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• 41. [Article] Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary

  The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have ...

  Citation × Citation Citation Abstract Copy Title: Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary Author: Sather, Nichole K. The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have been investigated in many coastal areas of the eastern Pacific Ocean, until recently, little was known about juvenile salmonid ecology within the Straits of Juan de Fuca. During the Spring/Summer outmigration period in 2006 and 2007, I examined the early life history of the five species of anadromous salmon in the Dungeness River estuary on the north Olympic Peninsula, Washington. I sampled multiple spatial scales within several habitat types to characterize salmon distribution and habitat use. My results presented in this thesis are segregated into two components: 1) tidal marsh ecology of juvenile salmonids in the Dungeness River estuary, and 2) the landscape-scale distribution of juvenile salmonids within the Dungeness River estuary. I examined the population of juvenile salmonids within blind tidal sloughs near the vicinity of the Dungeness River delta. Salmonids were present within the tidal marshes throughout the entire outmigration period (e.g., March through July). Juvenile Chinook salmon (Oncorhynchus tshawytscha) were the most abundant salmonid species within the marshes. Based on the temporal distribution and size structure of juvenile Chinook salmon in the estuary I identified at least four life history types: 1) a fry strategy included a large pulse of fish emigrating from the river at a small size (e.g., 35-45mm FL) during late winter and early spring months; 2) the second group of fish was the least abundant group emigrating from the river from April through mid May at sizes ranging from 50-75mm FL; 3) the third group of migrants entered the estuary between from late spring through the summer months at larger sizes than the initial groups (e.g., 60-90mm FL); and 4) the final group of Chinook salmon included a stream-type yearling strategy. In addition to the four life history strategies identified for Chinook salmon, I detected at least three groups of chum salmon migrating into the estuary. These groups were distinguished by their size and timing of migration and are further described according to different rearing strategies. The distribution of juvenile salmonids was most strongly influenced by the degree of connectivity (i.e., distance) between the tidal marshes and the mouth of the Dungeness River. Habitat complexity and opportunity also governed the distribution of juvenile salmonids within the tidal marshes. I also sampled three regions of the estuary with a beach seine to investigate the nearshore distribution of juvenile salmonids within the Dungeness River estuary: the delta face, inner Bay, and outer Bay. Among the three regions, species composition was highly variable between 2006 and 2007. The most common salmonids encountered within the beach seine sites included Chinook salmon, chum salmon (O. kisutch), and pink salmon (O. gorbuscha). The relative abundance of salmonids was highest near the delta face and lowest within the outer bay area. The landscape-scale distribution and habitat use of juvenile salmonids within the Dungeness River estuary is largely influenced by ecosystem connectivity, but is also linked to biotic characteristics of the fish (e.g., life history type and fish size). Although the Dungeness includes hydrogeomorphic characteristics (e.g., steep river gradient, composition of sand spits in the estuary) unique to other Pacific Northwest watersheds, this system produces a variety of life history types comparable to other estuaries. Understanding the mechanisms that drive the distribution of juvenile salmonids within the Dungeness will supply local resource managers with a baseline with which to establish ecosystem restoration goals. Title: Aspects of the early life history of juvenile salmonids in the Dungeness River Estuary Author: Sather, Nichole K. The decline of many Pacific salmon stocks has stimulated interest in the early life history and habitat requirements of juvenile salmon. Although estuarine habitat associations of juvenile salmon have been investigated in many coastal areas of the eastern Pacific Ocean, until recently, little was known about juvenile salmonid ecology within the Straits of Juan de Fuca. During the Spring/Summer outmigration period in 2006 and 2007, I examined the early life history of the five species of anadromous salmon in the Dungeness River estuary on the north Olympic Peninsula, Washington. I sampled multiple spatial scales within several habitat types to characterize salmon distribution and habitat use. My results presented in this thesis are segregated into two components: 1) tidal marsh ecology of juvenile salmonids in the Dungeness River estuary, and 2) the landscape-scale distribution of juvenile salmonids within the Dungeness River estuary. I examined the population of juvenile salmonids within blind tidal sloughs near the vicinity of the Dungeness River delta. Salmonids were present within the tidal marshes throughout the entire outmigration period (e.g., March through July). Juvenile Chinook salmon (Oncorhynchus tshawytscha) were the most abundant salmonid species within the marshes. Based on the temporal distribution and size structure of juvenile Chinook salmon in the estuary I identified at least four life history types: 1) a fry strategy included a large pulse of fish emigrating from the river at a small size (e.g., 35-45mm FL) during late winter and early spring months; 2) the second group of fish was the least abundant group emigrating from the river from April through mid May at sizes ranging from 50-75mm FL; 3) the third group of migrants entered the estuary between from late spring through the summer months at larger sizes than the initial groups (e.g., 60-90mm FL); and 4) the final group of Chinook salmon included a stream-type yearling strategy. In addition to the four life history strategies identified for Chinook salmon, I detected at least three groups of chum salmon migrating into the estuary. These groups were distinguished by their size and timing of migration and are further described according to different rearing strategies. The distribution of juvenile salmonids was most strongly influenced by the degree of connectivity (i.e., distance) between the tidal marshes and the mouth of the Dungeness River. Habitat complexity and opportunity also governed the distribution of juvenile salmonids within the tidal marshes. I also sampled three regions of the estuary with a beach seine to investigate the nearshore distribution of juvenile salmonids within the Dungeness River estuary: the delta face, inner Bay, and outer Bay. Among the three regions, species composition was highly variable between 2006 and 2007. The most common salmonids encountered within the beach seine sites included Chinook salmon, chum salmon (O. kisutch), and pink salmon (O. gorbuscha). The relative abundance of salmonids was highest near the delta face and lowest within the outer bay area. The landscape-scale distribution and habitat use of juvenile salmonids within the Dungeness River estuary is largely influenced by ecosystem connectivity, but is also linked to biotic characteristics of the fish (e.g., life history type and fish size). Although the Dungeness includes hydrogeomorphic characteristics (e.g., steep river gradient, composition of sand spits in the estuary) unique to other Pacific Northwest watersheds, this system produces a variety of life history types comparable to other estuaries. Understanding the mechanisms that drive the distribution of juvenile salmonids within the Dungeness will supply local resource managers with a baseline with which to establish ecosystem restoration goals. Close

• 42. [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

• 43. [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

• 44. [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

• 45. [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

• 46. [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

• 47. [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

• 48. [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