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• 1. [Article] Little Deschutes Subbasin Watershed Assessment

  Abstract -- Many of the impacts to fish and wildlife habitat and water quality in the Little Deschutes River Subbasin are concentrated in the areas of housing, roads, and other human development. Most ...

  Citation × Citation Citation Abstract Copy Title: Little Deschutes Subbasin Watershed Assessment Abstract -- Many of the impacts to fish and wildlife habitat and water quality in the Little Deschutes River Subbasin are concentrated in the areas of housing, roads, and other human development. Most of the human population in the subbasin is concentrated around the community centers of La Pine, Gilchrist, Crescent, and Crescent Lake. There is significant dispersed development along the lower reaches of the Little Deschutes River between the communities of Sunriver and La Pine -an area characterized by gentle topography and depressions with forested wetlands, marshes and shallow lakes. Streams in this area, as illustrated by the Little Deschutes River , are low gradient and originate in the high elevation areas in the southwest portion of the watershed where there is higher precipitation. This ownership pattern has significant implications for natural resource management, as lower gradient floodplain areas tend to provide important wetland, fish, and wildlife habitat. Key Findings Fuel Loading: Having homes safe from wildfires is a concern for many residents. Fire suppression has increased the amount of dry wood in the area, creating a ready source for major wildfires. Riparian Areas and Wetlands: Loss of wetland and riparian areas , especially in the lower areas along the Little Deschutes River , has affected a number of resources. Water quality has been affected by the reduced wetlands that act as filters of nitrogen; the loss of streamside trees and other vegetation reduces shade that helps to cool water temperatures. Finally, loss ofwetlands and riparian vegetation has reduced important fish and wildlife habitats. Wildlife: The growth and development have altered wildlife habitats. Loss of wetlands, streamside vegetation, and other changes in the watershed have reduced important wildlife habitat. Roads and development have impacted migrating mule deer, increasing collisions between deer and cars and altering their migration pathways. Fish: There has been a significant loss of native trout and an increase in introduced brook and brown trout in the Little Deschutes River and tributaries. Loss of native trout is from competition with introduced species and changes in aquatic habitat and water temperatures. Water Quality: A major concern about the water in the river is unusually high temperatures in the summer and the abnormal growth of algae. Other studies indicated that there are problems with groundwater loading ofnitrogen. The high water table (with associated wetlands), and porous pumice soils contributes to increased nitrates, a by-product of septic systems and an indicator of human pathogens. Title: Little Deschutes Subbasin Watershed Assessment Abstract -- Many of the impacts to fish and wildlife habitat and water quality in the Little Deschutes River Subbasin are concentrated in the areas of housing, roads, and other human development. Most of the human population in the subbasin is concentrated around the community centers of La Pine, Gilchrist, Crescent, and Crescent Lake. There is significant dispersed development along the lower reaches of the Little Deschutes River between the communities of Sunriver and La Pine -an area characterized by gentle topography and depressions with forested wetlands, marshes and shallow lakes. Streams in this area, as illustrated by the Little Deschutes River , are low gradient and originate in the high elevation areas in the southwest portion of the watershed where there is higher precipitation. This ownership pattern has significant implications for natural resource management, as lower gradient floodplain areas tend to provide important wetland, fish, and wildlife habitat. Key Findings Fuel Loading: Having homes safe from wildfires is a concern for many residents. Fire suppression has increased the amount of dry wood in the area, creating a ready source for major wildfires. Riparian Areas and Wetlands: Loss of wetland and riparian areas , especially in the lower areas along the Little Deschutes River , has affected a number of resources. Water quality has been affected by the reduced wetlands that act as filters of nitrogen; the loss of streamside trees and other vegetation reduces shade that helps to cool water temperatures. Finally, loss ofwetlands and riparian vegetation has reduced important fish and wildlife habitats. Wildlife: The growth and development have altered wildlife habitats. Loss of wetlands, streamside vegetation, and other changes in the watershed have reduced important wildlife habitat. Roads and development have impacted migrating mule deer, increasing collisions between deer and cars and altering their migration pathways. Fish: There has been a significant loss of native trout and an increase in introduced brook and brown trout in the Little Deschutes River and tributaries. Loss of native trout is from competition with introduced species and changes in aquatic habitat and water temperatures. Water Quality: A major concern about the water in the river is unusually high temperatures in the summer and the abnormal growth of algae. Other studies indicated that there are problems with groundwater loading ofnitrogen. The high water table (with associated wetlands), and porous pumice soils contributes to increased nitrates, a by-product of septic systems and an indicator of human pathogens. Close

• 2. [Article] AI - Rearing of Juvenile Salmon in Recovering Wetlands of the Salmon River Estuary

  Abstract -- The Salmon River estuary, on the central Oregon coast, provides an excellent opportunity to study salmonid use of restored tidal marsh. The U.S. Forest Service manages the estuary as part of ...

  Citation × Citation Citation Abstract Copy Title: AI - Rearing of Juvenile Salmon in Recovering Wetlands of the Salmon River Estuary Abstract -- The Salmon River estuary, on the central Oregon coast, provides an excellent opportunity to study salmonid use of restored tidal marsh. The U.S. Forest Service manages the estuary as part of the Cascade Head Scenic Research Area with the goal to rehabilitate the estuary “to its condition prior to the existing diking and agricultural use.” To achieve this goal, the U.S. Forest Service has completed three dike removal projects at 9-year intervals beginning in 1978. These projects created a patchwork of restored marshes in various stages of recovery, providing a natural laboratory for studying marsh restoration processes and their effects on estuarine rearing salmonids. Our Sea Grant-funded research, which is a cooperative study with researchers from the University of Washington, has four objectives: (1) describe salmon species use of undiked reference and recovering marshes; (2) compare diets of juvenile salmon among reference and diked marshes of different recovery ages; (3) compare availability and distribution of prey organisms consumed by juvenile salmon; and (4) assess geomorphological and ecological indicators (“metrics”) of restored wetlands and relationships to salmon use. This report describes the results of fish distribution and abundance surveys. Results of the other objectives are described in Gray et al. (In Review). Title: AI - Rearing of Juvenile Salmon in Recovering Wetlands of the Salmon River Estuary Abstract -- The Salmon River estuary, on the central Oregon coast, provides an excellent opportunity to study salmonid use of restored tidal marsh. The U.S. Forest Service manages the estuary as part of the Cascade Head Scenic Research Area with the goal to rehabilitate the estuary “to its condition prior to the existing diking and agricultural use.” To achieve this goal, the U.S. Forest Service has completed three dike removal projects at 9-year intervals beginning in 1978. These projects created a patchwork of restored marshes in various stages of recovery, providing a natural laboratory for studying marsh restoration processes and their effects on estuarine rearing salmonids. Our Sea Grant-funded research, which is a cooperative study with researchers from the University of Washington, has four objectives: (1) describe salmon species use of undiked reference and recovering marshes; (2) compare diets of juvenile salmon among reference and diked marshes of different recovery ages; (3) compare availability and distribution of prey organisms consumed by juvenile salmon; and (4) assess geomorphological and ecological indicators (“metrics”) of restored wetlands and relationships to salmon use. This report describes the results of fish distribution and abundance surveys. Results of the other objectives are described in Gray et al. (In Review). Close

• 3. [Article] AI - Stream Habitat Conditions on Industrial Forest Lands in Coastal Oregon

  Abstract -- In the summer of 1998 and 1999, watersheds in western Oregon were randomly sampled for stream habitat conditions. Sites were selected using a random tessellation stratified design. Oregon Department ...

  Citation × Citation Citation Abstract Copy Title: AI - Stream Habitat Conditions on Industrial Forest Lands in Coastal Oregon Abstract -- In the summer of 1998 and 1999, watersheds in western Oregon were randomly sampled for stream habitat conditions. Sites were selected using a random tessellation stratified design. Oregon Department of Fish and Wildlife Aquatic Inventories methods were used to quantify indicators of sediment supply and quality, riparian forest connectivity and health, habitat structure, in-stream complexity, and presence of salmonid species. As part of the overall sampling 47 sites in 1998 and 70 sites in 1999 were sampled on industrial forest lands. Of these sites 13 were sampled both in 1998 and 1999, and 37 sites were sampled for fish presence/absence. Approximately 44% of the sites sampled for habitat were within the range of anadromous salmonids. Upstream catchment area and gradient were the two major factors driving the overall patterns of habitat variables. Secondarily, land ownership and geology were other factors correlated with the habitat variables analyzed. The private non-industrial land ownership type was characterized by slightly higher fine sediment levels, lower wood volumes and number of key wood pieces, lower densities of deep pools, and lower levels of stream shading. State and industrial forest lands show moderate wood levels in the stream channel, although they show low levels of conifers in riparian zones. The sedimentary geologic type was characterized by higher levels of fine sediments in riffle units. Twelve, high quality, unconstrained stream reaches occurred in the 1998 and 1999 habitat sample on Industrial forest lands. Conditions on industrial forest lands in 1998-1999 were compared to conditions in 1993-1994 to detect any potential change over the five-year period. Three different datasets were analyzed. No significant changes in aquatic habitat or riparian conditions were detected. Electrofishing surveys were conducted at 37 sites outside or the expected range of coho salmon to determine fish presence/absence. Salmonid species were present at 19 of the sites that were electrofished. Title: AI - Stream Habitat Conditions on Industrial Forest Lands in Coastal Oregon Abstract -- In the summer of 1998 and 1999, watersheds in western Oregon were randomly sampled for stream habitat conditions. Sites were selected using a random tessellation stratified design. Oregon Department of Fish and Wildlife Aquatic Inventories methods were used to quantify indicators of sediment supply and quality, riparian forest connectivity and health, habitat structure, in-stream complexity, and presence of salmonid species. As part of the overall sampling 47 sites in 1998 and 70 sites in 1999 were sampled on industrial forest lands. Of these sites 13 were sampled both in 1998 and 1999, and 37 sites were sampled for fish presence/absence. Approximately 44% of the sites sampled for habitat were within the range of anadromous salmonids. Upstream catchment area and gradient were the two major factors driving the overall patterns of habitat variables. Secondarily, land ownership and geology were other factors correlated with the habitat variables analyzed. The private non-industrial land ownership type was characterized by slightly higher fine sediment levels, lower wood volumes and number of key wood pieces, lower densities of deep pools, and lower levels of stream shading. State and industrial forest lands show moderate wood levels in the stream channel, although they show low levels of conifers in riparian zones. The sedimentary geologic type was characterized by higher levels of fine sediments in riffle units. Twelve, high quality, unconstrained stream reaches occurred in the 1998 and 1999 habitat sample on Industrial forest lands. Conditions on industrial forest lands in 1998-1999 were compared to conditions in 1993-1994 to detect any potential change over the five-year period. Three different datasets were analyzed. No significant changes in aquatic habitat or riparian conditions were detected. Electrofishing surveys were conducted at 37 sites outside or the expected range of coho salmon to determine fish presence/absence. Salmonid species were present at 19 of the sites that were electrofished. Close

• 4. [Article] Neacoxie Watershed

  Abstract -- Previously, little information was known about the ecology or the condition of native habitats in the Neacoxie sub-watershed that drains from the city of Warrenton into the north section of ...

  Citation × Citation Citation Abstract Copy Title: Neacoxie Watershed Abstract -- Previously, little information was known about the ecology or the condition of native habitats in the Neacoxie sub-watershed that drains from the city of Warrenton into the north section of the Necanicum Estuary in the city of Seaside. In 2002, the Necanicum Watershed Council completed an assessment for the Necanicum River watershed, but with major knowledge gaps for the Neacoxie watershed, which includes the Neacoxie Creek corridor and the Clatsop Plains. In order for the North Coast Land Conservancy (NCLC) and other land managers to develop stewardship priorities and to make informed decisions about land management actions in this region, additional information was required. Together with the Necanicum Watershed Council and the North Coast Watershed Association, NCLC secured funding to conduct habitat inventories of the Neacoxie watershed. The Neacoxie Watershed Assessment summarizes the results of terrestrial plant transects and aquatic plant surveys completed in the summer of 2011 on ten properties owned by the North Coast Land Conservancy (NCLC) in the Neacoxie Creek watershed (please refer to Appendices A & B). Habitat types include stabilized sand dunes dominated by coastal prairie habitat, interdunal wetland swales and lakes, upland Sitka spruce forest, and forested wetlands. Percent composition of each plant community type observed was calculated. Invasive non-native plant species were recorded. Surveys were also conducted for both native and non-native plants in four water bodies owned by NCLC or adjacent to land trust properties. The plant community data that were collected will be used to evaluate baseline ecological conditions in the Neacoxie watershed. Plant communities can be used as indicators of long-term tidal and hydrologic conditions as well as the ecological health of the landscape. Repeated measurements can be used to assess community changes over time and to assess how plant community composition compares to that described for natural conditions. This information will assist the land trust in making science-based stewardship decisions on its properties, and can be used by other landowners to better understand changes occurring in plant communities in similar habitats on their properties as a result of human disturbance (e.g., land development, farming, grazing) and invasion by non-native plants. Title: Neacoxie Watershed Abstract -- Previously, little information was known about the ecology or the condition of native habitats in the Neacoxie sub-watershed that drains from the city of Warrenton into the north section of the Necanicum Estuary in the city of Seaside. In 2002, the Necanicum Watershed Council completed an assessment for the Necanicum River watershed, but with major knowledge gaps for the Neacoxie watershed, which includes the Neacoxie Creek corridor and the Clatsop Plains. In order for the North Coast Land Conservancy (NCLC) and other land managers to develop stewardship priorities and to make informed decisions about land management actions in this region, additional information was required. Together with the Necanicum Watershed Council and the North Coast Watershed Association, NCLC secured funding to conduct habitat inventories of the Neacoxie watershed. The Neacoxie Watershed Assessment summarizes the results of terrestrial plant transects and aquatic plant surveys completed in the summer of 2011 on ten properties owned by the North Coast Land Conservancy (NCLC) in the Neacoxie Creek watershed (please refer to Appendices A & B). Habitat types include stabilized sand dunes dominated by coastal prairie habitat, interdunal wetland swales and lakes, upland Sitka spruce forest, and forested wetlands. Percent composition of each plant community type observed was calculated. Invasive non-native plant species were recorded. Surveys were also conducted for both native and non-native plants in four water bodies owned by NCLC or adjacent to land trust properties. The plant community data that were collected will be used to evaluate baseline ecological conditions in the Neacoxie watershed. Plant communities can be used as indicators of long-term tidal and hydrologic conditions as well as the ecological health of the landscape. Repeated measurements can be used to assess community changes over time and to assess how plant community composition compares to that described for natural conditions. This information will assist the land trust in making science-based stewardship decisions on its properties, and can be used by other landowners to better understand changes occurring in plant communities in similar habitats on their properties as a result of human disturbance (e.g., land development, farming, grazing) and invasion by non-native plants. Close

• 5. [Article] NF - Effect of Bull Trout and Brook Trout Interactions on Foraging Habitat, Feeding Behavior, and Growth

  Abstract -- Observations of free-ranging sympatric bull trout Salvelinus confluentus and nonnative brook trout S. fontinalis in two eastern Oregon headwater streams provided little evidence of habitat ...

  Citation × Citation Citation Abstract Copy Title: NF - Effect of Bull Trout and Brook Trout Interactions on Foraging Habitat, Feeding Behavior, and Growth Abstract -- Observations of free-ranging sympatric bull trout Salvelinus confluentus and nonnative brook trout S. fontinalis in two eastern Oregon headwater streams provided little evidence of habitat partitioning. Both species held focal feeding points in similar microhabitats and fed primarily from the water column rather than from the surface or benthos. In an instream experiment, 20 enclosures were assigned one of three treatments: two bull trout, four bull trout, or a mix of two bull trout and two brook trout. In the enclosures, macroinvertebrate drift was restricted and trout densities were elevated, creating an environment of reduced food and habitat resources. Under these conditions, there was no indication of a niche shift by bull trout; feeding behavior and habitat use by bull trout did not differ depending on the presence or absence of brook trout. Brook trout in the mixed-species treatment were the most aggressive, maintained dominance in 75% of the enclosures, and exhibited significantly higher growth than sympatric bull trout. However, the effects of intra-and interspecific interactions on bull trout growth were equivalent. Given the absence of resource partitioning and a niche shift by bull trout in the presence of brook trout (despite obvious interference interactions), we suggest that the displacement of bull trout by brook trout is likely when resources are scarce. Title: NF - Effect of Bull Trout and Brook Trout Interactions on Foraging Habitat, Feeding Behavior, and Growth Abstract -- Observations of free-ranging sympatric bull trout Salvelinus confluentus and nonnative brook trout S. fontinalis in two eastern Oregon headwater streams provided little evidence of habitat partitioning. Both species held focal feeding points in similar microhabitats and fed primarily from the water column rather than from the surface or benthos. In an instream experiment, 20 enclosures were assigned one of three treatments: two bull trout, four bull trout, or a mix of two bull trout and two brook trout. In the enclosures, macroinvertebrate drift was restricted and trout densities were elevated, creating an environment of reduced food and habitat resources. Under these conditions, there was no indication of a niche shift by bull trout; feeding behavior and habitat use by bull trout did not differ depending on the presence or absence of brook trout. Brook trout in the mixed-species treatment were the most aggressive, maintained dominance in 75% of the enclosures, and exhibited significantly higher growth than sympatric bull trout. However, the effects of intra-and interspecific interactions on bull trout growth were equivalent. Given the absence of resource partitioning and a niche shift by bull trout in the presence of brook trout (despite obvious interference interactions), we suggest that the displacement of bull trout by brook trout is likely when resources are scarce. Close

• 6. [Article] Oregon South Coast Estuaries: Hunter Creek, Pistol River, Chetco River, & Winchuck River Tidal Wetlands Assessment (2012-2015)

  Abstract -- Although tidal wetlands on the Oregon South Coast are limited in extent, they may be particularly valuable for a variety of wetland functions. This assessment combines the Brophy (2007) and ...

  Citation × Citation Citation Abstract Copy Title: Oregon South Coast Estuaries: Hunter Creek, Pistol River, Chetco River, & Winchuck River Tidal Wetlands Assessment (2012-2015) Abstract -- Although tidal wetlands on the Oregon South Coast are limited in extent, they may be particularly valuable for a variety of wetland functions. This assessment combines the Brophy (2007) and Adamus (2005) approaches to quantify the extent and causes of habitat loss and hydrogeomorphic changes in tidal wetlands of four Oregon South Coast Estuaries. The potential for restoring critical habitat and wetland functions is ranked using Ecological Prioritization Criteria (Brophy, 2007), while indicators of function, risk, and integrity are evaluated using scoring models from the Adamus (2005) Hydrogeomorphic (HGM) Rapid Assessment Method. The extent of inundation (head of tide) during King Tide conditions was observed and documented by staff and volunteers. Field measurements of salinity concentrations and stratification during high and low flow were tabulated. The historic aerial photo record was examined to detect channel migration, floodplain re-vegetation, and human-caused alterations. Related studies were combined with these observations to provide a summary of estuary hydrology, sedimentation, and channel stability related to wetland establishment and loss in each of the four estuaries. Ecological priority scores (Brophy, 2007) varied with wetland size, tidal channel condition, connectivity, and diversity of vegetation classes. Wetlands were categorized as restoration or conservation types, and priority ranks for wetlands were depicted on orthophoto base maps. Tidal wetlands and nearby floodplain wetlands in a variety of geomorphic settings were surveyed using the HGM protocol, including one “reference” and one restoration site . The HGM survey scores 55 indicators, including botanical transects, used to rank wetland functions (calculated by indicator scoring models). Risks to wetlands include human disturbances in close proximity to the wetlands and floodplains, resulting from the narrow valley floors in this tectonically active region. Wetland integrity is threatened by a surprising large proportion of non-native species in the botanical transects, 40%. Wetland indicators that scored low, and could be restored or enhanced, are discussed in a restoration considerations narrative. Wetland descriptions include lists of plant species, grouped by wetland status, native/non-native, and perennial/annual persistence. In addition to the HGM scores, an analysis of cover and diversity of all plant species in plots, off-transect species diversity, and waterfowl food distribution was completed using a wetland vegetation database developed for the Oregon South Coast. Title: Oregon South Coast Estuaries: Hunter Creek, Pistol River, Chetco River, & Winchuck River Tidal Wetlands Assessment (2012-2015) Abstract -- Although tidal wetlands on the Oregon South Coast are limited in extent, they may be particularly valuable for a variety of wetland functions. This assessment combines the Brophy (2007) and Adamus (2005) approaches to quantify the extent and causes of habitat loss and hydrogeomorphic changes in tidal wetlands of four Oregon South Coast Estuaries. The potential for restoring critical habitat and wetland functions is ranked using Ecological Prioritization Criteria (Brophy, 2007), while indicators of function, risk, and integrity are evaluated using scoring models from the Adamus (2005) Hydrogeomorphic (HGM) Rapid Assessment Method. The extent of inundation (head of tide) during King Tide conditions was observed and documented by staff and volunteers. Field measurements of salinity concentrations and stratification during high and low flow were tabulated. The historic aerial photo record was examined to detect channel migration, floodplain re-vegetation, and human-caused alterations. Related studies were combined with these observations to provide a summary of estuary hydrology, sedimentation, and channel stability related to wetland establishment and loss in each of the four estuaries. Ecological priority scores (Brophy, 2007) varied with wetland size, tidal channel condition, connectivity, and diversity of vegetation classes. Wetlands were categorized as restoration or conservation types, and priority ranks for wetlands were depicted on orthophoto base maps. Tidal wetlands and nearby floodplain wetlands in a variety of geomorphic settings were surveyed using the HGM protocol, including one “reference” and one restoration site . The HGM survey scores 55 indicators, including botanical transects, used to rank wetland functions (calculated by indicator scoring models). Risks to wetlands include human disturbances in close proximity to the wetlands and floodplains, resulting from the narrow valley floors in this tectonically active region. Wetland integrity is threatened by a surprising large proportion of non-native species in the botanical transects, 40%. Wetland indicators that scored low, and could be restored or enhanced, are discussed in a restoration considerations narrative. Wetland descriptions include lists of plant species, grouped by wetland status, native/non-native, and perennial/annual persistence. In addition to the HGM scores, an analysis of cover and diversity of all plant species in plots, off-transect species diversity, and waterfowl food distribution was completed using a wetland vegetation database developed for the Oregon South Coast. Close

• 7. [Article] Willamette Biological Opinion Hatchery Research 2010 Annual Report

  Abstract -- Task 1.1: Distribution, Abundance, and Proportion of Hatchery and Natural-Origin Chinook Salmon: Counts of spring Chinook redds were similar in 2010 compared to the 2002–2009 averages for the ...

  Citation × Citation Citation Abstract Copy Title: Willamette Biological Opinion Hatchery Research 2010 Annual Report Abstract -- Task 1.1: Distribution, Abundance, and Proportion of Hatchery and Natural-Origin Chinook Salmon: Counts of spring Chinook redds were similar in 2010 compared to the 2002–2009 averages for the Middle Fork Willamette, McKenzie and the North Santiam rivers and significantly higher in the South Santiam River Preliminary analyses indicate that the proportions of hatchery fish recovered as carcasses from the spawning grounds varied significantly among all four surveyed sub-basins (South Santiam > M. Fork Willamette > North Santiam > McKenzie) Task 1.2: Monitor fin-clipped & unclipped fish passing Leaburg and Upper Bennett dams. Adult fish passage at Leaburg and Upper Bennett dams was continuously monitored in 2010. We estimated that 2,696 spring Chinook (52% unclipped) passed above Leaburg Dam and 5,956 passed above upper Bennett Dam (14% unclipped). Passage at Leaburg Dam of fin-clipped fish was strongly bimodal with peaks in June (coincident with passage of the majority of unclipped fish) and September (coincident with a smaller proportion of unclipped fish). This bimodal peak suggests that hatchery fish might be removed in September to reduce the proportion of hatchery origin spawners while simultaneously reducing the impacts of handling wild fish. Task 2.1: Collection, spawn timing, and Hatchery/Wild (H/W ) composition for broodstock management. Collection, spawn timing, and H/W composition for broodstock management were successfully monitored at all facilities in 2010. Task 2.2: Determine Survival of Outplanted Fish and Abundance of Spawners. Patterns of pre-spawning mortality were similar to results in 2009 with mortality below project dams significantly higher than that above project dams. We did not detect significant differences in mortality between clipped and unclipped spring Chinook. In comparisons of pre-spawning mortality among sub-basins above project dams, pre-spawning mortality was uniformly low in the Breitenbush and N. Santiam above Detroit, S. Santiam above Foster, and in the S. Fork McKenzie. Pre-spawning mortality was uniformly higher above project dams in the N. Fork Mid. Fork Willamette, Fall Creek and the Little N. Fork Santiam. No comprehensive surveys were conducted in the Middle Fork Willamette. Task 3.1: Determine the extent of summer steelhead reproduction in the wild: We developed a formal study plan to analyze and interpret genetic results from a collection of 299 tissue samples from unclipped juvenile steelhead at Willamette Falls, five from the mainstem Willamette River, and two from the South Santiam River in 2010 in addition to a single sample from an unclipped adult steelhead at the Minto fish collection facility. Samples were preserved 7 and cataloged and then shipped to the NOAA Fisheries Manchester, Washington (WA) laboratory for analysis. Task 3.2: Evaluate release strategies for summer steelhead to increase migration and reduce impacts on wild fish. Study plans to evaluate advantages and disadvantages of volitional release strategies were completed and presented in the 2009 annual report to USACE (Cannon et al. 2010). Funding to process the tissue samples was not available in 2010, and no progress was made in executing the proposed work. Title: Willamette Biological Opinion Hatchery Research 2010 Annual Report Abstract -- Task 1.1: Distribution, Abundance, and Proportion of Hatchery and Natural-Origin Chinook Salmon: Counts of spring Chinook redds were similar in 2010 compared to the 2002–2009 averages for the Middle Fork Willamette, McKenzie and the North Santiam rivers and significantly higher in the South Santiam River Preliminary analyses indicate that the proportions of hatchery fish recovered as carcasses from the spawning grounds varied significantly among all four surveyed sub-basins (South Santiam > M. Fork Willamette > North Santiam > McKenzie) Task 1.2: Monitor fin-clipped & unclipped fish passing Leaburg and Upper Bennett dams. Adult fish passage at Leaburg and Upper Bennett dams was continuously monitored in 2010. We estimated that 2,696 spring Chinook (52% unclipped) passed above Leaburg Dam and 5,956 passed above upper Bennett Dam (14% unclipped). Passage at Leaburg Dam of fin-clipped fish was strongly bimodal with peaks in June (coincident with passage of the majority of unclipped fish) and September (coincident with a smaller proportion of unclipped fish). This bimodal peak suggests that hatchery fish might be removed in September to reduce the proportion of hatchery origin spawners while simultaneously reducing the impacts of handling wild fish. Task 2.1: Collection, spawn timing, and Hatchery/Wild (H/W ) composition for broodstock management. Collection, spawn timing, and H/W composition for broodstock management were successfully monitored at all facilities in 2010. Task 2.2: Determine Survival of Outplanted Fish and Abundance of Spawners. Patterns of pre-spawning mortality were similar to results in 2009 with mortality below project dams significantly higher than that above project dams. We did not detect significant differences in mortality between clipped and unclipped spring Chinook. In comparisons of pre-spawning mortality among sub-basins above project dams, pre-spawning mortality was uniformly low in the Breitenbush and N. Santiam above Detroit, S. Santiam above Foster, and in the S. Fork McKenzie. Pre-spawning mortality was uniformly higher above project dams in the N. Fork Mid. Fork Willamette, Fall Creek and the Little N. Fork Santiam. No comprehensive surveys were conducted in the Middle Fork Willamette. Task 3.1: Determine the extent of summer steelhead reproduction in the wild: We developed a formal study plan to analyze and interpret genetic results from a collection of 299 tissue samples from unclipped juvenile steelhead at Willamette Falls, five from the mainstem Willamette River, and two from the South Santiam River in 2010 in addition to a single sample from an unclipped adult steelhead at the Minto fish collection facility. Samples were preserved 7 and cataloged and then shipped to the NOAA Fisheries Manchester, Washington (WA) laboratory for analysis. Task 3.2: Evaluate release strategies for summer steelhead to increase migration and reduce impacts on wild fish. Study plans to evaluate advantages and disadvantages of volitional release strategies were completed and presented in the 2009 annual report to USACE (Cannon et al. 2010). Funding to process the tissue samples was not available in 2010, and no progress was made in executing the proposed work. Close

• 8. [Article] Factors that Influence Evolutionary Significant Unit Boundaries and Status Assessment in a Highly Polymorphic Species, Oncorhynchus mykiss, in the Columbia Basin

  Abstract -- The species Oncorhynchus mykiss expresses a complex array of life histories across much of its range as well as considerable geographic variation. Several subspecies have been proposed (Behnke ...

  Citation × Citation Citation Abstract Copy Title: Factors that Influence Evolutionary Significant Unit Boundaries and Status Assessment in a Highly Polymorphic Species, Oncorhynchus mykiss, in the Columbia Basin Abstract -- The species Oncorhynchus mykiss expresses a complex array of life histories across much of its range as well as considerable geographic variation. Several subspecies have been proposed (Behnke 1992), although none of them are formally recognized. Two of the proposed subspecies in North America include both trout and steelhead life histories: O.m. irideus, or Coastal rainbow/steelhead, and O.m. gairdneri, or Inland redband/steelhead. A third subspecies that includes an anadromous life history occurs in Asia, while all other North American subspecies are entirely trout. In the Pacific Northwest, the boundary between the coastal and inland subspecies occurs in the Columbia Gorge, where the Columbia River cuts through the Cascade Mountain Range. The steelhead and trout life histories within these two subspecies are genetically more similar to each other than to fish with the same life history in the other subspecies, indicating that the different life histories within a geographic area share an evolutionary origin (Allendorf 1975). Recent molecular systematic surveys suggest that this proposed taxonomic model of North American 0. mykiss subspecies may be over simplified and inaccurate (Currens 1997, Busby et al. 1996, F. Utter, U. of Washington); however, it remains the available model until final revisions to the taxonomy are adopted. The NOAA Fisheries Service (NMFS) further divided 0. mykiss into multiple "Evolutionarily Significant Units" (ESUs)(Waples 1991, 56 FR 58612, Waples 1995) for listing consideration under the federal Endangered Species Act (ESA). The ESA considers "distinct" populations of taxonmnic species to be "species" eligible for legal protection (16 U.S.C. 1532[161). NMFS adopted the concept of ESUs to serve as distinct population segments in their ESA listing decisions, along with specific criteria for defining them. Evidence for whether or not rainbow trout and steelhead are in the same ESUs is presented in this report according to the criteria provided by NMFS policy (56 FR 58612). The U.S. Fish and Wildlife Service (USFWS) likewise recognizes "Distinct Population Segments" (DPSs) that may be listed under ESA. The agencies share jurisdiction over 0. mykiss for ESA decisions, with NMFS overseeing the anadromous steelhead and USFWS overseeing the freshwater trout. NMFS has described ESUs for all Northwest steelhead, whether they have been listed or not (Busby et al. 1996); however, the USFWS has not generally described DPSs for Northwest 0. mykiss trout. During the original coast-wide status review of steelhead conducted in the 1990s, the NMFS Biological Review Team concluded that, in general, 0. mykiss trout are part of steelhead ESUs in cases where the two forms are sympatric and have an opportunity to interbreed (Busby et al. 1996). The review team was less conclusive about whether trout above artificial barriers were part of the ESUs. Trout that are sympatric with steelhead were also included in the ESUs by NMFS in the final listing determinations, but they were not listed. The steelhead in five of the ESUs in the Pacific Northwest were listed, including the Lower Columbia (63 FR 13347), Willamette, Mid-Columbia (64 FR 14517), Upper Columbia and Snake ESUs (62 FR 43937), all of which are in the Columbia Basin. As a result of two recent court cases NMFS is now reexamming the biological relationship between trout and steelhead populations in the ESUs where steelhead are listed and is reassessing the extinction risk of the whole ESUs from the perspective of both life histories. First, the Hogan decision in Oregon concluded that the Services may describe distinct population segments for ESA listing, but once ESUs or DPSs are described, the Services cannot list only part of one of one of them (Alsea Valley Alliance v. Evans [161 F.Supp. 2d 1154, D. Oreg. 2001]). So if NMFS finds trout to be part of an ESU along with steelhead, the Service cannot assess the extinction risk of only the steelhead in the ESU or list only the steelhead. Second, lawsuits in California about non­anadromous 0. mykiss upstream of man-made barriers (mostly impassible dams) made a similar argument, stating that such populations are related to the steelhead populations below the barriers and should be included in the ESUs and listed (EDC v. Evans, SACV- 00-1212-AHS (EEA), United States District Court, C.D. California). The purpose of this report is to provide more detailed information about trout and steelhead in the Columbia Basin listed ESUs. This report will address two major issues. The first section provides information that will be used to review whether trout and steelhead populations are biologically part the same ESUs, as defined by NMFS criteria. The second section provides information that will be used to review the extinction risks of entire ESUs if trout are considered along with steelhead. A similar, separate report is being prepared for California ESUs where steelhead are listed. Title: Factors that Influence Evolutionary Significant Unit Boundaries and Status Assessment in a Highly Polymorphic Species, Oncorhynchus mykiss, in the Columbia Basin Abstract -- The species Oncorhynchus mykiss expresses a complex array of life histories across much of its range as well as considerable geographic variation. Several subspecies have been proposed (Behnke 1992), although none of them are formally recognized. Two of the proposed subspecies in North America include both trout and steelhead life histories: O.m. irideus, or Coastal rainbow/steelhead, and O.m. gairdneri, or Inland redband/steelhead. A third subspecies that includes an anadromous life history occurs in Asia, while all other North American subspecies are entirely trout. In the Pacific Northwest, the boundary between the coastal and inland subspecies occurs in the Columbia Gorge, where the Columbia River cuts through the Cascade Mountain Range. The steelhead and trout life histories within these two subspecies are genetically more similar to each other than to fish with the same life history in the other subspecies, indicating that the different life histories within a geographic area share an evolutionary origin (Allendorf 1975). Recent molecular systematic surveys suggest that this proposed taxonomic model of North American 0. mykiss subspecies may be over simplified and inaccurate (Currens 1997, Busby et al. 1996, F. Utter, U. of Washington); however, it remains the available model until final revisions to the taxonomy are adopted. The NOAA Fisheries Service (NMFS) further divided 0. mykiss into multiple "Evolutionarily Significant Units" (ESUs)(Waples 1991, 56 FR 58612, Waples 1995) for listing consideration under the federal Endangered Species Act (ESA). The ESA considers "distinct" populations of taxonmnic species to be "species" eligible for legal protection (16 U.S.C. 1532[161). NMFS adopted the concept of ESUs to serve as distinct population segments in their ESA listing decisions, along with specific criteria for defining them. Evidence for whether or not rainbow trout and steelhead are in the same ESUs is presented in this report according to the criteria provided by NMFS policy (56 FR 58612). The U.S. Fish and Wildlife Service (USFWS) likewise recognizes "Distinct Population Segments" (DPSs) that may be listed under ESA. The agencies share jurisdiction over 0. mykiss for ESA decisions, with NMFS overseeing the anadromous steelhead and USFWS overseeing the freshwater trout. NMFS has described ESUs for all Northwest steelhead, whether they have been listed or not (Busby et al. 1996); however, the USFWS has not generally described DPSs for Northwest 0. mykiss trout. During the original coast-wide status review of steelhead conducted in the 1990s, the NMFS Biological Review Team concluded that, in general, 0. mykiss trout are part of steelhead ESUs in cases where the two forms are sympatric and have an opportunity to interbreed (Busby et al. 1996). The review team was less conclusive about whether trout above artificial barriers were part of the ESUs. Trout that are sympatric with steelhead were also included in the ESUs by NMFS in the final listing determinations, but they were not listed. The steelhead in five of the ESUs in the Pacific Northwest were listed, including the Lower Columbia (63 FR 13347), Willamette, Mid-Columbia (64 FR 14517), Upper Columbia and Snake ESUs (62 FR 43937), all of which are in the Columbia Basin. As a result of two recent court cases NMFS is now reexamming the biological relationship between trout and steelhead populations in the ESUs where steelhead are listed and is reassessing the extinction risk of the whole ESUs from the perspective of both life histories. First, the Hogan decision in Oregon concluded that the Services may describe distinct population segments for ESA listing, but once ESUs or DPSs are described, the Services cannot list only part of one of one of them (Alsea Valley Alliance v. Evans [161 F.Supp. 2d 1154, D. Oreg. 2001]). So if NMFS finds trout to be part of an ESU along with steelhead, the Service cannot assess the extinction risk of only the steelhead in the ESU or list only the steelhead. Second, lawsuits in California about non­anadromous 0. mykiss upstream of man-made barriers (mostly impassible dams) made a similar argument, stating that such populations are related to the steelhead populations below the barriers and should be included in the ESUs and listed (EDC v. Evans, SACV- 00-1212-AHS (EEA), United States District Court, C.D. California). The purpose of this report is to provide more detailed information about trout and steelhead in the Columbia Basin listed ESUs. This report will address two major issues. The first section provides information that will be used to review whether trout and steelhead populations are biologically part the same ESUs, as defined by NMFS criteria. The second section provides information that will be used to review the extinction risks of entire ESUs if trout are considered along with steelhead. A similar, separate report is being prepared for California ESUs where steelhead are listed. Close

• 9. [Article] Fish Population Monitoring in the Middle Fork John Day River Intensively Monitored Watershed - Annual Technical Report 2008

  Abstract -- Within the Middle Fork John Day River IMW (MFJDR_IMW), several habitat factors have been identified as limiting for the recovery of summer steelhead. Degraded floodplain and channel structure, ...

  Citation × Citation Citation Abstract Copy Title: Fish Population Monitoring in the Middle Fork John Day River Intensively Monitored Watershed - Annual Technical Report 2008 Abstract -- Within the Middle Fork John Day River IMW (MFJDR_IMW), several habitat factors have been identified as limiting for the recovery of summer steelhead. Degraded floodplain and channel structure, altered sediment routing, altered hydrology, and water quality (temperature) are cited as limiting factors in the Draft Mid-Columbia Steelhead Recovery Plan (Carmichael 2008). Current and proposed restoration efforts for the MFJDR_IMW are anticipated to address these key limiting factors. In order to assess restoration effectiveness on focal fish species, monitoring and analyses must emphasize population level spatial scales. Fish population monitoring for the MFDJR_IMW includes evaluating summer steelhead and spring Chinook population productivity, survival, and abundance. While abundance is an important metric for population assessments, survival and production will also be key indicators of population responses to planned restoration activities. Freshwater survival is assessed from the parr to smolt life stages (parr to smolt survival) and ocean or out-of-basin survival is estimated as a smolt to adult return ratio (SAR). Freshwater productivity is assessed as smolts produced for constructed redds (smolts/redd). Originator: ODFW, Eastern Oregon Fish Research (EOFR). Funded by Oregon Watershed Enhancement Board (OWEB). Title: Fish Population Monitoring in the Middle Fork John Day River Intensively Monitored Watershed - Annual Technical Report 2008 Abstract -- Within the Middle Fork John Day River IMW (MFJDR_IMW), several habitat factors have been identified as limiting for the recovery of summer steelhead. Degraded floodplain and channel structure, altered sediment routing, altered hydrology, and water quality (temperature) are cited as limiting factors in the Draft Mid-Columbia Steelhead Recovery Plan (Carmichael 2008). Current and proposed restoration efforts for the MFJDR_IMW are anticipated to address these key limiting factors. In order to assess restoration effectiveness on focal fish species, monitoring and analyses must emphasize population level spatial scales. Fish population monitoring for the MFDJR_IMW includes evaluating summer steelhead and spring Chinook population productivity, survival, and abundance. While abundance is an important metric for population assessments, survival and production will also be key indicators of population responses to planned restoration activities. Freshwater survival is assessed from the parr to smolt life stages (parr to smolt survival) and ocean or out-of-basin survival is estimated as a smolt to adult return ratio (SAR). Freshwater productivity is assessed as smolts produced for constructed redds (smolts/redd). Originator: ODFW, Eastern Oregon Fish Research (EOFR). Funded by Oregon Watershed Enhancement Board (OWEB). Close

• 10. [Article] Fish Population Monitoring in the Middle Fork John Day River Intensively Monitored Watershed - Annual Technical Report 2009

  Abstract -- Within the Middle Fork John Day River IMW (MFJDR_IMW), several habitat factors have been identified as limiting for the recovery of summer steelhead. Degraded floodplain and channel structure, ...

  Citation × Citation Citation Abstract Copy Title: Fish Population Monitoring in the Middle Fork John Day River Intensively Monitored Watershed - Annual Technical Report 2009 Abstract -- Within the Middle Fork John Day River IMW (MFJDR_IMW), several habitat factors have been identified as limiting for the recovery of summer steelhead. Degraded floodplain and channel structure, altered sediment routing, altered hydrology, and water quality (temperature) are cited as limiting factors in the Draft Mid-Columbia Steelhead Recovery Plan (Carmichael 2008). Current and proposed restoration efforts for the MFJDR_IMW are anticipated to address these key limiting factors. In order to assess restoration effectiveness on focal fish species, monitoring and analyses must emphasize population level spatial scales. Fish population monitoring for the MFDJR_IMW includes evaluating summer steelhead and spring Chinook population productivity, survival, and abundance. While abundance is an important metric for population assessments, survival and production will also be key indicators of population responses to planned restoration activities. Freshwater survival is assessed from the parr to smolt life stages (parr to smolt survival) and ocean or out-of-basin survival is estimated as a smolt to adult return ratio (SAR). Freshwater productivity is assessed as smolts produced for constructed redds (smolts/redd). Originator: ODFW, Eastern Oregon Fish Research (EOFR). Funded by Oregon Watershed Enhancement Board (OWEB). Title: Fish Population Monitoring in the Middle Fork John Day River Intensively Monitored Watershed - Annual Technical Report 2009 Abstract -- Within the Middle Fork John Day River IMW (MFJDR_IMW), several habitat factors have been identified as limiting for the recovery of summer steelhead. Degraded floodplain and channel structure, altered sediment routing, altered hydrology, and water quality (temperature) are cited as limiting factors in the Draft Mid-Columbia Steelhead Recovery Plan (Carmichael 2008). Current and proposed restoration efforts for the MFJDR_IMW are anticipated to address these key limiting factors. In order to assess restoration effectiveness on focal fish species, monitoring and analyses must emphasize population level spatial scales. Fish population monitoring for the MFDJR_IMW includes evaluating summer steelhead and spring Chinook population productivity, survival, and abundance. While abundance is an important metric for population assessments, survival and production will also be key indicators of population responses to planned restoration activities. Freshwater survival is assessed from the parr to smolt life stages (parr to smolt survival) and ocean or out-of-basin survival is estimated as a smolt to adult return ratio (SAR). Freshwater productivity is assessed as smolts produced for constructed redds (smolts/redd). Originator: ODFW, Eastern Oregon Fish Research (EOFR). Funded by Oregon Watershed Enhancement Board (OWEB). Close