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• 1. [Article] Juvenile Rockfish (Sebastes spp.) Community Composition and Habitat use of Yaquina Bay, Oregon

  Estuaries, which provide viable habitat for a plethora of fish and invertebrate species, are being increasingly impacted by anthropogenic and natural forces. Estuaries are important nursery habitat for ...

  Citation × Citation Citation Abstract Copy Title: Juvenile Rockfish (Sebastes spp.) Community Composition and Habitat use of Yaquina Bay, Oregon Author: Lindsley, Amy J. Estuaries, which provide viable habitat for a plethora of fish and invertebrate species, are being increasingly impacted by anthropogenic and natural forces. Estuaries are important nursery habitat for young-of-the-year (YOY) Pacific rockfish (Sebastes spp.). Yaquina Bay, a marine-dominated estuary on the central Oregon Coast, served as a study site for the estuarine use of juvenile rockfishes, and large numbers of juvenile rockfish have been captured in this bay. Nursery habitats must provide rearing habitat, adequate food resources and refuge. A vital but lacking connection in our understanding of estuaries as nursery habitat is how rockfishes use the different microhabitats within an estuarine ecosystem. As habitats structure biotic communities, determining the ecological requirements for juvenile rockfish habitats that minimize mortality, maximize growth and increase population numbers will assist managers and biologists in managing and protecting critical high-quality nursery areas. This study provides insight into Oregon rockfish life history, evaluating the spatial and temporal use of estuarine nursery habitat by juvenile rockfishes. The primary objectives were to (1) determine which species of rockfish utilize Yaquina Bay, (2) determine seasonal variations in abundance, and (3) assess the utilization of natural (eelgrass beds, Zostera marina) versus anthropogenic (piers) estuarine habitat. I conducted a mark-recapture study of juvenile rockfishes to begin to elucidate how these species may be using different habitats in the bay. This study provides evidence for the presence of previously undocumented rockfish species, the overwinter persistence of juvenile rockfish in the estuary, some degree of site fidelity, and apparent minimal movement of juvenile rockfish in the Yaquina Bay estuary during the period of this study, as well as a shift in rockfish community dominance from S. melanops to S. maliger and S. caurinus. The survival and recapture of juveniles in both natural (Z. marina) and anthropogenic (piers) habitat demonstrates rockfishes’ successful use of multiple Yaquina Bay habitat types as nursery grounds year-round. There is seasonal variability in rockfish use of the anthropogenic and natural habitat, with the anthropogenic habitats having an overall higher capture rate and a higher occurrence of larger rockfish. All eight species S. melanops, S. maliger, S. caurinus, S. paucispinis, S. flavidus, S. nebulosus, S. pinniger and S. auriculatus are present in the natural, Z. marina habitat. Sebastes pinniger and S. auriculatus are absent from anthropogenic, pier habitat. The implications of determining habitat parameters, community interactions, seasonal changes of the fish community, and ecosystem mechanisms may be invaluable to support further recreational and commercial fishing and help sustain or increase adult populations. My findings present a significant contribution towards the proper management and conservation of essential habitat for rockfish, a group of species with high commercial value and substantial recreational harvest. Title: Juvenile Rockfish (Sebastes spp.) Community Composition and Habitat use of Yaquina Bay, Oregon Author: Lindsley, Amy J. Estuaries, which provide viable habitat for a plethora of fish and invertebrate species, are being increasingly impacted by anthropogenic and natural forces. Estuaries are important nursery habitat for young-of-the-year (YOY) Pacific rockfish (Sebastes spp.). Yaquina Bay, a marine-dominated estuary on the central Oregon Coast, served as a study site for the estuarine use of juvenile rockfishes, and large numbers of juvenile rockfish have been captured in this bay. Nursery habitats must provide rearing habitat, adequate food resources and refuge. A vital but lacking connection in our understanding of estuaries as nursery habitat is how rockfishes use the different microhabitats within an estuarine ecosystem. As habitats structure biotic communities, determining the ecological requirements for juvenile rockfish habitats that minimize mortality, maximize growth and increase population numbers will assist managers and biologists in managing and protecting critical high-quality nursery areas. This study provides insight into Oregon rockfish life history, evaluating the spatial and temporal use of estuarine nursery habitat by juvenile rockfishes. The primary objectives were to (1) determine which species of rockfish utilize Yaquina Bay, (2) determine seasonal variations in abundance, and (3) assess the utilization of natural (eelgrass beds, Zostera marina) versus anthropogenic (piers) estuarine habitat. I conducted a mark-recapture study of juvenile rockfishes to begin to elucidate how these species may be using different habitats in the bay. This study provides evidence for the presence of previously undocumented rockfish species, the overwinter persistence of juvenile rockfish in the estuary, some degree of site fidelity, and apparent minimal movement of juvenile rockfish in the Yaquina Bay estuary during the period of this study, as well as a shift in rockfish community dominance from S. melanops to S. maliger and S. caurinus. The survival and recapture of juveniles in both natural (Z. marina) and anthropogenic (piers) habitat demonstrates rockfishes’ successful use of multiple Yaquina Bay habitat types as nursery grounds year-round. There is seasonal variability in rockfish use of the anthropogenic and natural habitat, with the anthropogenic habitats having an overall higher capture rate and a higher occurrence of larger rockfish. All eight species S. melanops, S. maliger, S. caurinus, S. paucispinis, S. flavidus, S. nebulosus, S. pinniger and S. auriculatus are present in the natural, Z. marina habitat. Sebastes pinniger and S. auriculatus are absent from anthropogenic, pier habitat. The implications of determining habitat parameters, community interactions, seasonal changes of the fish community, and ecosystem mechanisms may be invaluable to support further recreational and commercial fishing and help sustain or increase adult populations. My findings present a significant contribution towards the proper management and conservation of essential habitat for rockfish, a group of species with high commercial value and substantial recreational harvest. Close

• 2. [Article] Habitat parameters associated with the distribution of seven willow species on a stream in southeastern Oregon

  Thirteen different habitat parameters were measured either quantitatively or qualitatively around seven different Salix (willow) species on a defined reach of stream on the southwestern slope of Steens ...

  Citation × Citation Citation Abstract Copy Title: Habitat parameters associated with the distribution of seven willow species on a stream in southeastern Oregon Author: Gilbert, Griffith J. Thirteen different habitat parameters were measured either quantitatively or qualitatively around seven different Salix (willow) species on a defined reach of stream on the southwestern slope of Steens Mountain in southeastern Oregon in order to both broaden the current information base of riparian ecology and inform future willow plantings aimed at improving riparian habitat. Willow species included in the research were: S. lemmonii (Lemmon willow), S. scouleriana (Scouler willow), S. boothii (Booth willow), S. geyeriana (Geyer willow), S. exigua (coyote willow), S. lasiandra (whiplash willow), and S. lutea (yellow willow). The habitat parameters measured were: height and distance of willow individual from stream channel bankfull elevation, stream channel slope, entrenchment ratio, width-to-depth ratio, watershed elevation, valley azimuth, valley width, soil rock size distribution, soil texture, and winter air temperature. Logistic regression models were built to describe probabilities of occurrence for five out of the seven willow species based on the habitat data collected. Multi-response permutation procedures were performed to describe differences between respective willow habitats. Booth and Geyer willow habitats were best described by watershed elevation as these species dominated the research stream channel’s upper reaches. Whiplash willow habitat was best described by stream channel entrenchment and width-to-depth ratio as this species occurred, on average, in habitats with high stream channel entrenchment and width-to-depth ratios. Specifically, the odds of whiplash willow occurrence are expected to increase by 17% with a unit increase in width-to-depth ratio. Yellow willow habitat was best described by watershed elevation and stream channel width-to-depth ratio as this species occurred only on the lower reaches of the research stream channel. Lemmon willow habitat was best described by interactions between watershed elevation and valley azimuth and between stream channel slope and width-to-depth ratio as the first of these interactions worked to create air temperatures favorable for species occurrence. Coyote willow habitat was best described by stream channel slope, entrenchment, and width-todepth ratio as this species occurred, on average, in habitats with combinations of stream channel slopes, entrenchment, and width-to-depth ratios able to promote frequent streambank rejuvenation. Scouler willow habitat was best described by stream channel entrenchment ratio, as well as interactions between watershed elevation and valley azimuth and between stream channel slope and width-to-depth ratio. Specifically, the odds of Scouler willow occurrence are expected to decrease by 89% with a unit increase in entrenchment ratio. Scouler willow, on average, occurs in habitats with air temperature dynamics similar to those described above for Lemmon willow, and on hydraulically efficient stream channels with low entrenchment and width-to-depth ratios. Title: Habitat parameters associated with the distribution of seven willow species on a stream in southeastern Oregon Author: Gilbert, Griffith J. Thirteen different habitat parameters were measured either quantitatively or qualitatively around seven different Salix (willow) species on a defined reach of stream on the southwestern slope of Steens Mountain in southeastern Oregon in order to both broaden the current information base of riparian ecology and inform future willow plantings aimed at improving riparian habitat. Willow species included in the research were: S. lemmonii (Lemmon willow), S. scouleriana (Scouler willow), S. boothii (Booth willow), S. geyeriana (Geyer willow), S. exigua (coyote willow), S. lasiandra (whiplash willow), and S. lutea (yellow willow). The habitat parameters measured were: height and distance of willow individual from stream channel bankfull elevation, stream channel slope, entrenchment ratio, width-to-depth ratio, watershed elevation, valley azimuth, valley width, soil rock size distribution, soil texture, and winter air temperature. Logistic regression models were built to describe probabilities of occurrence for five out of the seven willow species based on the habitat data collected. Multi-response permutation procedures were performed to describe differences between respective willow habitats. Booth and Geyer willow habitats were best described by watershed elevation as these species dominated the research stream channel’s upper reaches. Whiplash willow habitat was best described by stream channel entrenchment and width-to-depth ratio as this species occurred, on average, in habitats with high stream channel entrenchment and width-to-depth ratios. Specifically, the odds of whiplash willow occurrence are expected to increase by 17% with a unit increase in width-to-depth ratio. Yellow willow habitat was best described by watershed elevation and stream channel width-to-depth ratio as this species occurred only on the lower reaches of the research stream channel. Lemmon willow habitat was best described by interactions between watershed elevation and valley azimuth and between stream channel slope and width-to-depth ratio as the first of these interactions worked to create air temperatures favorable for species occurrence. Coyote willow habitat was best described by stream channel slope, entrenchment, and width-todepth ratio as this species occurred, on average, in habitats with combinations of stream channel slopes, entrenchment, and width-to-depth ratios able to promote frequent streambank rejuvenation. Scouler willow habitat was best described by stream channel entrenchment ratio, as well as interactions between watershed elevation and valley azimuth and between stream channel slope and width-to-depth ratio. Specifically, the odds of Scouler willow occurrence are expected to decrease by 89% with a unit increase in entrenchment ratio. Scouler willow, on average, occurs in habitats with air temperature dynamics similar to those described above for Lemmon willow, and on hydraulically efficient stream channels with low entrenchment and width-to-depth ratios. Close

• 3. [Article] Growth rates and species composition of juvenile rockfish (Sebastes spp.) in Oregon’s nearshore and estuarine habitats

  Identification of critical habitat for all life stages of commercially exploited fish populations is critical for effective management. Despite a clear need for basic biological information on juvenile ...

  Citation × Citation Citation Abstract Copy Title: Growth rates and species composition of juvenile rockfish (Sebastes spp.) in Oregon’s nearshore and estuarine habitats Author: Gallagher, M. Brett Identification of critical habitat for all life stages of commercially exploited fish populations is critical for effective management. Despite a clear need for basic biological information on juvenile rockfish life history, there have been very few efforts to describe distribution and habitat of this life stage, particularly along the Oregon coast. This study investigated the relationships between habitat-type, species composition and growth of juvenile rockfishes following settlement into nearshore reefs and estuaries. By using a four-level classification system to prioritize and identify Essential Fish Habitat, results of this study refine scientific knowledge of EFH for Oregon’s nearshore rockfish species. Four species of rockfish were collected during the summers of 2004 and 2005. blue rockfish (S. mystinus), black rockfish (S. melanops), yellowtail rockfish (S. flavidus) and widow rockfish (S. entomelas). Nearshore hand net samples were dominated by blue rockfish. Estuary samples were almost exclusively black rockfish, indicating that this species is common in Yaquina Bay. No black rockfish were collected from our nearshore sampling sites in either 2004 or 2005, although this habitat is listed as common for juveniles of this species. Identification of critical habitat for all life stages of commercially exploited fish populations is critical for effective management. Despite a clear need for basic biological information on juvenile rockfish life history, there have been very few efforts to describe distribution and habitat of this life stage, particularly along the Oregon coast. This study investigated the relationships between habitat-type, species composition and growth of juvenile rockfishes following settlement into nearshore reefs and estuaries. By using a four-level classification system to prioritize and identify Essential Fish Habitat, results of this study refine scientific knowledge of EFH for Oregon’s nearshore rockfish species. Four species of rockfish were collected during the summers of 2004 and 2005. blue rockfish (S. mystinus), black rockfish (S. melanops), yellowtail rockfish (S. flavidus) and widow rockfish (S. entomelas). Nearshore hand net samples were dominated by blue rockfish. Estuary samples were almost exclusively black rockfish, indicating that this species is common in Yaquina Bay. No black rockfish were collected from our nearshore sampling sites in either 2004 or 2005, although this habitat is listed as common for juveniles of this species. Blue rockfish settlement was detected from April thru July in 2004, and from May thru June in 2005. Peak settlement timing was in June of both years. Settlement for black rockfish ranged from March thru July both years, with peak settlement timing occurring in mid-May. Yellowtail and widow rockfish juveniles were rarely encountered, with settlement occurring in April and July respectively. Abundance, as estimated from catch per unit effort (CPUE) calculations, varied among years and habitats. Black rockfish were more abundant in 2004 than in 2005. Some of the highest densities were found around pilings, docks and other anthropogenic structures: CPUE decreased within rock, eelgrass, and sand habitats respectively. Growth was not significantly different among habitats for either black or blue rockfish. Growth rate differences were not significant among years for either black or blue rockfish. However, growth differences were significant between species (black 0.50 mm d-1 and blue .54 mm d-1 (two sample-t test, T stat = -3.19, df = 133 P-value <.002). Additionally, this thesis presents a tank validation experiment that investigated the validity of traps as a quantitative measure of habitat quality. This trap validation study showed that as habitat complexity increases, trap efficiency decreases. Trap attractiveness is an important source of bias when used for juvenile rockfish abundance estimation. This study demonstrates abundance estimates may be inflated in areas of low habitat complexity in the natural environment, or under-estimate the relative abundance of rockfishes within complex habitats. This study identifies estuaries as Essential Fish Habitat for black rockfish juveniles along the central Oregon coast, and nearshore reef as EFH for blue rockfish juveniles. Results of this study also provide specific information on spatial and temporal patterns of recruitment, habitat selection and growth, previously unknown for Oregon's nearshore Sebastes species. Title: Growth rates and species composition of juvenile rockfish (Sebastes spp.) in Oregon’s nearshore and estuarine habitats Author: Gallagher, M. Brett Identification of critical habitat for all life stages of commercially exploited fish populations is critical for effective management. Despite a clear need for basic biological information on juvenile rockfish life history, there have been very few efforts to describe distribution and habitat of this life stage, particularly along the Oregon coast. This study investigated the relationships between habitat-type, species composition and growth of juvenile rockfishes following settlement into nearshore reefs and estuaries. By using a four-level classification system to prioritize and identify Essential Fish Habitat, results of this study refine scientific knowledge of EFH for Oregon’s nearshore rockfish species. Four species of rockfish were collected during the summers of 2004 and 2005. blue rockfish (S. mystinus), black rockfish (S. melanops), yellowtail rockfish (S. flavidus) and widow rockfish (S. entomelas). Nearshore hand net samples were dominated by blue rockfish. Estuary samples were almost exclusively black rockfish, indicating that this species is common in Yaquina Bay. No black rockfish were collected from our nearshore sampling sites in either 2004 or 2005, although this habitat is listed as common for juveniles of this species. Identification of critical habitat for all life stages of commercially exploited fish populations is critical for effective management. Despite a clear need for basic biological information on juvenile rockfish life history, there have been very few efforts to describe distribution and habitat of this life stage, particularly along the Oregon coast. This study investigated the relationships between habitat-type, species composition and growth of juvenile rockfishes following settlement into nearshore reefs and estuaries. By using a four-level classification system to prioritize and identify Essential Fish Habitat, results of this study refine scientific knowledge of EFH for Oregon’s nearshore rockfish species. Four species of rockfish were collected during the summers of 2004 and 2005. blue rockfish (S. mystinus), black rockfish (S. melanops), yellowtail rockfish (S. flavidus) and widow rockfish (S. entomelas). Nearshore hand net samples were dominated by blue rockfish. Estuary samples were almost exclusively black rockfish, indicating that this species is common in Yaquina Bay. No black rockfish were collected from our nearshore sampling sites in either 2004 or 2005, although this habitat is listed as common for juveniles of this species. Blue rockfish settlement was detected from April thru July in 2004, and from May thru June in 2005. Peak settlement timing was in June of both years. Settlement for black rockfish ranged from March thru July both years, with peak settlement timing occurring in mid-May. Yellowtail and widow rockfish juveniles were rarely encountered, with settlement occurring in April and July respectively. Abundance, as estimated from catch per unit effort (CPUE) calculations, varied among years and habitats. Black rockfish were more abundant in 2004 than in 2005. Some of the highest densities were found around pilings, docks and other anthropogenic structures: CPUE decreased within rock, eelgrass, and sand habitats respectively. Growth was not significantly different among habitats for either black or blue rockfish. Growth rate differences were not significant among years for either black or blue rockfish. However, growth differences were significant between species (black 0.50 mm d-1 and blue .54 mm d-1 (two sample-t test, T stat = -3.19, df = 133 P-value <.002). Additionally, this thesis presents a tank validation experiment that investigated the validity of traps as a quantitative measure of habitat quality. This trap validation study showed that as habitat complexity increases, trap efficiency decreases. Trap attractiveness is an important source of bias when used for juvenile rockfish abundance estimation. This study demonstrates abundance estimates may be inflated in areas of low habitat complexity in the natural environment, or under-estimate the relative abundance of rockfishes within complex habitats. This study identifies estuaries as Essential Fish Habitat for black rockfish juveniles along the central Oregon coast, and nearshore reef as EFH for blue rockfish juveniles. Results of this study also provide specific information on spatial and temporal patterns of recruitment, habitat selection and growth, previously unknown for Oregon's nearshore Sebastes species. Close

• 4. [Article] The use of remote sensing for characterizing forests in wildlife habitat modeling

  Spatially explicit maps of habitat relationships have proven to be valuable tools for conservation and management applications including evaluating how and which species may be impacted by large scale ...

  Citation × Citation Citation Abstract Copy Title: The use of remote sensing for characterizing forests in wildlife habitat modeling Author: Vogeler, Jody C. Spatially explicit maps of habitat relationships have proven to be valuable tools for conservation and management applications including evaluating how and which species may be impacted by large scale climate change, ongoing fragmentation of habitat, and local land-use practices. Studies have turned to remote sensing datasets as a way to characterize vegetation for the examination of habitat selection and for mapping realized relationships across the landscape. Although the use of remote sensing in wildlife studies has increased in recent years, the use of these datasets is still limited and some data sources and methods are yet to be explored. The overall goal of this dissertation was to look at the state of the wildlife ecology discipline in the use of geospatial data for habitat mapping, and to advance this area through the fusion of remote sensing tools for the mapping of previously difficult to characterize forest metrics for inclusion in avian cavity-nester habitat models. Chapter 2 reviewed over 60 years of selected wildlife literature to examine the wildlife ecology disciple through historic trends and recent advances in the use of remote sensing for habitat characterization focusing on aspects of scale and the use of available technology. We discuss commonly used remote sensing data sources, point out recent advances in the use of geospatial data for characterizing forest wildlife habitat (the use of lidar data and the creation of spatially explicit habitat prediction maps), and provide future suggestions for increased utilization of available datasets (secondary lidar metrics and time series Landsat data). In chapters 3 and 4 we explored the use of remote sensing for characterizing forest components previously difficult to map across landscapes at scales relevant to local wildlife habitat selection. Chapter 3 found promise in the fusion of lidar structure and Landsat time series disturbance products in the modeling and mapping of post-fire snag and shrub distributions at fine scales and at size/cover thresholds relevant for habitat mapping applications for many wildlife species. The study was conducted within the 2003 B&B Fire Complex in central Oregon. Using 164 field calibration plots and remote sensing predictors, we modeled the presence/absence of snag classes (dbh ≥40cm, ≥50cm, and ≥75cm) and woody shrub cover resulting in 10m output predictive grid maps. Remote sensing predictors included various lidar structure and topography variables and Landsat time series products representing the pre-fire forest, disturbance magnitude, and current forest conditions. We were able to model and map all habitat metrics with acceptable predictive performance and low-moderate errors. The utility of these snag and shrub metrics for representing important nesting habitat features for a cavity-nesting species of conservation concern, the Lewis's Woodpecker (Melanerpes lewis), was demonstrated in Chapter 4. We were able to model nesting habitat with good accuracies according to multiple performance measures and then map realized relationships for this species of conservation concern in an identified source habitat type, providing a potential resource for local scale conservation and management efforts and adding to the regional knowledge of habitat selection for the Lewis's Woodpecker. To our knowledge, these chapters represent first attempts to fuse lidar and time series Landsat disturbance metrics in a post-fire landscape and for the mapping of snag and shrub distributions at scales relevant to avian cavity nesting habitat. Title: The use of remote sensing for characterizing forests in wildlife habitat modeling Author: Vogeler, Jody C. Spatially explicit maps of habitat relationships have proven to be valuable tools for conservation and management applications including evaluating how and which species may be impacted by large scale climate change, ongoing fragmentation of habitat, and local land-use practices. Studies have turned to remote sensing datasets as a way to characterize vegetation for the examination of habitat selection and for mapping realized relationships across the landscape. Although the use of remote sensing in wildlife studies has increased in recent years, the use of these datasets is still limited and some data sources and methods are yet to be explored. The overall goal of this dissertation was to look at the state of the wildlife ecology discipline in the use of geospatial data for habitat mapping, and to advance this area through the fusion of remote sensing tools for the mapping of previously difficult to characterize forest metrics for inclusion in avian cavity-nester habitat models. Chapter 2 reviewed over 60 years of selected wildlife literature to examine the wildlife ecology disciple through historic trends and recent advances in the use of remote sensing for habitat characterization focusing on aspects of scale and the use of available technology. We discuss commonly used remote sensing data sources, point out recent advances in the use of geospatial data for characterizing forest wildlife habitat (the use of lidar data and the creation of spatially explicit habitat prediction maps), and provide future suggestions for increased utilization of available datasets (secondary lidar metrics and time series Landsat data). In chapters 3 and 4 we explored the use of remote sensing for characterizing forest components previously difficult to map across landscapes at scales relevant to local wildlife habitat selection. Chapter 3 found promise in the fusion of lidar structure and Landsat time series disturbance products in the modeling and mapping of post-fire snag and shrub distributions at fine scales and at size/cover thresholds relevant for habitat mapping applications for many wildlife species. The study was conducted within the 2003 B&B Fire Complex in central Oregon. Using 164 field calibration plots and remote sensing predictors, we modeled the presence/absence of snag classes (dbh ≥40cm, ≥50cm, and ≥75cm) and woody shrub cover resulting in 10m output predictive grid maps. Remote sensing predictors included various lidar structure and topography variables and Landsat time series products representing the pre-fire forest, disturbance magnitude, and current forest conditions. We were able to model and map all habitat metrics with acceptable predictive performance and low-moderate errors. The utility of these snag and shrub metrics for representing important nesting habitat features for a cavity-nesting species of conservation concern, the Lewis's Woodpecker (Melanerpes lewis), was demonstrated in Chapter 4. We were able to model nesting habitat with good accuracies according to multiple performance measures and then map realized relationships for this species of conservation concern in an identified source habitat type, providing a potential resource for local scale conservation and management efforts and adding to the regional knowledge of habitat selection for the Lewis's Woodpecker. To our knowledge, these chapters represent first attempts to fuse lidar and time series Landsat disturbance metrics in a post-fire landscape and for the mapping of snag and shrub distributions at scales relevant to avian cavity nesting habitat. Close

• 5. [Article] Comparing Metacarcinus magister settlement preferences among the seagrasses Zostera marina and Zostera japonica

  Metacarcinus magister, the Dungeness crab, is a commercially important species on the Pacific Northwest coast as the most profitable fishery in Oregon and an important ecological player as both predator ...

  Citation × Citation Citation Abstract Copy Title: Comparing Metacarcinus magister settlement preferences among the seagrasses Zostera marina and Zostera japonica Author: Heidmann, Sarah, Jaco, Erin Metacarcinus magister, the Dungeness crab, is a commercially important species on the Pacific Northwest coast as the most profitable fishery in Oregon and an important ecological player as both predator and prey. Understanding the spatial distribution of Dungeness throughout different life history stages is beneficial both ecologically and economically. Zostera japonica is an established invasive species of seagrass in the Pacific Northwest and may also be important habitat for recently settled juvenile Dungeness. We examined the distribution of juvenile Dungeness in May 2013 among Z. japonica, Z. marina, and open habitats in the Yaquina Bay Estuary in Newport, Oregon. We correlated Dungeness abundance with habitat, shoot density and biomass of seagrass, tidal height, and abundance of Hemigrapsus oregonensis, another local species of crab. Our results indicate that Dungeness preferred seagrass habitats to open mud, but had no apparent preference among different species of seagrasses, despite the correlation of Dungeness abundance with seagrass biomass. This study increases scientific understanding of the life cycle of Dungeness crabs and the importance of estuarine habitats, which must be protected in order to achieve a sustainable fishery. Title: Comparing Metacarcinus magister settlement preferences among the seagrasses Zostera marina and Zostera japonica Author: Heidmann, Sarah, Jaco, Erin Metacarcinus magister, the Dungeness crab, is a commercially important species on the Pacific Northwest coast as the most profitable fishery in Oregon and an important ecological player as both predator and prey. Understanding the spatial distribution of Dungeness throughout different life history stages is beneficial both ecologically and economically. Zostera japonica is an established invasive species of seagrass in the Pacific Northwest and may also be important habitat for recently settled juvenile Dungeness. We examined the distribution of juvenile Dungeness in May 2013 among Z. japonica, Z. marina, and open habitats in the Yaquina Bay Estuary in Newport, Oregon. We correlated Dungeness abundance with habitat, shoot density and biomass of seagrass, tidal height, and abundance of Hemigrapsus oregonensis, another local species of crab. Our results indicate that Dungeness preferred seagrass habitats to open mud, but had no apparent preference among different species of seagrasses, despite the correlation of Dungeness abundance with seagrass biomass. This study increases scientific understanding of the life cycle of Dungeness crabs and the importance of estuarine habitats, which must be protected in order to achieve a sustainable fishery. Close

• 6. [Article] Modeling Large Wood Impacts on Stream Hydrodynamics and Juvenile Salmon Habitat

  Large wood (LW) pieces are recognized as an important habitat component for salmon freshwater habitat. As such, they are often used in stream habitat restoration practices despite a lack of knowledge about ...

  Citation × Citation Citation Abstract Copy Title: Modeling Large Wood Impacts on Stream Hydrodynamics and Juvenile Salmon Habitat Author: Bair, Russell Large wood (LW) pieces are recognized as an important habitat component for salmon freshwater habitat. As such, they are often used in stream habitat restoration practices despite a lack of knowledge about their impacts on spatial and temporal hydraulic characteristics relevant to fish habitat. In this thesis we present results on the impacts of LW on reach scale stream hydraulics. We use hydraulic models to identifying patterns and magnitudes of change in aspects of the flow field that are relevant to juvenile Coho Salmon after an addition of LW. The Nays2DH model was used because of its capacity to model unsteady flows around LW structures in-stream. Flow conditions after LW addition were modeled in three alluvial plane bed gravel reaches of Mill Creek in the Oregon Coast Range, a long term salmon life cycle study site. Study streams are small, with a bankfull (Q[subscript bf]) discharge between 2.2 and 8.7 m³/s and bankfull widths varying from 5.5 to 10.6 m. Survivable habitat was characterized for the flow field in terms of a) velocity (v) less than critical swim speed of juvenile Coho Salmon (v[subscript crit] = 0.5 m/s); b) and bed refuge estimated based on the likelihood of the movement of the reach median bed particle size (D₅₀). Spatial and temporal increases in wetted area were also determined. After the addition of LW, the area of acceptable habitat increased 17-26% in terms of velocity, 31-39% in terms of substrate stability, and 24-35% in terms of wetted area at Q[subscript bf]. Similar magnitudes of increase were observed over an entire storm hydrograph in each site. Patterns of change in the flow field showed deep pools of slower water forming upstream of LW jams which agreed with initial field observations of geomorphic change. Newly inundated flood plains and bars represented large portions of the additional habitat after the addition of LW. These areas had low velocity and shear stress values indicating that their contributions to additional habitat will be resilient to fluctuation even if acceptable habitat metrics were to be adjusted. Title: Modeling Large Wood Impacts on Stream Hydrodynamics and Juvenile Salmon Habitat Author: Bair, Russell Large wood (LW) pieces are recognized as an important habitat component for salmon freshwater habitat. As such, they are often used in stream habitat restoration practices despite a lack of knowledge about their impacts on spatial and temporal hydraulic characteristics relevant to fish habitat. In this thesis we present results on the impacts of LW on reach scale stream hydraulics. We use hydraulic models to identifying patterns and magnitudes of change in aspects of the flow field that are relevant to juvenile Coho Salmon after an addition of LW. The Nays2DH model was used because of its capacity to model unsteady flows around LW structures in-stream. Flow conditions after LW addition were modeled in three alluvial plane bed gravel reaches of Mill Creek in the Oregon Coast Range, a long term salmon life cycle study site. Study streams are small, with a bankfull (Q[subscript bf]) discharge between 2.2 and 8.7 m³/s and bankfull widths varying from 5.5 to 10.6 m. Survivable habitat was characterized for the flow field in terms of a) velocity (v) less than critical swim speed of juvenile Coho Salmon (v[subscript crit] = 0.5 m/s); b) and bed refuge estimated based on the likelihood of the movement of the reach median bed particle size (D₅₀). Spatial and temporal increases in wetted area were also determined. After the addition of LW, the area of acceptable habitat increased 17-26% in terms of velocity, 31-39% in terms of substrate stability, and 24-35% in terms of wetted area at Q[subscript bf]. Similar magnitudes of increase were observed over an entire storm hydrograph in each site. Patterns of change in the flow field showed deep pools of slower water forming upstream of LW jams which agreed with initial field observations of geomorphic change. Newly inundated flood plains and bars represented large portions of the additional habitat after the addition of LW. These areas had low velocity and shear stress values indicating that their contributions to additional habitat will be resilient to fluctuation even if acceptable habitat metrics were to be adjusted. Close

• 7. [Article] Influence of habitat characteristics on Greater sage-grouse reproductive success in the Montana Mountains, Nevada

  Greater sage-grouse (Centrocercus urophasianus) populations have declined across their geographic range during the last century. They were once widespread throughout the Intermountain West, but lower ...

  Citation × Citation Citation Abstract Copy Title: Influence of habitat characteristics on Greater sage-grouse reproductive success in the Montana Mountains, Nevada Author: Rebholz, James L. Greater sage-grouse (Centrocercus urophasianus) populations have declined across their geographic range during the last century. They were once widespread throughout the Intermountain West, but lower annual productivity, likely caused by degradation and loss of suitable habitat, has greatly reduced their distribution and population densities. Habitat used for reproduction has been well described, but relationships between habitat characteristics and reproductive output are less understood. Nesting success and chick survival are both important factors influencing annual productivity of sage-grouse. Several studies have investigated the effects of vegetation characteristics on nest success, but due to the variability of vegetation communities across the range, further work is necessary to clarify results from these studies. The relationships between habitat characteristics and chick survival are not as clearly understood. We initiated a study in the Montana Mountains of northwestern Nevada to describe nesting and early brood-rearing habitat and compare hypotheses describing potential relationships between habitat characteristics and reproductive success. In 2004 and 2005, we monitored 84 sage-grouse hens during the reproductive period and quantified fine-scale habitat characteristics at nest and brood sites. We quantified the vegetation structure at successful and unsuccessful nests and related individual habitat characteristics to the odds of a nest hatching successfully. Individually marked chicks were monitored for 3 weeks after hatching to measure associations of forb, grass and sagebrush cover, and food availability with chick survival. Grass cover beneath the nest shrub was the best predictor of nest outcome, and increasing amounts of grass cover improved the likelihood of a nest hatching successfully. Conversely, grass cover at early brood sites was negatively associated with chick survival. Early brood sites with greater forb cover were associated with higher sage-grouse chick survival. There was a weak relationship between sagebrush canopy cover at the nest shrub and hatch success, but sagebrush cover did not appear to have an effect on chick survival in the Montana Mountains. Finally, we examined the relative importance of maternally-influenced variables for chick survival. Total plasma protein levels (TPP) of pre-laying hens have been linked to reproductive success and may be an indication of early spring habitat quality. We evaluated the association of TPP levels with sage-grouse chick survival, and also tested chick weight and chick sex to determine if they influenced chick survival. Total plasma protein levels were a good indicator of chick survival and may indicate a relationship between early spring forb availability and chick survival. Chick survival did not appear to be related to sex or weight at capture. These results are similar to earlier studies that described the importance of herbaceous understory for both nest success and early brood-rearing. Management activities focusing on the restoration and maintenance of vegetation communities with intact herbaceous understories will likely improve sage-grouse reproductive success and annual production. Title: Influence of habitat characteristics on Greater sage-grouse reproductive success in the Montana Mountains, Nevada Author: Rebholz, James L. Greater sage-grouse (Centrocercus urophasianus) populations have declined across their geographic range during the last century. They were once widespread throughout the Intermountain West, but lower annual productivity, likely caused by degradation and loss of suitable habitat, has greatly reduced their distribution and population densities. Habitat used for reproduction has been well described, but relationships between habitat characteristics and reproductive output are less understood. Nesting success and chick survival are both important factors influencing annual productivity of sage-grouse. Several studies have investigated the effects of vegetation characteristics on nest success, but due to the variability of vegetation communities across the range, further work is necessary to clarify results from these studies. The relationships between habitat characteristics and chick survival are not as clearly understood. We initiated a study in the Montana Mountains of northwestern Nevada to describe nesting and early brood-rearing habitat and compare hypotheses describing potential relationships between habitat characteristics and reproductive success. In 2004 and 2005, we monitored 84 sage-grouse hens during the reproductive period and quantified fine-scale habitat characteristics at nest and brood sites. We quantified the vegetation structure at successful and unsuccessful nests and related individual habitat characteristics to the odds of a nest hatching successfully. Individually marked chicks were monitored for 3 weeks after hatching to measure associations of forb, grass and sagebrush cover, and food availability with chick survival. Grass cover beneath the nest shrub was the best predictor of nest outcome, and increasing amounts of grass cover improved the likelihood of a nest hatching successfully. Conversely, grass cover at early brood sites was negatively associated with chick survival. Early brood sites with greater forb cover were associated with higher sage-grouse chick survival. There was a weak relationship between sagebrush canopy cover at the nest shrub and hatch success, but sagebrush cover did not appear to have an effect on chick survival in the Montana Mountains. Finally, we examined the relative importance of maternally-influenced variables for chick survival. Total plasma protein levels (TPP) of pre-laying hens have been linked to reproductive success and may be an indication of early spring habitat quality. We evaluated the association of TPP levels with sage-grouse chick survival, and also tested chick weight and chick sex to determine if they influenced chick survival. Total plasma protein levels were a good indicator of chick survival and may indicate a relationship between early spring forb availability and chick survival. Chick survival did not appear to be related to sex or weight at capture. These results are similar to earlier studies that described the importance of herbaceous understory for both nest success and early brood-rearing. Management activities focusing on the restoration and maintenance of vegetation communities with intact herbaceous understories will likely improve sage-grouse reproductive success and annual production. Close

• 8. [Article] Terrestrial amphibian distribution, habitat associations and downed wood temperature profiles in managed headwater forests with riparian buffers in the Oregon Coast Range

  Western forests have become increasingly fragmented landscapes dominated by young stands. Given that western Oregon forests largely consist of headwater systems, there is a need to better understand how ...

  Citation × Citation Citation Abstract Copy Title: Terrestrial amphibian distribution, habitat associations and downed wood temperature profiles in managed headwater forests with riparian buffers in the Oregon Coast Range Author: Kluber, Matthew R. Western forests have become increasingly fragmented landscapes dominated by young stands. Given that western Oregon forests largely consist of headwater systems, there is a need to better understand how headwater forest taxa and their habitats are impacted by forest management practices. Several amphibian species associated with forested headwater systems have emerged as management concerns. Forest management strategies, such as harvests that remove only part of the canopy and retention of riparian buffer strips, may help ameliorate some of the negative effects on amphibians in managed forests. Pre-existing site conditions, such as legacy downed wood, also may play a role in buffering the impacts of silvicultural practices on terrestrial amphibians. Downed wood is an important habitat component for many amphibians, because the cool, moist microclimates of downed wood can provide refugia for terrestrial amphibians during warmer summer months. However, downed wood habitat suitability is another emerging concern as the rate of input and size of downed wood declines in managed forests. As part of the USDI Bureau of Land Managements Density Management Study, we investigated how untreated streamside buffers modify impacts of upland thinning on headwater forest terrestrial amphibians and their habitat at three sites in the Oregon Coast Range. To further assess habitat associations of these animals, we conducted a field experiment to address amphibian cover use, including downed wood, moss and coarse and fine substrates. In addition, we examined how temperature profiles inside small- and large-diameter downed wood and soil temperatures differed from ambient air temperatures. Temperatures of wood and soil were monitored at different slope positions (near streams and upslope) and overstory regimes (thinned and unthinned stands) to assess potential habitat suitability and buffering capabilities against seasonal temperature extremes for plethodontid salamanders. Our results suggest that pre-existing site conditions (e.g., amount of rocky or fine substrate) play an important role in determining the response of terrestrial amphibians to upland forest thinning. However, retention of stream buffers is important in maintaining unaltered stream and riparian conditions. Moderate thinning and preservation of vital habitat in riparian and nearby upland areas by way of variable-width buffers (15 m minimum width) may be sufficient in maintaining suitable habitat and microclimatic conditions vital to amphibian assemblages in managed headwater forests. Additionally, logs of a wide size range and soils may provide sufficient protection against thermal extremes harmful to plethodontid salamanders in thinned stands with limited overstory. However, this alone cannot support plethodontid salamanders. These salamanders require exposed areas (e.g., leaf litter, soil surface, rock faces) where much of their foraging and well as courtship occurs. Partial retention of the canopy through moderate thinning coupled with variable-width riparain buffers that may increase in width when suitable terrestrial habitat is encountered, may provide sufficient microhabitat, microclimate, and protection in maintaining terrestrial amphibian assemblages in managed headwater forests. Title: Terrestrial amphibian distribution, habitat associations and downed wood temperature profiles in managed headwater forests with riparian buffers in the Oregon Coast Range Author: Kluber, Matthew R. Western forests have become increasingly fragmented landscapes dominated by young stands. Given that western Oregon forests largely consist of headwater systems, there is a need to better understand how headwater forest taxa and their habitats are impacted by forest management practices. Several amphibian species associated with forested headwater systems have emerged as management concerns. Forest management strategies, such as harvests that remove only part of the canopy and retention of riparian buffer strips, may help ameliorate some of the negative effects on amphibians in managed forests. Pre-existing site conditions, such as legacy downed wood, also may play a role in buffering the impacts of silvicultural practices on terrestrial amphibians. Downed wood is an important habitat component for many amphibians, because the cool, moist microclimates of downed wood can provide refugia for terrestrial amphibians during warmer summer months. However, downed wood habitat suitability is another emerging concern as the rate of input and size of downed wood declines in managed forests. As part of the USDI Bureau of Land Managements Density Management Study, we investigated how untreated streamside buffers modify impacts of upland thinning on headwater forest terrestrial amphibians and their habitat at three sites in the Oregon Coast Range. To further assess habitat associations of these animals, we conducted a field experiment to address amphibian cover use, including downed wood, moss and coarse and fine substrates. In addition, we examined how temperature profiles inside small- and large-diameter downed wood and soil temperatures differed from ambient air temperatures. Temperatures of wood and soil were monitored at different slope positions (near streams and upslope) and overstory regimes (thinned and unthinned stands) to assess potential habitat suitability and buffering capabilities against seasonal temperature extremes for plethodontid salamanders. Our results suggest that pre-existing site conditions (e.g., amount of rocky or fine substrate) play an important role in determining the response of terrestrial amphibians to upland forest thinning. However, retention of stream buffers is important in maintaining unaltered stream and riparian conditions. Moderate thinning and preservation of vital habitat in riparian and nearby upland areas by way of variable-width buffers (15 m minimum width) may be sufficient in maintaining suitable habitat and microclimatic conditions vital to amphibian assemblages in managed headwater forests. Additionally, logs of a wide size range and soils may provide sufficient protection against thermal extremes harmful to plethodontid salamanders in thinned stands with limited overstory. However, this alone cannot support plethodontid salamanders. These salamanders require exposed areas (e.g., leaf litter, soil surface, rock faces) where much of their foraging and well as courtship occurs. Partial retention of the canopy through moderate thinning coupled with variable-width riparain buffers that may increase in width when suitable terrestrial habitat is encountered, may provide sufficient microhabitat, microclimate, and protection in maintaining terrestrial amphibian assemblages in managed headwater forests. Close

• 9. [Article] Greater sage-grouse movements and habitat use during winter in central Oregon

  Greater sage-grouse (Centrocercus urophasianus), a sagebrush obligate species, has contracted in extent by nearly half its original distribution. This is primarily due to habitat loss and degradation over ...

  Citation × Citation Citation Abstract Copy Title: Greater sage-grouse movements and habitat use during winter in central Oregon Author: Bruce, Jennifer R. Greater sage-grouse (Centrocercus urophasianus), a sagebrush obligate species, has contracted in extent by nearly half its original distribution. This is primarily due to habitat loss and degradation over the past 150 years. During winter, sage-grouse depend completely on sagebrush habitat for food and cover, yet sage-grouse winter ecology has been poorly studied in the past. We studied greater sage-grouse winter habitat use and movement in central Oregon by tracking 22 radio-collared sage-grouse (7 female, 15 male) from January through mid March 2007 to record specific characteristics of sagebrush used and patterns of movement for each sex during winter. We quantified winter habitat characteristics such as canopy height and topography at each sage-grouse location, estimated winter distances moved using weekly to biweekly point locations, and compared this information between males and females. The sage-grouse we studied moved extensively across the landscape in central Oregon, using approximately 1,480 km2 during winter. Sagebrush canopy height in sites used by sage-grouse varied from 0.25 to 0.75 m, with females tending to use sites with taller sagebrush plants and less total foliar cover than sites used by males. The difference in foliar cover between sexes was related to a seasonal change in habitat use; four females found in low sagebrush in January and early February stopped using it after 15 Feb 2007. Also by this date, most male sage-grouse had stopped using big sagebrush as they migrated to lekking areas. During our study there was half as much snow cover on average, which may explain why sage-grouse mortality rates were low. Managers interested in preserving sage-grouse populations should provide large areas (thousands of square km) of habitat that contain heterogeneous sagebrush habitat, specifically with both low and big sagebrush so that food and cover are available for greater sage-grouse during winter. Title: Greater sage-grouse movements and habitat use during winter in central Oregon Author: Bruce, Jennifer R. Greater sage-grouse (Centrocercus urophasianus), a sagebrush obligate species, has contracted in extent by nearly half its original distribution. This is primarily due to habitat loss and degradation over the past 150 years. During winter, sage-grouse depend completely on sagebrush habitat for food and cover, yet sage-grouse winter ecology has been poorly studied in the past. We studied greater sage-grouse winter habitat use and movement in central Oregon by tracking 22 radio-collared sage-grouse (7 female, 15 male) from January through mid March 2007 to record specific characteristics of sagebrush used and patterns of movement for each sex during winter. We quantified winter habitat characteristics such as canopy height and topography at each sage-grouse location, estimated winter distances moved using weekly to biweekly point locations, and compared this information between males and females. The sage-grouse we studied moved extensively across the landscape in central Oregon, using approximately 1,480 km2 during winter. Sagebrush canopy height in sites used by sage-grouse varied from 0.25 to 0.75 m, with females tending to use sites with taller sagebrush plants and less total foliar cover than sites used by males. The difference in foliar cover between sexes was related to a seasonal change in habitat use; four females found in low sagebrush in January and early February stopped using it after 15 Feb 2007. Also by this date, most male sage-grouse had stopped using big sagebrush as they migrated to lekking areas. During our study there was half as much snow cover on average, which may explain why sage-grouse mortality rates were low. Managers interested in preserving sage-grouse populations should provide large areas (thousands of square km) of habitat that contain heterogeneous sagebrush habitat, specifically with both low and big sagebrush so that food and cover are available for greater sage-grouse during winter. Close

• 10. [Article] Defining habitat preferences of pelagic loggerhead sea turtles (Caretta caretta) in the North Atlantic through analysis of behavior and bycatch

  For many species of marine turtle the characteristics that define pelagic habitat have yet to be fully identified. A better understanding of these habitat characteristics is critical to reduce high seas ...

  Citation × Citation Citation Abstract Copy Title: Defining habitat preferences of pelagic loggerhead sea turtles (Caretta caretta) in the North Atlantic through analysis of behavior and bycatch Author: McCarthy, Abigail L. For many species of marine turtle the characteristics that define pelagic habitat have yet to be fully identified. A better understanding of these habitat characteristics is critical to reduce high seas fisheries interactions with turtles, especially as the status of many turtle populations has placed them on the threatened or endangered species list. The combination of high-resolution satellite-tracking data with remotely sensed oceanographic data makes it possible to identify habitat for loggerhead turtles by analyzing the behavior of individual animals. Bycatch of loggerhead turtles in longline fisheries can also be examined using the same high-resolution oceanographic data to determine if there are identifiable habitat differences in high- and low- bycatch areas. I analyzed the tracks of ten loggerhead turtles tagged in the spring and fall of 1998 near Madeira, Portugal in relation to the marine environment they occupied. To determine the relationship between an individual turtle and its environment, some measure of behavior was necessary. I calculated the straightness index (SI), the ratio of the displacement of the animal to the total distance traveled, for individual weekly segments of the ten tracks as a measure of individual behavior. I then extracted information about the chlorophyll, sea-surface temperature (SST), bathymetry, and geostrophic current of the ocean in a 20km buffer surrounding the tracks, and examined the relationship between the straightness index and those characteristics using logistic regression. Chlorophyll a value, bathymetry, and movement of the turtle with geostrophic currents were consistently related to the straightness index of the tracks of all ten animals (two-sided p-value from Wald's test: 0.005, 0.0017, and 0.0018, respectively). Tracks were less straight in high chlorophyll regions and in shallower ocean areas, and animals were more likely to be moving with prevailing geostrophic currents during straighter track segments. These results confirm comparable analyses of loggerhead tracks in the Pacific, and indicate that sea turtles alter their behavior (likely representing a shift from traveling to foraging) when they encounter high-chlorophyll regions. Turtles with highly sinuous tracks spend more time in a given area or habitat than those who pass straight through, and therefore may be more susceptible to incidental capture by fisheries operating in those habitats. To address the fisheries bycatch/ habitat interactions I analyzed longline bycatch data to determine whether the marine environmental variables identified in the first part of my study were related to the probability of catching a turtle on a given longline set. I performed a logistic regression analysis using bycatch of turtles as the response variable, and bathymetry, SST, SST gradient (indicative of frontal activity), chlorophyll a, and chlorophyll a gradient as the independent variables. I also included the location and the date of the longline sets as potential predictor variables. I found that the most important variables predicting the odds that a turtle would be caught on a given set were chlorophyll a value in the area of the haul ( Wald's test, p=0.009) and the latitude at the beginning of the haul (Wald's test, p=0.0005). Turtles were more likely to be caught on sets in lower chlorophyll regions and in higher latitude regions of the data set, and there was no indication of important effects of bathymetry. These results disagree with my predictions from the tracking analysis, either because the fisheries-dependent bycatch data set did not provide enough contrast of habitat types, or because bycatch probability is not related to turtle behavior. My results indicate a difference between the critical variables selected as predictors of turtle habitat using the bycatch data and those selected using the behavior of individual tracked animals. While bycatch information is important, the distribution of fisheries data is highly biased towards frontal zones and regions of historic high catch. Judgments about turtle behavior based on only fisheries interactions could lead to incorrect conclusions about where animals spend the majority of their time. Assuming that animals are more likely to have an increased probability of interaction with longlines in areas where they spend more time foraging, fishing pressure should be reduced in those areas of high-use for pelagic loggerheads. It is crucial to base fisheries time-area closures and the design of marine protected areas on the behavior of tracked animals, and not just on fisheries bycatch data. Title: Defining habitat preferences of pelagic loggerhead sea turtles (Caretta caretta) in the North Atlantic through analysis of behavior and bycatch Author: McCarthy, Abigail L. For many species of marine turtle the characteristics that define pelagic habitat have yet to be fully identified. A better understanding of these habitat characteristics is critical to reduce high seas fisheries interactions with turtles, especially as the status of many turtle populations has placed them on the threatened or endangered species list. The combination of high-resolution satellite-tracking data with remotely sensed oceanographic data makes it possible to identify habitat for loggerhead turtles by analyzing the behavior of individual animals. Bycatch of loggerhead turtles in longline fisheries can also be examined using the same high-resolution oceanographic data to determine if there are identifiable habitat differences in high- and low- bycatch areas. I analyzed the tracks of ten loggerhead turtles tagged in the spring and fall of 1998 near Madeira, Portugal in relation to the marine environment they occupied. To determine the relationship between an individual turtle and its environment, some measure of behavior was necessary. I calculated the straightness index (SI), the ratio of the displacement of the animal to the total distance traveled, for individual weekly segments of the ten tracks as a measure of individual behavior. I then extracted information about the chlorophyll, sea-surface temperature (SST), bathymetry, and geostrophic current of the ocean in a 20km buffer surrounding the tracks, and examined the relationship between the straightness index and those characteristics using logistic regression. Chlorophyll a value, bathymetry, and movement of the turtle with geostrophic currents were consistently related to the straightness index of the tracks of all ten animals (two-sided p-value from Wald's test: 0.005, 0.0017, and 0.0018, respectively). Tracks were less straight in high chlorophyll regions and in shallower ocean areas, and animals were more likely to be moving with prevailing geostrophic currents during straighter track segments. These results confirm comparable analyses of loggerhead tracks in the Pacific, and indicate that sea turtles alter their behavior (likely representing a shift from traveling to foraging) when they encounter high-chlorophyll regions. Turtles with highly sinuous tracks spend more time in a given area or habitat than those who pass straight through, and therefore may be more susceptible to incidental capture by fisheries operating in those habitats. To address the fisheries bycatch/ habitat interactions I analyzed longline bycatch data to determine whether the marine environmental variables identified in the first part of my study were related to the probability of catching a turtle on a given longline set. I performed a logistic regression analysis using bycatch of turtles as the response variable, and bathymetry, SST, SST gradient (indicative of frontal activity), chlorophyll a, and chlorophyll a gradient as the independent variables. I also included the location and the date of the longline sets as potential predictor variables. I found that the most important variables predicting the odds that a turtle would be caught on a given set were chlorophyll a value in the area of the haul ( Wald's test, p=0.009) and the latitude at the beginning of the haul (Wald's test, p=0.0005). Turtles were more likely to be caught on sets in lower chlorophyll regions and in higher latitude regions of the data set, and there was no indication of important effects of bathymetry. These results disagree with my predictions from the tracking analysis, either because the fisheries-dependent bycatch data set did not provide enough contrast of habitat types, or because bycatch probability is not related to turtle behavior. My results indicate a difference between the critical variables selected as predictors of turtle habitat using the bycatch data and those selected using the behavior of individual tracked animals. While bycatch information is important, the distribution of fisheries data is highly biased towards frontal zones and regions of historic high catch. Judgments about turtle behavior based on only fisheries interactions could lead to incorrect conclusions about where animals spend the majority of their time. Assuming that animals are more likely to have an increased probability of interaction with longlines in areas where they spend more time foraging, fishing pressure should be reduced in those areas of high-use for pelagic loggerheads. It is crucial to base fisheries time-area closures and the design of marine protected areas on the behavior of tracked animals, and not just on fisheries bycatch data. Close

• 11. [Article] Determination of Trade-offs between Wetland Ecosystem Services in an Agricultural Landscape

  Wetland restoration mitigates effects of agricultural development on water quality, flooding, and habitat loss. Multi-objective optimization for wetland locations and sizes has not included objective functions ...

  Citation × Citation Citation Abstract Copy Title: Determination of Trade-offs between Wetland Ecosystem Services in an Agricultural Landscape Author: Garrison, Stacey L. Wetland restoration mitigates effects of agricultural development on water quality, flooding, and habitat loss. Multi-objective optimization for wetland locations and sizes has not included objective functions for water quality, hydrology, and habitat in unison, limiting analysis of trade-offs among these ecosystem services. This study establishes two methods to improve the accuracy of simulating wetland restoration with an optimization-simulation framework for analysis of trade-offs: identification of wetland type and constraining wetland and drainage area configurations to potential field-scale wetlands in the study area. Determination of a wetland habitat type used characteristics of the Hydrogeomorphic Method, and this type was utilized in a land-use/land-cover simulation linked to a species-habitat model. Multi-objective optimization identified optimal wetlands and drainage areas. These wetlands demonstrated redundancy among treatment ecosystem services. Modifying wetlands and drainage areas from the optimally-identified values caused shifts to the trade-off relationships. The habitat objective function conflicted with the treatment objective functions, but at low levels of confidence, demonstrating the necessity to incorporate all the objective function types together into a multi-objective optimization. The methods to increase accurate representation from this study can be incorporated into future studies to improve understanding of wetland ecosystem service processes for land-use planning. Title: Determination of Trade-offs between Wetland Ecosystem Services in an Agricultural Landscape Author: Garrison, Stacey L. Wetland restoration mitigates effects of agricultural development on water quality, flooding, and habitat loss. Multi-objective optimization for wetland locations and sizes has not included objective functions for water quality, hydrology, and habitat in unison, limiting analysis of trade-offs among these ecosystem services. This study establishes two methods to improve the accuracy of simulating wetland restoration with an optimization-simulation framework for analysis of trade-offs: identification of wetland type and constraining wetland and drainage area configurations to potential field-scale wetlands in the study area. Determination of a wetland habitat type used characteristics of the Hydrogeomorphic Method, and this type was utilized in a land-use/land-cover simulation linked to a species-habitat model. Multi-objective optimization identified optimal wetlands and drainage areas. These wetlands demonstrated redundancy among treatment ecosystem services. Modifying wetlands and drainage areas from the optimally-identified values caused shifts to the trade-off relationships. The habitat objective function conflicted with the treatment objective functions, but at low levels of confidence, demonstrating the necessity to incorporate all the objective function types together into a multi-objective optimization. The methods to increase accurate representation from this study can be incorporated into future studies to improve understanding of wetland ecosystem service processes for land-use planning. Close

• 12. [Article] Distribution of bats in Southeast Alaska and selection of day-roosts in trees by Keen’s myotis on Prince of Wales Island, Southeast Alaska

  We conducted capture and acoustic surveys for bats in six areas along a latitudinal gradient in Southeast Alaska from mid-May to September in 2005 and we continued surveys on Prince of Wales Island from ...

  Citation × Citation Citation Abstract Copy Title: Distribution of bats in Southeast Alaska and selection of day-roosts in trees by Keen’s myotis on Prince of Wales Island, Southeast Alaska Author: Boland, Julia L. We conducted capture and acoustic surveys for bats in six areas along a latitudinal gradient in Southeast Alaska from mid-May to September in 2005 and we continued surveys on Prince of Wales Island from mid-May to September in 2006. We determined the level of effort required to catch each species and documented ranges in morphology and periods of reproduction. We captured little brown myotis, Myotis lucifugus; California myotis, M. californicus; long-legged myotis, M. volans; and Keen’s myotis, M. keenii, and we acoustically detected and sighted the silver-haired bat, Lasionycteris noctivagans. Capture success varied by species, year, and type of capture site. Our surveys support prior research suggesting that the little brown myotis is the most abundant species in the region, although densities appear to be low relative to other parts of its range. California myotis and Keen’s myotis were captured as far north as Juneau. The long-legged myotis was captured on Wrangell and Prince of Wales Islands and the silver-haired bat was detected on Prince of Wales Island. Prince of Wales Island is the southernmost area we sampled and was the only area where all species were detected. Given low rates of detection, all species appear to occur in low densities in Southeast Alaska. Better understanding of population status and trends and examination of habitat ecology and response to forest management in the region is needed to prioritize conservation strategies. The Keen’s myotis is rare and has one of the most limited distributions of any bat species in North America. Understanding gender-specific roosting ecologies of bats at relevant spatial scales is necessary to effectively evaluate the impact of habitat alteration and prioritize conservation efforts for bats in temperate forests. We examined selection of day-roosts in trees by Keen’s myotis from mid-May to September, 2006 on Prince of Wales Island, Southeast Alaska. Our objectives were to 1) examine relationships between and determine relative importance of habitat characteristics on selection of day-roosts at three spatial scales and 2) determine if habitat associations for males and females differed at each scale. We tracked 13 females to 62 roosts in trees and 6 males to 24 roosts in trees. Features at each spatial scale appeared to influence selection of day-roosts by female Keen’s myotis, but associations were strongest at the tree scale and trees used as roosts were primarily large in diameter with structural defects and located in old-growth forests. Trees in plots around roosts of females had large mean diameters and these plots had a high abundance of roost-like trees. Roosts were generally located near to roads and streams and surrounded by landscapes with a high abundance of old-growth and riparian habitat. Associations were evident for male Keen’s myotis at each spatial scale, but associations at the landscape scale were strongest. Male Keen’s myotis exhibited flexibility with the types of roosts they chose, but tree roosts were primarily snags in early to intermediate decay surrounded by a high relative abundance of roost-like trees that were closer to roads and further from riparian habitat. Habitat associations differed between males and females at each spatial scale and differences are likely a reflection of higher energetic constraints associated with reproduction for females. Energetic benefits gained from optimal roosting habitat may be critical for successful reproduction by females. Females primarily roosted in old-growth habitat and we suggest that maintaining structural components characteristic of old growth will promote conservation of Keen’s myotis in Southeast Alaska. Title: Distribution of bats in Southeast Alaska and selection of day-roosts in trees by Keen’s myotis on Prince of Wales Island, Southeast Alaska Author: Boland, Julia L. We conducted capture and acoustic surveys for bats in six areas along a latitudinal gradient in Southeast Alaska from mid-May to September in 2005 and we continued surveys on Prince of Wales Island from mid-May to September in 2006. We determined the level of effort required to catch each species and documented ranges in morphology and periods of reproduction. We captured little brown myotis, Myotis lucifugus; California myotis, M. californicus; long-legged myotis, M. volans; and Keen’s myotis, M. keenii, and we acoustically detected and sighted the silver-haired bat, Lasionycteris noctivagans. Capture success varied by species, year, and type of capture site. Our surveys support prior research suggesting that the little brown myotis is the most abundant species in the region, although densities appear to be low relative to other parts of its range. California myotis and Keen’s myotis were captured as far north as Juneau. The long-legged myotis was captured on Wrangell and Prince of Wales Islands and the silver-haired bat was detected on Prince of Wales Island. Prince of Wales Island is the southernmost area we sampled and was the only area where all species were detected. Given low rates of detection, all species appear to occur in low densities in Southeast Alaska. Better understanding of population status and trends and examination of habitat ecology and response to forest management in the region is needed to prioritize conservation strategies. The Keen’s myotis is rare and has one of the most limited distributions of any bat species in North America. Understanding gender-specific roosting ecologies of bats at relevant spatial scales is necessary to effectively evaluate the impact of habitat alteration and prioritize conservation efforts for bats in temperate forests. We examined selection of day-roosts in trees by Keen’s myotis from mid-May to September, 2006 on Prince of Wales Island, Southeast Alaska. Our objectives were to 1) examine relationships between and determine relative importance of habitat characteristics on selection of day-roosts at three spatial scales and 2) determine if habitat associations for males and females differed at each scale. We tracked 13 females to 62 roosts in trees and 6 males to 24 roosts in trees. Features at each spatial scale appeared to influence selection of day-roosts by female Keen’s myotis, but associations were strongest at the tree scale and trees used as roosts were primarily large in diameter with structural defects and located in old-growth forests. Trees in plots around roosts of females had large mean diameters and these plots had a high abundance of roost-like trees. Roosts were generally located near to roads and streams and surrounded by landscapes with a high abundance of old-growth and riparian habitat. Associations were evident for male Keen’s myotis at each spatial scale, but associations at the landscape scale were strongest. Male Keen’s myotis exhibited flexibility with the types of roosts they chose, but tree roosts were primarily snags in early to intermediate decay surrounded by a high relative abundance of roost-like trees that were closer to roads and further from riparian habitat. Habitat associations differed between males and females at each spatial scale and differences are likely a reflection of higher energetic constraints associated with reproduction for females. Energetic benefits gained from optimal roosting habitat may be critical for successful reproduction by females. Females primarily roosted in old-growth habitat and we suggest that maintaining structural components characteristic of old growth will promote conservation of Keen’s myotis in Southeast Alaska. Close

• 13. [Article] Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers

  I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical ...

  Citation × Citation Citation Abstract Copy Title: Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers Author: Lewis, Sierra Koch I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical salmonid-bearing rivers, little documentation exists for anadromous fish presence above potential natural obstacles upstream of Soda Springs Dam. My prediction was that if migratory salmonids are allowed to move upstream of the dam using a new fish ladder they would utilize available upstream spawning habitat. I captured, radio-tagged, and transplanted wild adult summer steelhead, O. mykiss, above Soda Springs Dam and tracked daily movements for 1 year to observe habitat preferences. I also investigated evidence of historical anadromy throughout the North Umpqua River basin using stable isotope analysis of salmon-derived nitrogen (¹⁵N) in foliar samples from Douglas fir trees, P. menziesii, (>100 years old). I tested the hypothesis that I could identify undocumented, historical salmon spawning reaches above natural and anthropogenic obstacles based solely upon δ¹⁵N foliar deposition patterns. While tracking radio-tagged steelhead, I documented holding locations, the timing of spawning activities, and the outmigration of kelts. Tagged fish did not show any extensive movement in the river or tributaries above the dam. Most of the tagged adults showed incremental daily movements near the release site or downstream into the hydropower reservoir but did not travel further than 1 kilometer upstream in the main river channel. I recorded movements and localized activities that suggested some of the fish spawned and subsequently moved downstream towards the Pacific Ocean. My observations indicated that spawning behavior of tagged fish above Soda Springs Dam was delayed several weeks relative to fish spawning below the dam. There was no evidence from telemetry that any fish moved upstream in Fish Creek, the newly accessible habitat of interest in this project. My data suggest that steelhead will use restored habitat above dams, but that re-colonization activities are variable and may be affected by altered flow regimes within the restored habitat upstream of the dam and intra-specific density dependence. My stable isotope data indicated that the foliar δ¹⁵N deposition patterns were confounded with elevation. I documented potential "salmon-derived" false positives on the Umpqua National Forest above impassable waterfalls. Overall I found that foliar δ¹⁵N deposition patterns were highly variable and unexpectedly indicated a statistically significant negative correlation of foliar δ¹⁵N values with historical salmon presence. My linear mixed-effects modeling suggests that the presence of salmon is the most important indicator of foliar δ¹⁵N values, rather than the proximity of a sampled tree to stream flow above or below migratory barriers. I was not able to use the mixed effects model to identify previously undocumented salmon spawning habitat. My results from the foliar technique suggest that the method may not be universally applicable as has been previously suggested in the literature. Title: Reconnecting aquatic habitats : validating historical habitat use by anadromous fishes using telemetry and stable isotope analysis above barriers Author: Lewis, Sierra Koch I conducted a study to identify potential spawning habitat for anadromous salmonids above a 60-year-old hydropower dam in the headwaters of the North Umpqua River in Oregon. Like many other historical salmonid-bearing rivers, little documentation exists for anadromous fish presence above potential natural obstacles upstream of Soda Springs Dam. My prediction was that if migratory salmonids are allowed to move upstream of the dam using a new fish ladder they would utilize available upstream spawning habitat. I captured, radio-tagged, and transplanted wild adult summer steelhead, O. mykiss, above Soda Springs Dam and tracked daily movements for 1 year to observe habitat preferences. I also investigated evidence of historical anadromy throughout the North Umpqua River basin using stable isotope analysis of salmon-derived nitrogen (¹⁵N) in foliar samples from Douglas fir trees, P. menziesii, (>100 years old). I tested the hypothesis that I could identify undocumented, historical salmon spawning reaches above natural and anthropogenic obstacles based solely upon δ¹⁵N foliar deposition patterns. While tracking radio-tagged steelhead, I documented holding locations, the timing of spawning activities, and the outmigration of kelts. Tagged fish did not show any extensive movement in the river or tributaries above the dam. Most of the tagged adults showed incremental daily movements near the release site or downstream into the hydropower reservoir but did not travel further than 1 kilometer upstream in the main river channel. I recorded movements and localized activities that suggested some of the fish spawned and subsequently moved downstream towards the Pacific Ocean. My observations indicated that spawning behavior of tagged fish above Soda Springs Dam was delayed several weeks relative to fish spawning below the dam. There was no evidence from telemetry that any fish moved upstream in Fish Creek, the newly accessible habitat of interest in this project. My data suggest that steelhead will use restored habitat above dams, but that re-colonization activities are variable and may be affected by altered flow regimes within the restored habitat upstream of the dam and intra-specific density dependence. My stable isotope data indicated that the foliar δ¹⁵N deposition patterns were confounded with elevation. I documented potential "salmon-derived" false positives on the Umpqua National Forest above impassable waterfalls. Overall I found that foliar δ¹⁵N deposition patterns were highly variable and unexpectedly indicated a statistically significant negative correlation of foliar δ¹⁵N values with historical salmon presence. My linear mixed-effects modeling suggests that the presence of salmon is the most important indicator of foliar δ¹⁵N values, rather than the proximity of a sampled tree to stream flow above or below migratory barriers. I was not able to use the mixed effects model to identify previously undocumented salmon spawning habitat. My results from the foliar technique suggest that the method may not be universally applicable as has been previously suggested in the literature. Close

• 14. [Article] thesisFIGS.PPT

  Citation × Citation Citation Abstract Copy Title: thesisFIGS.PPT Author: Nasby, Nicole M. Title: thesisFIGS.PPT Author: Nasby, Nicole M. Close

• 15. [Article] Nasby_Thesis.doc

  Citation × Citation Citation Abstract Copy Title: Nasby_Thesis.doc Author: Nasby, Nicole M. Title: Nasby_Thesis.doc Author: Nasby, Nicole M. Close

• 16. [Article] Integration of submersible transect data and high-resolution sonar imagery for a habitat-based groundfish assessment of Heceta Bank, Oregon

  Citation × Citation Citation Abstract Copy Title: Integration of submersible transect data and high-resolution sonar imagery for a habitat-based groundfish assessment of Heceta Bank, Oregon Author: Nasby, Nicole M. Title: Integration of submersible transect data and high-resolution sonar imagery for a habitat-based groundfish assessment of Heceta Bank, Oregon Author: Nasby, Nicole M. Close

• 17. [Article] A GIS investigation of indigenous intensification of native food plants : humans as environmental variable in maxent habitat suitability modeling of Camassia in Oregon

  This thesis merges the fields of Ecology and Anthropology by applying Habitat Suitability Modeling to the relationship between people and plants in the Pacific Northwest. In it, I create and optimize two ...

  Citation × Citation Citation Abstract Copy Title: A GIS investigation of indigenous intensification of native food plants : humans as environmental variable in maxent habitat suitability modeling of Camassia in Oregon Author: Elliott, Braden T. This thesis merges the fields of Ecology and Anthropology by applying Habitat Suitability Modeling to the relationship between people and plants in the Pacific Northwest. In it, I create and optimize two Maxent habitat suitability models for camas (Camassia spp.) in Oregon. The first model describes the physical environment of camas using precipitation and maximum temperature. The second model incorporates the cultural environment of camas by adding cultural centrality and cost distance to known earth ovens. Cultural centrality is inferred by combining culture and language area maps of the Pacific Northwest around Euroamerican contact. Centrality is measured by agreement between these maps, peripherality is measured by disagreement. Earth ovens, used to prepare camas for human consumption, are mapped on a slope map of Oregon to measure cost distance--the energy necessary to travel--to the nearest known oven. The first (ecological) model performs acceptably well, but the second (socioecological) model outperforms the first on standard measures which reward fit and penalize complexity. This demonstrates a strong relationship between indigenous cultural geography and the distribution of camas on the Oregon landscape, visible through centuries of nonindigenous landscape management with a necessarily incomplete dataset. Title: A GIS investigation of indigenous intensification of native food plants : humans as environmental variable in maxent habitat suitability modeling of Camassia in Oregon Author: Elliott, Braden T. This thesis merges the fields of Ecology and Anthropology by applying Habitat Suitability Modeling to the relationship between people and plants in the Pacific Northwest. In it, I create and optimize two Maxent habitat suitability models for camas (Camassia spp.) in Oregon. The first model describes the physical environment of camas using precipitation and maximum temperature. The second model incorporates the cultural environment of camas by adding cultural centrality and cost distance to known earth ovens. Cultural centrality is inferred by combining culture and language area maps of the Pacific Northwest around Euroamerican contact. Centrality is measured by agreement between these maps, peripherality is measured by disagreement. Earth ovens, used to prepare camas for human consumption, are mapped on a slope map of Oregon to measure cost distance--the energy necessary to travel--to the nearest known oven. The first (ecological) model performs acceptably well, but the second (socioecological) model outperforms the first on standard measures which reward fit and penalize complexity. This demonstrates a strong relationship between indigenous cultural geography and the distribution of camas on the Oregon landscape, visible through centuries of nonindigenous landscape management with a necessarily incomplete dataset. Close

• 18. [Article] Mason’s Run brook trout (Salvelinus fontinalis): history, management challenges, and recommendations

  Graduation date: 2016

  Citation × Citation Citation Abstract Copy Title: Mason’s Run brook trout (Salvelinus fontinalis): history, management challenges, and recommendations Author: Russell, Joseph D. III Graduation date: 2016 Title: Mason’s Run brook trout (Salvelinus fontinalis): history, management challenges, and recommendations Author: Russell, Joseph D. III Graduation date: 2016 Close

• 19. [Article] Dungeness Settlement Paper.docx

  Citation × Citation Citation Abstract Copy Title: Dungeness Settlement Paper.docx Author: Heidmann, Sarah, Jaco, Erin Title: Dungeness Settlement Paper.docx Author: Heidmann, Sarah, Jaco, Erin Close

• 20. [Article] Dungeness Settlement Paper.pdf

  Citation × Citation Citation Abstract Copy Title: Dungeness Settlement Paper.pdf Author: Heidmann, Sarah, Jaco, Erin Title: Dungeness Settlement Paper.pdf Author: Heidmann, Sarah, Jaco, Erin Close

• 21. [Article] TNC_ASPEN_SEC 1.pdf

  Citation × Citation Citation Abstract Copy Title: TNC_ASPEN_SEC 1.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Title: TNC_ASPEN_SEC 1.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Close

• 22. [Article] TNC_ASPEN_SEC 2.pdf

  Citation × Citation Citation Abstract Copy Title: TNC_ASPEN_SEC 2.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Title: TNC_ASPEN_SEC 2.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Close

• 23. [Article] TNC_ASPEN_SEC 3.pdf

  Citation × Citation Citation Abstract Copy Title: TNC_ASPEN_SEC 3.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Title: TNC_ASPEN_SEC 3.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Close

• 24. [Article] TNC_ASPEN_SEC 4.pdf

  Citation × Citation Citation Abstract Copy Title: TNC_ASPEN_SEC 4.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Title: TNC_ASPEN_SEC 4.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Close

• 25. [Article] TNC_ASPEN_SEC 5.pdf

  Citation × Citation Citation Abstract Copy Title: TNC_ASPEN_SEC 5.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Title: TNC_ASPEN_SEC 5.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Close

• 26. [Article] TNC_ASPEN_FULL DOC_FINAL for web.pdf

  Citation × Citation Citation Abstract Copy Title: TNC_ASPEN_FULL DOC_FINAL for web.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Title: TNC_ASPEN_FULL DOC_FINAL for web.pdf Author: Ediger, Vernita, Seager, S Trent, Davis, Emily Jane Close

• 27. [Article] Distributional patterns of 0-group Pacific cod (Gadus macrocephalus) in the eastern Bering Sea under variable recruitment and thermal conditions

  Despite the importance of Pacific cod in Bering Sea fisheries and foodwebs, little is known about the habitat use and the distribution of early life stages. We analysed 6 years of catch data for 0-group ...

  Citation × Citation Citation Abstract Copy Title: Distributional patterns of 0-group Pacific cod (Gadus macrocephalus) in the eastern Bering Sea under variable recruitment and thermal conditions Author: Miller, Jessica A., Hurst, Thomas P., Moss, Jamal H. Despite the importance of Pacific cod in Bering Sea fisheries and foodwebs, little is known about the habitat use and the distribution of early life stages. We analysed 6 years of catch data for 0-group Pacific cod in fishery-independent surveys of the Bering Sea shelf. Juvenile cod were most commonly captured on the middle shelf over depths of 50–80 m and were rarely captured north of 58°N. Consistently high catches were observed east of the Pribilof Islands and north of Port Moller along the Alaska Peninsula. There was evidence of density-dependent habitat selection at the local scale as the frequency of occurrence increased with regional catch per unit effort. At the basin scale, the southerly distribution of the weak 2009 cohort suggested the possibility of a range contraction for small cohorts. There was no consistent shift in the distribution of juvenile Pacific cod in response to interannual climate variability. These results for Pacific cod contrast with those observed for walleye pollock, which appears to exhibit greater variance in distribution, but are similar to patterns observed for juvenile Atlantic cod. Future work should focus on distribution in nearshore habitats and examine the patterns of dispersal and the connectivity of the Bering Sea and Gulf of Alaska populations. Title: Distributional patterns of 0-group Pacific cod (Gadus macrocephalus) in the eastern Bering Sea under variable recruitment and thermal conditions Author: Miller, Jessica A., Hurst, Thomas P., Moss, Jamal H. Despite the importance of Pacific cod in Bering Sea fisheries and foodwebs, little is known about the habitat use and the distribution of early life stages. We analysed 6 years of catch data for 0-group Pacific cod in fishery-independent surveys of the Bering Sea shelf. Juvenile cod were most commonly captured on the middle shelf over depths of 50–80 m and were rarely captured north of 58°N. Consistently high catches were observed east of the Pribilof Islands and north of Port Moller along the Alaska Peninsula. There was evidence of density-dependent habitat selection at the local scale as the frequency of occurrence increased with regional catch per unit effort. At the basin scale, the southerly distribution of the weak 2009 cohort suggested the possibility of a range contraction for small cohorts. There was no consistent shift in the distribution of juvenile Pacific cod in response to interannual climate variability. These results for Pacific cod contrast with those observed for walleye pollock, which appears to exhibit greater variance in distribution, but are similar to patterns observed for juvenile Atlantic cod. Future work should focus on distribution in nearshore habitats and examine the patterns of dispersal and the connectivity of the Bering Sea and Gulf of Alaska populations. Close

• 28. [Article] Short-tailed weasel space use in managed forests of western Oregon

  Although short-tailed weasels (Mustela erminea) are important predators of small mammals, little is known about their space use, habitat selection, or vulnerability to predation in North America. To evaluate ...

  Citation × Citation Citation Abstract Copy Title: Short-tailed weasel space use in managed forests of western Oregon Author: Linnell, Mark A Although short-tailed weasels (Mustela erminea) are important predators of small mammals, little is known about their space use, habitat selection, or vulnerability to predation in North America. To evaluate the effects of forest management and social structure on home range size and habitat selection of short-tailed weasels, I conducted a telemetry study in the Coast Ranges of western Oregon, USA. I used fixed kernel utilization distributions, multiple linear regression, and weighted compositional analysis to assess factors associated with home range size and habitat selection for 25 radio-marked short-tailed weasels. The radio-collared weasels selected early seral forest (5-15 years post-harvest) over closed canopy forest (>16 years postharvest). Females showed the strongest selection for early seral forest and had smaller home ranges than males (♀♀ x̄ = 10.4 hectares, 95% CI = 6.6-14.1 ha; ♂♂ x̄ = 53.3 hectares, 95% CI = 30.4-76.2 ha). Based on these observations, I proposed that weasels in my study exhibited a competitive hierarchy whereby the best exploitation competitors (females) selected the most productive cover types (early seral, fields) and appeared to be unaffected by interference competition from the larger males. Additionally, while radio-tracking weasels, I observed several mortalities, most of which I attributed to owls (4 out of 5 confirmed mortalities). Using Kaplan- Meier analysis, I estimated the estimated survival rate for the 9 month period of my study (June 2012-March 2013) was 0.36; 95% CI = 0.13-0.6. This estimate indicated an annual survival rate that was similar to the mean for 6 studies elsewhere in temperate North America in which the fate of weasels (Mustela spp.) was tracked (x̄ = 0.31 ± 0.09). I concluded that predation was an important factor limiting short-tailed weasel populations. Furthermore, strong selection for early seral cover, an ephemeral cover type, indicated that habitat for weasels in my study area may be limited to relatively short time periods. This may be due to forest management practices, including high density re-planting of conifers to accelerate the re-establishment of conifer trees after timber harvest. I suggest that reducing tree planting densities would favor weasel occupancy of managed forest by increasing the duration in which early seral vegetation is available. Title: Short-tailed weasel space use in managed forests of western Oregon Author: Linnell, Mark A Although short-tailed weasels (Mustela erminea) are important predators of small mammals, little is known about their space use, habitat selection, or vulnerability to predation in North America. To evaluate the effects of forest management and social structure on home range size and habitat selection of short-tailed weasels, I conducted a telemetry study in the Coast Ranges of western Oregon, USA. I used fixed kernel utilization distributions, multiple linear regression, and weighted compositional analysis to assess factors associated with home range size and habitat selection for 25 radio-marked short-tailed weasels. The radio-collared weasels selected early seral forest (5-15 years post-harvest) over closed canopy forest (>16 years postharvest). Females showed the strongest selection for early seral forest and had smaller home ranges than males (♀♀ x̄ = 10.4 hectares, 95% CI = 6.6-14.1 ha; ♂♂ x̄ = 53.3 hectares, 95% CI = 30.4-76.2 ha). Based on these observations, I proposed that weasels in my study exhibited a competitive hierarchy whereby the best exploitation competitors (females) selected the most productive cover types (early seral, fields) and appeared to be unaffected by interference competition from the larger males. Additionally, while radio-tracking weasels, I observed several mortalities, most of which I attributed to owls (4 out of 5 confirmed mortalities). Using Kaplan- Meier analysis, I estimated the estimated survival rate for the 9 month period of my study (June 2012-March 2013) was 0.36; 95% CI = 0.13-0.6. This estimate indicated an annual survival rate that was similar to the mean for 6 studies elsewhere in temperate North America in which the fate of weasels (Mustela spp.) was tracked (x̄ = 0.31 ± 0.09). I concluded that predation was an important factor limiting short-tailed weasel populations. Furthermore, strong selection for early seral cover, an ephemeral cover type, indicated that habitat for weasels in my study area may be limited to relatively short time periods. This may be due to forest management practices, including high density re-planting of conifers to accelerate the re-establishment of conifer trees after timber harvest. I suggest that reducing tree planting densities would favor weasel occupancy of managed forest by increasing the duration in which early seral vegetation is available. Close

• 29. [Article] Identifying habitat factors for canary rockfish (Sebastes pinniger) off Washington and Oregon using environmental data and trawl logbooks

  If fisheries managers are to effectively manage commercially exploited fish populations, a basic understanding of the factors that influence fish distribution and abundance is required. In 2005, efforts ...

  Citation × Citation Citation Abstract Copy Title: Identifying habitat factors for canary rockfish (Sebastes pinniger) off Washington and Oregon using environmental data and trawl logbooks Author: Vestfals, Cathleen D. If fisheries managers are to effectively manage commercially exploited fish populations, a basic understanding of the factors that influence fish distribution and abundance is required. In 2005, efforts to identify Essential Fish Habitat (EFH) for the 82 groundfish species managed by the Pacific Fishery Management Council along the West Coast resulted in the entire continental margin being designated as EFH. Clearly, our knowledge of EFH needs to be refined, which can be accomplished by gaining insight into how environmental variables shape the distribution of managed species. Habitat is commonly used to describe a set of environmental variables that are thought to influence occupancy. The aim of this thesis research is to detect and analyze the quantitative relationships between canary rockfish (Sebastes pinniger) presence/absence data, their spatial distribution, and various biotic and abiotic factors. The presence of canary rockfish at various locations was correlated against co-located environmental variables including bottom depths, temperatures, locations (latitude and longitude), seafloor substrate types, canary rockfish hotspots, and the presence/absence of other groundfish and invertebrate species. The statistical analysis was conducted using the generalized additive model (GAM), which is a nonparametric regression technique very well suited to model nonlinear speciesenvironment interactions. The GAM analysis was conducted using information collected from four different data sources. Data collected by the Alaska Fisheries Science Center (AFSC) from 1986 to 2001 provided information at distinct locations and times on the presence/absence of canary rockfish and other groundfish and invertebrate species, and associated depths and temperatures. Seafloor lithology maps for Oregon and Washington and 100-meter gridded bathymetric data, obtained from the Active Tectonics and Seafloor Mapping Lab at Oregon State University, provided information on the physical characteristics of the seafloor. These data were used in conjunction with the AFSC bottom trawl survey data to investigate the relationships between substrate type, slope and rugosity, and the presence of canary rockfish. Finally, locations of canary rockfish hotspots, or areas with high canary rockfish catch, were identified from Oregon commercial trawl logbook data (1995-2001) and provided information on distinct areas where the trawl fishing fleet had successfully caught canary rockfish in the past. Canary rockfish presence in trawl survey tows was associated with specific locations and ranges of bathymetry, temperatures, and substrate types, as well as proximity to canary rockfish hotspots, and particular fish and invertebrate communities. Survey year had a strong effect on the presence of canary rockfish, as did location (latitude and longitude) and depth. The geographic location of a survey tow had a negative effect on the presence of canary rockfish in the nearshore region, and a positive effect the further the location was from the coastline, with canary rockfish presence being highest off the Washington coast between 47.5°N and 48.5°N. While canary rockfish were found at depths between 57 m and 307 m in the survey, the majority of the tows with canary rockfish catch, over 90%, occurred between the depths of 57 m and 199 m. Though temperature did not have a significant effect on canary rockfish presence in the GAM, canary rockfish were associated with specific temperature ranges, only being caught at temperatures between 6.2°C and 9.0°C in the survey. Over 89% of the tows with canary rockfish catch occurred between 6.2°C and 7.9°C. Since temperature and bottom depth of the trawl survey tows were highly correlated, it was difficult to determine which variable was the causative factor in determining the probability of a canary rockfish being present. Canary rockfish presence was higher in survey tows made closer to canary rockfish hotspots, as well as hard bottom types. Finally, the presence of lingcod, yellowtail, silvergray, or redstripe rockfish in a survey tow increased the likelihood of canary rockfish being present, as did the presence of basketstars and corals. By studying the relationships between species and their environment, we can begin to understand the relative importance of how environmental variables shape the distribution of managed species. For ecosystem-based management strategies to be successful, the functional relationships between organisms and their habitat must be understood. The predictive model developed in this study can be used to identify areas off Oregon and Washington where canary rockfish are likely to be found in relation to various habitat factors, and can potentially be used to delineate areas that should be sampled in future surveys of canary rockfish. Additionally, this research will help to improve our understanding of the factors that influence canary rockfish distribution, which may produce a more realistic definition of canary rockfish habitat, and improve assessment. This study specifically focuses on canary rockfish, because this species currently constrains many West Coast fisheries for groundfish, however, the methods outlined here could be applied more generally to other species of interest. Title: Identifying habitat factors for canary rockfish (Sebastes pinniger) off Washington and Oregon using environmental data and trawl logbooks Author: Vestfals, Cathleen D. If fisheries managers are to effectively manage commercially exploited fish populations, a basic understanding of the factors that influence fish distribution and abundance is required. In 2005, efforts to identify Essential Fish Habitat (EFH) for the 82 groundfish species managed by the Pacific Fishery Management Council along the West Coast resulted in the entire continental margin being designated as EFH. Clearly, our knowledge of EFH needs to be refined, which can be accomplished by gaining insight into how environmental variables shape the distribution of managed species. Habitat is commonly used to describe a set of environmental variables that are thought to influence occupancy. The aim of this thesis research is to detect and analyze the quantitative relationships between canary rockfish (Sebastes pinniger) presence/absence data, their spatial distribution, and various biotic and abiotic factors. The presence of canary rockfish at various locations was correlated against co-located environmental variables including bottom depths, temperatures, locations (latitude and longitude), seafloor substrate types, canary rockfish hotspots, and the presence/absence of other groundfish and invertebrate species. The statistical analysis was conducted using the generalized additive model (GAM), which is a nonparametric regression technique very well suited to model nonlinear speciesenvironment interactions. The GAM analysis was conducted using information collected from four different data sources. Data collected by the Alaska Fisheries Science Center (AFSC) from 1986 to 2001 provided information at distinct locations and times on the presence/absence of canary rockfish and other groundfish and invertebrate species, and associated depths and temperatures. Seafloor lithology maps for Oregon and Washington and 100-meter gridded bathymetric data, obtained from the Active Tectonics and Seafloor Mapping Lab at Oregon State University, provided information on the physical characteristics of the seafloor. These data were used in conjunction with the AFSC bottom trawl survey data to investigate the relationships between substrate type, slope and rugosity, and the presence of canary rockfish. Finally, locations of canary rockfish hotspots, or areas with high canary rockfish catch, were identified from Oregon commercial trawl logbook data (1995-2001) and provided information on distinct areas where the trawl fishing fleet had successfully caught canary rockfish in the past. Canary rockfish presence in trawl survey tows was associated with specific locations and ranges of bathymetry, temperatures, and substrate types, as well as proximity to canary rockfish hotspots, and particular fish and invertebrate communities. Survey year had a strong effect on the presence of canary rockfish, as did location (latitude and longitude) and depth. The geographic location of a survey tow had a negative effect on the presence of canary rockfish in the nearshore region, and a positive effect the further the location was from the coastline, with canary rockfish presence being highest off the Washington coast between 47.5°N and 48.5°N. While canary rockfish were found at depths between 57 m and 307 m in the survey, the majority of the tows with canary rockfish catch, over 90%, occurred between the depths of 57 m and 199 m. Though temperature did not have a significant effect on canary rockfish presence in the GAM, canary rockfish were associated with specific temperature ranges, only being caught at temperatures between 6.2°C and 9.0°C in the survey. Over 89% of the tows with canary rockfish catch occurred between 6.2°C and 7.9°C. Since temperature and bottom depth of the trawl survey tows were highly correlated, it was difficult to determine which variable was the causative factor in determining the probability of a canary rockfish being present. Canary rockfish presence was higher in survey tows made closer to canary rockfish hotspots, as well as hard bottom types. Finally, the presence of lingcod, yellowtail, silvergray, or redstripe rockfish in a survey tow increased the likelihood of canary rockfish being present, as did the presence of basketstars and corals. By studying the relationships between species and their environment, we can begin to understand the relative importance of how environmental variables shape the distribution of managed species. For ecosystem-based management strategies to be successful, the functional relationships between organisms and their habitat must be understood. The predictive model developed in this study can be used to identify areas off Oregon and Washington where canary rockfish are likely to be found in relation to various habitat factors, and can potentially be used to delineate areas that should be sampled in future surveys of canary rockfish. Additionally, this research will help to improve our understanding of the factors that influence canary rockfish distribution, which may produce a more realistic definition of canary rockfish habitat, and improve assessment. This study specifically focuses on canary rockfish, because this species currently constrains many West Coast fisheries for groundfish, however, the methods outlined here could be applied more generally to other species of interest. Close

• 30. [Article] Twenty-year changes in riparian bird communities of east-central Oregon

  Over the last 50 years, riparian zones in the semi-arid West have gained recognition as disproportionately important habitats for both breeding bird communities and agricultural operations. Despite growing ...

  Citation × Citation Citation Abstract Copy Title: Twenty-year changes in riparian bird communities of east-central Oregon Author: Ellis, Michael S. Over the last 50 years, riparian zones in the semi-arid West have gained recognition as disproportionately important habitats for both breeding bird communities and agricultural operations. Despite growing interest in exploring avian-habitat relationships in these systems to better inform land management, few studies have attempted to describe temporal changes in the region's riparian bird communities. To provide a frame of reference for these changes, we compared indices of avian abundance and diversity from three streamside vegetation associations in east-central Oregon during the 2014 breeding season with baseline data collected by TA Sanders and WD Edge in 1993 and 1994 (Sanders and Edge 1998). Our objectives were to identify patterns of change in the avian community with a focus on riparian shrub-dependent species, to re-examine previously reported relationships between avian abundance and vegetation volume, and to identify possible causes of declines in abundance and diversity with the goal of providing land managers in the semi-arid region information to be used in the guidance and adaptation of management practices. We combined field protocols used by Sanders and Edge to survey birds along point count transects and to measure riparian vegetation with modern analytical techniques. We found few major differences in overall diversity between study periods, but documented precipitous declines in detections for two of three riparian shrub-dependent focal species - Yellow Warbler (Setophaga petechia) and Willow Flycatcher (Empidonax trailii). Song Sparrow (Melospiza melodia) detections declined by a smaller margin. Changes in number of detections for these species did not reflect trends in mesic shrub volume, which had been identified as a likely driver of obligate species abundance by Sanders and Edge but remained relatively unchanged between study periods. Declines of all three focal species reflected regional Breeding Bird Survey trends, corroborating our finding that their declines may not be a result of changes in local site conditions. Compositional similarity between avian communities was significantly higher in 2014 than in 1993-1994, exhibiting a shift toward greater homogenization between structurally distinct riparian habitats. Our results suggest managing working lands for riparian shrub cover or volume, an important metric of grazing intensity and riparian system health, may not be enough to conserve diversity and abundance of riparian-shrub dependent birds, and more work should be done to identify and alleviate factors contributing to these species' declines. Title: Twenty-year changes in riparian bird communities of east-central Oregon Author: Ellis, Michael S. Over the last 50 years, riparian zones in the semi-arid West have gained recognition as disproportionately important habitats for both breeding bird communities and agricultural operations. Despite growing interest in exploring avian-habitat relationships in these systems to better inform land management, few studies have attempted to describe temporal changes in the region's riparian bird communities. To provide a frame of reference for these changes, we compared indices of avian abundance and diversity from three streamside vegetation associations in east-central Oregon during the 2014 breeding season with baseline data collected by TA Sanders and WD Edge in 1993 and 1994 (Sanders and Edge 1998). Our objectives were to identify patterns of change in the avian community with a focus on riparian shrub-dependent species, to re-examine previously reported relationships between avian abundance and vegetation volume, and to identify possible causes of declines in abundance and diversity with the goal of providing land managers in the semi-arid region information to be used in the guidance and adaptation of management practices. We combined field protocols used by Sanders and Edge to survey birds along point count transects and to measure riparian vegetation with modern analytical techniques. We found few major differences in overall diversity between study periods, but documented precipitous declines in detections for two of three riparian shrub-dependent focal species - Yellow Warbler (Setophaga petechia) and Willow Flycatcher (Empidonax trailii). Song Sparrow (Melospiza melodia) detections declined by a smaller margin. Changes in number of detections for these species did not reflect trends in mesic shrub volume, which had been identified as a likely driver of obligate species abundance by Sanders and Edge but remained relatively unchanged between study periods. Declines of all three focal species reflected regional Breeding Bird Survey trends, corroborating our finding that their declines may not be a result of changes in local site conditions. Compositional similarity between avian communities was significantly higher in 2014 than in 1993-1994, exhibiting a shift toward greater homogenization between structurally distinct riparian habitats. Our results suggest managing working lands for riparian shrub cover or volume, an important metric of grazing intensity and riparian system health, may not be enough to conserve diversity and abundance of riparian-shrub dependent birds, and more work should be done to identify and alleviate factors contributing to these species' declines. Close

• 31. [Article] The Responses of Slope-spawning Flatfish to Environmental Variability in the Eastern Bering Sea

  When adult spawning and juvenile settling locations of marine fishes are geographically separated, their early life history stages must rely on transport and their own behavior to move them toward suitable ...

  Citation × Citation Citation Abstract Copy Title: The Responses of Slope-spawning Flatfish to Environmental Variability in the Eastern Bering Sea Author: Vestfals, Cathleen D. When adult spawning and juvenile settling locations of marine fishes are geographically separated, their early life history stages must rely on transport and their own behavior to move them toward suitable habitats for successful recruitment to the juvenile phase. Variations in climate may reduce the availability of spawning and juvenile nursery habitats and alter ocean circulation patterns, which can disrupt dispersal pathways and affect life cycle closure. This research focused on two commercially- and ecologically-important flatfish species in the eastern Bering Sea (EBS), Greenland halibut (Reinhardtius hippoglossoides) and Pacific halibut (Hippoglossus stenolepis), which may be especially sensitive to climate variability due to strong seasonally and ontogenetically variable distributions and extended pelagic larval phases. Data from fishery-dependent and fishery-independent sources were analyzed to determine the influence of environmental variability on adult habitat use, thus gaining a uniquely comprehensive range of seasonal and geographic coverage of each species' distribution. Transport along and across the Bering Slope was characterized from 23 years (1982 - 2004) of simulations from a Regional Ocean Modeling System (ROMS) ocean circulation model, with the expectation that changes in the strength and position of the Bering Slope Current (BSC) would affect recruitment, and that circulation features along and across the shelf edge would be strongly influenced by atmospheric forcing. To understand the physical mechanisms of larval delivery to shelf nursery areas, Greenland and Pacific halibut dispersal pathways were simulated from their source (e.g., spawning areas over the continental slope) to settlement locations (e.g., juvenile nursery areas on the continental shelf) using DisMELS (Dispersal Model for Early Life Stages), an individual-based particle-tracking model. Spatial patterns of dispersal were characterized for each species and for years with contrasting settlement success to understand the influence of local oceanographic and atmospheric conditions on dispersal corridor use. Adult Greenland and Pacific halibut exhibited strong and contrasting responses to changes in temperature on the shelf, with catches decreasing and increasing, respectively, at approximately 1°C. The effect of temperature was not as prominent along the slope, suggesting that slope habitats may provide some insulation from shelf-associated environmental variability, particularly for Greenland halibut. With warming, Greenland halibut exhibited more of a bathymetric shift in distribution, while the shift was more latitudinal for Pacific halibut. Habitat partitioning may, in part, explain differences in Greenland and Pacific halibut adult distributions. Analysis of modeled circulation revealed strong variations in the strength and position of the BSC, with changes in along-shelf and cross-shelf flow associated with changes in recruitment. Greenland halibut benefitted from decreased along-shelf and on-shelf flow, while Pacific halibut benefitted from on-shelf flows through Bering and Pribilof canyons. Variability in transport and the BSC position was strongly influenced by winds, ice cover, and large-scale climatic drivers. Greenland and Pacific halibut dispersal pathways varied between years, with distinct differences in dispersal characteristics found between the two species. In general, Greenland halibut connected to shelf nursery areas via more northern corridors, while Pacific halibut connected through more southern ones. In years with poor settlement success, the reverse pattern was observed. Greenland halibut dispersal metrics were strongly correlated with along- and cross-shelf transport, as well as NW along-shelf winds and ice, while Pacific halibut had strong associations with SW onshelf winds. Spawning time and location, along with climate-induced changes in circulation, appear to differentially affect Greenland and Pacific halibut dispersal pathways, which can lead to variations in their recruitment. Overall, Greenland and Pacific halibut had contrasting responses to similar environmental forcing, and predicted climate change is expected to impact these species in different ways. With increasing warming on the EBS shelf, they will likely further partition their habitats, with Greenland halibut finding colder refuges along the slope and Pacific halibut inhabiting larger portions of the shelf. Climate-induced changes in circulation were found to affect the transport of halibut eggs and larvae and their recruitment to the juvenile phase, which suggests an important role in their slope-shelf connectivity. Results of this study suggest that Greenland and Pacific halibut use different mechanisms to move from their spawning locations along the slope to their settlement areas on the shelf, and that environmental conditions that increase slope-shelf connectivity for one species will likely result in reduced connectivity for the other. This research improves our understanding of how slopespawning flatfish respond to a changing ocean environment, which is important for effective management of their populations, as predicted climate change will likely alter their habitat use and population dynamics. Title: The Responses of Slope-spawning Flatfish to Environmental Variability in the Eastern Bering Sea Author: Vestfals, Cathleen D. When adult spawning and juvenile settling locations of marine fishes are geographically separated, their early life history stages must rely on transport and their own behavior to move them toward suitable habitats for successful recruitment to the juvenile phase. Variations in climate may reduce the availability of spawning and juvenile nursery habitats and alter ocean circulation patterns, which can disrupt dispersal pathways and affect life cycle closure. This research focused on two commercially- and ecologically-important flatfish species in the eastern Bering Sea (EBS), Greenland halibut (Reinhardtius hippoglossoides) and Pacific halibut (Hippoglossus stenolepis), which may be especially sensitive to climate variability due to strong seasonally and ontogenetically variable distributions and extended pelagic larval phases. Data from fishery-dependent and fishery-independent sources were analyzed to determine the influence of environmental variability on adult habitat use, thus gaining a uniquely comprehensive range of seasonal and geographic coverage of each species' distribution. Transport along and across the Bering Slope was characterized from 23 years (1982 - 2004) of simulations from a Regional Ocean Modeling System (ROMS) ocean circulation model, with the expectation that changes in the strength and position of the Bering Slope Current (BSC) would affect recruitment, and that circulation features along and across the shelf edge would be strongly influenced by atmospheric forcing. To understand the physical mechanisms of larval delivery to shelf nursery areas, Greenland and Pacific halibut dispersal pathways were simulated from their source (e.g., spawning areas over the continental slope) to settlement locations (e.g., juvenile nursery areas on the continental shelf) using DisMELS (Dispersal Model for Early Life Stages), an individual-based particle-tracking model. Spatial patterns of dispersal were characterized for each species and for years with contrasting settlement success to understand the influence of local oceanographic and atmospheric conditions on dispersal corridor use. Adult Greenland and Pacific halibut exhibited strong and contrasting responses to changes in temperature on the shelf, with catches decreasing and increasing, respectively, at approximately 1°C. The effect of temperature was not as prominent along the slope, suggesting that slope habitats may provide some insulation from shelf-associated environmental variability, particularly for Greenland halibut. With warming, Greenland halibut exhibited more of a bathymetric shift in distribution, while the shift was more latitudinal for Pacific halibut. Habitat partitioning may, in part, explain differences in Greenland and Pacific halibut adult distributions. Analysis of modeled circulation revealed strong variations in the strength and position of the BSC, with changes in along-shelf and cross-shelf flow associated with changes in recruitment. Greenland halibut benefitted from decreased along-shelf and on-shelf flow, while Pacific halibut benefitted from on-shelf flows through Bering and Pribilof canyons. Variability in transport and the BSC position was strongly influenced by winds, ice cover, and large-scale climatic drivers. Greenland and Pacific halibut dispersal pathways varied between years, with distinct differences in dispersal characteristics found between the two species. In general, Greenland halibut connected to shelf nursery areas via more northern corridors, while Pacific halibut connected through more southern ones. In years with poor settlement success, the reverse pattern was observed. Greenland halibut dispersal metrics were strongly correlated with along- and cross-shelf transport, as well as NW along-shelf winds and ice, while Pacific halibut had strong associations with SW onshelf winds. Spawning time and location, along with climate-induced changes in circulation, appear to differentially affect Greenland and Pacific halibut dispersal pathways, which can lead to variations in their recruitment. Overall, Greenland and Pacific halibut had contrasting responses to similar environmental forcing, and predicted climate change is expected to impact these species in different ways. With increasing warming on the EBS shelf, they will likely further partition their habitats, with Greenland halibut finding colder refuges along the slope and Pacific halibut inhabiting larger portions of the shelf. Climate-induced changes in circulation were found to affect the transport of halibut eggs and larvae and their recruitment to the juvenile phase, which suggests an important role in their slope-shelf connectivity. Results of this study suggest that Greenland and Pacific halibut use different mechanisms to move from their spawning locations along the slope to their settlement areas on the shelf, and that environmental conditions that increase slope-shelf connectivity for one species will likely result in reduced connectivity for the other. This research improves our understanding of how slopespawning flatfish respond to a changing ocean environment, which is important for effective management of their populations, as predicted climate change will likely alter their habitat use and population dynamics. Close

• 32. [Article] Lidar-derived canopy architecture predicts brown creeper occupancy of two western coniferous forests

  This is the publisher’s final pdf. The published article is copyrighted by The Cooper Ornithological Society and can be found at: http://www.cooper.org/.

  Citation × Citation Citation Abstract Copy Title: Lidar-derived canopy architecture predicts brown creeper occupancy of two western coniferous forests Author: Vogeler, Jody C., Vierling, Lee A., Vierling, Kerri T., Hudak, Andrew T. This is the publisher’s final pdf. The published article is copyrighted by The Cooper Ornithological Society and can be found at: http://www.cooper.org/. Title: Lidar-derived canopy architecture predicts brown creeper occupancy of two western coniferous forests Author: Vogeler, Jody C., Vierling, Lee A., Vierling, Kerri T., Hudak, Andrew T. This is the publisher’s final pdf. The published article is copyrighted by The Cooper Ornithological Society and can be found at: http://www.cooper.org/. Close

• 33. [Article] Natural-Channel-Design Restorations That Changed Geomorphology Have Little Effect on Macroinvertebrate Communities in Headwater Streams

  This is the publisher’s final pdf. The published article is copyrighted by John Wiley & Sons, Inc. and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291526-100X. To the best of ...

  Citation × Citation Citation Abstract Copy Title: Natural-Channel-Design Restorations That Changed Geomorphology Have Little Effect on Macroinvertebrate Communities in Headwater Streams Author: Ernst, Anne G., Baldigo, Barry P., Warren, Dana R. This is the publisher’s final pdf. The published article is copyrighted by John Wiley & Sons, Inc. and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291526-100X. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Title: Natural-Channel-Design Restorations That Changed Geomorphology Have Little Effect on Macroinvertebrate Communities in Headwater Streams Author: Ernst, Anne G., Baldigo, Barry P., Warren, Dana R. This is the publisher’s final pdf. The published article is copyrighted by John Wiley & Sons, Inc. and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291526-100X. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Close

• 34. [Article] Aspen Restoration and Social Agreements: An Introductory Guide for Forest Collaboratives in Central and Eastern Oregon

  Collaborative Regional Learning This document is part of a forest collaborative regional learning project on aspen restoration and social agreements. Thanks to all the individuals, collaborative groups, ...

  Citation × Citation Citation Abstract Copy Title: Aspen Restoration and Social Agreements: An Introductory Guide for Forest Collaboratives in Central and Eastern Oregon Author: Davis, Emily Jane, Seager, S Trent, Ediger, Vernita Collaborative Regional Learning This document is part of a forest collaborative regional learning project on aspen restoration and social agreements. Thanks to all the individuals, collaborative groups, and organizations who provided feedback and suggestions. We appreciate the participation of members from: Blue Mountains Forest Partners, Deschutes Collaborative Forest Project, Harney County Restoration Collaborative, Ochoco Forest Restoration Collaborative, Umatilla Forest Collaborative Group, and Wallow-Whitman Forest Collaborative. Title: Aspen Restoration and Social Agreements: An Introductory Guide for Forest Collaboratives in Central and Eastern Oregon Author: Davis, Emily Jane, Seager, S Trent, Ediger, Vernita Collaborative Regional Learning This document is part of a forest collaborative regional learning project on aspen restoration and social agreements. Thanks to all the individuals, collaborative groups, and organizations who provided feedback and suggestions. We appreciate the participation of members from: Blue Mountains Forest Partners, Deschutes Collaborative Forest Project, Harney County Restoration Collaborative, Ochoco Forest Restoration Collaborative, Umatilla Forest Collaborative Group, and Wallow-Whitman Forest Collaborative. Close

• 35. [Article] Bird-vegetation relationships across ten years after thinning in young thinned and unthinned Douglas-fir forests

  Bird-vegetation associations are a base for bird conservation and management, as well as for predictions of the effects of resource management and climate change on wildlife populations. A recent shift ...

  Citation × Citation Citation Abstract Copy Title: Bird-vegetation relationships across ten years after thinning in young thinned and unthinned Douglas-fir forests Author: Yegorova, Svetlana Bird-vegetation associations are a base for bird conservation and management, as well as for predictions of the effects of resource management and climate change on wildlife populations. A recent shift in forest management priorities from timber production to native species' habitat conservation on federal lands has emphasized the need to understand the mechanisms underlying the effects of vegetation management on wildlife. The assumption of strong bird-vegetation relationships is rarely tested for forest birds, especially at large temporal extents, which are more likely to reveal instabilities in bird-vegetation relationships than short-term studies. This study aimed to quantify bird-vegetation relationships and investigate their strength in young thinned and unthinned Douglas-fir forest stands over ten to years post thinning. Additionally, this study investigated whether disturbance associated with forest thinning decoupled bird-vegetation relationships in the thinned and unthinned stands. I used abundance or occurrence data for eight bird species collected at 58 point count surveys, conducted during six breeding seasons over ten years following forest thinning. I obtained detailed local-scale vegetation characteristics associated with bird sampling points and modeled bird occurrence or abundance as a function of vegetation characteristics. Vegetation characteristics explaining individual species occurrence or abundance varied among species and among years for any given species. Six out of eight species showed responses to examined vegetation characteristics. For three out of six species, the effects of vegetation characteristics on bird occurrence or abundance remained consistently positive or negative over time. For the other three species the absolute effect of vegetation decreased over time to that of not statistically different from zero. The estimates of vegetation effects on bird response varied in size among years, though they were not statistically different among years. Magnitude of vegetation effect on bird occurrence or abundance did not increase with time, nor was it related to species prevalence or abundance. I found evidence of a response threshold for one species, Swainson's thrush. I suggest that changing abundance of resources, associated with thinning disturbance, demographic stochasticity associated with small population sizes, as well as large-scale demographic processes and possibly life history traits of examined species, mediate the strength of local-level bird-vegetation associations. Variability of vegetation effects on bird occurrence or abundance over time suggests a greater uncertainty of results of vegetation-related wildlife management efforts than has previously been suggested by short-term studies. Therefore, incorporation of the uncertainty of bird-vegetation relationships into predictive models and continued long-term monitoring of species response to management may be crucial for future successful and effective management decisions. Title: Bird-vegetation relationships across ten years after thinning in young thinned and unthinned Douglas-fir forests Author: Yegorova, Svetlana Bird-vegetation associations are a base for bird conservation and management, as well as for predictions of the effects of resource management and climate change on wildlife populations. A recent shift in forest management priorities from timber production to native species' habitat conservation on federal lands has emphasized the need to understand the mechanisms underlying the effects of vegetation management on wildlife. The assumption of strong bird-vegetation relationships is rarely tested for forest birds, especially at large temporal extents, which are more likely to reveal instabilities in bird-vegetation relationships than short-term studies. This study aimed to quantify bird-vegetation relationships and investigate their strength in young thinned and unthinned Douglas-fir forest stands over ten to years post thinning. Additionally, this study investigated whether disturbance associated with forest thinning decoupled bird-vegetation relationships in the thinned and unthinned stands. I used abundance or occurrence data for eight bird species collected at 58 point count surveys, conducted during six breeding seasons over ten years following forest thinning. I obtained detailed local-scale vegetation characteristics associated with bird sampling points and modeled bird occurrence or abundance as a function of vegetation characteristics. Vegetation characteristics explaining individual species occurrence or abundance varied among species and among years for any given species. Six out of eight species showed responses to examined vegetation characteristics. For three out of six species, the effects of vegetation characteristics on bird occurrence or abundance remained consistently positive or negative over time. For the other three species the absolute effect of vegetation decreased over time to that of not statistically different from zero. The estimates of vegetation effects on bird response varied in size among years, though they were not statistically different among years. Magnitude of vegetation effect on bird occurrence or abundance did not increase with time, nor was it related to species prevalence or abundance. I found evidence of a response threshold for one species, Swainson's thrush. I suggest that changing abundance of resources, associated with thinning disturbance, demographic stochasticity associated with small population sizes, as well as large-scale demographic processes and possibly life history traits of examined species, mediate the strength of local-level bird-vegetation associations. Variability of vegetation effects on bird occurrence or abundance over time suggests a greater uncertainty of results of vegetation-related wildlife management efforts than has previously been suggested by short-term studies. Therefore, incorporation of the uncertainty of bird-vegetation relationships into predictive models and continued long-term monitoring of species response to management may be crucial for future successful and effective management decisions. Close

• 36. [Article] Pacific lamprey Entosphenus tridentatus : integrating traditional ecological knowledge and contemporary values into conservation planning, and stream substrate associations with larval abundance in the Willamette River Basin, Oregon, U.S.A.

  Pacific lamprey Entosphenus tridentatus is a valuable icon and traditional food source for Indigenous people of western North America. Native Americans have utilized traditional ecological knowledge (TEK) ...

  Citation × Citation Citation Abstract Copy Title: Pacific lamprey Entosphenus tridentatus : integrating traditional ecological knowledge and contemporary values into conservation planning, and stream substrate associations with larval abundance in the Willamette River Basin, Oregon, U.S.A. Author: Sheoships, Gabe Pacific lamprey Entosphenus tridentatus is a valuable icon and traditional food source for Indigenous people of western North America. Native Americans have utilized traditional ecological knowledge (TEK) since time immemorial to guide their ways of life, transmitting cultural values and natural history to further generational knowledge. Pacific lamprey are in decline throughout their range, and have historically been disregarded in western science. The Willamette River Basin, Oregon, U.S.A currently supports a traditional harvest location, Willamette Falls, which continues to persist, despite great losses in adjacent basins and remains a harvest stronghold amongst Columbia River Basin Tribes. To further understand Pacific lamprey, we utilized both Indigenous knowledge and western science to gain information that would aid recovery. My first goal was to determine traditional ecological knowledge and the cultural values of Pacific lamprey to provide guidance for future conservation planning. My second goal was to evaluate the fine scale habitat characteristics of larval Pacific lamprey. To determine tribal values for the purpose of informing conservation planning of Pacific lamprey, I used: 1) oral history interviews of tribal elders, and 2) questionnaires distributed across entire adult (18 years and older) tribal populations. We conducted semi-structured interviews with tribal elders to gain insights into the biology, distribution, and cultural value of lamprey. I interviewed 32 tribal elders, 11 from the Grand Ronde, 10 from the Siletz, and 11 from the Umatilla. To understand modern fishing practices and current values of lamprey, I distributed a standardized questionnaire (n = 753) to a sample of each adult (18 years and older) tribal population, and received a total of 188 responses total: 38 from the Grand Ronde, 60 from the Siletz, and 90 from the Umatilla. From my interviews, I found that each tribe has noticed a decline in Pacific lamprey populations within their ceded areas, and has witnessed traditional harvest locations lost due to population declines and/or anthropogenic damage, leaving Willamette Falls as the sole harvest site for the three tribes. Questionnaire results showed that the strongest issues relating to the traditional usage of Pacific lamprey amongst each tribe are cultural awareness, harvest accessibility, and Pacific lamprey populations. I evaluated two fine scale habitat associations of larval Pacific lamprey in the Willamette River Basin to understand the association of stream sediment and larval abundance. Study objectives were to: 1) evaluate the substrate size most closely associated with larval abundance, and 2) to evaluate the influence of organic material upon larval abundance. We used a backpack electrofisher to enumerate larval lamprey in six wadeable Willamette River tributaries, using a nested two-pass sample design at a lower, middle, and upper reach (each reach composed of ten 1-m² quadrats). Stream sediment cores were collected for subsequent determination of particle size and organic composition content. I used particle size sieve analysis to estimate dominant substrate size class per sample, from the following size classes: silt (< 0.063 mm), very fine sand (0.063–0.125 mm), fine sand (0.125-0.25 mm), medium fine sand (0.25-0.50 mm), coarse sand (0.50-1.0 mm), very coarse sand (1.0-2.36 mm), and fine gravel (>2.36 mm). I analyzed organic content by loss of weight through combustion. Larvae were present in 17 of 18 reaches (94%) 18), but only detected in 37% of the quadrats. Larval Pacific lamprey abundance was highest in habitats with predominantly medium fine sand (0.25-0.50 mm) substrate. I fit negative binomial mixed models using parameters for sediment depth, percentage of medium fine sand (0.25-0.50 mm), organic material and a random effect for basin. My top model consisted of percentage of medium fine sand (0.25-0.50 mm), organic material and a random effect for basin. At the fine scale, substrate characteristics were associated with the abundance of larval Pacific lamprey. Appropriate conservation measures should be taken to address the restoration of Pacific lamprey, activities that promote natural river flow and distribution of sediment could be of benefit. Efforts that educate mainstream society should be implemented to reduce further species decline. With the continued decline of Pacific lamprey, there is potential for further degradation of tribal cultural values. Conservation work that promotes the restoration of Pacific lamprey is crucial to the tradition and culture of the Grand Ronde, Siletz, and Umatilla Tribes. Title: Pacific lamprey Entosphenus tridentatus : integrating traditional ecological knowledge and contemporary values into conservation planning, and stream substrate associations with larval abundance in the Willamette River Basin, Oregon, U.S.A. Author: Sheoships, Gabe Pacific lamprey Entosphenus tridentatus is a valuable icon and traditional food source for Indigenous people of western North America. Native Americans have utilized traditional ecological knowledge (TEK) since time immemorial to guide their ways of life, transmitting cultural values and natural history to further generational knowledge. Pacific lamprey are in decline throughout their range, and have historically been disregarded in western science. The Willamette River Basin, Oregon, U.S.A currently supports a traditional harvest location, Willamette Falls, which continues to persist, despite great losses in adjacent basins and remains a harvest stronghold amongst Columbia River Basin Tribes. To further understand Pacific lamprey, we utilized both Indigenous knowledge and western science to gain information that would aid recovery. My first goal was to determine traditional ecological knowledge and the cultural values of Pacific lamprey to provide guidance for future conservation planning. My second goal was to evaluate the fine scale habitat characteristics of larval Pacific lamprey. To determine tribal values for the purpose of informing conservation planning of Pacific lamprey, I used: 1) oral history interviews of tribal elders, and 2) questionnaires distributed across entire adult (18 years and older) tribal populations. We conducted semi-structured interviews with tribal elders to gain insights into the biology, distribution, and cultural value of lamprey. I interviewed 32 tribal elders, 11 from the Grand Ronde, 10 from the Siletz, and 11 from the Umatilla. To understand modern fishing practices and current values of lamprey, I distributed a standardized questionnaire (n = 753) to a sample of each adult (18 years and older) tribal population, and received a total of 188 responses total: 38 from the Grand Ronde, 60 from the Siletz, and 90 from the Umatilla. From my interviews, I found that each tribe has noticed a decline in Pacific lamprey populations within their ceded areas, and has witnessed traditional harvest locations lost due to population declines and/or anthropogenic damage, leaving Willamette Falls as the sole harvest site for the three tribes. Questionnaire results showed that the strongest issues relating to the traditional usage of Pacific lamprey amongst each tribe are cultural awareness, harvest accessibility, and Pacific lamprey populations. I evaluated two fine scale habitat associations of larval Pacific lamprey in the Willamette River Basin to understand the association of stream sediment and larval abundance. Study objectives were to: 1) evaluate the substrate size most closely associated with larval abundance, and 2) to evaluate the influence of organic material upon larval abundance. We used a backpack electrofisher to enumerate larval lamprey in six wadeable Willamette River tributaries, using a nested two-pass sample design at a lower, middle, and upper reach (each reach composed of ten 1-m² quadrats). Stream sediment cores were collected for subsequent determination of particle size and organic composition content. I used particle size sieve analysis to estimate dominant substrate size class per sample, from the following size classes: silt (< 0.063 mm), very fine sand (0.063–0.125 mm), fine sand (0.125-0.25 mm), medium fine sand (0.25-0.50 mm), coarse sand (0.50-1.0 mm), very coarse sand (1.0-2.36 mm), and fine gravel (>2.36 mm). I analyzed organic content by loss of weight through combustion. Larvae were present in 17 of 18 reaches (94%) 18), but only detected in 37% of the quadrats. Larval Pacific lamprey abundance was highest in habitats with predominantly medium fine sand (0.25-0.50 mm) substrate. I fit negative binomial mixed models using parameters for sediment depth, percentage of medium fine sand (0.25-0.50 mm), organic material and a random effect for basin. My top model consisted of percentage of medium fine sand (0.25-0.50 mm), organic material and a random effect for basin. At the fine scale, substrate characteristics were associated with the abundance of larval Pacific lamprey. Appropriate conservation measures should be taken to address the restoration of Pacific lamprey, activities that promote natural river flow and distribution of sediment could be of benefit. Efforts that educate mainstream society should be implemented to reduce further species decline. With the continued decline of Pacific lamprey, there is potential for further degradation of tribal cultural values. Conservation work that promotes the restoration of Pacific lamprey is crucial to the tradition and culture of the Grand Ronde, Siletz, and Umatilla Tribes. Close

• 37. [Article] Defining and evaluating recovery of OCN coho salmon stocks: implications for rebuilding stocks under the Oregon Plan : summary of a workshop organized by the Independent Multidisciplinary Science Team, August 4-5, 1999

  This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds.

  Citation × Citation Citation Abstract Copy Title: Defining and evaluating recovery of OCN coho salmon stocks: implications for rebuilding stocks under the Oregon Plan : summary of a workshop organized by the Independent Multidisciplinary Science Team, August 4-5, 1999 Author: Independent Multidisciplinary Science Team (Or.) This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Title: Defining and evaluating recovery of OCN coho salmon stocks: implications for rebuilding stocks under the Oregon Plan : summary of a workshop organized by the Independent Multidisciplinary Science Team, August 4-5, 1999 Author: Independent Multidisciplinary Science Team (Or.) This report was written by the Independent Multidisciplinary Science Team of the Oregon Plan for Salmon and Watersheds. Close