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• 1. [Image] The Water Report - The Oregon Water Resources Department: an interview with director Paul Cleary

  	Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. See the full report at http://www.thewaterreport.com/
  	Citation × Citation Citation Abstract Copy Title: The Water Report - The Oregon Water Resources Department: an interview with director Paul Cleary Author: Envirotech Publications Year: 2004, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. See the full report at http://www.thewaterreport.com/ Title: The Water Report - The Oregon Water Resources Department: an interview with director Paul Cleary Author: Envirotech Publications Year: 2004, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. See the full report at http://www.thewaterreport.com/ Close

• 2. [Image] The Water Report - Hydro relicensing OR/CA: fish passage

  	Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. See the full report at http://www.thewaterreport.com/
  	Citation × Citation Citation Abstract Copy Title: The Water Report - Hydro relicensing OR/CA: fish passage Author: Envirotech Publications Year: 2006, 2008 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. See the full report at http://www.thewaterreport.com/ Title: The Water Report - Hydro relicensing OR/CA: fish passage Author: Envirotech Publications Year: 2006, 2008 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. See the full report at http://www.thewaterreport.com/ Close

• 3. [Image] The Water Report. Klamath Fishery Science: Controversy in the Klamath River Basin

  	Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographic references. See the full report at http://www.thewaterreport.com/.
  	Citation × Citation Citation Abstract Copy Title: The Water Report. Klamath Fishery Science: Controversy in the Klamath River Basin Author: Envirotech Publications Year: 2005, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographic references. See the full report at http://www.thewaterreport.com/. Title: The Water Report. Klamath Fishery Science: Controversy in the Klamath River Basin Author: Envirotech Publications Year: 2005, 2008, 2006 Only portions of issues of The Water Report are available in the Klamath Waters Digital Library. Includes bibliographic references. See the full report at http://www.thewaterreport.com/. Close

• 4. [Article] Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths

  Published March 1989. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog...

  Citation × Citation Citation Abstract Copy Title: Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths Author: Hankin, David G., Oregon State University. Extension Service, Oregon. Fish Division, Nicholas, Jay W., Oregon. Dept. of Fish and Wildlife. Research and Development Section Published March 1989. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog Title: Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths Author: Hankin, David G., Oregon State University. Extension Service, Oregon. Fish Division, Nicholas, Jay W., Oregon. Dept. of Fish and Wildlife. Research and Development Section Published March 1989. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog Close

• 5. [Article] An investigation into the genetic basis of migration timing in Chinook salmon (Oncorhynchus tshawytscha)

  The genetic basis of adaptation is complex as many fitness-related traits are quantitative and likely influenced by multiple genes with variable effects across different selective environments. One important ...

  Citation × Citation Citation Abstract Copy Title: An investigation into the genetic basis of migration timing in Chinook salmon (Oncorhynchus tshawytscha) Author: O'Malley, Kathleen Gallen, 1976- The genetic basis of adaptation is complex as many fitness-related traits are quantitative and likely influenced by multiple genes with variable effects across different selective environments. One important adaptation for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which individuals return to natal breeding sites within a reproductive season. Here, I tested for adaptive genetic differentiation among temporally divergent migratory runs using candidate loci. First, I isolated and characterized two copies of the circadian rhythm gene, Clock, from Chinook salmon (OtsClock1a and OtsClock1b). Phylogenetic analysis revealed that these copies likely arose subsequent to the salmonid genome-wide duplication event. Each copy contains a polyglutamine repeat motif (PolyQ), an essential binding domain of this transcription factor. However, a 1200bp non-coding segment, showing >90% sequence identity to the Salmo salar Transferrin gene, is located downstream of the OtsClock1a PolyQ, yet absent from OtsClock1b providing evidence for nonhomologous recombination. Another candidate, Ots515NWFSC, shows sequence identity to three salmonid genes central to reproductive development: Gonadotropin-releasing hormone, CYP19b-I, and Ghrelin. I employed OtsClock1b and Ots515NWFSC to test for differentiation in two unique systems: Feather River, California; and Waitaki and Poulter Rivers, New Zealand. Based on length variation in these candidate genes, Feather River fall and spring run Chinook salmon are genetically differentiated. In contrast, these seasonal runs are genetically indistinguishable based on neutral microsatellite loci. Correspondingly, temporally divergent Chinook salmon runs in the Waitaki and Poulter Rivers show greater differentiation based on variation in OtsClock1b and Ots515NWFSC than microsatellite loci. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC are likely under selection in both systems. In addition, I found evidence for a latitudinal cline in two OtsClock1b PolyQ alleles among 42 Chinook salmon runs which is likely maintained by selection and thus may reflect an adaptation to photoperiodic parameters. Lastly, a hierarchical gene diversity analysis of OtsClock1b PolyQ variation revealed that run timing explained 43.7% of the overall genetic variance which contrast sharply with the 8.1% calculated for microsatellite loci. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration timing of Chinook salmon. Title: An investigation into the genetic basis of migration timing in Chinook salmon (Oncorhynchus tshawytscha) Author: O'Malley, Kathleen Gallen, 1976- The genetic basis of adaptation is complex as many fitness-related traits are quantitative and likely influenced by multiple genes with variable effects across different selective environments. One important adaptation for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which individuals return to natal breeding sites within a reproductive season. Here, I tested for adaptive genetic differentiation among temporally divergent migratory runs using candidate loci. First, I isolated and characterized two copies of the circadian rhythm gene, Clock, from Chinook salmon (OtsClock1a and OtsClock1b). Phylogenetic analysis revealed that these copies likely arose subsequent to the salmonid genome-wide duplication event. Each copy contains a polyglutamine repeat motif (PolyQ), an essential binding domain of this transcription factor. However, a 1200bp non-coding segment, showing >90% sequence identity to the Salmo salar Transferrin gene, is located downstream of the OtsClock1a PolyQ, yet absent from OtsClock1b providing evidence for nonhomologous recombination. Another candidate, Ots515NWFSC, shows sequence identity to three salmonid genes central to reproductive development: Gonadotropin-releasing hormone, CYP19b-I, and Ghrelin. I employed OtsClock1b and Ots515NWFSC to test for differentiation in two unique systems: Feather River, California; and Waitaki and Poulter Rivers, New Zealand. Based on length variation in these candidate genes, Feather River fall and spring run Chinook salmon are genetically differentiated. In contrast, these seasonal runs are genetically indistinguishable based on neutral microsatellite loci. Correspondingly, temporally divergent Chinook salmon runs in the Waitaki and Poulter Rivers show greater differentiation based on variation in OtsClock1b and Ots515NWFSC than microsatellite loci. Tests for selective neutrality indicate that OtsClock1b and Ots515NWFSC are likely under selection in both systems. In addition, I found evidence for a latitudinal cline in two OtsClock1b PolyQ alleles among 42 Chinook salmon runs which is likely maintained by selection and thus may reflect an adaptation to photoperiodic parameters. Lastly, a hierarchical gene diversity analysis of OtsClock1b PolyQ variation revealed that run timing explained 43.7% of the overall genetic variance which contrast sharply with the 8.1% calculated for microsatellite loci. Evidence presented here suggests that OtsClock1b and Ots515NWFSC may influence migration timing of Chinook salmon. Close

• 6. [Article] The Willamette River Spring Chinook Sport Fishery, 1947

  "The Willamette River has the largest runs of spring chinook salmon of any tributary of the Columbia River rising in Oregon. The run to the Willamette is most unique in that the migrating fish pass up ...

  Citation × Citation Citation Abstract Copy Title: The Willamette River Spring Chinook Sport Fishery, 1947 Author: Jensen, Christopher, Johnson, Donald R. "The Willamette River has the largest runs of spring chinook salmon of any tributary of the Columbia River rising in Oregon. The run to the Willamette is most unique in that the migrating fish pass up the river through Portland, a city of several hundred thousand people, and support a large sport fishery in the metropolitan area. This river is the major tributary of the Columbia west of the Cascade Mountains and joins that river about 100 miles from the sea. Anadromous forms, other than spring chinook frequenting the Willamette, include fall chinook and silver salmon, steelhead, trout, and shad. Spring chinook populations of the Columbia have declined steadily since about 1890 and those of the Willamette have probably done likewise. An investigation is being conducted to assess the causes of the decline in Willamette spring chinook. A study of the spot fishery is part of the program." (From Introduction) Title: The Willamette River Spring Chinook Sport Fishery, 1947 Author: Jensen, Christopher, Johnson, Donald R. "The Willamette River has the largest runs of spring chinook salmon of any tributary of the Columbia River rising in Oregon. The run to the Willamette is most unique in that the migrating fish pass up the river through Portland, a city of several hundred thousand people, and support a large sport fishery in the metropolitan area. This river is the major tributary of the Columbia west of the Cascade Mountains and joins that river about 100 miles from the sea. Anadromous forms, other than spring chinook frequenting the Willamette, include fall chinook and silver salmon, steelhead, trout, and shad. Spring chinook populations of the Columbia have declined steadily since about 1890 and those of the Willamette have probably done likewise. An investigation is being conducted to assess the causes of the decline in Willamette spring chinook. A study of the spot fishery is part of the program." (From Introduction) Close

• 7. [Article] Habitat Improvement Project, No. 21

  "A view-window counting station was operated at the Pacific Power and Light Company's dam on the North Umpqua River at Winchester, Douglas County, Oregon. The fish passing the dam each season were enumerated ...

  Citation × Citation Citation Abstract Copy Title: Habitat Improvement Project, No. 21 Author: Bauer, Jerry A., Oregon. State Game Commission. Fishery Division "A view-window counting station was operated at the Pacific Power and Light Company's dam on the North Umpqua River at Winchester, Douglas County, Oregon. The fish passing the dam each season were enumerated by species, according to a statistical sampling program established at Oregon State University. The counter recorded the marked fish of hatchery origin contained in each run of fish. The data collected were used to project total figures for each species of fish, evaluate hatchery production, provide information to the public, and in formulating angling regulations." (Abstract From Author) Title: Habitat Improvement Project, No. 21 Author: Bauer, Jerry A., Oregon. State Game Commission. Fishery Division "A view-window counting station was operated at the Pacific Power and Light Company's dam on the North Umpqua River at Winchester, Douglas County, Oregon. The fish passing the dam each season were enumerated by species, according to a statistical sampling program established at Oregon State University. The counter recorded the marked fish of hatchery origin contained in each run of fish. The data collected were used to project total figures for each species of fish, evaluate hatchery production, provide information to the public, and in formulating angling regulations." (Abstract From Author) Close

• 8. [Article] Distribution and movements of Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin

  Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin and other large river systems in western Alaska have declined dramatically since the late 1990s. This continuing trend has ...

  Citation × Citation Citation Abstract Copy Title: Distribution and movements of Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin Author: Eiler, John H. Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin and other large river systems in western Alaska have declined dramatically since the late 1990s. This continuing trend has raised concerns over the future status of the returns, and severely impacted commercial and subsistence fisheries within the drainage. Management is further complicated by the mixed-stock composition of the run, the presence of other temporally similar salmon species, and the need to equitably allocate harvests between the numerous fisheries and user groups scattered throughout the basin. Detailed information is needed on Chinook salmon run characteristics to better understand and manage the returns, and facilitate conservation efforts. However, this goal is exacerbated by the massive size and remote nature of the basin, the large number of highly mobile fish, and the compressed timing of the run. To address these challenges, radio telemetry was used to determine the stock composition and spawning distribution of the returns, and the migratory characteristics of the fish. The migratory patterns exhibited by returning salmon provide a number of insights into the status of the run. Since the Yukon River is essentially free-flowing (i.e., not regulated), this study also presented an opportunity to document the distribution and upriver movements of large returns of wild Chinook salmon under natural conditions. During 2002-2004, returning adult Chinook salmon were captured in the lower Yukon River (approximately 300 km upriver from the river mouth), tagged with radio transmitters, and tracked upriver using remote tracking stations located on important migratory routes and major spawning tributaries. Aerial tracking surveys were used to locate fish in spawning areas and between stations. The fish responded well to the capture and handling procedures, with most (2,790, 98%) resuming upriver movements. Although the fish initially displayed a negative tagging response, with slower migration rates observed immediately after release, the duration of this response was relatively short (several days) and less severe as the fish moved upriver. Independent measures indicated that the swimming speeds and timing of the fish upriver from the tagging area were comparable to untagged fish, suggesting that the tagging methods used were relatively benign. Fish returned to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging area. Distribution patterns were similar across years, suggesting that the principal components of the run were identified. Most spawning fish were clustered in a number of key tributaries, with smaller numbers of fish located in other spatially isolated areas. The fish typically returned to clear water tributaries that were relatively entrenched, had moderate gradients, and were associated with upland areas. Fish were largely absent in lowland reaches characterized by meandering, low gradient, highly alluvial channels often associated with main river floodplains. There was suggestive evidence of mainstem spawning in reaches of the Upper Yukon. The status of fish remaining in other mainstem areas was less certain, and may represent local spawning activity or fish that died while in-transit to upriver areas. Although Chinook salmon spawned throughout the basin, the run was dominated by two regional components (Tanana and Upper Yukon), which annually comprised over 70% of the return. Substantially fewer fish returned to other areas ranging from 2-9% of the return, although the collective contribution of these stocks was appreciable. Most regional returns consisted of several principal stocks and a number of small, spatially isolated populations. Regional and stock composition estimates were similar across years even though differences in run abundance were reported, suggesting that these abundance differences were not related to regional or stock-specific differences. Run timing was relatively compressed compared to rivers in the southern portion of the range, with most stocks passing through the lower river over a 6-week period, ranging from 16 to 38 d. Run timing was generally earlier for stocks traveling farther upriver, although exceptions were noted. Lower basin stocks were primarily later run fish. Pronounced differences were observed in the migration rates (km/d) exhibited by regional stocks. Substantially slower swimming speeds were observed for fish returning to terminal tributaries in the lower basin ranging from 28-40 km/d compared to 52-62 km/d for upper basin stocks. The migratory patterns (migration rates in sequential reaches) of the fish also showed distinct regional differences. Average migration rates through the lower river were remarkably similar for the different stocks, ranging from 57-62 km/d, with most stocks exhibiting a general decline as the fish moved farther upriver. Tanana River stocks displayed a pronounced reduction in swimming speed after leaving the Yukon River main stem, with migration rates declining to 24 km/d on average as the fish approached their terminal tributaries. Conversely, upper basin stocks exhibited a relatively gradual (but variable) overall decline in migration rate even though these fish were traveling substantially greater distances upriver. Average migration rates for upper basin stocks ranged from 43-61 km/d as the fish approached their terminal tributaries. There was substantial variation in the migratory patterns exhibited by individual fish, although these patterns tended to be similar to the patterns exhibited by the regional stocks, particularly as the fish moved farther upriver from the tagging area. The dominant source of variation among fish reflected the average migration rate, with individual fish traveling slower in the lower basin exhibiting consistently slower migration rates as they moved upriver compared to their faster moving counterparts. This migratory pattern was consistent across stocks, and on average explained 74% of the within-stock variation in migration rate represented by the multivariate data. The second source of variation in migration rate reflected a shift in the relative swimming speeds of the individual fish as they progressed upriver. Although movement rates declined for nearly all of the fish during the migration, differences were observed in the pattern of the decline. Fish with faster migration rates in the lower river exhibited a pronounced decline in swimming speed as they moved upriver, whereas fish moving slower in the lower river displayed a more gradual decline in migration rate. On average, this migratory pattern explained 22% of the within-stock variation in migration rate represented by the multivariate data. Most fish (98%) exhibited continuous upriver movements and strong fidelity to the rivers they entered. However a small number of fish (n = 66) deviated from this pattern. Some of these individuals initially passed their final destination and continued upriver for varying distances before reversing direction, swimming back downstream, and entering their terminal tributary. Although most of these excursions were relatively short (< 30 km), there were several instances where fish traveled hundreds of kilometers out of their way. Thirty-four fish tracked to terminal tributaries subsequently left these rivers, and traveled to other terminal tributaries within the basin (n = 31) or were harvested in upriver fisheries (n = 3). Although most of these incidents involved nearby tributaries, major diversions were also observed, with several fish traveling over 300 km to natal rivers after leaving the initial tributary. Chinook salmon returns to the Yukon River typically consisted of a series of distinct and sizable increases in the number fish entering the river over the course of the run, commonly referred to as pulses. A large number of fish (n = 251) were radio tagged over a 4-day period during a pulse in 2003 to provide information on the progression of the pulse as it moved upriver. The time taken by the pulse to move past subsequent upriver locations increased as the fish moved farther upriver from the tagging area, with the fish passing sites located 580 and 800 km upriver over a span of 14 and 21 d, respectively. Although not surprising considering the extensive variation in migration rates observed among individual fish, this finding does suggest that these pulses do not represent cohesive aggregates of fish moving upriver. Unlike the well established methods used to estimate other life history characteristics, the development of quantitative methods for analyzing and modeling fish movements has lagged noticeably behind, due in part to the complexity associated with movement data and (prior to the advent of telemetry) the difficulty of collecting this type of information on free-ranging individuals. Two fundamentally different analytical approaches, hierarchical linear regression models and multivariate ordination, were used during this study to evaluate factors thought to influence the upriver movements of the fish. In spite of the inherent differences, both methods provided strikingly similar results, indicating that the study findings were not dependent on the approach used, and suggesting that the results were plausible based on the information available and the weight of evidence. Both analytical methods had advantages, and provided complementary information. With hierarchical linear models, it was possible to simultaneously evaluate a wide range of explanatory variables (in our case, both biological and environmental), which provided standardized comparisons and simplified the interpretation of the results. Since both fixed and random effects were incorporated in the models, it was possible to account for sources of variation when insufficient information was available to identify the underlining factors – an important consideration since few field studies provide comprehensive data. With multivariate ordination, separate analyzes were needed to examine the relationships between the migration rates and the biotic and physical variables. In addition to being cumbersome, this limitation made it more difficult to compare the relative influence of the different factors and interactions between factors. However, ordination was very useful as an exploratory tool. Although compartmentalized by stock, across fish comparisons were simple and relatively straightforward. Because the explanatory variables were evaluated separately in relation to the ordination score assigned to the fish, it was possible to examine and compare highly correlated variables. Ordination was also able to identify overall patterns within the data and assess the relative importance. While this can be accomplished within the framework of linear regression using mixture models to determine whether multiple distributions exist within the data, the process is much simpler with ordination. The migratory patterns of the fish were influenced by a wide range of factors, with evidentiary support for complex, multi-faceted relationships. Physical features of the basin demonstrated stronger explanatory power, accounting for over 70% of the observed variation in migration rate compared to 18% for the biological characteristics of the fish. Parameter estimates associated with the steepness of the migratory route and remaining distance the fish had to travel to reach their natal rivers were most strongly correlated with migration rate, with consistent relationships observed across stocks. Migration rates were also noticeably slower in extensively braided reaches of the basin. The weaker relationships between migration rate and biotic factors may reflect stabilizing selection on long-distance migrants. Smaller fish exhibited minimally faster swimming speeds on average than larger individuals. This relationship was stronger in highly braided reaches. Run timing was positively related to migration rate for most stocks. Surprisingly, upper basin stocks traveling farther upriver displayed progressively negative relationships, suggesting that late-run fish were moving slower. Ancillary information suggests that this decline may relate to deteriorating fish condition later in the season. Title: Distribution and movements of Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin Author: Eiler, John H. Chinook salmon, Oncorhynchus tshawytscha, returning to the Yukon River basin and other large river systems in western Alaska have declined dramatically since the late 1990s. This continuing trend has raised concerns over the future status of the returns, and severely impacted commercial and subsistence fisheries within the drainage. Management is further complicated by the mixed-stock composition of the run, the presence of other temporally similar salmon species, and the need to equitably allocate harvests between the numerous fisheries and user groups scattered throughout the basin. Detailed information is needed on Chinook salmon run characteristics to better understand and manage the returns, and facilitate conservation efforts. However, this goal is exacerbated by the massive size and remote nature of the basin, the large number of highly mobile fish, and the compressed timing of the run. To address these challenges, radio telemetry was used to determine the stock composition and spawning distribution of the returns, and the migratory characteristics of the fish. The migratory patterns exhibited by returning salmon provide a number of insights into the status of the run. Since the Yukon River is essentially free-flowing (i.e., not regulated), this study also presented an opportunity to document the distribution and upriver movements of large returns of wild Chinook salmon under natural conditions. During 2002-2004, returning adult Chinook salmon were captured in the lower Yukon River (approximately 300 km upriver from the river mouth), tagged with radio transmitters, and tracked upriver using remote tracking stations located on important migratory routes and major spawning tributaries. Aerial tracking surveys were used to locate fish in spawning areas and between stations. The fish responded well to the capture and handling procedures, with most (2,790, 98%) resuming upriver movements. Although the fish initially displayed a negative tagging response, with slower migration rates observed immediately after release, the duration of this response was relatively short (several days) and less severe as the fish moved upriver. Independent measures indicated that the swimming speeds and timing of the fish upriver from the tagging area were comparable to untagged fish, suggesting that the tagging methods used were relatively benign. Fish returned to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging area. Distribution patterns were similar across years, suggesting that the principal components of the run were identified. Most spawning fish were clustered in a number of key tributaries, with smaller numbers of fish located in other spatially isolated areas. The fish typically returned to clear water tributaries that were relatively entrenched, had moderate gradients, and were associated with upland areas. Fish were largely absent in lowland reaches characterized by meandering, low gradient, highly alluvial channels often associated with main river floodplains. There was suggestive evidence of mainstem spawning in reaches of the Upper Yukon. The status of fish remaining in other mainstem areas was less certain, and may represent local spawning activity or fish that died while in-transit to upriver areas. Although Chinook salmon spawned throughout the basin, the run was dominated by two regional components (Tanana and Upper Yukon), which annually comprised over 70% of the return. Substantially fewer fish returned to other areas ranging from 2-9% of the return, although the collective contribution of these stocks was appreciable. Most regional returns consisted of several principal stocks and a number of small, spatially isolated populations. Regional and stock composition estimates were similar across years even though differences in run abundance were reported, suggesting that these abundance differences were not related to regional or stock-specific differences. Run timing was relatively compressed compared to rivers in the southern portion of the range, with most stocks passing through the lower river over a 6-week period, ranging from 16 to 38 d. Run timing was generally earlier for stocks traveling farther upriver, although exceptions were noted. Lower basin stocks were primarily later run fish. Pronounced differences were observed in the migration rates (km/d) exhibited by regional stocks. Substantially slower swimming speeds were observed for fish returning to terminal tributaries in the lower basin ranging from 28-40 km/d compared to 52-62 km/d for upper basin stocks. The migratory patterns (migration rates in sequential reaches) of the fish also showed distinct regional differences. Average migration rates through the lower river were remarkably similar for the different stocks, ranging from 57-62 km/d, with most stocks exhibiting a general decline as the fish moved farther upriver. Tanana River stocks displayed a pronounced reduction in swimming speed after leaving the Yukon River main stem, with migration rates declining to 24 km/d on average as the fish approached their terminal tributaries. Conversely, upper basin stocks exhibited a relatively gradual (but variable) overall decline in migration rate even though these fish were traveling substantially greater distances upriver. Average migration rates for upper basin stocks ranged from 43-61 km/d as the fish approached their terminal tributaries. There was substantial variation in the migratory patterns exhibited by individual fish, although these patterns tended to be similar to the patterns exhibited by the regional stocks, particularly as the fish moved farther upriver from the tagging area. The dominant source of variation among fish reflected the average migration rate, with individual fish traveling slower in the lower basin exhibiting consistently slower migration rates as they moved upriver compared to their faster moving counterparts. This migratory pattern was consistent across stocks, and on average explained 74% of the within-stock variation in migration rate represented by the multivariate data. The second source of variation in migration rate reflected a shift in the relative swimming speeds of the individual fish as they progressed upriver. Although movement rates declined for nearly all of the fish during the migration, differences were observed in the pattern of the decline. Fish with faster migration rates in the lower river exhibited a pronounced decline in swimming speed as they moved upriver, whereas fish moving slower in the lower river displayed a more gradual decline in migration rate. On average, this migratory pattern explained 22% of the within-stock variation in migration rate represented by the multivariate data. Most fish (98%) exhibited continuous upriver movements and strong fidelity to the rivers they entered. However a small number of fish (n = 66) deviated from this pattern. Some of these individuals initially passed their final destination and continued upriver for varying distances before reversing direction, swimming back downstream, and entering their terminal tributary. Although most of these excursions were relatively short (< 30 km), there were several instances where fish traveled hundreds of kilometers out of their way. Thirty-four fish tracked to terminal tributaries subsequently left these rivers, and traveled to other terminal tributaries within the basin (n = 31) or were harvested in upriver fisheries (n = 3). Although most of these incidents involved nearby tributaries, major diversions were also observed, with several fish traveling over 300 km to natal rivers after leaving the initial tributary. Chinook salmon returns to the Yukon River typically consisted of a series of distinct and sizable increases in the number fish entering the river over the course of the run, commonly referred to as pulses. A large number of fish (n = 251) were radio tagged over a 4-day period during a pulse in 2003 to provide information on the progression of the pulse as it moved upriver. The time taken by the pulse to move past subsequent upriver locations increased as the fish moved farther upriver from the tagging area, with the fish passing sites located 580 and 800 km upriver over a span of 14 and 21 d, respectively. Although not surprising considering the extensive variation in migration rates observed among individual fish, this finding does suggest that these pulses do not represent cohesive aggregates of fish moving upriver. Unlike the well established methods used to estimate other life history characteristics, the development of quantitative methods for analyzing and modeling fish movements has lagged noticeably behind, due in part to the complexity associated with movement data and (prior to the advent of telemetry) the difficulty of collecting this type of information on free-ranging individuals. Two fundamentally different analytical approaches, hierarchical linear regression models and multivariate ordination, were used during this study to evaluate factors thought to influence the upriver movements of the fish. In spite of the inherent differences, both methods provided strikingly similar results, indicating that the study findings were not dependent on the approach used, and suggesting that the results were plausible based on the information available and the weight of evidence. Both analytical methods had advantages, and provided complementary information. With hierarchical linear models, it was possible to simultaneously evaluate a wide range of explanatory variables (in our case, both biological and environmental), which provided standardized comparisons and simplified the interpretation of the results. Since both fixed and random effects were incorporated in the models, it was possible to account for sources of variation when insufficient information was available to identify the underlining factors – an important consideration since few field studies provide comprehensive data. With multivariate ordination, separate analyzes were needed to examine the relationships between the migration rates and the biotic and physical variables. In addition to being cumbersome, this limitation made it more difficult to compare the relative influence of the different factors and interactions between factors. However, ordination was very useful as an exploratory tool. Although compartmentalized by stock, across fish comparisons were simple and relatively straightforward. Because the explanatory variables were evaluated separately in relation to the ordination score assigned to the fish, it was possible to examine and compare highly correlated variables. Ordination was also able to identify overall patterns within the data and assess the relative importance. While this can be accomplished within the framework of linear regression using mixture models to determine whether multiple distributions exist within the data, the process is much simpler with ordination. The migratory patterns of the fish were influenced by a wide range of factors, with evidentiary support for complex, multi-faceted relationships. Physical features of the basin demonstrated stronger explanatory power, accounting for over 70% of the observed variation in migration rate compared to 18% for the biological characteristics of the fish. Parameter estimates associated with the steepness of the migratory route and remaining distance the fish had to travel to reach their natal rivers were most strongly correlated with migration rate, with consistent relationships observed across stocks. Migration rates were also noticeably slower in extensively braided reaches of the basin. The weaker relationships between migration rate and biotic factors may reflect stabilizing selection on long-distance migrants. Smaller fish exhibited minimally faster swimming speeds on average than larger individuals. This relationship was stronger in highly braided reaches. Run timing was positively related to migration rate for most stocks. Surprisingly, upper basin stocks traveling farther upriver displayed progressively negative relationships, suggesting that late-run fish were moving slower. Ancillary information suggests that this decline may relate to deteriorating fish condition later in the season. Close

• 9. [Article] Evidence for selective mortality in marine environments: the role of fish migration size, timing, and production type

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Inter-Research ...

  Citation × Citation Citation Abstract Copy Title: Evidence for selective mortality in marine environments: the role of fish migration size, timing, and production type Author: Teel, David J., Emmett, Robert L., Miller, Jessica A., Weitkamp, Laurie A., Claiborne, Andrew M. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Inter-Research and can be found at: http://www.int-res.com/journals/meps/meps-home/. Title: Evidence for selective mortality in marine environments: the role of fish migration size, timing, and production type Author: Teel, David J., Emmett, Robert L., Miller, Jessica A., Weitkamp, Laurie A., Claiborne, Andrew M. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Inter-Research and can be found at: http://www.int-res.com/journals/meps/meps-home/. Close

• 10. [Article] Factors affecting the abundance of fall chinook salmon in the Columbia River

  A study of the population ecology of Columbia River fall chinook salmon, Oncorhynchus tshawytscha (Walbaum), was made in an attempt to determine the cause of a serious decline in this run which occurred in ...

  Citation × Citation Citation Abstract Copy Title: Factors affecting the abundance of fall chinook salmon in the Columbia River Author: Van Hyning, Jack M. A study of the population ecology of Columbia River fall chinook salmon, Oncorhynchus tshawytscha (Walbaum), was made in an attempt to determine the cause of a serious decline in this run which occurred in the early 1950's. Fluctuations in abundance of major salmon runs the North Pacific were examined to detect any coastwide pattern. Only chinook salmon in Cook Inlet, Alaska, and chum salmon from Oregon to southwestern Alaska showed a similar trend. The following life history stages broken down into pre- and post-decline years were examined: (1) marine life including distribution and migration, growth and maturity, survival rate, oceanography, and commercial and sport fisheries; (2) upstream migration including river fisheries, gear selectivity, size and age composition of the run, escapement, and influence of dams, diseases, and water quality; (3) reproduction and incubation including spawning areas and spawning and incubation conditions; and (4) downstream migration which included predation, dams and reservoirs, diseases, flow, turbidity and temperature, and estuary life. Salient points of the analysis were: (1) a change in the maturity and survival pattern based on tagged and fin-clipped fish recovered before and after 1950; (2) a significant negative correlation between sea-water temperature during a year class' first year at sea and subsequent survival; (3) a large increase in the ocean fisheries coincident with the decline in the run; (4) catch-effort statistics of the ocean fishery show a near classic example of the effect of overexploitation; (5) estimates of the contribution of Columbia River chinook to the ocean fisheries based on tag recoveries could be underestimates rather than overestimates; (6) a significant inverse correlation between estimated ocean catch of Columbia River fall chinook and numbers entering the river; (7) size and age composition of the ocean and river catches decreased coincident with the decline in the run; (8) the gill-net fishery shows little size selectivity by age, size, or sex in the dominant group; (9) fluctuations in abundance of hatchery stocks are related to differences in survival between fingerling and adult; (10) hatchery, lower river, and upriver populations fluctuate in abundance in much the same pattern; (11) optimum escapement is between 90,000 and 100,000 adults, a value that was exceeded during most years; (12) a highly significant negative correlation between numbers of spawners and return per spawner; (13) most of the early dams had no direct effect on fall chinook and the decline in productivity occurred when river conditions were relatively stable; (14) temperatures at time of migration and spawning for fall chinook have not increased enough to be a serious mortality factor; (15) little relationship between flow, turbidity, and temperature at time of downstream migration and subsequent return was evident except that high temperatures and high flows (and turbidities) tended to produce poorer runs during certain time periods; and (16) predation and delay of smolts in reservoirs are largely unknown factors, but circumstantial evidence suggests that they were not important in regulating fall chinook numbers during the period of the study. Finally, variables that appeared to bear some relationship to fluctuations in abundance of fall chinook were submitted to multiple regression analysis. For the predecline period (1938-46 brood years), sea-water temperature and ocean troll fishing effort were significant variables (R² = 0.74). For post decline years (1947-59 broods), troll had the most influence on total return with ocean temperature and escapement having lesser effects. For the combined years, troll intensity and ocean temperature were the significant variables (R² = 0.572). Entering interaction of river flow at downstream migration with the other variables brought R² to 0.754 which means that 75% of the variability in the returning run could be accounted for by these three factors. Return per spawner was so heavily influenced by numbers of spawners that the other factors assumed negligible importance. Equations were derived that predicted the returning run in close agreement with the actual run size. Substituting a low and constant troll fishing effort in the equation resulted in the predicted run maintaining the average predecline level. The increase in ocean fishing was the main contributor to the decline of the Columbia River fall chinook run as shown by correlation, by analogy, and by the process of elimination. To demonstrate why other chinook runs have not shown similar declines, it was shown that due to several unique features in Columbia River fall chinook life history they are exposed to much more ocean fishing than other populations. It was emphasized that these conclusions should not be extrapolated to the future or to other species or runs of salmon. Title: Factors affecting the abundance of fall chinook salmon in the Columbia River Author: Van Hyning, Jack M. A study of the population ecology of Columbia River fall chinook salmon, Oncorhynchus tshawytscha (Walbaum), was made in an attempt to determine the cause of a serious decline in this run which occurred in the early 1950's. Fluctuations in abundance of major salmon runs the North Pacific were examined to detect any coastwide pattern. Only chinook salmon in Cook Inlet, Alaska, and chum salmon from Oregon to southwestern Alaska showed a similar trend. The following life history stages broken down into pre- and post-decline years were examined: (1) marine life including distribution and migration, growth and maturity, survival rate, oceanography, and commercial and sport fisheries; (2) upstream migration including river fisheries, gear selectivity, size and age composition of the run, escapement, and influence of dams, diseases, and water quality; (3) reproduction and incubation including spawning areas and spawning and incubation conditions; and (4) downstream migration which included predation, dams and reservoirs, diseases, flow, turbidity and temperature, and estuary life. Salient points of the analysis were: (1) a change in the maturity and survival pattern based on tagged and fin-clipped fish recovered before and after 1950; (2) a significant negative correlation between sea-water temperature during a year class' first year at sea and subsequent survival; (3) a large increase in the ocean fisheries coincident with the decline in the run; (4) catch-effort statistics of the ocean fishery show a near classic example of the effect of overexploitation; (5) estimates of the contribution of Columbia River chinook to the ocean fisheries based on tag recoveries could be underestimates rather than overestimates; (6) a significant inverse correlation between estimated ocean catch of Columbia River fall chinook and numbers entering the river; (7) size and age composition of the ocean and river catches decreased coincident with the decline in the run; (8) the gill-net fishery shows little size selectivity by age, size, or sex in the dominant group; (9) fluctuations in abundance of hatchery stocks are related to differences in survival between fingerling and adult; (10) hatchery, lower river, and upriver populations fluctuate in abundance in much the same pattern; (11) optimum escapement is between 90,000 and 100,000 adults, a value that was exceeded during most years; (12) a highly significant negative correlation between numbers of spawners and return per spawner; (13) most of the early dams had no direct effect on fall chinook and the decline in productivity occurred when river conditions were relatively stable; (14) temperatures at time of migration and spawning for fall chinook have not increased enough to be a serious mortality factor; (15) little relationship between flow, turbidity, and temperature at time of downstream migration and subsequent return was evident except that high temperatures and high flows (and turbidities) tended to produce poorer runs during certain time periods; and (16) predation and delay of smolts in reservoirs are largely unknown factors, but circumstantial evidence suggests that they were not important in regulating fall chinook numbers during the period of the study. Finally, variables that appeared to bear some relationship to fluctuations in abundance of fall chinook were submitted to multiple regression analysis. For the predecline period (1938-46 brood years), sea-water temperature and ocean troll fishing effort were significant variables (R² = 0.74). For post decline years (1947-59 broods), troll had the most influence on total return with ocean temperature and escapement having lesser effects. For the combined years, troll intensity and ocean temperature were the significant variables (R² = 0.572). Entering interaction of river flow at downstream migration with the other variables brought R² to 0.754 which means that 75% of the variability in the returning run could be accounted for by these three factors. Return per spawner was so heavily influenced by numbers of spawners that the other factors assumed negligible importance. Equations were derived that predicted the returning run in close agreement with the actual run size. Substituting a low and constant troll fishing effort in the equation resulted in the predicted run maintaining the average predecline level. The increase in ocean fishing was the main contributor to the decline of the Columbia River fall chinook run as shown by correlation, by analogy, and by the process of elimination. To demonstrate why other chinook runs have not shown similar declines, it was shown that due to several unique features in Columbia River fall chinook life history they are exposed to much more ocean fishing than other populations. It was emphasized that these conclusions should not be extrapolated to the future or to other species or runs of salmon. Close