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• 641. [Article] Lower Snake River Compensation Plan; Oregon Summer Steelhead Evaluation Studies - 2015 Annual Progress Report

  Abstract -- The objectives of this report are to document fish culture practices, describe adult returns, and assess progress toward meeting LSRCP goals for Grande Ronde and Imnaha steelhead (Oncorhynchus ...

  Citation × Citation Citation Abstract Copy Title: Lower Snake River Compensation Plan; Oregon Summer Steelhead Evaluation Studies - 2015 Annual Progress Report Abstract -- The objectives of this report are to document fish culture practices, describe adult returns, and assess progress toward meeting LSRCP goals for Grande Ronde and Imnaha steelhead (Oncorhynchus mykiss). We report on juvenile steelhead rearing and release activities for the 2014 brood year (BY) released in 2015. Included are collection, spawning, and adult characteristics for the 2015 returns, returns from experimental releases, supplementation in Little Sheep Creek, and success toward achieving compensation goals. The Grande Ronde and Imnaha river steelhead hatchery programs were initiated in 1976 and 1982 in response to the rapid decline in Snake River steelhead abundance. Annual adult mitigation, brood year specific smolt-to-adult return and total smolt-to-adult survival rates, and annual smolt production goals were established to compensate for the estimated annual loss of 48% of adult production. Adaptive management has resulted in current interim smolt production goals of 800,000 (ODFW Wallowa stock released into the Grande Ronde) and 215,000 (Imnaha stock) smolts; less than the original goals of 1,350,000 and 330,000 smolts. Based on original smolt production goals it was assumed that 27,552 Wallowa stock and 6,000 Imnaha stock adults would be produced annually. Furthermore, 66.7% of these fish were expected to be harvested below the compensation area, defined as the watershed above Lower Granite Dam, resulting in compensation area adult return goals of 9,184 Wallowa stock and 2,000 Imnaha stock. In general, the data in this report were derived from hatchery inventories and standard databases (e.g., Pacific States Marine Fisheries Commission Regional Mark Information System (RMIS), ODFW mark recovery) or through standard measuring techniques. As such, specific protocols are usually not described. In cases where expansions of data or unique methodologies were used, protocols are described in more detail. Additional descriptions of protocols can be found in our work statements (Carmichael et al. 2012, Carmichael et al. 2013). Coded-wire tag (CWT) data collected from 2015 adult returns were used to evaluate smolt-to-adult survival rates in experimental rearing and release groups. In 2015, the only experimental treatments from which fish returned were second generation progeny from early returning (fall-collected) broodstock. In 2015, smolts were released at Wallowa Hatchery that were third generation progeny of early returning (fall-collected) broodstock for an experimental comparison with progeny of standard production broodstock. Methods for the fall broodstock experiment are described in Warren et al. (2011a). Analysis of specific survival studies will be completed and published in separate reports once all brood years have returned and CWT data are complete for each experiment. In addition, much of the data that we discuss in this report will be used in separate and specific evaluations of ongoing supplementation programs for steelhead in the Imnaha River basin. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Title: Lower Snake River Compensation Plan; Oregon Summer Steelhead Evaluation Studies - 2015 Annual Progress Report Abstract -- The objectives of this report are to document fish culture practices, describe adult returns, and assess progress toward meeting LSRCP goals for Grande Ronde and Imnaha steelhead (Oncorhynchus mykiss). We report on juvenile steelhead rearing and release activities for the 2014 brood year (BY) released in 2015. Included are collection, spawning, and adult characteristics for the 2015 returns, returns from experimental releases, supplementation in Little Sheep Creek, and success toward achieving compensation goals. The Grande Ronde and Imnaha river steelhead hatchery programs were initiated in 1976 and 1982 in response to the rapid decline in Snake River steelhead abundance. Annual adult mitigation, brood year specific smolt-to-adult return and total smolt-to-adult survival rates, and annual smolt production goals were established to compensate for the estimated annual loss of 48% of adult production. Adaptive management has resulted in current interim smolt production goals of 800,000 (ODFW Wallowa stock released into the Grande Ronde) and 215,000 (Imnaha stock) smolts; less than the original goals of 1,350,000 and 330,000 smolts. Based on original smolt production goals it was assumed that 27,552 Wallowa stock and 6,000 Imnaha stock adults would be produced annually. Furthermore, 66.7% of these fish were expected to be harvested below the compensation area, defined as the watershed above Lower Granite Dam, resulting in compensation area adult return goals of 9,184 Wallowa stock and 2,000 Imnaha stock. In general, the data in this report were derived from hatchery inventories and standard databases (e.g., Pacific States Marine Fisheries Commission Regional Mark Information System (RMIS), ODFW mark recovery) or through standard measuring techniques. As such, specific protocols are usually not described. In cases where expansions of data or unique methodologies were used, protocols are described in more detail. Additional descriptions of protocols can be found in our work statements (Carmichael et al. 2012, Carmichael et al. 2013). Coded-wire tag (CWT) data collected from 2015 adult returns were used to evaluate smolt-to-adult survival rates in experimental rearing and release groups. In 2015, the only experimental treatments from which fish returned were second generation progeny from early returning (fall-collected) broodstock. In 2015, smolts were released at Wallowa Hatchery that were third generation progeny of early returning (fall-collected) broodstock for an experimental comparison with progeny of standard production broodstock. Methods for the fall broodstock experiment are described in Warren et al. (2011a). Analysis of specific survival studies will be completed and published in separate reports once all brood years have returned and CWT data are complete for each experiment. In addition, much of the data that we discuss in this report will be used in separate and specific evaluations of ongoing supplementation programs for steelhead in the Imnaha River basin. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR) Close

• 642. [Article] Status of Winter Rearing Habitat in Four Coho Population Units_ODFW AQI Winter Report Final 2008

  Abstract -- We described the status of habitat in four Oregon coastal coho salmon (Oncorhynchus kisutch) population units (Nehalem, Siuslaw, Coquille, South Umpqua) during winter 2007, estimated the potential ...

  Citation × Citation Citation Abstract Copy Title: Status of Winter Rearing Habitat in Four Coho Population Units_ODFW AQI Winter Report Final 2008 Abstract -- We described the status of habitat in four Oregon coastal coho salmon (Oncorhynchus kisutch) population units (Nehalem, Siuslaw, Coquille, South Umpqua) during winter 2007, estimated the potential winter rearing capacity of streams within those population units, and described the differences observed in stream habitat between winter and summer with emphasis on slow water and secondary channel habitats. Sample sites were randomly selected and spatially balanced within the distribution of coho salmon (juvenile and adult) in Oregon coastal watersheds south of the Columbia River. Twenty five sites were targeted within each of the four population units. Each survey was approximately 1000 m in length and adhered to protocols in Moore et al (2007). The Habitat Limiting Factors Model (HLFM) was used to estimate habitat capacity and quality for rearing juvenile coho. The HLFM predicted that the Nehalem and Siuslaw basins could support the highest density of juvenile coho, and the South Umpqua the least. Seasonal changes in habitat were similar to that reported in a previous study. Winter surveys facilitated the assessment of habitat status and estimating capacity because the surveys were conducted at the time when habitat is most limiting to survival of juvenile coho. Winter surveys were particularly valuable in capturing secondary channel and slow water habitat units such as beaver ponds and alcoves. We also performed a sensitivity analysis to determine the number of survey sites necessary to represent each population unit within the desired confidence range of 30% recommended in the Coho Conservation Plan. Twenty five target sites were not adequate to describe the winter parr capacity within a 95% confidence interval of +30% in each population unit. Confidence intervals of estimates of parr per km ranged from 34 to 60% and mean parr per m2 ranged from 20 to 45%. Title: Status of Winter Rearing Habitat in Four Coho Population Units_ODFW AQI Winter Report Final 2008 Abstract -- We described the status of habitat in four Oregon coastal coho salmon (Oncorhynchus kisutch) population units (Nehalem, Siuslaw, Coquille, South Umpqua) during winter 2007, estimated the potential winter rearing capacity of streams within those population units, and described the differences observed in stream habitat between winter and summer with emphasis on slow water and secondary channel habitats. Sample sites were randomly selected and spatially balanced within the distribution of coho salmon (juvenile and adult) in Oregon coastal watersheds south of the Columbia River. Twenty five sites were targeted within each of the four population units. Each survey was approximately 1000 m in length and adhered to protocols in Moore et al (2007). The Habitat Limiting Factors Model (HLFM) was used to estimate habitat capacity and quality for rearing juvenile coho. The HLFM predicted that the Nehalem and Siuslaw basins could support the highest density of juvenile coho, and the South Umpqua the least. Seasonal changes in habitat were similar to that reported in a previous study. Winter surveys facilitated the assessment of habitat status and estimating capacity because the surveys were conducted at the time when habitat is most limiting to survival of juvenile coho. Winter surveys were particularly valuable in capturing secondary channel and slow water habitat units such as beaver ponds and alcoves. We also performed a sensitivity analysis to determine the number of survey sites necessary to represent each population unit within the desired confidence range of 30% recommended in the Coho Conservation Plan. Twenty five target sites were not adequate to describe the winter parr capacity within a 95% confidence interval of +30% in each population unit. Confidence intervals of estimates of parr per km ranged from 34 to 60% and mean parr per m2 ranged from 20 to 45%. Close

• 643. [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

• 644. [Article] Escapement and Productivity of Summer Steelhead and Spring Chinook Salmon in the John Day River; Annual Report 2017

  Abstract -- The John Day River, located in northeastern Oregon, supports five wild populations of summer steelhead (Oncorhynchus mykiss) and three populations of wild spring chinook (Oncorhynchus tschawytscha) ...

  Citation × Citation Citation Abstract Copy Title: Escapement and Productivity of Summer Steelhead and Spring Chinook Salmon in the John Day River; Annual Report 2017 Abstract -- The John Day River, located in northeastern Oregon, supports five wild populations of summer steelhead (Oncorhynchus mykiss) and three populations of wild spring chinook (Oncorhynchus tschawytscha) with no hatchery supplementation. However, these populations remain depressed relative to historic levels. In 1999, the National Marine Fisheries Service (NMFS) listed the Middle Columbia River summer steelhead Distinct Population Segment (DPS), which includes the John Day River Major Population Group (MPG), as threatened under the Endangered Species Act (ESA). Although numerous habitat protection and rehabilitation projects have been implemented within the John Day River basin to improve steelhead and other salmonid freshwater production and survival, it has been difficult to estimate the effectiveness of these projects without a systematic program in place to collect information on the status, trends, and distribution of spawning activity, juvenile salmonids, and aquatic habitat conditions within the basin. Prior to the inception of this project, population and environmental monitoring of steelhead in the basin consisted of a combination of index spawning surveys and periodic monitoring of some status and trend indicators. While index spawning data is useful for drawing inference about long-term trends in adult steelhead abundance, they are limited for determining the status of steelhead escapement or distribution at the population or MPG scale because survey sites are not randomly selected and are likely biased towards streams with higher fish abundance. A broader approach to the monitoring and evaluation of status and trends in anadromous and resident salmonid populations and their habitats was needed to provide data to effectively support restoration efforts and guide alternative future management actions in the basin. The Independent Scientific Review Panel (ISRP) recommended that the region move away from index surveys and embrace probabilistic sampling for most population and habitat monitoring. To meet the ISRP recommendation, the structure and methods employed by the Oregon Plan for Salmon and Watersheds Monitoring Program were extended to the John Day basin. This approach incorporates the sampling strategy of the United States Environmental Protection Agency’s (EPA) Environmental Monitoring and Assessment Program (EMAP). This research effort employs a statistically based and spatially explicit sampling design to answer key monitoring questions, integrate on-going sampling efforts, and improve agency coordination. The current program seeks to integrate project objectives focused on summer steelhead spawning metrics, juvenile salmonid metrics, and aquatic habitat conditions. Title: Escapement and Productivity of Summer Steelhead and Spring Chinook Salmon in the John Day River; Annual Report 2017 Abstract -- The John Day River, located in northeastern Oregon, supports five wild populations of summer steelhead (Oncorhynchus mykiss) and three populations of wild spring chinook (Oncorhynchus tschawytscha) with no hatchery supplementation. However, these populations remain depressed relative to historic levels. In 1999, the National Marine Fisheries Service (NMFS) listed the Middle Columbia River summer steelhead Distinct Population Segment (DPS), which includes the John Day River Major Population Group (MPG), as threatened under the Endangered Species Act (ESA). Although numerous habitat protection and rehabilitation projects have been implemented within the John Day River basin to improve steelhead and other salmonid freshwater production and survival, it has been difficult to estimate the effectiveness of these projects without a systematic program in place to collect information on the status, trends, and distribution of spawning activity, juvenile salmonids, and aquatic habitat conditions within the basin. Prior to the inception of this project, population and environmental monitoring of steelhead in the basin consisted of a combination of index spawning surveys and periodic monitoring of some status and trend indicators. While index spawning data is useful for drawing inference about long-term trends in adult steelhead abundance, they are limited for determining the status of steelhead escapement or distribution at the population or MPG scale because survey sites are not randomly selected and are likely biased towards streams with higher fish abundance. A broader approach to the monitoring and evaluation of status and trends in anadromous and resident salmonid populations and their habitats was needed to provide data to effectively support restoration efforts and guide alternative future management actions in the basin. The Independent Scientific Review Panel (ISRP) recommended that the region move away from index surveys and embrace probabilistic sampling for most population and habitat monitoring. To meet the ISRP recommendation, the structure and methods employed by the Oregon Plan for Salmon and Watersheds Monitoring Program were extended to the John Day basin. This approach incorporates the sampling strategy of the United States Environmental Protection Agency’s (EPA) Environmental Monitoring and Assessment Program (EMAP). This research effort employs a statistically based and spatially explicit sampling design to answer key monitoring questions, integrate on-going sampling efforts, and improve agency coordination. The current program seeks to integrate project objectives focused on summer steelhead spawning metrics, juvenile salmonid metrics, and aquatic habitat conditions. Close

• 645. [Article] A Proposal for an Integrated Research Monitoring Program for Oregon Coastal Chinook Populations

  Abstract -- Among the many chinook salmon populations contributing to large, mixed stock ocean net, troll, and recreational fisheries managed by the Pacific Salmon Commission (PSC) there is a good deal ...

  Citation × Citation Citation Abstract Copy Title: A Proposal for an Integrated Research Monitoring Program for Oregon Coastal Chinook Populations Abstract -- Among the many chinook salmon populations contributing to large, mixed stock ocean net, troll, and recreational fisheries managed by the Pacific Salmon Commission (PSC) there is a good deal of diversity with respect to productivity, life history characteristics, and ocean distribution. During the years immediately following the adoption of the original 1985 Pacific Salmon Treaty (PST), lack of adequate data prevented the PSC from managing effectively for these differences. Instead, chinook management outlined in Annex IV of the original treaty was based upon long term population trends for very large aggregates of stocks. Although harvest ceilings were established as part of a PST recovery plan for over-exploited stocks, they were based on average coast-wide production trends and resulted in over harvest of weak stocks in some years and failure to take advantage of large returns in other years. By the mid-l 990's, data relative to the distribution and abundance of many salmon stocks contributing to PST fisheries was improving. At the same time, there was increasing dissatisfaction with quota-based management and strong interest in instituting annual abundance-based management for stock aggregates that share geographic proximity of spawning areas, similar life history and genetic characteristics, and similar distributions in the ocean. Abundance-based management for aggregated stocks would establish and implement annual fishery exploitation rates in fisheries that insure long-term sustainability for all aggregates and related individual stocks. In the absence of bilateral agreement between the U.S. and Canada regarding implementation of abundance-based management, the three voting U.S. PSC Commissioners signed the 1996 Letter of Agreement (LOA) that defined elements of an abundance-based management approach for chinook salmon fisheries in southeast Alaska. The LOA was designed to: 1) set the stage for future bilateral negotiations regarding abundance based management; 2) clarify the role of PST fisheries in rebuilding depressed natural stocks; and 3) provide a means for sharing conservation responsibility of far-north migrating stocks originating from watersheds in Oregon and Washington. The foundation for abundance-based management set forth in the LOA was subsequently expanded upon and incorporated as Aggregate Abundance-Based Management (AABM) in Annex IV, Chapter 3 of the 1999 PST. Application of the abundance-based management outlined in the 1996 LOA and the subsequent 1999 amendments to the PST requires knowledge of the stock recruitment relationships, biological spawning escapement goals, and annual forecasts of ocean abundance and distribution for stocks in each aggregate to regulate fishery harvest. Managers must also have annual post-season estimates of aggregate specific exploitation rates and in-river escapements to assess the effectiveness of regulatory measures. The base-monitoring program for Oregon's coastal chinook under the 1985 PSC met only a few of these data requirements. In recognition of requirements for new and more precise data, the signatories of the original LOA sought out additional federal funds for new and expanded monitoring programs. Since 1997 Congress has annually approved approximately $1.8 million for additional research and monitoring needed to implement terms of the LOA. The PSC delegated discretionary authority for the use of those funds to the U.S. Section's Chinook Technical Committee (CTC). Title: A Proposal for an Integrated Research Monitoring Program for Oregon Coastal Chinook Populations Abstract -- Among the many chinook salmon populations contributing to large, mixed stock ocean net, troll, and recreational fisheries managed by the Pacific Salmon Commission (PSC) there is a good deal of diversity with respect to productivity, life history characteristics, and ocean distribution. During the years immediately following the adoption of the original 1985 Pacific Salmon Treaty (PST), lack of adequate data prevented the PSC from managing effectively for these differences. Instead, chinook management outlined in Annex IV of the original treaty was based upon long term population trends for very large aggregates of stocks. Although harvest ceilings were established as part of a PST recovery plan for over-exploited stocks, they were based on average coast-wide production trends and resulted in over harvest of weak stocks in some years and failure to take advantage of large returns in other years. By the mid-l 990's, data relative to the distribution and abundance of many salmon stocks contributing to PST fisheries was improving. At the same time, there was increasing dissatisfaction with quota-based management and strong interest in instituting annual abundance-based management for stock aggregates that share geographic proximity of spawning areas, similar life history and genetic characteristics, and similar distributions in the ocean. Abundance-based management for aggregated stocks would establish and implement annual fishery exploitation rates in fisheries that insure long-term sustainability for all aggregates and related individual stocks. In the absence of bilateral agreement between the U.S. and Canada regarding implementation of abundance-based management, the three voting U.S. PSC Commissioners signed the 1996 Letter of Agreement (LOA) that defined elements of an abundance-based management approach for chinook salmon fisheries in southeast Alaska. The LOA was designed to: 1) set the stage for future bilateral negotiations regarding abundance based management; 2) clarify the role of PST fisheries in rebuilding depressed natural stocks; and 3) provide a means for sharing conservation responsibility of far-north migrating stocks originating from watersheds in Oregon and Washington. The foundation for abundance-based management set forth in the LOA was subsequently expanded upon and incorporated as Aggregate Abundance-Based Management (AABM) in Annex IV, Chapter 3 of the 1999 PST. Application of the abundance-based management outlined in the 1996 LOA and the subsequent 1999 amendments to the PST requires knowledge of the stock recruitment relationships, biological spawning escapement goals, and annual forecasts of ocean abundance and distribution for stocks in each aggregate to regulate fishery harvest. Managers must also have annual post-season estimates of aggregate specific exploitation rates and in-river escapements to assess the effectiveness of regulatory measures. The base-monitoring program for Oregon's coastal chinook under the 1985 PSC met only a few of these data requirements. In recognition of requirements for new and more precise data, the signatories of the original LOA sought out additional federal funds for new and expanded monitoring programs. Since 1997 Congress has annually approved approximately $1.8 million for additional research and monitoring needed to implement terms of the LOA. The PSC delegated discretionary authority for the use of those funds to the U.S. Section's Chinook Technical Committee (CTC). Close

• 646. [Article] The historic and contemporary ecology of western Cascade meadows : archeology, vegetation, and macromoth ecology

  Montane meadows in the western Cascades of Oregon occupy approximately 5% of the landscape, but contribute greatly to the region's biodiversity. Western Cascades meadows are dynamic parts of the landscape ...

  Citation × Citation Citation Abstract Copy Title: The historic and contemporary ecology of western Cascade meadows : archeology, vegetation, and macromoth ecology Author: Highland, Steven A. Montane meadows in the western Cascades of Oregon occupy approximately 5% of the landscape, but contribute greatly to the region's biodiversity. Western Cascades meadows are dynamic parts of the landscape and have contracted by over 50% in the past two hundred years in the HJ Andrews Experimental Forest (hereafter Andrews Forest). Many studies have linked the loss of meadows with local extirpation of species and loss of regional biodiversity, but these processes depend upon the factors that create and maintain meadows, and how species respond to meadow configuration. The prehistory of these meadows is poorly understood, as is the contemporary ecology. This study combined previously collected archeological and moth datasets, aerial photographs, and new plant, tree core, and moth data to investigate interactions between landforms, disturbance, vegetation, and moth abundance and diversity in montane meadows of the western Cascades of Oregon. Burning by prehistoric people may have created and maintained montane meadows, but relatively little evidence remains of the activities of prehistoric peoples in the western Cascades. This study assessed the extent to which prehistoric people preferentially used different landforms and vegetation types by inferring use from landscape distributions of archaeological sites. Descriptions of 359 previously recorded and four newly discovered archeological sites in the McKenzie River watershed of western Oregon were examined using GIS and chi-square analysis to determine how sites were distributed relative to classified vegetation and landforms of the 3700-km² McKenzie River watershed. The high ridges of the HJ Andrews Experimental Forest were analyzed using air photo change detection and archaeological field surveys to identify how archeological sites were distributed relative to landforms and vegetation communities, including meadows. The field surveys documented physical evidence (archeological sites) confirming Native American use of the meadows and surrounding open forests. The locations of these sites indicate that Native Americans utilized the edges between large open meadows and open forests, as well as gently sloping open meadows. The prior extent of meadows (before air photos) was estimated by dendrochronology of 220 trees along present-day and inferred past meadow edges. Forest age structure and the open-grown forms of Douglas fir suggests a much more open habitat, potentially due to fire, was present more than 200 years ago. Moths are major consumers of vegetation when in caterpillar stage and are food sources for many birds and mammals, and contribute greatly to the insect diversity in a region. Moth species richness and abundance may be associated with the distribution of vegetation communities and seasonal timing, and the conservation of rare moths may depend on the conservation of rare vegetation habitats. A dataset of moths sampled 10 times/year at 20 locations in the 64-km² Andrews Forest over the period 2004-2008 was analyzed using generalized linear mixed models (GLMM), non-metric multidimensional scaling (NMS), multi-response permutation procedure (MRPP), analysis of variance (ANOVA), and two tailed t-test to identify the overall patterns of rare and common moth distribution as well as moth community relationships to structurally and taxonomically derived vegetation classes and seasonality. Five hundred fourteen species and 69,168 macromoth individuals were identified. Moth species abundance and diversity were significantly higher in low elevation coniferous forests than in other vegetation types, according to the GLMM. Sixty-six rare moth species were significantly associated with high elevation open habitats. Species associated with meadows also were significantly more likely to be hardwood or herb-feeders than conifer-feeders as caterpillars, based on ANOVAs. The 26 most common moth species were significantly associated with low elevation coniferous forests and were more likely to be conifer-feeders as caterpillars, based on ANOVAs. Common moth species were significantly more likely to emerge earlier in warmer years than in cooler years, based on a two-tailed t-test. Managing the western Cascades landscape for moth biodiversity and for moth abundance requires maintenance and potentially expansion of rare upland habitats as well as lowland coniferous forests. Montane meadows in the Andrews Forest are contracting in size, but it is not known how these changes have affected moth and plant biodiversity. The rate and pattern of meadow contraction from 1949 to 2005 along the high ridges of the Andrews Forest were analyzed using air photo change detection. Overall meadows contracted by nearly 50% from 1949 to 2005, but rates of meadow loss were much higher for the largest meadow complexes. Plant community diversity in seventeen meadows and the diversity, abundance, and community structure of moths at 98 locations sampled in the summers of 2008, 2009, and 2010 were related to measures of meadow size, isolation, and other variables using cluster analysis (CLA), MRPP, NMS, and generalized additive models (GAMs). Plant diversity in meadows was significantly positively related to meadow area in 1949 and the distance of the meadow from the road, based on GAM analysis. Plant community structure was most closely correlated with meadow area in 1949 and slope, based on CLA, MRPP, and NMS analysis. Calendar day explained the most variation in moth species richness, abundance, and community structure, but the next most important explanatory variables differed according to feeding guild, based on GAMs. Richness, abundance, and community structure of herb-feeding moths was related to meadow area in 1949 and elevation. For angiosperm-feeding moths, area-perimeter ratio in 2005 explained the most variation in richness, abundance, and community structure after calendar day. For gymnosperm-feeding moths, meadow area change from 1949-2005, a variable measuring the amount of increase in coniferous tree cover, explained the most variation in richness, abundance, and community structure after calendar day. The abundance and diversity of herb-feeding moths and meadow plants exhibited a lagged response to habitat loss, which may indicate an extinction debt. In contrast, angiosperm-and gymnosperm-feeding moths responded quickly (within 50 years) to increases in their habitat. Managing for the conservation of biodiversity in the upper elevations of the Andrews Forest will require targeted management strategies for different groups of organisms. Herb-feeding moths and meadow plants will benefit from expansion of open meadow habitat, while angiosperm and gymnosperm-feeders will require the maintenance of edge environments and coniferous forests. Title: The historic and contemporary ecology of western Cascade meadows : archeology, vegetation, and macromoth ecology Author: Highland, Steven A. Montane meadows in the western Cascades of Oregon occupy approximately 5% of the landscape, but contribute greatly to the region's biodiversity. Western Cascades meadows are dynamic parts of the landscape and have contracted by over 50% in the past two hundred years in the HJ Andrews Experimental Forest (hereafter Andrews Forest). Many studies have linked the loss of meadows with local extirpation of species and loss of regional biodiversity, but these processes depend upon the factors that create and maintain meadows, and how species respond to meadow configuration. The prehistory of these meadows is poorly understood, as is the contemporary ecology. This study combined previously collected archeological and moth datasets, aerial photographs, and new plant, tree core, and moth data to investigate interactions between landforms, disturbance, vegetation, and moth abundance and diversity in montane meadows of the western Cascades of Oregon. Burning by prehistoric people may have created and maintained montane meadows, but relatively little evidence remains of the activities of prehistoric peoples in the western Cascades. This study assessed the extent to which prehistoric people preferentially used different landforms and vegetation types by inferring use from landscape distributions of archaeological sites. Descriptions of 359 previously recorded and four newly discovered archeological sites in the McKenzie River watershed of western Oregon were examined using GIS and chi-square analysis to determine how sites were distributed relative to classified vegetation and landforms of the 3700-km² McKenzie River watershed. The high ridges of the HJ Andrews Experimental Forest were analyzed using air photo change detection and archaeological field surveys to identify how archeological sites were distributed relative to landforms and vegetation communities, including meadows. The field surveys documented physical evidence (archeological sites) confirming Native American use of the meadows and surrounding open forests. The locations of these sites indicate that Native Americans utilized the edges between large open meadows and open forests, as well as gently sloping open meadows. The prior extent of meadows (before air photos) was estimated by dendrochronology of 220 trees along present-day and inferred past meadow edges. Forest age structure and the open-grown forms of Douglas fir suggests a much more open habitat, potentially due to fire, was present more than 200 years ago. Moths are major consumers of vegetation when in caterpillar stage and are food sources for many birds and mammals, and contribute greatly to the insect diversity in a region. Moth species richness and abundance may be associated with the distribution of vegetation communities and seasonal timing, and the conservation of rare moths may depend on the conservation of rare vegetation habitats. A dataset of moths sampled 10 times/year at 20 locations in the 64-km² Andrews Forest over the period 2004-2008 was analyzed using generalized linear mixed models (GLMM), non-metric multidimensional scaling (NMS), multi-response permutation procedure (MRPP), analysis of variance (ANOVA), and two tailed t-test to identify the overall patterns of rare and common moth distribution as well as moth community relationships to structurally and taxonomically derived vegetation classes and seasonality. Five hundred fourteen species and 69,168 macromoth individuals were identified. Moth species abundance and diversity were significantly higher in low elevation coniferous forests than in other vegetation types, according to the GLMM. Sixty-six rare moth species were significantly associated with high elevation open habitats. Species associated with meadows also were significantly more likely to be hardwood or herb-feeders than conifer-feeders as caterpillars, based on ANOVAs. The 26 most common moth species were significantly associated with low elevation coniferous forests and were more likely to be conifer-feeders as caterpillars, based on ANOVAs. Common moth species were significantly more likely to emerge earlier in warmer years than in cooler years, based on a two-tailed t-test. Managing the western Cascades landscape for moth biodiversity and for moth abundance requires maintenance and potentially expansion of rare upland habitats as well as lowland coniferous forests. Montane meadows in the Andrews Forest are contracting in size, but it is not known how these changes have affected moth and plant biodiversity. The rate and pattern of meadow contraction from 1949 to 2005 along the high ridges of the Andrews Forest were analyzed using air photo change detection. Overall meadows contracted by nearly 50% from 1949 to 2005, but rates of meadow loss were much higher for the largest meadow complexes. Plant community diversity in seventeen meadows and the diversity, abundance, and community structure of moths at 98 locations sampled in the summers of 2008, 2009, and 2010 were related to measures of meadow size, isolation, and other variables using cluster analysis (CLA), MRPP, NMS, and generalized additive models (GAMs). Plant diversity in meadows was significantly positively related to meadow area in 1949 and the distance of the meadow from the road, based on GAM analysis. Plant community structure was most closely correlated with meadow area in 1949 and slope, based on CLA, MRPP, and NMS analysis. Calendar day explained the most variation in moth species richness, abundance, and community structure, but the next most important explanatory variables differed according to feeding guild, based on GAMs. Richness, abundance, and community structure of herb-feeding moths was related to meadow area in 1949 and elevation. For angiosperm-feeding moths, area-perimeter ratio in 2005 explained the most variation in richness, abundance, and community structure after calendar day. For gymnosperm-feeding moths, meadow area change from 1949-2005, a variable measuring the amount of increase in coniferous tree cover, explained the most variation in richness, abundance, and community structure after calendar day. The abundance and diversity of herb-feeding moths and meadow plants exhibited a lagged response to habitat loss, which may indicate an extinction debt. In contrast, angiosperm-and gymnosperm-feeding moths responded quickly (within 50 years) to increases in their habitat. Managing for the conservation of biodiversity in the upper elevations of the Andrews Forest will require targeted management strategies for different groups of organisms. Herb-feeding moths and meadow plants will benefit from expansion of open meadow habitat, while angiosperm and gymnosperm-feeders will require the maintenance of edge environments and coniferous forests. Close

• 647. [Article] Hood River Bull Trout Abundance, Life History, and Habitat Connectivity, 2007 Progress Reports 2007

  Abstract -- Hood River bull trout are thought to exist as two independent reproductive units (USFWS 2004), known as local populations (Rieman and McIntyre 1995). The Clear Branch local population is isolated ...

  Citation × Citation Citation Abstract Copy Title: Hood River Bull Trout Abundance, Life History, and Habitat Connectivity, 2007 Progress Reports 2007 Abstract -- Hood River bull trout are thought to exist as two independent reproductive units (USFWS 2004), known as local populations (Rieman and McIntyre 1995). The Clear Branch local population is isolated above Clear Branch Dam, which provides limited downstream fish passage during infrequent and sporadic periods of spill and no upstream passage. Bull trout in this population inhabit Laurance Lake Reservoir and tributaries upstream of Clear Branch Dam. The Hood River local population occurs in the mainstem Hood River and Middle Fork Hood River downstream of the Clear Branch Dam and a small number of adult bull trout migrate each year into the Hood River from the Columbia River (Figure 1). The status of both populations is extremely precarious. The Clear Branch population is at risk of a random extinction event due to low numbers, negative interactions with non-native smallmouth bass, isolation and limited spawning habitat (USFWS, 1998). The Hood River population also appears to be small and is threatened by passage barriers, unscreened irrigation systems, impaired water quality and periodic siltation of spawning substrate by glacial outbursts. Clear Branch bull trout spawn in Clear Branch and Pinnacle Creek. After rearing in these two natal streams for an unknown time period, most are believed to migrate downstream to Laurance Lake Reservoir. Clear Branch bull trout have been documented passing over the dam spillway during high water events (Pribyl et al. 1996) and may provide a recruitment source for the Hood River local population. Adult bull trout tagged at Powerdale Dam have been observed at Coe Branch irrigation diversion and in a trap at the base of Clear Branch dam. These fish may have been attempting to reach spawning areas located upstream of the dam. However, the success of bull trout migrating downstream via the spillway or the possibility of successfully navigating through the diversion network has never been determined. Depending on the water year, the Middle Fork Irrigation District (MFID) may not spill at all, or the timing of the spill may not coincide with the timing of downstream migration, which is currently unknown (East Fork Hood River and Middle Fork Hood River Watershed analysis). Smallmouth bass were discovered in Lake Laurance Reservoir in the 1990s. Creel surveys have shown that large adult bass are caught occasionally in the reservoir and schools of bass fry have been seen by district fish biologist (Rod French, ODFW, personal communication), suggesting that they are spawning successfully. This illegal introduction poses a potential threat to the Clear Branch bull trout population, but its magnitude is unknown because the bass population size and degree of interaction between the two species are unknown. Bull trout and smallmouth bass have significantly different temperature preferences and tolerances, with bull trout being one of the most sensitive coldwater species and bass being a warm water species. Lake Laurance, a relatively high-altitude reservoir at 890 m (2,920 feet), does not provide ideal bass habitat so these two species may have largely non-overlapping distributions or differing activity periods (Terry Shrader, ODFW warmwater fish biologist, personal communication). However, based on past reservoir temperature data (Berger et al. 2005), there are periods in the reservoir when there is potential for bull trout and bass interaction: periods when bull trout are susceptible to bass predation and when juvenile fish might compete for resources. Spawning activity of the Hood River local population has been observed in a few locations within the Middle Fork of Hood River (Figure 1). Although consistent and extensive spawning areas for this population are not known, some of the locations where juvenile rearing or potential bull trout redds have been observed include the Middle Fork Hood River and some of its tributaries: Bear Creek, Compass Creek and Coe Branch (USFWS 2004). However, Coe Branch, Compass Creek, and the Middle Fork are glacial streams with a high volume of sand and silt which may compromise spawning success. No bull trout spawning or rearing has been observed on the East and West Forks of Hood River. The Middle Fork and mainstem Hood River provide foraging, migration and overwintering habitat. Hood River bull trout are also known to migrate into the Columbia River. Two bull trout tagged at Powerdale Dam (RK 7.2 of mainstem Hood River) were recovered near Drano Lake in Washington State; and one was captured 11 kilometers downstream of the confluence of the Hood and Columbia Rivers (USFWS 2004). Every year (usually between May and July), adult bull trout, presumably migrating upstream from the Columbia River, are captured and anchor tagged at Powerdale Dam. Although some of these tagged fish have been observed upstream (one in Coe Branch and three below Clear Branch dam), the spawning destination of fluvial adults within the Hood River basin is largely unknown. Dispersing juvenile bull trout and migrating adults in this local population are threatened by flow diversions with inadequate screening and passage facilities. Several structures are suspected to impede upstream migration or entrain juvenile and adult bull trout into irrigation works (Pribyl et al. 1996, HRWG 1999). These structures include: the diversion at Clear Branch Dam (passage and screening), Coe Branch (passage and screening), and the Farmers Irrigation District diversion (screening) on the mainstem Hood River (HRWG 1999). However, little research has been conducted to assess the impacts of these structures on migrating bull trout. Beyond a general knowledge of the distribution of Hood River bull trout and the nature of anthropogenic factors that potentially restrict their life history and habitat connectivity, little is known about this recovery unit. Baseline information about adult abundance is lacking for both local populations, the potential of a source (Clear Branch) and sink (Hood River) relationship between the two local populations has not been explored, and the migratory life history of adult fish caught at Powerdale Dam is unknown. The degree to which irrigation and hydropower diversions hamper connectivity within the Hood River basin is also poorly understood. Migratory life histories have been viewed as key to species persistence (Rieman and McIntyre 1995; Dunham and Rieman 1999), and understanding movement patterns and associated habitat requirements are critical to maintaining those migratory forms (Muhlfeld and Morotz 2005; Hostettler 2005). Gaining this information is also critical to evaluating bull trout recovery in the Hood River Subbasin (Coccoli 2004). The Oregon Department of Fish and Wildlife (ODFW) initiated a study in 2006 to improve our understanding of the abundance, life history, and potential limiting factors of the bull trout in this recovery unit. This report describes findings for the first two years of the study (2006-2007). Specific study objectives for the first two years were: 1. Determine the migratory life history of Hood River bull trout and assess the potential impacts of flow diversions and two new falls on the Middle Fork Hood River (scoured by the November 2006 glacial outburst) on bull trout migrations. 2. Determine current distribution of bull trout reproduction and early rearing in historical and potential bull trout streams in the Hood River Subbasin. 3. Determine the juvenile and adult life history the Clear Branch local population and develop a statistically reliable and cost-effective protocol for monitoring the abundance of adult Clear Branch bull trout. 4. Assess the potential impact of smallmouth bass on bull trout in Laurance Lake Reservoir. Title: Hood River Bull Trout Abundance, Life History, and Habitat Connectivity, 2007 Progress Reports 2007 Abstract -- Hood River bull trout are thought to exist as two independent reproductive units (USFWS 2004), known as local populations (Rieman and McIntyre 1995). The Clear Branch local population is isolated above Clear Branch Dam, which provides limited downstream fish passage during infrequent and sporadic periods of spill and no upstream passage. Bull trout in this population inhabit Laurance Lake Reservoir and tributaries upstream of Clear Branch Dam. The Hood River local population occurs in the mainstem Hood River and Middle Fork Hood River downstream of the Clear Branch Dam and a small number of adult bull trout migrate each year into the Hood River from the Columbia River (Figure 1). The status of both populations is extremely precarious. The Clear Branch population is at risk of a random extinction event due to low numbers, negative interactions with non-native smallmouth bass, isolation and limited spawning habitat (USFWS, 1998). The Hood River population also appears to be small and is threatened by passage barriers, unscreened irrigation systems, impaired water quality and periodic siltation of spawning substrate by glacial outbursts. Clear Branch bull trout spawn in Clear Branch and Pinnacle Creek. After rearing in these two natal streams for an unknown time period, most are believed to migrate downstream to Laurance Lake Reservoir. Clear Branch bull trout have been documented passing over the dam spillway during high water events (Pribyl et al. 1996) and may provide a recruitment source for the Hood River local population. Adult bull trout tagged at Powerdale Dam have been observed at Coe Branch irrigation diversion and in a trap at the base of Clear Branch dam. These fish may have been attempting to reach spawning areas located upstream of the dam. However, the success of bull trout migrating downstream via the spillway or the possibility of successfully navigating through the diversion network has never been determined. Depending on the water year, the Middle Fork Irrigation District (MFID) may not spill at all, or the timing of the spill may not coincide with the timing of downstream migration, which is currently unknown (East Fork Hood River and Middle Fork Hood River Watershed analysis). Smallmouth bass were discovered in Lake Laurance Reservoir in the 1990s. Creel surveys have shown that large adult bass are caught occasionally in the reservoir and schools of bass fry have been seen by district fish biologist (Rod French, ODFW, personal communication), suggesting that they are spawning successfully. This illegal introduction poses a potential threat to the Clear Branch bull trout population, but its magnitude is unknown because the bass population size and degree of interaction between the two species are unknown. Bull trout and smallmouth bass have significantly different temperature preferences and tolerances, with bull trout being one of the most sensitive coldwater species and bass being a warm water species. Lake Laurance, a relatively high-altitude reservoir at 890 m (2,920 feet), does not provide ideal bass habitat so these two species may have largely non-overlapping distributions or differing activity periods (Terry Shrader, ODFW warmwater fish biologist, personal communication). However, based on past reservoir temperature data (Berger et al. 2005), there are periods in the reservoir when there is potential for bull trout and bass interaction: periods when bull trout are susceptible to bass predation and when juvenile fish might compete for resources. Spawning activity of the Hood River local population has been observed in a few locations within the Middle Fork of Hood River (Figure 1). Although consistent and extensive spawning areas for this population are not known, some of the locations where juvenile rearing or potential bull trout redds have been observed include the Middle Fork Hood River and some of its tributaries: Bear Creek, Compass Creek and Coe Branch (USFWS 2004). However, Coe Branch, Compass Creek, and the Middle Fork are glacial streams with a high volume of sand and silt which may compromise spawning success. No bull trout spawning or rearing has been observed on the East and West Forks of Hood River. The Middle Fork and mainstem Hood River provide foraging, migration and overwintering habitat. Hood River bull trout are also known to migrate into the Columbia River. Two bull trout tagged at Powerdale Dam (RK 7.2 of mainstem Hood River) were recovered near Drano Lake in Washington State; and one was captured 11 kilometers downstream of the confluence of the Hood and Columbia Rivers (USFWS 2004). Every year (usually between May and July), adult bull trout, presumably migrating upstream from the Columbia River, are captured and anchor tagged at Powerdale Dam. Although some of these tagged fish have been observed upstream (one in Coe Branch and three below Clear Branch dam), the spawning destination of fluvial adults within the Hood River basin is largely unknown. Dispersing juvenile bull trout and migrating adults in this local population are threatened by flow diversions with inadequate screening and passage facilities. Several structures are suspected to impede upstream migration or entrain juvenile and adult bull trout into irrigation works (Pribyl et al. 1996, HRWG 1999). These structures include: the diversion at Clear Branch Dam (passage and screening), Coe Branch (passage and screening), and the Farmers Irrigation District diversion (screening) on the mainstem Hood River (HRWG 1999). However, little research has been conducted to assess the impacts of these structures on migrating bull trout. Beyond a general knowledge of the distribution of Hood River bull trout and the nature of anthropogenic factors that potentially restrict their life history and habitat connectivity, little is known about this recovery unit. Baseline information about adult abundance is lacking for both local populations, the potential of a source (Clear Branch) and sink (Hood River) relationship between the two local populations has not been explored, and the migratory life history of adult fish caught at Powerdale Dam is unknown. The degree to which irrigation and hydropower diversions hamper connectivity within the Hood River basin is also poorly understood. Migratory life histories have been viewed as key to species persistence (Rieman and McIntyre 1995; Dunham and Rieman 1999), and understanding movement patterns and associated habitat requirements are critical to maintaining those migratory forms (Muhlfeld and Morotz 2005; Hostettler 2005). Gaining this information is also critical to evaluating bull trout recovery in the Hood River Subbasin (Coccoli 2004). The Oregon Department of Fish and Wildlife (ODFW) initiated a study in 2006 to improve our understanding of the abundance, life history, and potential limiting factors of the bull trout in this recovery unit. This report describes findings for the first two years of the study (2006-2007). Specific study objectives for the first two years were: 1. Determine the migratory life history of Hood River bull trout and assess the potential impacts of flow diversions and two new falls on the Middle Fork Hood River (scoured by the November 2006 glacial outburst) on bull trout migrations. 2. Determine current distribution of bull trout reproduction and early rearing in historical and potential bull trout streams in the Hood River Subbasin. 3. Determine the juvenile and adult life history the Clear Branch local population and develop a statistically reliable and cost-effective protocol for monitoring the abundance of adult Clear Branch bull trout. 4. Assess the potential impact of smallmouth bass on bull trout in Laurance Lake Reservoir. Close

• 648. [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

• 649. [Article] The influence of climate change and restoration on stream temperature

  Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, ...

  Citation × Citation Citation Abstract Copy Title: The influence of climate change and restoration on stream temperature Author: Diabat, Mousa Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, and channel structure directly influence stream temperature. Numerous studies indicate that increased average air temperature during the past century has led to stream warming across the world. The trend of stream warming was also present in spring-fed watersheds, where summer flow has decreased. In addition, anthropogenic practices that alter the natural landscape and channel structure, such as forest management, agriculture, and mining contributed to stream warming. For example, deforested and unshaded stream reaches or dredged channels were warmer than shaded reaches and meandering streams. Stream temperatures in North American lotic habitats are of a specific concern due to their significant economic, cultural, and ecological value. With climate projections indicating that air temperature will only continue to rise throughout the 21st century, cold- or cool-water organisms, especially fishes, will be affected. Therefore, there is a strong need to better understand the impacts of changing climate, riparian landscape, and channel structure on a stream's heat budget. This may assist in restoring the historic thermal regime in impacted sites and mitigating the impacts of future climate change. This study looks into the relative influences of the different factors on a stream's heat budget with three manuscripts: one on stream temperature response to diel timing of air warming, one on stream temperature response to changes in air temperature, flow, and riparian vegetation, and one on stream temperature response to air warming and channel reconstruction. I used the software Heat Source version 8.05 to simulate stream temperature for all three analyses along the Middle Fork John Day River, Oregon USA. Two of the manuscripts were applied to an upper 37 km section of the Middle Fork John Day River (presented in chapter 2 and 3), where the third manuscript was applied to a 1.5-km section. The sensitivity analysis of stream temperature response to diel timing of air warming (Chapter 2: Diel Timing of Warmer Air under Climate Change Affects Magnitude, Timing, and Duration of Stream Temperature Change) was based on scenarios representing uniform air warming over the diel period, daytime warming, and nighttime warming. Uniform warming of air temperature is a simple representation of increases in the average daily or monthly temperatures generated by the 'delta method'. The delta method relies on adding a constant value to the air temperature time-series data. This constant value is the difference (delta) between base case average air temperatures and the projected one. Scenarios of daytime or nighttime warming represent conditions under which most of the warming of the air occurs during the daytime or the nighttime, respectively. I simulated the stream temperature response to warmer air conditions of +2 °C and +4 °C in daily average for all three cases of air warming conditions. The three cases of different diel distributions of air warming generated 7-day average daily maximum stream temperature (7DADM) increases of approximately +1.8 °C ± 0.1 °C at the downstream end of the study section relative to the base case. In most parts of the reach, the three distributions of air warming generated different ranges of stream temperatures, different 7DADM values, different durations of stream temperature changes, and different average daily temperatures. Changes of stream temperature were out of phase with imposed changes of air temperature. Therefore, nighttime warming of air temperatures would cause the greatest increase in maximum daily stream temperature, which typically occurs during the daytime. The sensitivity analysis of the relative influences of changes in air temperature, stream flow, and riparian vegetation on stream temperature (Chapter 3: Assessing Stream Temperature Response to Cumulative Influence of Changing Air Temperature, Flow, and Riparian Vegetation). This study summarized stream temperature simulation in 36 scenarios representing possible manifestations of 21st century climate conditions and land management strategies. In addition to existing conditions (base case) of flow, air temperature, and riparian vegetation, scenarios consisted of: two air temperature increases of 2 °C and 4 °C, two stream flow variations of +30% and -30%, three spatially uniform riparian vegetation conditions that create averages of effective shade 7%, 34%, and 79%, in addition to 14% for base case conditions. Results suggest that variation in riparian vegetation was the dominant factor influencing stream temperature because it regulates incoming shortwave radiation, the largest heat input to the stream, while variation in stream flow has a negligible influence. Results indicated that increasing the effective shade along the study section, particularly in the currently unshaded sections, could mitigate the influence of increasing air temperature, and would reduce stream temperature maxima below current values even under future climate conditions of warmer air. With the small influence it had, increasing stream flow reduced the 7DADM under low shade conditions. However, increasing stream flow showed counterintuitive results as it contributed to increasing stream temperature maxima when the stream was heavily shaded. The applied study examined the stream temperature response to restoration practices and their potential to mitigate the influence of warmer air conditions (Chapter 4: Estimating Stream Temperature Response to Restoring Channel and Riparian Vegetation and the Potential to Mitigate Warmer Air Conditions). This study focused on a 1.5 km section along the upper part of the Middle Fork John Day River that was modified due to past anthropogenic activities of mining for gold and timber harvest. Currently, the riparian vegetation of the study site is mostly shrubs and stands of short trees. Restoration designs call for the restoration of both the channel structure and replanting the riparian vegetation. Simulation results showed that the 7DADM was higher in the restored channel than the existing channel with both conditions of low and high effective shade conditions. However, a combined restoration practice of channel reconstruction and medium effective shade conditions reduced stream temperature maxima more than restoring riparian vegetation alone. In addition, results showed that restoring riparian vegetation was sufficient to mitigate the influence of warmer air on stream temperature, while restoring the channel alone is not. Heat budget analysis showed that heat accumulation during the daytime increased in the restored channel, which was longer, narrower, and deeper than the existing channel. It is important to emphasize that stream temperature is one of many goals that restoration activities aim to improve. Furthermore, differences in 7DADM among the different scenarios of restoration are negligible. Such small differences could hardly be measure. While this study examined a short section of 1.5 km, longer stream sections may increase the differences in 7DADM. Primary conclusions of this study are: 1) daily maxima of stream temperature will increase in response to increased air temperature regardless of the distribution of air warming during the diel cycle; 2) nighttime air warming caused a greater increase in stream temperature maximum than daytime warming; 3) riparian vegetation was the dominant factor on stream's heat budget, more than air temperature or stream flow; 4) restoring riparian vegetation mitigated the influence of warmer air; 5) restoring channel structure alone was not sufficient to lower temperature maxima; and 6) restoration project was most successful in improving degraded stream temperature when combined with channel reconstruction and improved riparian shade. Title: The influence of climate change and restoration on stream temperature Author: Diabat, Mousa Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, and channel structure directly influence stream temperature. Numerous studies indicate that increased average air temperature during the past century has led to stream warming across the world. The trend of stream warming was also present in spring-fed watersheds, where summer flow has decreased. In addition, anthropogenic practices that alter the natural landscape and channel structure, such as forest management, agriculture, and mining contributed to stream warming. For example, deforested and unshaded stream reaches or dredged channels were warmer than shaded reaches and meandering streams. Stream temperatures in North American lotic habitats are of a specific concern due to their significant economic, cultural, and ecological value. With climate projections indicating that air temperature will only continue to rise throughout the 21st century, cold- or cool-water organisms, especially fishes, will be affected. Therefore, there is a strong need to better understand the impacts of changing climate, riparian landscape, and channel structure on a stream's heat budget. This may assist in restoring the historic thermal regime in impacted sites and mitigating the impacts of future climate change. This study looks into the relative influences of the different factors on a stream's heat budget with three manuscripts: one on stream temperature response to diel timing of air warming, one on stream temperature response to changes in air temperature, flow, and riparian vegetation, and one on stream temperature response to air warming and channel reconstruction. I used the software Heat Source version 8.05 to simulate stream temperature for all three analyses along the Middle Fork John Day River, Oregon USA. Two of the manuscripts were applied to an upper 37 km section of the Middle Fork John Day River (presented in chapter 2 and 3), where the third manuscript was applied to a 1.5-km section. The sensitivity analysis of stream temperature response to diel timing of air warming (Chapter 2: Diel Timing of Warmer Air under Climate Change Affects Magnitude, Timing, and Duration of Stream Temperature Change) was based on scenarios representing uniform air warming over the diel period, daytime warming, and nighttime warming. Uniform warming of air temperature is a simple representation of increases in the average daily or monthly temperatures generated by the 'delta method'. The delta method relies on adding a constant value to the air temperature time-series data. This constant value is the difference (delta) between base case average air temperatures and the projected one. Scenarios of daytime or nighttime warming represent conditions under which most of the warming of the air occurs during the daytime or the nighttime, respectively. I simulated the stream temperature response to warmer air conditions of +2 °C and +4 °C in daily average for all three cases of air warming conditions. The three cases of different diel distributions of air warming generated 7-day average daily maximum stream temperature (7DADM) increases of approximately +1.8 °C ± 0.1 °C at the downstream end of the study section relative to the base case. In most parts of the reach, the three distributions of air warming generated different ranges of stream temperatures, different 7DADM values, different durations of stream temperature changes, and different average daily temperatures. Changes of stream temperature were out of phase with imposed changes of air temperature. Therefore, nighttime warming of air temperatures would cause the greatest increase in maximum daily stream temperature, which typically occurs during the daytime. The sensitivity analysis of the relative influences of changes in air temperature, stream flow, and riparian vegetation on stream temperature (Chapter 3: Assessing Stream Temperature Response to Cumulative Influence of Changing Air Temperature, Flow, and Riparian Vegetation). This study summarized stream temperature simulation in 36 scenarios representing possible manifestations of 21st century climate conditions and land management strategies. In addition to existing conditions (base case) of flow, air temperature, and riparian vegetation, scenarios consisted of: two air temperature increases of 2 °C and 4 °C, two stream flow variations of +30% and -30%, three spatially uniform riparian vegetation conditions that create averages of effective shade 7%, 34%, and 79%, in addition to 14% for base case conditions. Results suggest that variation in riparian vegetation was the dominant factor influencing stream temperature because it regulates incoming shortwave radiation, the largest heat input to the stream, while variation in stream flow has a negligible influence. Results indicated that increasing the effective shade along the study section, particularly in the currently unshaded sections, could mitigate the influence of increasing air temperature, and would reduce stream temperature maxima below current values even under future climate conditions of warmer air. With the small influence it had, increasing stream flow reduced the 7DADM under low shade conditions. However, increasing stream flow showed counterintuitive results as it contributed to increasing stream temperature maxima when the stream was heavily shaded. The applied study examined the stream temperature response to restoration practices and their potential to mitigate the influence of warmer air conditions (Chapter 4: Estimating Stream Temperature Response to Restoring Channel and Riparian Vegetation and the Potential to Mitigate Warmer Air Conditions). This study focused on a 1.5 km section along the upper part of the Middle Fork John Day River that was modified due to past anthropogenic activities of mining for gold and timber harvest. Currently, the riparian vegetation of the study site is mostly shrubs and stands of short trees. Restoration designs call for the restoration of both the channel structure and replanting the riparian vegetation. Simulation results showed that the 7DADM was higher in the restored channel than the existing channel with both conditions of low and high effective shade conditions. However, a combined restoration practice of channel reconstruction and medium effective shade conditions reduced stream temperature maxima more than restoring riparian vegetation alone. In addition, results showed that restoring riparian vegetation was sufficient to mitigate the influence of warmer air on stream temperature, while restoring the channel alone is not. Heat budget analysis showed that heat accumulation during the daytime increased in the restored channel, which was longer, narrower, and deeper than the existing channel. It is important to emphasize that stream temperature is one of many goals that restoration activities aim to improve. Furthermore, differences in 7DADM among the different scenarios of restoration are negligible. Such small differences could hardly be measure. While this study examined a short section of 1.5 km, longer stream sections may increase the differences in 7DADM. Primary conclusions of this study are: 1) daily maxima of stream temperature will increase in response to increased air temperature regardless of the distribution of air warming during the diel cycle; 2) nighttime air warming caused a greater increase in stream temperature maximum than daytime warming; 3) riparian vegetation was the dominant factor on stream's heat budget, more than air temperature or stream flow; 4) restoring riparian vegetation mitigated the influence of warmer air; 5) restoring channel structure alone was not sufficient to lower temperature maxima; and 6) restoration project was most successful in improving degraded stream temperature when combined with channel reconstruction and improved riparian shade. Close