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• 61. [Article] Assessment of the potential for conflict between existing ocean space use and renewable energy development off the coast of Oregon

  Oregon's ocean waters are a potential source of wind, wave, and tidal energy; of interest to renewable energy entrepreneurs and to the U.S. government as it seeks to bolster energy security. In order to ...

  Citation × Citation Citation Abstract Copy Title: Assessment of the potential for conflict between existing ocean space use and renewable energy development off the coast of Oregon Author: Sullivan, Colleen M. (Colleen Marie) Oregon's ocean waters are a potential source of wind, wave, and tidal energy; of interest to renewable energy entrepreneurs and to the U.S. government as it seeks to bolster energy security. In order to install technology to capture this energy, however, it may be necessary to mitigate conflict with existing ocean space users. The objective of this research was to construct a conflict analysis model in a GIS to answer the following research questions: (1) Within the study area off the coast of Oregon, where are stakeholders currently using ocean space and how many uses overlap? (2) To what extent might existing ocean space use present potential for conflict with renewable energy development? (3) How do various types of uncertainty affect analysis results? (4) What are the implications of these findings for ecosystem based management of the ocean? All available spatial information on ocean space usage by commercial fishing, commercial non-fishing, recreational, Native American, and scientific communities was gathered. Stakeholder outreach with these communities was used to vet the collected data and allow each to contribute knowledge not previously available through GIS data clearinghouses maintained by government or interest groups. The resulting data were used as inputs to a conflict visualization model written in Python and imported to an ArcGIS tool. Results showed extensive coverage and overlap of existing ocean space uses; specifically that 99.7% of the 1-nm² grid cells of the study area are occupied by at least 6 different categories of ocean space use. The six uses with the greatest coverage were: Fishing – Trolling, Habitat, Military, Fishing - Closure Areas, Protected, and Marine Transportation - Low Intensity. An uncertainty analysis was also completed to illustrate the margin for error and therefore the necessity of appropriate stakeholder outreach during the renewable energy siting process, as opposed to relying only on a GIS. Ranking of each category by its potential for conflict with renewable energy development demonstrated which areas of the ocean may be particularly contentious. Because rankings are subjective, a tool was created to allow users to input their own rankings. For the purpose of this report, default rankings were assigned to each as justified by the literature. Results under these assumptions showed that space use and potential for conflict were highest between the coast and approximately 30 nm at sea. This is likely because certain space use is limited by depth (e.g., recreational use); there is increased shipping density as vessels approach and depart major ports; and increased fuel costs associated with traveling further from shore. Two potential applications of model results were demonstrated. First, comparison with existing wave energy permit sites highlighted relative potential for conflict among the sites and the input data detailed the specific uses present. Second, comparison with areas determined most suitable for development by the wave energy industry illustrated that areas of high suitability often also had high rankings for potential for conflict. It appeared that the factors that determined development suitability were often the same factors that drew current ocean space users to those locations. Current support at the state, regional and federal level under the National Ocean Policy for the use of marine spatial planning as a tool to implement ecosystem based management of the oceans requires that tools such as the one developed in this research are used, to ensure that all components of the marine ecosystem are considered prior to implementation of a management plan. The addition of renewable energy to the current social landscape of the ocean will reduce the resource base for many categories of ocean space use. Model results demonstrated that mitigation of conflict between development and existing space use is not merely a best practice supported by current policy, but a necessity. Results presented a visualization of the social landscape of the ocean that could help managers determine which stakeholders to engage during the initial stage of choosing a site for development. Title: Assessment of the potential for conflict between existing ocean space use and renewable energy development off the coast of Oregon Author: Sullivan, Colleen M. (Colleen Marie) Oregon's ocean waters are a potential source of wind, wave, and tidal energy; of interest to renewable energy entrepreneurs and to the U.S. government as it seeks to bolster energy security. In order to install technology to capture this energy, however, it may be necessary to mitigate conflict with existing ocean space users. The objective of this research was to construct a conflict analysis model in a GIS to answer the following research questions: (1) Within the study area off the coast of Oregon, where are stakeholders currently using ocean space and how many uses overlap? (2) To what extent might existing ocean space use present potential for conflict with renewable energy development? (3) How do various types of uncertainty affect analysis results? (4) What are the implications of these findings for ecosystem based management of the ocean? All available spatial information on ocean space usage by commercial fishing, commercial non-fishing, recreational, Native American, and scientific communities was gathered. Stakeholder outreach with these communities was used to vet the collected data and allow each to contribute knowledge not previously available through GIS data clearinghouses maintained by government or interest groups. The resulting data were used as inputs to a conflict visualization model written in Python and imported to an ArcGIS tool. Results showed extensive coverage and overlap of existing ocean space uses; specifically that 99.7% of the 1-nm² grid cells of the study area are occupied by at least 6 different categories of ocean space use. The six uses with the greatest coverage were: Fishing – Trolling, Habitat, Military, Fishing - Closure Areas, Protected, and Marine Transportation - Low Intensity. An uncertainty analysis was also completed to illustrate the margin for error and therefore the necessity of appropriate stakeholder outreach during the renewable energy siting process, as opposed to relying only on a GIS. Ranking of each category by its potential for conflict with renewable energy development demonstrated which areas of the ocean may be particularly contentious. Because rankings are subjective, a tool was created to allow users to input their own rankings. For the purpose of this report, default rankings were assigned to each as justified by the literature. Results under these assumptions showed that space use and potential for conflict were highest between the coast and approximately 30 nm at sea. This is likely because certain space use is limited by depth (e.g., recreational use); there is increased shipping density as vessels approach and depart major ports; and increased fuel costs associated with traveling further from shore. Two potential applications of model results were demonstrated. First, comparison with existing wave energy permit sites highlighted relative potential for conflict among the sites and the input data detailed the specific uses present. Second, comparison with areas determined most suitable for development by the wave energy industry illustrated that areas of high suitability often also had high rankings for potential for conflict. It appeared that the factors that determined development suitability were often the same factors that drew current ocean space users to those locations. Current support at the state, regional and federal level under the National Ocean Policy for the use of marine spatial planning as a tool to implement ecosystem based management of the oceans requires that tools such as the one developed in this research are used, to ensure that all components of the marine ecosystem are considered prior to implementation of a management plan. The addition of renewable energy to the current social landscape of the ocean will reduce the resource base for many categories of ocean space use. Model results demonstrated that mitigation of conflict between development and existing space use is not merely a best practice supported by current policy, but a necessity. Results presented a visualization of the social landscape of the ocean that could help managers determine which stakeholders to engage during the initial stage of choosing a site for development. Close

• 62. [Article] The epidemiology of sudden oak death in Oregon forests

  The phytopathogen Phytophthora ramorum (Werres, DeCock & Man in't Veld), causal agent of Sudden Oak Death (SOD) of oaks (Quercus spp.) and tanoaks (Notholithocarpus densiflorus syn. Lithocarpus densiflorus), ...

  Citation × Citation Citation Abstract Copy Title: The epidemiology of sudden oak death in Oregon forests Author: Peterson, Ebba K. The phytopathogen Phytophthora ramorum (Werres, DeCock & Man in't Veld), causal agent of Sudden Oak Death (SOD) of oaks (Quercus spp.) and tanoaks (Notholithocarpus densiflorus syn. Lithocarpus densiflorus), is established in coastal forests of the western United States. Since the discovery of SOD in the Douglas-fir / tanoak forests of southwest Oregon in 2001, a multiagency effort has ensued with the goal of fully eliminating P. ramorum from this originally small and isolated area. In this study we investigated the epidemiology of SOD in Oregon, particularly as it affects the success of the eradication program. Two approaches were taken to discern the mechanism of long distance dispersal: first, a landscape analysis of the spatial relationship between SOD sites and roads or streams, features associated with movement of infested soils, and, second, a local analysis to discern if understory infection is originating from soil or stream-borne inoculum. Using a restricted randomization test we concluded that SOD sites were no closer to roads than expected by chance, which is inconsistent with soil dispersal by people. While we found evidence that SOD sites were preferentially closer to waterways, inoculum had not moved away from streams into adjacent understory foliage. The local distribution of understory infection around SOD positive trees indicated that primary inoculum is infecting overstory canopies first, suggesting that P. ramorum is dispersing in air currents. Regression modeling indicated that weather conditions two years before detection could explain variation in the maximum distance inoculum moved each year of the epidemic between 2001 and 2010. This two year delay between infection and detection has allowed ample time for infested sites to contribute to further spread. Model results were consistent with observations made the summer of 2011, when trees likely infected by secondary inoculum at non-eradicated sites developed symptoms but were still undetectable by aerial surveys. Due to the prevalence of infection on tanoak, opportunities for sporulation and infection occur more often in Oregon than in California. These data can explain the failure to eliminate P. ramorum. Nevertheless, we did find evidence that the eradication program has significantly reduced the potential size of the SOD epidemic in Oregon. Title: The epidemiology of sudden oak death in Oregon forests Author: Peterson, Ebba K. The phytopathogen Phytophthora ramorum (Werres, DeCock & Man in't Veld), causal agent of Sudden Oak Death (SOD) of oaks (Quercus spp.) and tanoaks (Notholithocarpus densiflorus syn. Lithocarpus densiflorus), is established in coastal forests of the western United States. Since the discovery of SOD in the Douglas-fir / tanoak forests of southwest Oregon in 2001, a multiagency effort has ensued with the goal of fully eliminating P. ramorum from this originally small and isolated area. In this study we investigated the epidemiology of SOD in Oregon, particularly as it affects the success of the eradication program. Two approaches were taken to discern the mechanism of long distance dispersal: first, a landscape analysis of the spatial relationship between SOD sites and roads or streams, features associated with movement of infested soils, and, second, a local analysis to discern if understory infection is originating from soil or stream-borne inoculum. Using a restricted randomization test we concluded that SOD sites were no closer to roads than expected by chance, which is inconsistent with soil dispersal by people. While we found evidence that SOD sites were preferentially closer to waterways, inoculum had not moved away from streams into adjacent understory foliage. The local distribution of understory infection around SOD positive trees indicated that primary inoculum is infecting overstory canopies first, suggesting that P. ramorum is dispersing in air currents. Regression modeling indicated that weather conditions two years before detection could explain variation in the maximum distance inoculum moved each year of the epidemic between 2001 and 2010. This two year delay between infection and detection has allowed ample time for infested sites to contribute to further spread. Model results were consistent with observations made the summer of 2011, when trees likely infected by secondary inoculum at non-eradicated sites developed symptoms but were still undetectable by aerial surveys. Due to the prevalence of infection on tanoak, opportunities for sporulation and infection occur more often in Oregon than in California. These data can explain the failure to eliminate P. ramorum. Nevertheless, we did find evidence that the eradication program has significantly reduced the potential size of the SOD epidemic in Oregon. Close

• 63. [Article] Geomorphic and Climatic Controls on Water Temperature and Streambed Scour, Copper River Delta, Alaska : Implications for Understanding Climate Change Impacts to the Pacific Salmon Egg Incubation Environment

  Pacific salmon (Oncorhynchus spp.) face numerous challenges associated with climate change. Most research has emphasized the potential effects of elevated summer water temperatures; however, climatic changes ...

  Citation × Citation Citation Abstract Copy Title: Geomorphic and Climatic Controls on Water Temperature and Streambed Scour, Copper River Delta, Alaska : Implications for Understanding Climate Change Impacts to the Pacific Salmon Egg Incubation Environment Author: Adelfio, Luca A. Pacific salmon (Oncorhynchus spp.) face numerous challenges associated with climate change. Most research has emphasized the potential effects of elevated summer water temperatures; however, climatic changes are also projected to significantly alter incubation and rearing habitats during the late autumn, winter, and spring months ("the incubation period"). Along the southern coast of Alaska, projected climatic changes include increases in the frequency of above freezing winter temperatures and reductions in low elevation snowpack. These changes are expected to impact the hydrology of salmon streams by increasing both water temperatures and the magnitude and frequency of winter floods. Projected increases in water temperature may accelerate embryo development, impacting juvenile viability. More powerful and more frequent winter floods could reduce the survival of salmon eggs by increasing streambed scour. Here, I investigate climatic and geomorphic controls of water temperature and potential scour depth at salmon spawning and rearing sites on the Copper River Delta, a large coastal foreland in Southcentral Alaska. In chapter 2, I utilized surface water temperature data collected at 18 sites to test the abilities of regression models to project year-round water temperature metrics based on catchment characteristics (elevation, slope, area, percent lake area) and air-water temperature correlations. Considerable variability in water temperature was observed on spatial and temporal scales. Both temperature maxima and the frequency of freezing conditions were positively correlated with percent lake area and negatively correlated with catchment elevation and slope. Sites with upwelling groundwater and sites with high-relief, high elevation catchments exhibited lower thermal sensitivity and water temperatures are anticipated to be less impacted by projected climatic changes. In chapter 3, I utilized surface and streambed water temperature data collected at 8 spawning sites to compare water temperatures during incubation periods under climatological mean ("severe winter") and anomalously warm ("mild winter") conditions. I also collected stream stage and channel geometry data at a subset of 3 sites and calculated streambed scour at bankfull discharge. The magnitude and seasonality of accumulated thermal units (°C/day) (ATU) within spawning gravels varied significantly between severe and mild winters at shallow flowpath sites, but not at upwelling groundwater sites. When seasonal snow and ice was absent, increases in spring ATU at shallow flowpath sites were particularly significant. Modelled mean scour depths varied from 3 to 72 cm, suggesting the impacts of scour on egg mortality will be variable across the landscape. I conclude that the impacts of projected climatic changes are likely to vary in magnitude across the Copper River Delta, even at small spatial scales, due to heterogeneity in climatic and geomorphic controls. Title: Geomorphic and Climatic Controls on Water Temperature and Streambed Scour, Copper River Delta, Alaska : Implications for Understanding Climate Change Impacts to the Pacific Salmon Egg Incubation Environment Author: Adelfio, Luca A. Pacific salmon (Oncorhynchus spp.) face numerous challenges associated with climate change. Most research has emphasized the potential effects of elevated summer water temperatures; however, climatic changes are also projected to significantly alter incubation and rearing habitats during the late autumn, winter, and spring months ("the incubation period"). Along the southern coast of Alaska, projected climatic changes include increases in the frequency of above freezing winter temperatures and reductions in low elevation snowpack. These changes are expected to impact the hydrology of salmon streams by increasing both water temperatures and the magnitude and frequency of winter floods. Projected increases in water temperature may accelerate embryo development, impacting juvenile viability. More powerful and more frequent winter floods could reduce the survival of salmon eggs by increasing streambed scour. Here, I investigate climatic and geomorphic controls of water temperature and potential scour depth at salmon spawning and rearing sites on the Copper River Delta, a large coastal foreland in Southcentral Alaska. In chapter 2, I utilized surface water temperature data collected at 18 sites to test the abilities of regression models to project year-round water temperature metrics based on catchment characteristics (elevation, slope, area, percent lake area) and air-water temperature correlations. Considerable variability in water temperature was observed on spatial and temporal scales. Both temperature maxima and the frequency of freezing conditions were positively correlated with percent lake area and negatively correlated with catchment elevation and slope. Sites with upwelling groundwater and sites with high-relief, high elevation catchments exhibited lower thermal sensitivity and water temperatures are anticipated to be less impacted by projected climatic changes. In chapter 3, I utilized surface and streambed water temperature data collected at 8 spawning sites to compare water temperatures during incubation periods under climatological mean ("severe winter") and anomalously warm ("mild winter") conditions. I also collected stream stage and channel geometry data at a subset of 3 sites and calculated streambed scour at bankfull discharge. The magnitude and seasonality of accumulated thermal units (°C/day) (ATU) within spawning gravels varied significantly between severe and mild winters at shallow flowpath sites, but not at upwelling groundwater sites. When seasonal snow and ice was absent, increases in spring ATU at shallow flowpath sites were particularly significant. Modelled mean scour depths varied from 3 to 72 cm, suggesting the impacts of scour on egg mortality will be variable across the landscape. I conclude that the impacts of projected climatic changes are likely to vary in magnitude across the Copper River Delta, even at small spatial scales, due to heterogeneity in climatic and geomorphic controls. Close

• 64. [Article] On the estimation and application of spatial and temporal autocorrelation in headwater streams

  This collection of three manuscripts serves to improve methods for collecting, interpreting, and utilizing autocorrelated data from headwater stream networks. Each stream network is comprised of linear ...

  Citation × Citation Citation Abstract Copy Title: On the estimation and application of spatial and temporal autocorrelation in headwater streams Author: Som, Nicholas A. This collection of three manuscripts serves to improve methods for collecting, interpreting, and utilizing autocorrelated data from headwater stream networks. Each stream network is comprised of linear segments. These segments lie within a unique branching structure that connects the segments via flowing water, and the connectivity provided by water varies seasonally. These aspects separate stream networks from other landscapes, and provide unique challenges to the statistical analysis of stream-based phenomenon. Two chapters of this work relied on a unique and comprehensive set of data. These data constitute a complete census of habitat unit fish counts from 40 randomly selected headwater basins in western Oregon. The first objective of this work was to evaluate how different sampling designs captured spatial autocorrelation, given the samples were drawn from a population of spatially autocorrelated observations. Spatially distributed clusters of sampling locations were more apt to capture spatial autocorrelation than samples without clusters or small clusters located at tributary junctions. A similar investigation was made concerning sampling design performance in relation to estimating autocorrelation function values. All sampling designs lead generally to negatively biased estimates, and practical differences among the sampling designs were not observed. The second objective was to investigate spatial autocorrelation model range parameters as measures of patch sizes. It is common practice to use range parameters to infer the size of patches within spatially autocorrelated data, but this methodology lacks sufficient justification. The census data were used to compute range parameter values, and another proposed autocorrelative measure of patch size: the integral scale. The same data were used to compute patch sizes under several patch definitions, and the relationship of range parameters and integral scale values with patch sizes was explored. Range parameter values did not equal and were not strongly correlated with average patch sizes, though range parameter values were more correlated with maximum patch and gap sizes. Integral scale values matched the magnitude of, but were not strongly correlated with, average patch sizes. The third objective was to refine the analysis of temporally autocorrelated hydrology data from paired watershed studies. Paired watershed studies are used to evaluate forest harvesting effects on stream biota and hydrology (i.e. fish, amphibians, insects, stream flow, and sediment yield). Traditionally, treatment effects are discerned using prediction intervals. This work provided an improved method for constructing prediction intervals for use in change detection in paired watershed studies. The improved prediction intervals included variation associated with estimating linear and autocorrelation model parameters. Title: On the estimation and application of spatial and temporal autocorrelation in headwater streams Author: Som, Nicholas A. This collection of three manuscripts serves to improve methods for collecting, interpreting, and utilizing autocorrelated data from headwater stream networks. Each stream network is comprised of linear segments. These segments lie within a unique branching structure that connects the segments via flowing water, and the connectivity provided by water varies seasonally. These aspects separate stream networks from other landscapes, and provide unique challenges to the statistical analysis of stream-based phenomenon. Two chapters of this work relied on a unique and comprehensive set of data. These data constitute a complete census of habitat unit fish counts from 40 randomly selected headwater basins in western Oregon. The first objective of this work was to evaluate how different sampling designs captured spatial autocorrelation, given the samples were drawn from a population of spatially autocorrelated observations. Spatially distributed clusters of sampling locations were more apt to capture spatial autocorrelation than samples without clusters or small clusters located at tributary junctions. A similar investigation was made concerning sampling design performance in relation to estimating autocorrelation function values. All sampling designs lead generally to negatively biased estimates, and practical differences among the sampling designs were not observed. The second objective was to investigate spatial autocorrelation model range parameters as measures of patch sizes. It is common practice to use range parameters to infer the size of patches within spatially autocorrelated data, but this methodology lacks sufficient justification. The census data were used to compute range parameter values, and another proposed autocorrelative measure of patch size: the integral scale. The same data were used to compute patch sizes under several patch definitions, and the relationship of range parameters and integral scale values with patch sizes was explored. Range parameter values did not equal and were not strongly correlated with average patch sizes, though range parameter values were more correlated with maximum patch and gap sizes. Integral scale values matched the magnitude of, but were not strongly correlated with, average patch sizes. The third objective was to refine the analysis of temporally autocorrelated hydrology data from paired watershed studies. Paired watershed studies are used to evaluate forest harvesting effects on stream biota and hydrology (i.e. fish, amphibians, insects, stream flow, and sediment yield). Traditionally, treatment effects are discerned using prediction intervals. This work provided an improved method for constructing prediction intervals for use in change detection in paired watershed studies. The improved prediction intervals included variation associated with estimating linear and autocorrelation model parameters. Close

• 65. [Article] Geographic factors as retardants to the development of Alaska's mineral industries

  The various elements of physical geography are commonly entertained as factors retarding the mineral industries of Alaska. It has been shown by numerous writers that the mineral industries of Alaska are, ...

  Citation × Citation Citation Abstract Copy Title: Geographic factors as retardants to the development of Alaska's mineral industries Author: Francis, Karl Earvil The various elements of physical geography are commonly entertained as factors retarding the mineral industries of Alaska. It has been shown by numerous writers that the mineral industries of Alaska are, indeed, in a difficult situation. Only the petroleum industry and sand and gravel for construction are of much significance to the Alaskan economy. Alaska's location makes it difficult to use domestic markets and turns the attention of all the resource-based primary industry toward the Orient. Though close to Europe, Alaskan trade across the Arctic Ocean yet awaits future transportation developments. The strategic position of Alaska has very significantly affected Alaska's primary industries by imposing stifling inflation on the state through emergency military activity little concerned with economics. Statehood and increased concern with the economy of Alaska by the Federal government promises to improve Alaska's locational problems. Alaska's size to some extent limits accessibility to the interior, but it also provides Alaska with a high mineral resource potential of great diversity and a very diverse landscape. The diversity of the land is a retardant to the extent that complexity of environment is a characteristic of Alaskan operations requiring a wide range of field experience and field equipment. Experience in all Alaskan terrain is quite rare. The topography of Alaska limits the development of new transportational routes to the interior from the south coast. It does not appreciably affect operational costs on existing roads and rails. Low terrain subject to frost action is a greater operational problem. As an underdeveloped land, Alaska is not unusually disadvantaged by topography; it does, in fact, have some advantages. A great hydroelectric potential exists in Alaska, but there is little chance that it will be of any great value to the mineral industries at this stage. Alaska has many diverse climates. South coastal Alaska has a climate similar enough to southern climates to be considered insignificant as a retardant to the mineral industries. In providing frozen coasts to western and northern Alaska, climate seriously retards development in these areas. Permafrost is a climatic resultant offering some considerable but yet largely undetermined effect on the mineral industries. The colder parts of Alaska have their biggest effect on the mineral industries in being different and, consequently, foreign and discouraging to southern people. The inherent disadvantage of cold is still largely obscured by blundering and inefficiency. Alaska has a considerable and diverse mineral resource that can, at this time, only be inferred. The unknown of Alaskan geology is its most striking feature. Exploration in all aspects is seriously discouraged by the economy and the obscuration of bed rock. Geophysical and geochemical prospecting has met with little success. It is felt that the lack of knowledge of and experience with the land is the biggest retardant to Alaska's mineral industries. The land is not inherently hostile, but rather it is different from that familiar to most of the people on it. A two-pronged attack on ignorance of the land is suggested, one to disseminate present knowledge and the other to seek out the unknown. When Alaska acquires a people familiar with and fully oriented toward the land, the effect of the geographic factors presently retarding the mineral industries will be greatly reduced. Title: Geographic factors as retardants to the development of Alaska's mineral industries Author: Francis, Karl Earvil The various elements of physical geography are commonly entertained as factors retarding the mineral industries of Alaska. It has been shown by numerous writers that the mineral industries of Alaska are, indeed, in a difficult situation. Only the petroleum industry and sand and gravel for construction are of much significance to the Alaskan economy. Alaska's location makes it difficult to use domestic markets and turns the attention of all the resource-based primary industry toward the Orient. Though close to Europe, Alaskan trade across the Arctic Ocean yet awaits future transportation developments. The strategic position of Alaska has very significantly affected Alaska's primary industries by imposing stifling inflation on the state through emergency military activity little concerned with economics. Statehood and increased concern with the economy of Alaska by the Federal government promises to improve Alaska's locational problems. Alaska's size to some extent limits accessibility to the interior, but it also provides Alaska with a high mineral resource potential of great diversity and a very diverse landscape. The diversity of the land is a retardant to the extent that complexity of environment is a characteristic of Alaskan operations requiring a wide range of field experience and field equipment. Experience in all Alaskan terrain is quite rare. The topography of Alaska limits the development of new transportational routes to the interior from the south coast. It does not appreciably affect operational costs on existing roads and rails. Low terrain subject to frost action is a greater operational problem. As an underdeveloped land, Alaska is not unusually disadvantaged by topography; it does, in fact, have some advantages. A great hydroelectric potential exists in Alaska, but there is little chance that it will be of any great value to the mineral industries at this stage. Alaska has many diverse climates. South coastal Alaska has a climate similar enough to southern climates to be considered insignificant as a retardant to the mineral industries. In providing frozen coasts to western and northern Alaska, climate seriously retards development in these areas. Permafrost is a climatic resultant offering some considerable but yet largely undetermined effect on the mineral industries. The colder parts of Alaska have their biggest effect on the mineral industries in being different and, consequently, foreign and discouraging to southern people. The inherent disadvantage of cold is still largely obscured by blundering and inefficiency. Alaska has a considerable and diverse mineral resource that can, at this time, only be inferred. The unknown of Alaskan geology is its most striking feature. Exploration in all aspects is seriously discouraged by the economy and the obscuration of bed rock. Geophysical and geochemical prospecting has met with little success. It is felt that the lack of knowledge of and experience with the land is the biggest retardant to Alaska's mineral industries. The land is not inherently hostile, but rather it is different from that familiar to most of the people on it. A two-pronged attack on ignorance of the land is suggested, one to disseminate present knowledge and the other to seek out the unknown. When Alaska acquires a people familiar with and fully oriented toward the land, the effect of the geographic factors presently retarding the mineral industries will be greatly reduced. Close

• 66. [Article] THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus)

  Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary ...

  Citation × Citation Citation Abstract Copy Title: THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus) Author: Nelson, Thomas Year: 2017 Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species. Title: THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus) Author: Nelson, Thomas Year: 2017 Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species. Close

• 67. [Article] Influences of island characteristics on community structure and species incidence of desert bats in a near-shore archipelago, Baja California, Mexico

  Island biogeography has strongly influenced the study of biodiversity because archipelagos provide natural model systems for investigating patterns of diversity and the processes that shape ecological ...

  Citation × Citation Citation Abstract Copy Title: Influences of island characteristics on community structure and species incidence of desert bats in a near-shore archipelago, Baja California, Mexico Author: Frick, Winifred F. Island biogeography has strongly influenced the study of biodiversity because archipelagos provide natural model systems for investigating patterns of diversity and the processes that shape ecological communities. I investigated the influence of area and isolation of islands (n = 32) in the Gulf of California, Mexico on patterns of richness, nestedness, and incidence of desert bats to determine factors important in shaping community structure and patterns of occurrence of bats in a naturally insular landscape. Species richness of bats was positively influenced by island size and declined with isolation from the Baja peninsula in two distinct subarchipelagos. Southern islands, which are associated with greater density of vegetation from summer rainfall, supported more species than dry, barren islands in the northern subarchipelago, suggesting that both area and habitat characteristics contribute to species richness of bats. Community composition of bats was nested by area and isolation, such that species found on smaller and more isolated islands were subsets of communities found on large, less isolated islands that harbored higher richness. The influences of area and isolation on community nestedness suggest species differ in immigration and persistence rates on islands. Bat communities were also nested at 27 sites in coastal habitat on the Baja peninsula, indicating that nestedness may occur in contiguous habitats that lack immigration and extinction filters. Probability of species occurrence on islands was influenced by area for five species of insectivorous bat (Pipistrellus hesperus, Myotis californicus, Macrotus californicus, Antrozous pallidus, and Mormoops megalophylla), suggesting occupancy of islands by these species is limited by resource requirements. The threshold of island size for occupancy of most species was ca. 100 ha, which is similar to area thresholds of incidence for many landbirds in the same archipelago. Isolation also influenced incidence of insectivorous bat species. My research shows that area and isolation influence both community structure and occupancy of bat species in a near-shore archipelago. My results raise important questions about connectivity and persistence of populations of bats in isolated habitats, especially when patch size is small. Title: Influences of island characteristics on community structure and species incidence of desert bats in a near-shore archipelago, Baja California, Mexico Author: Frick, Winifred F. Island biogeography has strongly influenced the study of biodiversity because archipelagos provide natural model systems for investigating patterns of diversity and the processes that shape ecological communities. I investigated the influence of area and isolation of islands (n = 32) in the Gulf of California, Mexico on patterns of richness, nestedness, and incidence of desert bats to determine factors important in shaping community structure and patterns of occurrence of bats in a naturally insular landscape. Species richness of bats was positively influenced by island size and declined with isolation from the Baja peninsula in two distinct subarchipelagos. Southern islands, which are associated with greater density of vegetation from summer rainfall, supported more species than dry, barren islands in the northern subarchipelago, suggesting that both area and habitat characteristics contribute to species richness of bats. Community composition of bats was nested by area and isolation, such that species found on smaller and more isolated islands were subsets of communities found on large, less isolated islands that harbored higher richness. The influences of area and isolation on community nestedness suggest species differ in immigration and persistence rates on islands. Bat communities were also nested at 27 sites in coastal habitat on the Baja peninsula, indicating that nestedness may occur in contiguous habitats that lack immigration and extinction filters. Probability of species occurrence on islands was influenced by area for five species of insectivorous bat (Pipistrellus hesperus, Myotis californicus, Macrotus californicus, Antrozous pallidus, and Mormoops megalophylla), suggesting occupancy of islands by these species is limited by resource requirements. The threshold of island size for occupancy of most species was ca. 100 ha, which is similar to area thresholds of incidence for many landbirds in the same archipelago. Isolation also influenced incidence of insectivorous bat species. My research shows that area and isolation influence both community structure and occupancy of bat species in a near-shore archipelago. My results raise important questions about connectivity and persistence of populations of bats in isolated habitats, especially when patch size is small. Close

• 68. [Article] The Role of Plant-soil Feedback in the Invasion of Brachypodium sylvaticum in Douglas-fir Forests

  Invasive plants have the capacity to transform landscapes and alter ecosystem function, causing significant economic and ecological damage. These effects include displacement and reduction of native flora ...

  Citation × Citation Citation Abstract Copy Title: The Role of Plant-soil Feedback in the Invasion of Brachypodium sylvaticum in Douglas-fir Forests Author: Esterson, Andrew Invasive plants have the capacity to transform landscapes and alter ecosystem function, causing significant economic and ecological damage. These effects include displacement and reduction of native flora and fauna, altered fire regimes, modification of biotic and abiotic soil properties, as well as local, regional, and global economic impacts. With such large impacts it is important that we better understand invasion dynamics to help with prevention, control and mitigation of invasive species. One process that has been associated with plant invasion is plant-soil feedback (PSF). A PSF occurs when plants alter biotic and abiotic soil properties through a variety of root exudates and litter decomposition such that subsequent plant growth is either positively or negatively affected. Positive conspecific and negative heterospecific responses have been theorized to be invasive species traits that promote invasion. Once an invasive species is removed from a system, there is a chance that PSFs generated by that species will persist in the soil, which is often referred to as 'plant legacies' or 'legacy effects' and may negatively influence restoration efforts. In the U.S. Pacific Northwest (PNW), Brachypodium sylvaticum (slender false brome), a perennial bunch grass native to Eurasia, is listed as a quarantined invasive species in California, Oregon, and Washington. Currently, B. sylvaticum is in the midst of rapid population growth and range expansion with populations in New York, Virginia, and Ontario, Canada. With a quickly expanding range research is critical for successful efforts to reduce the spread of B. sylvaticum. We developed two experiments to determine if PSF is a contributing factor to B. sylvaticum invasion in PNW forests. We hypothesized that 1) B. sylvaticum has positive conspecific and negative heterospecific PSF, 2) native species PSF has no effect on B. sylvaticum, and 3) PSF generated by B. sylvaticum will persist in the soil once removed, but over time, response of native species, soil nutrients and bacterial community composition will change from the invaded conditioned. To test our first two hypotheses, B. sylvaticum and five common native plants from the Oregon Coastal range, including the economically important tree, Pseudotsuga menziesii (Douglas-fir), were grown in a greenhouse on wild forest soils that had either been sterilized or kept live to condition the soil biotic community to the invader and the native species. Brachypodium sylvaticum was then grown on soil conditioned by itself and soil conditioned by natives; each of the five native species was grown on soil conditioned by B. sylvaticum and on their own conditioned soils. Plant biomass along with species specific measurements (number of leaves, stems, tillers, stem diameter and height) were recorded and a relative response (RR) index was used to determine the direction of PSF for the invader and native species. To test our third hypothesis, in March, 2015, ten plots were established in the McDonald-Dunn Research Forest located in Corvallis, OR where B. sylvaticum had at least 75% cover. Herbicide was applied to half of each plot to make two soil treatments: soil with B. sylvaticum and soil without B. sylvaticum. Over a nine-month period three soil collections took place where soil was collected from all plots and treatments. Plant response was evaluated by growing four native species and B. sylvaticum on both soil treatments and evaluating total biomass with a RR index; plant response (via growth), soil nutrients and bacterial communities were measured for each collection period. Bacterial communities were measured with phospholipid fatty acid (PLFA) analysis and high throughput 16s rRNA amplicon sequencing. Contrary to our hypotheses, the RR to PSF generated by B. sylvaticum was negative for the invader and P. menziesii and neutral for all other natives. Soils conditioned by Bromus vulgaris inhibited B. sylvaticum growth whereas soils conditioned by Prunella vulgaris and P. menziesii promoted B. sylvaticum growth. When testing for legacy effects, the RR of P. menziesii was negative when grown on soils where B. sylvaticum had been removed for six-months (six-month soils) but when grown on soils where B. sylvaticum had been removed for nine-months (nine-month soil) the RR of P. menziesii was neutral. The RR of P. vulgaris to six-month soils was positive while its RR to nine-month soils was negative. Nutrient and bacterial communities did not change in response to B. sylvaticum removal suggesting that the biotic and abiotic legacy requires longer than nine-months to be observed or B. sylvaticum does not affect the response variables measured. Overall, our data suggest that PSF generated by B. sylvaticum does not facilitate the invasion process but does differentially affect native species growth over time. PSF generated by native grasses may be a useful restoration tool to help prevent B. sylvaticum invasion and we suggest planting native species at least nine-months after B. sylvaticum removal. Title: The Role of Plant-soil Feedback in the Invasion of Brachypodium sylvaticum in Douglas-fir Forests Author: Esterson, Andrew Invasive plants have the capacity to transform landscapes and alter ecosystem function, causing significant economic and ecological damage. These effects include displacement and reduction of native flora and fauna, altered fire regimes, modification of biotic and abiotic soil properties, as well as local, regional, and global economic impacts. With such large impacts it is important that we better understand invasion dynamics to help with prevention, control and mitigation of invasive species. One process that has been associated with plant invasion is plant-soil feedback (PSF). A PSF occurs when plants alter biotic and abiotic soil properties through a variety of root exudates and litter decomposition such that subsequent plant growth is either positively or negatively affected. Positive conspecific and negative heterospecific responses have been theorized to be invasive species traits that promote invasion. Once an invasive species is removed from a system, there is a chance that PSFs generated by that species will persist in the soil, which is often referred to as 'plant legacies' or 'legacy effects' and may negatively influence restoration efforts. In the U.S. Pacific Northwest (PNW), Brachypodium sylvaticum (slender false brome), a perennial bunch grass native to Eurasia, is listed as a quarantined invasive species in California, Oregon, and Washington. Currently, B. sylvaticum is in the midst of rapid population growth and range expansion with populations in New York, Virginia, and Ontario, Canada. With a quickly expanding range research is critical for successful efforts to reduce the spread of B. sylvaticum. We developed two experiments to determine if PSF is a contributing factor to B. sylvaticum invasion in PNW forests. We hypothesized that 1) B. sylvaticum has positive conspecific and negative heterospecific PSF, 2) native species PSF has no effect on B. sylvaticum, and 3) PSF generated by B. sylvaticum will persist in the soil once removed, but over time, response of native species, soil nutrients and bacterial community composition will change from the invaded conditioned. To test our first two hypotheses, B. sylvaticum and five common native plants from the Oregon Coastal range, including the economically important tree, Pseudotsuga menziesii (Douglas-fir), were grown in a greenhouse on wild forest soils that had either been sterilized or kept live to condition the soil biotic community to the invader and the native species. Brachypodium sylvaticum was then grown on soil conditioned by itself and soil conditioned by natives; each of the five native species was grown on soil conditioned by B. sylvaticum and on their own conditioned soils. Plant biomass along with species specific measurements (number of leaves, stems, tillers, stem diameter and height) were recorded and a relative response (RR) index was used to determine the direction of PSF for the invader and native species. To test our third hypothesis, in March, 2015, ten plots were established in the McDonald-Dunn Research Forest located in Corvallis, OR where B. sylvaticum had at least 75% cover. Herbicide was applied to half of each plot to make two soil treatments: soil with B. sylvaticum and soil without B. sylvaticum. Over a nine-month period three soil collections took place where soil was collected from all plots and treatments. Plant response was evaluated by growing four native species and B. sylvaticum on both soil treatments and evaluating total biomass with a RR index; plant response (via growth), soil nutrients and bacterial communities were measured for each collection period. Bacterial communities were measured with phospholipid fatty acid (PLFA) analysis and high throughput 16s rRNA amplicon sequencing. Contrary to our hypotheses, the RR to PSF generated by B. sylvaticum was negative for the invader and P. menziesii and neutral for all other natives. Soils conditioned by Bromus vulgaris inhibited B. sylvaticum growth whereas soils conditioned by Prunella vulgaris and P. menziesii promoted B. sylvaticum growth. When testing for legacy effects, the RR of P. menziesii was negative when grown on soils where B. sylvaticum had been removed for six-months (six-month soils) but when grown on soils where B. sylvaticum had been removed for nine-months (nine-month soil) the RR of P. menziesii was neutral. The RR of P. vulgaris to six-month soils was positive while its RR to nine-month soils was negative. Nutrient and bacterial communities did not change in response to B. sylvaticum removal suggesting that the biotic and abiotic legacy requires longer than nine-months to be observed or B. sylvaticum does not affect the response variables measured. Overall, our data suggest that PSF generated by B. sylvaticum does not facilitate the invasion process but does differentially affect native species growth over time. PSF generated by native grasses may be a useful restoration tool to help prevent B. sylvaticum invasion and we suggest planting native species at least nine-months after B. sylvaticum removal. Close

• 69. [Article] Recovery of Wild Coho Salmon In Salmon River Basin, 2008-2010 Report Number: OPSW-ODFW-2011-10

  Abstract -- Hatcheries have been a centerpiece of salmon management in the Pacific Northwest for more than a century but recent evidence of adverse interactions between hatchery and naturally-produced ...

  Citation × Citation Citation Abstract Copy Title: Recovery of Wild Coho Salmon In Salmon River Basin, 2008-2010 Report Number: OPSW-ODFW-2011-10 Abstract -- Hatcheries have been a centerpiece of salmon management in the Pacific Northwest for more than a century but recent evidence of adverse interactions between hatchery and naturally-produced salmon have resulted in substantial changes in many hatchery programs. In 2007 the Oregon Department of Fish and Wildlife terminated a 30-year artificial propagation program for coho salmon in the Salmon River basin after a status assessment concluded that wild population viability was threatened by hatchery effects on salmon productivity (Chilcote et al. 2005). Hatchery-reared coho comprised 50-100% of the naturally spawning population in recent years. Low productivity was reflected in a low spawner to recruit ratio, and life-stage specific survival was lower than that of nearby populations. The temporal distribution of adult spawning in the basin was truncated and peaked 1.5 months earlier relative to the pre-hatchery period and adjacent coastal populations. The cessation of hatchery releases into Salmon River not only removed the primary factor believed to limit productivity of the local population, it also constituted a rare management experiment to test whether a naturally-spawning population can recover from a prolonged period of low abundance after interactions with hatchery-produced coho salmon are eliminated. This report summarizes the results of coho population studies at Salmon River for the first three years after the hatchery program was discontinued. The study in Salmon River is timely because ecological interactions between hatchery and wild fish have been implicated in the reduced survival and decreased productivity of wild coho and other salmonid populations (Nickelson 2003, Buhle et al. 2009, Chilcote et al. 2011). Recent studies involving a diversity of salmonid species and watersheds have shown a negative relationship between hatchery spawner abundance and wild population productivity regardless of the duration of hatchery influence (Chilcote et al. 2011). Yet neither the mechanisms of these productivity declines nor their potential reversibility have been investigated. Recent management changes at Salmon River provide an opportunity to experimentally evaluate coho salmon survival and productivity following the elimination of a decades-long hatchery program. The results will provide new insights into the reversibility of hatchery effects and the rate, mechanisms, and trajectory of response by a naturally spawning coho salmon population. Hatchery programs have been shown to change the timing and distribution of naturally spawning adults, but ecological and genetic influences on the spatial structure and life history diversity of juvenile populations are poorly understood. Conventional understanding of the life history of juvenile coho has presumed a relatively fixed pattern of rearing and migration. However, recent studies have found much greater variation in juvenile life history and habitat-use patterns than previously expected (Miller and Sadro 2003, Koski 2009), including evidence that estuaries may play a prominent role in the life histories of some coho salmon populations. A recent study in the Salmon River basin found considerable diversity in the life histories of juvenile Chinook salmon, including extended rearing by fry and other subyearling migrants within the complex network of natural and restored estuarine wetlands (Bottom et al. 2005). Unfortunately, interpretation of juvenile life history variations at Salmon River was confounded by the Chinook hatchery program, which has concentrated spawning activity in the lower river near the hatchery and may directly influence juvenile migration and rearing patterns. Discontinuation of the coho hatchery program at Salmon River provides an opportunity to quantify changes in juvenile life history following the elimination of all hatchery-fish interactions with the naturally spawning population. Such responses may provide important insights into the mechanisms of hatchery influence on wild salmon productivity and population resilience. Our research integrates adult and juvenile life stages, examines linkages to physical habitat conditions in fresh water and the estuary, and describes variability between juvenile performance and adult returns. It also monitors the coho salmon population across habitat types and life history stages to identify population responses at a landscape scale. We will determine productivity and survival at each salmon life stage and monitor the response of the adult population following the cessation of the coho salmon hatchery program. From these indicators, we will determine the potential resiliency of the coho salmon population, and evaluate the biological benefits or tradeoffs of returning the ecosystem to natural salmon production. Our study design encompasses four population phases: (1) pre-hatchery conditions (Mullen 1979), (2) dominance by hatchery-reared spawners (2008), (3) first generation naturally produced juveniles (2009-2011), and (4) second generation naturally produced juveniles (starting in 2012). This research will validate assumptions about factors limiting coho recovery and determine whether recovery actions have been effective. Here, we report on findings from 2008-2010 to address four principal objectives: 1. Quantify life stage specific survival and recruits per spawner ratio of the coho salmon population before and after hatchery coho salmon are removed from Salmon River. 2. Assess whether the Salmon River coho population is limited by capacity and complexity of stream habitat. 3. Describe the diversity of juvenile and adult life histories of coho salmon in the Salmon River basin, and estimate the relative contributions of various juvenile life histories to adult returns. 4. Determine seasonal use of the Salmon River estuary and its tidally-inundated wetlands by juvenile coho salmon. The field sampling that supported the study on coho salmon also captured Chinook salmon and steelhead and cutthroat trout during routine sampling in the watershed and estuary. This report emphasizes coho salmon results, but also summarizes catch, distribution, and migration data for other salmonids to compare densities and abundances in freshwater and the estuary. Additional results for Chinook, steelhead, and cutthroat are presented in Appendix A. See Stein et al. (2011) for more detailed information on life history diversity, migration patterns, habitat use, and abundance of cutthroat trout. Title: Recovery of Wild Coho Salmon In Salmon River Basin, 2008-2010 Report Number: OPSW-ODFW-2011-10 Abstract -- Hatcheries have been a centerpiece of salmon management in the Pacific Northwest for more than a century but recent evidence of adverse interactions between hatchery and naturally-produced salmon have resulted in substantial changes in many hatchery programs. In 2007 the Oregon Department of Fish and Wildlife terminated a 30-year artificial propagation program for coho salmon in the Salmon River basin after a status assessment concluded that wild population viability was threatened by hatchery effects on salmon productivity (Chilcote et al. 2005). Hatchery-reared coho comprised 50-100% of the naturally spawning population in recent years. Low productivity was reflected in a low spawner to recruit ratio, and life-stage specific survival was lower than that of nearby populations. The temporal distribution of adult spawning in the basin was truncated and peaked 1.5 months earlier relative to the pre-hatchery period and adjacent coastal populations. The cessation of hatchery releases into Salmon River not only removed the primary factor believed to limit productivity of the local population, it also constituted a rare management experiment to test whether a naturally-spawning population can recover from a prolonged period of low abundance after interactions with hatchery-produced coho salmon are eliminated. This report summarizes the results of coho population studies at Salmon River for the first three years after the hatchery program was discontinued. The study in Salmon River is timely because ecological interactions between hatchery and wild fish have been implicated in the reduced survival and decreased productivity of wild coho and other salmonid populations (Nickelson 2003, Buhle et al. 2009, Chilcote et al. 2011). Recent studies involving a diversity of salmonid species and watersheds have shown a negative relationship between hatchery spawner abundance and wild population productivity regardless of the duration of hatchery influence (Chilcote et al. 2011). Yet neither the mechanisms of these productivity declines nor their potential reversibility have been investigated. Recent management changes at Salmon River provide an opportunity to experimentally evaluate coho salmon survival and productivity following the elimination of a decades-long hatchery program. The results will provide new insights into the reversibility of hatchery effects and the rate, mechanisms, and trajectory of response by a naturally spawning coho salmon population. Hatchery programs have been shown to change the timing and distribution of naturally spawning adults, but ecological and genetic influences on the spatial structure and life history diversity of juvenile populations are poorly understood. Conventional understanding of the life history of juvenile coho has presumed a relatively fixed pattern of rearing and migration. However, recent studies have found much greater variation in juvenile life history and habitat-use patterns than previously expected (Miller and Sadro 2003, Koski 2009), including evidence that estuaries may play a prominent role in the life histories of some coho salmon populations. A recent study in the Salmon River basin found considerable diversity in the life histories of juvenile Chinook salmon, including extended rearing by fry and other subyearling migrants within the complex network of natural and restored estuarine wetlands (Bottom et al. 2005). Unfortunately, interpretation of juvenile life history variations at Salmon River was confounded by the Chinook hatchery program, which has concentrated spawning activity in the lower river near the hatchery and may directly influence juvenile migration and rearing patterns. Discontinuation of the coho hatchery program at Salmon River provides an opportunity to quantify changes in juvenile life history following the elimination of all hatchery-fish interactions with the naturally spawning population. Such responses may provide important insights into the mechanisms of hatchery influence on wild salmon productivity and population resilience. Our research integrates adult and juvenile life stages, examines linkages to physical habitat conditions in fresh water and the estuary, and describes variability between juvenile performance and adult returns. It also monitors the coho salmon population across habitat types and life history stages to identify population responses at a landscape scale. We will determine productivity and survival at each salmon life stage and monitor the response of the adult population following the cessation of the coho salmon hatchery program. From these indicators, we will determine the potential resiliency of the coho salmon population, and evaluate the biological benefits or tradeoffs of returning the ecosystem to natural salmon production. Our study design encompasses four population phases: (1) pre-hatchery conditions (Mullen 1979), (2) dominance by hatchery-reared spawners (2008), (3) first generation naturally produced juveniles (2009-2011), and (4) second generation naturally produced juveniles (starting in 2012). This research will validate assumptions about factors limiting coho recovery and determine whether recovery actions have been effective. Here, we report on findings from 2008-2010 to address four principal objectives: 1. Quantify life stage specific survival and recruits per spawner ratio of the coho salmon population before and after hatchery coho salmon are removed from Salmon River. 2. Assess whether the Salmon River coho population is limited by capacity and complexity of stream habitat. 3. Describe the diversity of juvenile and adult life histories of coho salmon in the Salmon River basin, and estimate the relative contributions of various juvenile life histories to adult returns. 4. Determine seasonal use of the Salmon River estuary and its tidally-inundated wetlands by juvenile coho salmon. The field sampling that supported the study on coho salmon also captured Chinook salmon and steelhead and cutthroat trout during routine sampling in the watershed and estuary. This report emphasizes coho salmon results, but also summarizes catch, distribution, and migration data for other salmonids to compare densities and abundances in freshwater and the estuary. Additional results for Chinook, steelhead, and cutthroat are presented in Appendix A. See Stein et al. (2011) for more detailed information on life history diversity, migration patterns, habitat use, and abundance of cutthroat trout. Close