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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