in coastal and lower Columbia River drainages. The purpose of the habitat surveys is to describe stream morphology, instream physical habitat, and riparian vegetation. Because the surveyors were already observing features within and alongside the stream channel, they were able to record observations of amphibians. The amphibian component was consistent with the survey protocol used by the US Geological Survey’s Amphibian Research and Monitoring Initiative (http://armi.usgs.gov/). The advantage of coupling an amphibian component with the OR Plan aquatic surveys was that it not only was an efficient use of resources, but more importantly, provided information using a statistically rigorous survey design across a broad geographic area. The Native Fish Investigations Project began a six year study in 2007 to document the distribution and abundance of redband trout in the Great Basin region of Eastern Oregon. The site selection procedure is comparable to the statistical standards as the Oregon Plan survey design. Amphibian data are also collected during three other survey projects, and although the site selection procedure does not conform to the same statistical standards as the Oregon Plan survey design, the projects offer a number of opportunities to collect amphibian occurrence information over a wide variety of habitats. The amphibian observations from these three projects are also included in this report. The three projects are as follows: • AIP conducts aquatic habitat surveys on selected streams throughout the state. • AIP conducts aquatic habitat surveys at stream habitat restoration projects in Western Oregon. • Native Fish Project conducts surveys of pond and slough sites for Oregon chub in the Willamette Valley. Due to the success of the 2006 and 2007 field studies, we continued our research during the summer of 2008 to improve our knowledge of distribution and community structure of amphibians. The summer 2008 surveys took place in 9 of Oregon’s 10 ecoregions (Figure 1) (Thorson et al. 2003). Ecoregions provide a framework for discussing amphibian distribution across the state because they are relatively large areas defined by distinctive geographic and ecological (flora and fauna) characteristics. The goals of our 2008 work were to: • Increase the consistency, efficiency and ability of habitat crews in identifying amphibians through improved training. • Increase knowledge of distribution, community structure, and habitat associations of amphibians in streams in: o Western Oregon coastal and lower Columbia drainages. o Ponds, sloughs and other off-channel aquatic habitats in the Willamette Valley. o Great Basin of eastern Oregon and selected streams in central Oregon. • Combine the 2008 observations with the 2006-07 results. Title: 2008 Amphibian Distribution Surveys in Wadeable Streams and Ponds in Western and Southeast Oregon, Information Reports Number 2010-05 Abstract -- The ODFW Oregon Conservation Strategy identified monitoring needs for 17 amphibian species native to the state of Oregon that are designated as “Strategy species”, or Species of Greatest Conservation Need (per USFWS requirements for State Wildlife Action Plans). The distribution of many species of amphibians in western Oregon is sparsely documented (Oregon Conservation Strategy, page 27). Although a broad-scale survey for amphibian presence would provide important baseline information about amphibian species composition and distribution, most studies have focused on limited areas. The majority of Oregon’s amphibians rely on aquatic habitats at some point of their life, either for breeding and juvenile development or to inhabit as adults. Most aquatic amphibians breed from late winter to early summer, and adults frequently remain in or near their breeding sites into the summer. Most tadpoles and juvenile amphibians are also active in and occupy aquatic habitats during the summer. Ongoing aquatic habitat and fish surveys are opportunities to observe species and life stages (breeding adults, tadpoles and juveniles) that occupy aquatic or riparian habitats during the summer. One cost-effective approach is to combine amphibian surveys with existing aquatic habitat and fish surveys such as those conducted as part of the Oregon Plan for Salmon and Watersheds (OCSRI 1997). The Oregon Plan has been in place since 1997 and the monitoring component provides a survey framework for streams in the lower Columbia River and Oregon coast drainages. The sampling framework is also compatible with implementation of the aquatic components of the Conservation Strategy, as demonstrated by this study. This study describes the presence of amphibians in and along wadeable streams in coast and lower Columbia River drainages of Oregon, ponds and sloughs in the Willamette Valley, and selected streams in the Great Basin of southeast and central Oregon. As a component of monitoring under the Oregon Plan, the Aquatic Inventories Project (AIP) conducts aquatic habitat surveys at randomly selected and spatially balanced sites across all 1st through 4th order streams in coastal and lower Columbia River drainages. The purpose of the habitat surveys is to describe stream morphology, instream physical habitat, and riparian vegetation. Because the surveyors were already observing features within and alongside the stream channel, they were able to record observations of amphibians. The amphibian component was consistent with the survey protocol used by the US Geological Survey’s Amphibian Research and Monitoring Initiative (http://armi.usgs.gov/). The advantage of coupling an amphibian component with the OR Plan aquatic surveys was that it not only was an efficient use of resources, but more importantly, provided information using a statistically rigorous survey design across a broad geographic area. The Native Fish Investigations Project began a six year study in 2007 to document the distribution and abundance of redband trout in the Great Basin region of Eastern Oregon. The site selection procedure is comparable to the statistical standards as the Oregon Plan survey design. Amphibian data are also collected during three other survey projects, and although the site selection procedure does not conform to the same statistical standards as the Oregon Plan survey design, the projects offer a number of opportunities to collect amphibian occurrence information over a wide variety of habitats. The amphibian observations from these three projects are also included in this report. The three projects are as follows: • AIP conducts aquatic habitat surveys on selected streams throughout the state. • AIP conducts aquatic habitat surveys at stream habitat restoration projects in Western Oregon. • Native Fish Project conducts surveys of pond and slough sites for Oregon chub in the Willamette Valley. Due to the success of the 2006 and 2007 field studies, we continued our research during the summer of 2008 to improve our knowledge of distribution and community structure of amphibians. The summer 2008 surveys took place in 9 of Oregon’s 10 ecoregions (Figure 1) (Thorson et al. 2003). Ecoregions provide a framework for discussing amphibian distribution across the state because they are relatively large areas defined by distinctive geographic and ecological (flora and fauna) characteristics. The goals of our 2008 work were to: • Increase the consistency, efficiency and ability of habitat crews in identifying amphibians through improved training. • Increase knowledge of distribution, community structure, and habitat associations of amphibians in streams in: o Western Oregon coastal and lower Columbia drainages. o Ponds, sloughs and other off-channel aquatic habitats in the Willamette Valley. o Great Basin of eastern Oregon and selected streams in central Oregon. • Combine the 2008 observations with the 2006-07 results. Close

• 950. [Article] Amphibian Distribution in Wadeable Streams and Ponds in Western and Southeast Oregon, 2009-2010 Progress Reports 2011

  Abstract -- The ODFW Oregon Conservation Strategy identified monitoring needs for 17 amphibian species native to the state of Oregon that are designated as “Strategy Species”, or “Species of Greatest Conservation ...

  Citation × Citation Citation Abstract Copy Title: Amphibian Distribution in Wadeable Streams and Ponds in Western and Southeast Oregon, 2009-2010 Progress Reports 2011 Abstract -- The ODFW Oregon Conservation Strategy identified monitoring needs for 17 amphibian species native to the state of Oregon that are designated as “Strategy Species”, or “Species of Greatest Conservation Need” (per USFWS requirements for State Wildlife Action Plans). The distribution of many species of amphibians in western Oregon is sparsely documented (Oregon Conservation Strategy, page 27). Although a broad-scale survey for amphibian presence would provide important baseline information about amphibian species composition and distribution, most studies have focused on limited areas. The majority of Oregon’s amphibians rely on aquatic habitats at some point of their life, either for breeding and juvenile development or to inhabit as adults. Most aquatic amphibians breed from late winter to early summer, and adults frequently remain in or near their breeding sites into the summer. Most tadpoles and juvenile amphibians are also active in and occupy aquatic habitats during the summer. Ongoing aquatic habitat and fish surveys are opportunities to observe species and life stages (breeding adults, tadpoles and juveniles) that occupy aquatic or riparian habitats during the summer. One cost-effective approach is to combine amphibian surveys with existing aquatic habitat and fish surveys such as those conducted as part of the Oregon Plan for Salmon and Watersheds (OCSRI 1997). The Oregon Plan has been in place since 1997 and the monitoring component provides a survey framework for streams in the lower Columbia River and Oregon coast drainages. The sampling framework is also compatible with implementation of the aquatic components of the Conservation Strategy, as demonstrated by this study. This study describes the presence of amphibians in and along wadeable streams in coast and lower Columbia River drainages of Oregon, ponds and sloughs in the Willamette Valley, and selected streams in the Great Basin of southeast and central Oregon. As a component of monitoring under the Oregon Plan, the Aquatic Inventories Project (AIP) conducts aquatic habitat surveys at randomly selected and spatially balanced sites across all 1st through 4th order streams in coastal and lower Columbia River drainages. The purpose of the habitat surveys is to describe stream morphology, instream physical habitat, and riparian vegetation. Because the surveyors were already observing features within and alongside the stream channel, they were able to record observations of amphibians. The advantage of coupling an amphibian component with the OR Plan aquatic surveys was that it not only was an efficient use of resources, but more importantly, provided information using a statistically rigorous survey design across a broad geographic area. The Native Fish Investigations Project began a six year study in 2007 to document the distribution and abundance of redband trout in the Great Basin region of Eastern Oregon. The site selection procedure is comparable to the statistical standards as the Oregon Plan survey design. Amphibian data are also collected during three other survey projects, and although the site selection procedure does not conform to the same statistical standards as the Oregon Plan survey design, the projects offer a number of opportunities to collect amphibian occurrence information over a wide variety of habitats. The amphibian observations from these three projects are also included in this report. The three projects are as follows: AIP conducts aquatic habitat surveys on selected streams throughout the state. AIP conducts aquatic habitat surveys at stream habitat restoration projects in Western Oregon. Native Fish Project conducts surveys of pond and slough sites for Oregon chub in the Willamette Valley. Due to the success of the 2007 and 2008 field studies, we continued our research during the summer of 2009 and 2010 to improve our knowledge of distribution and community structure of amphibians. The summer 2009 and 2010 surveys took place in 9 of Oregon’s 10 ecoregions (Figure 1) (Thorson et al. 2003). Ecoregions provide a framework for discussing amphibian distribution across the state because they are relatively large areas defined by distinctive geographic and ecological (flora and fauna) characteristics. The goals of our 2009-2010 work were to: Increase the consistency, efficiency and ability of habitat crews in identifying amphibians through improved training. Increase knowledge of distribution, community structure, and habitat associations of amphibians in streams in: Western Oregon coastal and lower Columbia drainages. Ponds, sloughs and other off-channel aquatic habitats in the Willamette Valley. Great Basin of eastern Oregon and selected streams in central Oregon. Combine the 2009-2010 observations with the 2007-2008 results. Title: Amphibian Distribution in Wadeable Streams and Ponds in Western and Southeast Oregon, 2009-2010 Progress Reports 2011 Abstract -- The ODFW Oregon Conservation Strategy identified monitoring needs for 17 amphibian species native to the state of Oregon that are designated as “Strategy Species”, or “Species of Greatest Conservation Need” (per USFWS requirements for State Wildlife Action Plans). The distribution of many species of amphibians in western Oregon is sparsely documented (Oregon Conservation Strategy, page 27). Although a broad-scale survey for amphibian presence would provide important baseline information about amphibian species composition and distribution, most studies have focused on limited areas. The majority of Oregon’s amphibians rely on aquatic habitats at some point of their life, either for breeding and juvenile development or to inhabit as adults. Most aquatic amphibians breed from late winter to early summer, and adults frequently remain in or near their breeding sites into the summer. Most tadpoles and juvenile amphibians are also active in and occupy aquatic habitats during the summer. Ongoing aquatic habitat and fish surveys are opportunities to observe species and life stages (breeding adults, tadpoles and juveniles) that occupy aquatic or riparian habitats during the summer. One cost-effective approach is to combine amphibian surveys with existing aquatic habitat and fish surveys such as those conducted as part of the Oregon Plan for Salmon and Watersheds (OCSRI 1997). The Oregon Plan has been in place since 1997 and the monitoring component provides a survey framework for streams in the lower Columbia River and Oregon coast drainages. The sampling framework is also compatible with implementation of the aquatic components of the Conservation Strategy, as demonstrated by this study. This study describes the presence of amphibians in and along wadeable streams in coast and lower Columbia River drainages of Oregon, ponds and sloughs in the Willamette Valley, and selected streams in the Great Basin of southeast and central Oregon. As a component of monitoring under the Oregon Plan, the Aquatic Inventories Project (AIP) conducts aquatic habitat surveys at randomly selected and spatially balanced sites across all 1st through 4th order streams in coastal and lower Columbia River drainages. The purpose of the habitat surveys is to describe stream morphology, instream physical habitat, and riparian vegetation. Because the surveyors were already observing features within and alongside the stream channel, they were able to record observations of amphibians. The advantage of coupling an amphibian component with the OR Plan aquatic surveys was that it not only was an efficient use of resources, but more importantly, provided information using a statistically rigorous survey design across a broad geographic area. The Native Fish Investigations Project began a six year study in 2007 to document the distribution and abundance of redband trout in the Great Basin region of Eastern Oregon. The site selection procedure is comparable to the statistical standards as the Oregon Plan survey design. Amphibian data are also collected during three other survey projects, and although the site selection procedure does not conform to the same statistical standards as the Oregon Plan survey design, the projects offer a number of opportunities to collect amphibian occurrence information over a wide variety of habitats. The amphibian observations from these three projects are also included in this report. The three projects are as follows: AIP conducts aquatic habitat surveys on selected streams throughout the state. AIP conducts aquatic habitat surveys at stream habitat restoration projects in Western Oregon. Native Fish Project conducts surveys of pond and slough sites for Oregon chub in the Willamette Valley. Due to the success of the 2007 and 2008 field studies, we continued our research during the summer of 2009 and 2010 to improve our knowledge of distribution and community structure of amphibians. The summer 2009 and 2010 surveys took place in 9 of Oregon’s 10 ecoregions (Figure 1) (Thorson et al. 2003). Ecoregions provide a framework for discussing amphibian distribution across the state because they are relatively large areas defined by distinctive geographic and ecological (flora and fauna) characteristics. The goals of our 2009-2010 work were to: Increase the consistency, efficiency and ability of habitat crews in identifying amphibians through improved training. Increase knowledge of distribution, community structure, and habitat associations of amphibians in streams in: Western Oregon coastal and lower Columbia drainages. Ponds, sloughs and other off-channel aquatic habitats in the Willamette Valley. Great Basin of eastern Oregon and selected streams in central Oregon. Combine the 2009-2010 observations with the 2007-2008 results. Close