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• 471. [Article] Political economy and trade effects of invasive species regulation : the case of noxious weeds

  Many non-native weed pests of food, fiber, and nursery crops pose threats to U.S. environment and agriculture. Noxious weed regulations play an important role in preventing the introduction and spread ...

  Citation × Citation Citation Abstract Copy Title: Political economy and trade effects of invasive species regulation : the case of noxious weeds Author: Min, He Many non-native weed pests of food, fiber, and nursery crops pose threats to U.S. environment and agriculture. Noxious weed regulations play an important role in preventing the introduction and spread of non-native plants, thereby protecting the local biodiversity, environment and economic activities. However, these regulations could also hamper agricultural trade. The three essays of this dissertation address the causes and consequences of cross-state differences in noxious weed regulations. In the first essay, a political-economic model is developed to derive cross-state regulatory congruence as a function of ecological and agronomic characteristics, and interest-group lobbying through political contributions. Econometric estimation suggests ecological and agronomic dissimilarities are primary causes of cross-state differences in noxious weed regulation. However, evidence of lobbying effects is statistically and economically significant. In particular, agricultural seed producers favor more uniform weed regulations across states, while commodity producers and consumers prefer that their state maintain a distinct weed list to protect its ecosystem and agronomic conditions. The impact of noxious weed regulations on inter-state agricultural trade is measured in the second essay. In particular, the extent of trade distortions arising from interest-groups' lobbying is estimated. For this purpose, each state’s net trade in three industries - agricultural seeds, nursery products and commodities - is derived as a function of weed regulatory congruence. The resulting spatial-autoregressive tobit model of inter-state agricultural trade is estimated using a modified Expectation-Maximization algorithm. The empirical results show that the noxious weed regulatory congruence has a positive and significant effect on inter-state trade flows. Moreover, the inter-state trade distortion from consumer and commodity-producers lobbies is estimated to be as much as $1.1 billion. In the third essay, a leader-follower framework is used to examine when a weed species on one state's (leader) regulation is added to that of another (follower) state. For this purpose, an ordered logit model of noxious weeds' listing time is specified as a function of invader characteristics and ecosystem invasibility. The empirical results suggest that the invader status and attributes are relatively more important than ecosystem characteristics in determining the weed listing time. Together, the three essays suggest greater emphasis on the use of science than interest-group lobbying for listing noxious weeds. Moreover, a better documentation of potential invaders, their characteristics and impacts on non-native environments, is important in controlling the introduction and spread of noxious weeds, and the consequent economic and ecological damages. Title: Political economy and trade effects of invasive species regulation : the case of noxious weeds Author: Min, He Many non-native weed pests of food, fiber, and nursery crops pose threats to U.S. environment and agriculture. Noxious weed regulations play an important role in preventing the introduction and spread of non-native plants, thereby protecting the local biodiversity, environment and economic activities. However, these regulations could also hamper agricultural trade. The three essays of this dissertation address the causes and consequences of cross-state differences in noxious weed regulations. In the first essay, a political-economic model is developed to derive cross-state regulatory congruence as a function of ecological and agronomic characteristics, and interest-group lobbying through political contributions. Econometric estimation suggests ecological and agronomic dissimilarities are primary causes of cross-state differences in noxious weed regulation. However, evidence of lobbying effects is statistically and economically significant. In particular, agricultural seed producers favor more uniform weed regulations across states, while commodity producers and consumers prefer that their state maintain a distinct weed list to protect its ecosystem and agronomic conditions. The impact of noxious weed regulations on inter-state agricultural trade is measured in the second essay. In particular, the extent of trade distortions arising from interest-groups' lobbying is estimated. For this purpose, each state’s net trade in three industries - agricultural seeds, nursery products and commodities - is derived as a function of weed regulatory congruence. The resulting spatial-autoregressive tobit model of inter-state agricultural trade is estimated using a modified Expectation-Maximization algorithm. The empirical results show that the noxious weed regulatory congruence has a positive and significant effect on inter-state trade flows. Moreover, the inter-state trade distortion from consumer and commodity-producers lobbies is estimated to be as much as $1.1 billion. In the third essay, a leader-follower framework is used to examine when a weed species on one state's (leader) regulation is added to that of another (follower) state. For this purpose, an ordered logit model of noxious weeds' listing time is specified as a function of invader characteristics and ecosystem invasibility. The empirical results suggest that the invader status and attributes are relatively more important than ecosystem characteristics in determining the weed listing time. Together, the three essays suggest greater emphasis on the use of science than interest-group lobbying for listing noxious weeds. Moreover, a better documentation of potential invaders, their characteristics and impacts on non-native environments, is important in controlling the introduction and spread of noxious weeds, and the consequent economic and ecological damages. Close

• 472. [Article] Advancing marine reserve science : from field experiments to marine conservation planning tools

  This dissertation focuses on science relevant to the design and implementation of marine reserves. The chapters explore a range of topics related to among-site variation in population, community, and ecosystem ...

  Citation × Citation Citation Abstract Copy Title: Advancing marine reserve science : from field experiments to marine conservation planning tools Author: Leslie, Heather M. This dissertation focuses on science relevant to the design and implementation of marine reserves. The chapters explore a range of topics related to among-site variation in population, community, and ecosystem dynamics. My results demonstrate the value and feasibility of integrating this knowledge into more comprehensive conservation and management approaches. While the threats facing the oceans are serious, we in the scientific community have considerable information and tools to contribute to the development and implementation of solutions. In Chapter 2, I report on the effects of conspecific density on multiple traits of the intertidal barnacle Balanus glandula. The primary effects of increased density were enhanced survival and higher reproductive rates. My results provide a strategy for evaluating the relative importance of positive vs. negative intraspecific interactions when implementing reserves. In Chapter 3, my co-authors and I investigated how variation in nearshore primary productivity influenced survival, growth, and reproduction in B. glandula. We found strong evidence for bottom-up (i.e. productivity) forcing of barnacle population dynamics. One site produced substantially more larvae than the others, demonstrating the importance of among-site variability. Our findings advance understanding of bottom-up influences on marine populations, and demonstrate the value of embedding reserves within a network. In Chapter 4, my co-authors and I used benthic habitat data from the Florida Keys to show how a computer-based siting tool could be used to help design reserve networks. We found that many different combinations of sites produced satisfactory networks, and highlighted areas as potential conservation priorities. Our work was the first marine application of this tool and provided a starting point for applications in California and Australia. In Chapter 5, I report on a synthesis of marine conservation planning cases globally. I found that the majority occurred in North and Central America, were based on biogeographic boundaries, and that biodiversity conservation was the primary objective. One of the most striking findings was the paucity of well-documented cases. My results suggested that planners consider knowledge of marine populations, communities, and ecosystems important when identifying priorities, but that they do not have clear guidelines for how to integrate this information appropriately. Title: Advancing marine reserve science : from field experiments to marine conservation planning tools Author: Leslie, Heather M. This dissertation focuses on science relevant to the design and implementation of marine reserves. The chapters explore a range of topics related to among-site variation in population, community, and ecosystem dynamics. My results demonstrate the value and feasibility of integrating this knowledge into more comprehensive conservation and management approaches. While the threats facing the oceans are serious, we in the scientific community have considerable information and tools to contribute to the development and implementation of solutions. In Chapter 2, I report on the effects of conspecific density on multiple traits of the intertidal barnacle Balanus glandula. The primary effects of increased density were enhanced survival and higher reproductive rates. My results provide a strategy for evaluating the relative importance of positive vs. negative intraspecific interactions when implementing reserves. In Chapter 3, my co-authors and I investigated how variation in nearshore primary productivity influenced survival, growth, and reproduction in B. glandula. We found strong evidence for bottom-up (i.e. productivity) forcing of barnacle population dynamics. One site produced substantially more larvae than the others, demonstrating the importance of among-site variability. Our findings advance understanding of bottom-up influences on marine populations, and demonstrate the value of embedding reserves within a network. In Chapter 4, my co-authors and I used benthic habitat data from the Florida Keys to show how a computer-based siting tool could be used to help design reserve networks. We found that many different combinations of sites produced satisfactory networks, and highlighted areas as potential conservation priorities. Our work was the first marine application of this tool and provided a starting point for applications in California and Australia. In Chapter 5, I report on a synthesis of marine conservation planning cases globally. I found that the majority occurred in North and Central America, were based on biogeographic boundaries, and that biodiversity conservation was the primary objective. One of the most striking findings was the paucity of well-documented cases. My results suggested that planners consider knowledge of marine populations, communities, and ecosystems important when identifying priorities, but that they do not have clear guidelines for how to integrate this information appropriately. Close

• 473. [Article] Interactive effects of silvicultural herbicides and cervid herbivory on early seral plant communities of the northern Oregon Coast Range

  Intensive forest management (IFM, dense conifer plantings and herbicide applications) may alter the characteristics of early seral plant communities that function as major habitat resources for a host ...

  Citation × Citation Citation Abstract Copy Title: Interactive effects of silvicultural herbicides and cervid herbivory on early seral plant communities of the northern Oregon Coast Range Author: Stokely, Thomas Intensive forest management (IFM, dense conifer plantings and herbicide applications) may alter the characteristics of early seral plant communities that function as major habitat resources for a host of wildlife species, including cervid herbivores such as Cervus elaphus and Odocoileus hemionus. Such large herbivores can also substantially affect plant community characteristics and succession, especially in disturbed early seral habitats. I hypothesized that the effect of cervid herbivory on early seral plant communities is mediated by the effect of silvicultural herbicide treatments. If that is the case, intensively treated stands with low plant cover and diversity should be most susceptible to herbivory, as cervids are less selective and herbivory impacts are highly concentrated where forage has been diminished. To test this hypothesis, I experimentally established paired 225 m² cervid Exclusion and Open-Herbivory treatment plots in 28, 12-15 ha early seral plantation stands throughout the northern Oregon Coast Range, USA, representing a gradient in IFM. The gradient included three herbicide treatments and a no-spray Control applied at the stand scale and replicated using a randomized complete block design. I compared estimates of cover, height and diversity for entire plant communities and specific functional groups among herbivory and herbicide treatments using mixed-effects models with a blocked split-plot design. I found convincing evidence that the effect of herbivory was mediated by herbicide treatment. No-spray Control stands were too vigorous, diverse and rich with native perennial herb and deciduous shrub forage to be substantially impacted by cervid herbivory. The herbaceous specific, Light herbicide treatment reduced Shannon diversity and the cover and richness of native-perennial herbs, releasing deciduous shrub height growth where cervids where excluded. Highly selective herbivory suppressed the shrub height response by 20.5 cm, increasing the abundance and richness of introduced herb species. The broad spectrum, Moderate herbicide treatment reduced diversity, forage cover and diminished the cover and richness of deciduous shrubs and native-perennial herbs, favoring the dominance of introduced-ruderal herbs. Herbivory in the Moderate treatment reduced total cover by 17.7 percent cover, moderate-quality forage cover by 13.2 percent cover and native perennial herb richness by 1.5 species, while suppressing the cover of introduced-ruderal herbs by 4.58 percent cover and reducing the height of ferns and introduced-perennial herbs by 19.9 and 17.3 cm, respectively. Plant communities subject to the Heavy treatment were the most depauperate of all and herbivory exacerbated the effect of this treatment on native-perennial herbs only. Average height of dominant vegetation was consistently lower with cervid access across all stands, especially with Moderate herbicide treatment. My results provide evidence that by reducing diversity and the abundance of native forage species, herbicide treatments altered herbivory selectivity and pressure. The alteration of herbivory pressure in turn influenced the outcome of herbicide treatments, resulting in an exacerbated effect with Moderate and Heavy treatments. The effect of herbivory in controlling vegetation in managed stands may have positive implications for conifer seedling growth, constituting a possible 'ecosystem service' by cervids in the Pacific Northwest. This 'service' may be to the detriment of biodiversity and other early seral associates when coupled with common intensive forest management practices. Title: Interactive effects of silvicultural herbicides and cervid herbivory on early seral plant communities of the northern Oregon Coast Range Author: Stokely, Thomas Intensive forest management (IFM, dense conifer plantings and herbicide applications) may alter the characteristics of early seral plant communities that function as major habitat resources for a host of wildlife species, including cervid herbivores such as Cervus elaphus and Odocoileus hemionus. Such large herbivores can also substantially affect plant community characteristics and succession, especially in disturbed early seral habitats. I hypothesized that the effect of cervid herbivory on early seral plant communities is mediated by the effect of silvicultural herbicide treatments. If that is the case, intensively treated stands with low plant cover and diversity should be most susceptible to herbivory, as cervids are less selective and herbivory impacts are highly concentrated where forage has been diminished. To test this hypothesis, I experimentally established paired 225 m² cervid Exclusion and Open-Herbivory treatment plots in 28, 12-15 ha early seral plantation stands throughout the northern Oregon Coast Range, USA, representing a gradient in IFM. The gradient included three herbicide treatments and a no-spray Control applied at the stand scale and replicated using a randomized complete block design. I compared estimates of cover, height and diversity for entire plant communities and specific functional groups among herbivory and herbicide treatments using mixed-effects models with a blocked split-plot design. I found convincing evidence that the effect of herbivory was mediated by herbicide treatment. No-spray Control stands were too vigorous, diverse and rich with native perennial herb and deciduous shrub forage to be substantially impacted by cervid herbivory. The herbaceous specific, Light herbicide treatment reduced Shannon diversity and the cover and richness of native-perennial herbs, releasing deciduous shrub height growth where cervids where excluded. Highly selective herbivory suppressed the shrub height response by 20.5 cm, increasing the abundance and richness of introduced herb species. The broad spectrum, Moderate herbicide treatment reduced diversity, forage cover and diminished the cover and richness of deciduous shrubs and native-perennial herbs, favoring the dominance of introduced-ruderal herbs. Herbivory in the Moderate treatment reduced total cover by 17.7 percent cover, moderate-quality forage cover by 13.2 percent cover and native perennial herb richness by 1.5 species, while suppressing the cover of introduced-ruderal herbs by 4.58 percent cover and reducing the height of ferns and introduced-perennial herbs by 19.9 and 17.3 cm, respectively. Plant communities subject to the Heavy treatment were the most depauperate of all and herbivory exacerbated the effect of this treatment on native-perennial herbs only. Average height of dominant vegetation was consistently lower with cervid access across all stands, especially with Moderate herbicide treatment. My results provide evidence that by reducing diversity and the abundance of native forage species, herbicide treatments altered herbivory selectivity and pressure. The alteration of herbivory pressure in turn influenced the outcome of herbicide treatments, resulting in an exacerbated effect with Moderate and Heavy treatments. The effect of herbivory in controlling vegetation in managed stands may have positive implications for conifer seedling growth, constituting a possible 'ecosystem service' by cervids in the Pacific Northwest. This 'service' may be to the detriment of biodiversity and other early seral associates when coupled with common intensive forest management practices. Close

• 474. [Article] Connecting local values and forest policy to the international forest sustainability dialogue

  Sustainable management of the world’s forests is a key component for conserving biodiversity, soil and water resources, mitigating climate change, strengthening economies, and promoting sustainable communities ...

  Citation × Citation Citation Abstract Copy Title: Connecting local values and forest policy to the international forest sustainability dialogue Author: Morre, Susan K. Sustainable management of the world’s forests is a key component for conserving biodiversity, soil and water resources, mitigating climate change, strengthening economies, and promoting sustainable communities and human well-being, now and in the future. While international cooperation is important, the actual policies and management actions that affect forest conditions and trends are decided at the national and local level, and are influenced by local community values and individual attitudes toward natural resource management. It is important to understand the breadth of ways that people value forests if we want to sustain those specific forest values (benefits, products, and amenities) over time. I compared values identified in forest policies to values identified by individuals from six demographic groups in Oregon. The 2010 U.S. Census shows that Oregon is becoming more racially and ethnically diverse (U.S. Census Bureau 2011). The purpose of this research was to learn what forest values are most important to individuals from six demographic groups, are included in the policies and regulations that guide the management of Oregon’s forests, and in the international forest sustainability discussions. I triangulated qualitative data from multiple sources: previous literature; forest policy document analysis; participant observation of state, national, and international policy discussions; and 14 purposive focus groups with individuals from six racial and ethnic groups in Oregon. Data were individual words and language segments that expressed forest values. Analyses were conducted based on the Montreal Process Criteria and Indicators of Sustainable Forest Management (MPCI), a subset of those indicators and metrics that comprise the Oregon Indicators of Sustainable Forest Management, and focus group transcripts. The most common forest values expressed in the focus groups and previous national and state surveys that are currently included in the Oregon Indicators, Oregon forest policy documents and the MPCI are recreation, clean water, wood products, and economic values, including jobs, income, and revenues for public services. However, the current Oregon forest policies and indicator metrics do not include some forest values expressed in the focus groups and surveys: spiritual values, cultural heritage values, natural forest appearance, and protection of diverse native understory plants for wildlife habitat and cultural uses. The revised set of MPCI used in the 2010 and 2011 national reports includes indicators and metrics for understory plant and animal species diversity, as well as the new indicator 44 "the importance of forests to people" which is intended to capture these important spiritual and cultural values. I recommend revised Oregon Indicators, metrics, and forest policies to measure current conditions and trends of these values in Oregon's forests.  Title: Connecting local values and forest policy to the international forest sustainability dialogue Author: Morre, Susan K. Sustainable management of the world’s forests is a key component for conserving biodiversity, soil and water resources, mitigating climate change, strengthening economies, and promoting sustainable communities and human well-being, now and in the future. While international cooperation is important, the actual policies and management actions that affect forest conditions and trends are decided at the national and local level, and are influenced by local community values and individual attitudes toward natural resource management. It is important to understand the breadth of ways that people value forests if we want to sustain those specific forest values (benefits, products, and amenities) over time. I compared values identified in forest policies to values identified by individuals from six demographic groups in Oregon. The 2010 U.S. Census shows that Oregon is becoming more racially and ethnically diverse (U.S. Census Bureau 2011). The purpose of this research was to learn what forest values are most important to individuals from six demographic groups, are included in the policies and regulations that guide the management of Oregon’s forests, and in the international forest sustainability discussions. I triangulated qualitative data from multiple sources: previous literature; forest policy document analysis; participant observation of state, national, and international policy discussions; and 14 purposive focus groups with individuals from six racial and ethnic groups in Oregon. Data were individual words and language segments that expressed forest values. Analyses were conducted based on the Montreal Process Criteria and Indicators of Sustainable Forest Management (MPCI), a subset of those indicators and metrics that comprise the Oregon Indicators of Sustainable Forest Management, and focus group transcripts. The most common forest values expressed in the focus groups and previous national and state surveys that are currently included in the Oregon Indicators, Oregon forest policy documents and the MPCI are recreation, clean water, wood products, and economic values, including jobs, income, and revenues for public services. However, the current Oregon forest policies and indicator metrics do not include some forest values expressed in the focus groups and surveys: spiritual values, cultural heritage values, natural forest appearance, and protection of diverse native understory plants for wildlife habitat and cultural uses. The revised set of MPCI used in the 2010 and 2011 national reports includes indicators and metrics for understory plant and animal species diversity, as well as the new indicator 44 "the importance of forests to people" which is intended to capture these important spiritual and cultural values. I recommend revised Oregon Indicators, metrics, and forest policies to measure current conditions and trends of these values in Oregon's forests.  Close

• 475. [Article] Interactive visualization of diversity in multivariate data sets unified across fields of study

  The study of the diversity of multivariate objects shares common characteristics across disciplines, including ecology and organizational management. Nevertheless, experts in these two disciplines have ...

  Citation × Citation Citation Abstract Copy Title: Interactive visualization of diversity in multivariate data sets unified across fields of study Author: Pham, Tuan N. T. (Tuan Nguyen Tha) The study of the diversity of multivariate objects shares common characteristics across disciplines, including ecology and organizational management. Nevertheless, experts in these two disciplines have adopted somewhat separate diversity concepts and analysis techniques, limiting the ability of potentially sharing and cross comparing these concerns. Moreover, while complex diversity data may benefit from exploratory data analysis, most of the existing techniques emphasize confirmatory analysis based on statistical metrics and models. To bridge these gaps, interactive visualization is especially appealing because of its potential to allow users to explore diversity data in a direct and holistic way, prior to further statistical analysis. This dissertation addresses the problem of designing multivariate visualizations that support exploration and communication of diversity patterns and processes in multivariate data. To this aim, the dissertation presents design considerations as well as implementation and evaluation of interactive visualizations targeting diversity analysis. The contributing visualization techniques and tools include (1) Diversity Map -- a novel multivariate space-filling representation emphasizing diversity patterns in separate attributes; (2) Ecological Distributions and Trends Explorer (EcoDATE) -- a web-based visual-analysis tool that is built upon the Diversity Map and facilitates the exploratory analysis of long-term ecological data with an emphasis on distribution patterns and temporal trends; and (3) HIST -- a visual representation for communicating team diversity faultlines across multiple attributes that is based on multiple linked, stacked histograms. Further, drawing upon lessons from these designs, this dissertation cross compares analyses of species diversity (ecology), microbial diversity (microbiology), and workgroup diversity (organizational management) and introduces a unified taxonomy of analytical tasks to guide the creation and evaluation of future diversity visualizations. The design considerations, visualization techniques, tools, and task taxonomy are evaluated and refined in empirical user studies involving human participants and subject-matter experts. Title: Interactive visualization of diversity in multivariate data sets unified across fields of study Author: Pham, Tuan N. T. (Tuan Nguyen Tha) The study of the diversity of multivariate objects shares common characteristics across disciplines, including ecology and organizational management. Nevertheless, experts in these two disciplines have adopted somewhat separate diversity concepts and analysis techniques, limiting the ability of potentially sharing and cross comparing these concerns. Moreover, while complex diversity data may benefit from exploratory data analysis, most of the existing techniques emphasize confirmatory analysis based on statistical metrics and models. To bridge these gaps, interactive visualization is especially appealing because of its potential to allow users to explore diversity data in a direct and holistic way, prior to further statistical analysis. This dissertation addresses the problem of designing multivariate visualizations that support exploration and communication of diversity patterns and processes in multivariate data. To this aim, the dissertation presents design considerations as well as implementation and evaluation of interactive visualizations targeting diversity analysis. The contributing visualization techniques and tools include (1) Diversity Map -- a novel multivariate space-filling representation emphasizing diversity patterns in separate attributes; (2) Ecological Distributions and Trends Explorer (EcoDATE) -- a web-based visual-analysis tool that is built upon the Diversity Map and facilitates the exploratory analysis of long-term ecological data with an emphasis on distribution patterns and temporal trends; and (3) HIST -- a visual representation for communicating team diversity faultlines across multiple attributes that is based on multiple linked, stacked histograms. Further, drawing upon lessons from these designs, this dissertation cross compares analyses of species diversity (ecology), microbial diversity (microbiology), and workgroup diversity (organizational management) and introduces a unified taxonomy of analytical tasks to guide the creation and evaluation of future diversity visualizations. The design considerations, visualization techniques, tools, and task taxonomy are evaluated and refined in empirical user studies involving human participants and subject-matter experts. Close

• 476. [Article] Environmental influences on host-pathogen dynamics of the amphibian chytrid fungus

  The causes of the global biodiversity crisis are varied and complex. Anthropogenic threats may act in isolation, or interact additively or synergistically with each other or with natural stressors to affect ...

  Citation × Citation Citation Abstract Copy Title: Environmental influences on host-pathogen dynamics of the amphibian chytrid fungus Author: Buck, Julia C. The causes of the global biodiversity crisis are varied and complex. Anthropogenic threats may act in isolation, or interact additively or synergistically with each other or with natural stressors to affect sensitive taxa. The recent emergence of many infectious diseases in wildlife has brought attention to the role of disease in population declines and species extinctions. Both abiotic and biotic components of the environment may mitigate or exacerbate effects of pathogens on their hosts through direct or indirect mechanisms. The effects of the environment on host-pathogen dynamics are complex, context-dependent, and in need of further examination. One particularly sensitive group, amphibians, is at the leading edge of the sixth mass extinction. The emerging infectious disease (EID) chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatis (Bd), is implicated in population declines and extinctions of amphibians globally. My disseration addresses questions pertaining to environmental influences on disease dynamics of Bd. As described in chapter 1, various abiotic and biotic components of the environment may affect host-pathogen dynamics of Bd, resulting in changes to the dynamics of Bd transmission and spread. Chapter 2 examines the influence of an abiotic factor, the insecticide (carbaryl) and three different assemblages of larval Pacific treefrogs (Pseudacris regilla) and Cascades frogs (Rana cascadae) on host-pathogen dynamics of Bd within a community context. I found separate effects of each treatment on amphibian growth and development, but no interactive effects among the treatments. However, Bd appeared to reduce phytoplankton abundance and increase periphyton biomass, an unexpected result that merited further investigation. One possible explanation for the results described in chapter 2 is that zooplankton might consume Bd zoospores, the infective stage of the pathogen, a hypothesis that I examine in chapter 3. I conducted laboratory experiments and confirmed the presence of Bd zoospores in the gut of Daphnia sp. through quantitative PCR and visual inspection. I discuss conservation implications of this finding. To determine whether predation on Bd zoospores by zooplankton could reduce infection in amphibians, I conducted a mesocosm experiment, which is described in chapter 4. I found complex effects on species interactions: competition between larval Cascades frogs and zooplankton for phytoplankton resources reduced phytoplankton concentration, zooplankton abundance, and survival of amphibians. These effects were diminished in the presence of Bd, suggesting that zooplankton may have at least partially substituted Bd zoospores for phytoplankton in their diet, thus stimulating competitive release. However, competitive effects between zooplankton and larval amphibians overshadowed indirect positive benefits of zooplankton predation on Bd zoospores. In chapter 4, competitive effects between zooplankton and larval amphibians for phytoplankton suggested that host-pathogen dynamics might be affected by the host’s supply of resources. Chapter 5 describes a mesocosm experiment that examined how eutrophication might affect Bd-infected Pacific treefrogs and other members of the aquatic community. Nutrient additions caused increased algal growth, which benefitted herbivorous larval amphibians. Larvae exposed to Bd altered their growth, development, and diet, and allocated resources differently than unexposed individuals. However, nutrient supplementation did not alter the response of larval amphibians to Bd. As described in chapter 6, consideration of hosts and pathogens as functional members of the ecological communities in which they exist can lead to important insights in host-pathogen dynamics. My PhD research may contribute to control measures for the emerging infectious disease chytridiomycosis. Title: Environmental influences on host-pathogen dynamics of the amphibian chytrid fungus Author: Buck, Julia C. The causes of the global biodiversity crisis are varied and complex. Anthropogenic threats may act in isolation, or interact additively or synergistically with each other or with natural stressors to affect sensitive taxa. The recent emergence of many infectious diseases in wildlife has brought attention to the role of disease in population declines and species extinctions. Both abiotic and biotic components of the environment may mitigate or exacerbate effects of pathogens on their hosts through direct or indirect mechanisms. The effects of the environment on host-pathogen dynamics are complex, context-dependent, and in need of further examination. One particularly sensitive group, amphibians, is at the leading edge of the sixth mass extinction. The emerging infectious disease (EID) chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatis (Bd), is implicated in population declines and extinctions of amphibians globally. My disseration addresses questions pertaining to environmental influences on disease dynamics of Bd. As described in chapter 1, various abiotic and biotic components of the environment may affect host-pathogen dynamics of Bd, resulting in changes to the dynamics of Bd transmission and spread. Chapter 2 examines the influence of an abiotic factor, the insecticide (carbaryl) and three different assemblages of larval Pacific treefrogs (Pseudacris regilla) and Cascades frogs (Rana cascadae) on host-pathogen dynamics of Bd within a community context. I found separate effects of each treatment on amphibian growth and development, but no interactive effects among the treatments. However, Bd appeared to reduce phytoplankton abundance and increase periphyton biomass, an unexpected result that merited further investigation. One possible explanation for the results described in chapter 2 is that zooplankton might consume Bd zoospores, the infective stage of the pathogen, a hypothesis that I examine in chapter 3. I conducted laboratory experiments and confirmed the presence of Bd zoospores in the gut of Daphnia sp. through quantitative PCR and visual inspection. I discuss conservation implications of this finding. To determine whether predation on Bd zoospores by zooplankton could reduce infection in amphibians, I conducted a mesocosm experiment, which is described in chapter 4. I found complex effects on species interactions: competition between larval Cascades frogs and zooplankton for phytoplankton resources reduced phytoplankton concentration, zooplankton abundance, and survival of amphibians. These effects were diminished in the presence of Bd, suggesting that zooplankton may have at least partially substituted Bd zoospores for phytoplankton in their diet, thus stimulating competitive release. However, competitive effects between zooplankton and larval amphibians overshadowed indirect positive benefits of zooplankton predation on Bd zoospores. In chapter 4, competitive effects between zooplankton and larval amphibians for phytoplankton suggested that host-pathogen dynamics might be affected by the host’s supply of resources. Chapter 5 describes a mesocosm experiment that examined how eutrophication might affect Bd-infected Pacific treefrogs and other members of the aquatic community. Nutrient additions caused increased algal growth, which benefitted herbivorous larval amphibians. Larvae exposed to Bd altered their growth, development, and diet, and allocated resources differently than unexposed individuals. However, nutrient supplementation did not alter the response of larval amphibians to Bd. As described in chapter 6, consideration of hosts and pathogens as functional members of the ecological communities in which they exist can lead to important insights in host-pathogen dynamics. My PhD research may contribute to control measures for the emerging infectious disease chytridiomycosis. Close

• 477. [Article] Aquatic community responses to drought disturbance: experimental manipulations of top predator extinctions and stream drying

  Although it is generally assumed that the intensifying abiotic environment is the primary effect of drought on aquatic organisms, drought-induced top predator extinctions may be an important underlying ...

  Citation × Citation Citation Abstract Copy Title: Aquatic community responses to drought disturbance: experimental manipulations of top predator extinctions and stream drying Author: Boersma, Kate S. Although it is generally assumed that the intensifying abiotic environment is the primary effect of drought on aquatic organisms, drought-induced top predator extinctions may be an important underlying mechanism. I used manipulative experiments to disentangle the impacts of drying and top predator extinctions on arid-land aquatic invertebrate communities. I then created a general conceptual framework that specifies how biotic and abiotic disturbances affect the composition of biological traits of species in a community (functional trait composition) and tested the framework with data from the manipulative experiments and a field study. Finally, I proposed a new metric to calculate the difference in functional trait composition between undisturbed and disturbed communities (called “functional distance”) and used it to understand trait turnover between undisturbed and disturbed arid-land stream communities. In Chapter 2, I describe two manipulative experiments in which I removed an invertebrate top predator from mesocosms containing arid-land stream invertebrates and recorded changes in the aquatic community. I found that top predator removal consistently decreased the abundance of detritivores and increased the abundance of mesopredators, even under different background environmental conditions. Chapter 3 describes a second mesocosm study in which I manipulated drying severity and measured aquatic community responses. My severe drying treatment allowed mesocosms to desiccate to a depth of ~1cm, yet I still I found that taxonomic and functional trait composition did not vary between treatments. The only discernable effect of drying was a decrease in abundance and increase in density of invertebrates. This result suggests that arid-land aquatic communities are highly resistant to drying disturbance that falls within the range of natural seasonal and interannual droughts but not resistant to the novel disturbance of top predator extinctions. In Chapter 4 I describe a conceptual framework that uses functional trait diversity to understand the mechanisms behind community responses to disturbances. I applied the framework to datasets from Chapters 2 and 3 and an observational field study during severe drought. While the biotic disturbance of top predator removal did not affect species diversity in the taxonomic analysis, it increased the overall functional trait diversity and favored trait combinations associated with aerial dispersal and predatory feeding modes. Interestingly, although natural stream drying occurred concurrently with the local extinction of the invertebrate top predator in the field, this extreme abiotic disturbance was associated with a reduction in functional trait diversity. The contradictory effects of these two novel disturbance types highlight the importance of colonization and spatial context in the resilience of arid-land aquatic communities to future disturbances; differences between disturbed and undisturbed communities in both top predator removal and catastrophic stream drying studies were associated with aerially dispersing invertebrates. My work suggests that combining taxonomic and functional trait analyses in a rigorous hypothesis-testing framework can reveal hidden mechanisms behind the effects of drought on aquatic communities. Ultimately, I hope that this framework can be applied to other disturbed systems to better understand the effects of human actions on ecological communities. Title: Aquatic community responses to drought disturbance: experimental manipulations of top predator extinctions and stream drying Author: Boersma, Kate S. Although it is generally assumed that the intensifying abiotic environment is the primary effect of drought on aquatic organisms, drought-induced top predator extinctions may be an important underlying mechanism. I used manipulative experiments to disentangle the impacts of drying and top predator extinctions on arid-land aquatic invertebrate communities. I then created a general conceptual framework that specifies how biotic and abiotic disturbances affect the composition of biological traits of species in a community (functional trait composition) and tested the framework with data from the manipulative experiments and a field study. Finally, I proposed a new metric to calculate the difference in functional trait composition between undisturbed and disturbed communities (called “functional distance”) and used it to understand trait turnover between undisturbed and disturbed arid-land stream communities. In Chapter 2, I describe two manipulative experiments in which I removed an invertebrate top predator from mesocosms containing arid-land stream invertebrates and recorded changes in the aquatic community. I found that top predator removal consistently decreased the abundance of detritivores and increased the abundance of mesopredators, even under different background environmental conditions. Chapter 3 describes a second mesocosm study in which I manipulated drying severity and measured aquatic community responses. My severe drying treatment allowed mesocosms to desiccate to a depth of ~1cm, yet I still I found that taxonomic and functional trait composition did not vary between treatments. The only discernable effect of drying was a decrease in abundance and increase in density of invertebrates. This result suggests that arid-land aquatic communities are highly resistant to drying disturbance that falls within the range of natural seasonal and interannual droughts but not resistant to the novel disturbance of top predator extinctions. In Chapter 4 I describe a conceptual framework that uses functional trait diversity to understand the mechanisms behind community responses to disturbances. I applied the framework to datasets from Chapters 2 and 3 and an observational field study during severe drought. While the biotic disturbance of top predator removal did not affect species diversity in the taxonomic analysis, it increased the overall functional trait diversity and favored trait combinations associated with aerial dispersal and predatory feeding modes. Interestingly, although natural stream drying occurred concurrently with the local extinction of the invertebrate top predator in the field, this extreme abiotic disturbance was associated with a reduction in functional trait diversity. The contradictory effects of these two novel disturbance types highlight the importance of colonization and spatial context in the resilience of arid-land aquatic communities to future disturbances; differences between disturbed and undisturbed communities in both top predator removal and catastrophic stream drying studies were associated with aerially dispersing invertebrates. My work suggests that combining taxonomic and functional trait analyses in a rigorous hypothesis-testing framework can reveal hidden mechanisms behind the effects of drought on aquatic communities. Ultimately, I hope that this framework can be applied to other disturbed systems to better understand the effects of human actions on ecological communities. Close

• 478. [Article] Life history variables of Dicamptodon salamanders

  It is good practice to fully understand components of an ecosystem if we hope to preserve its biodiversity. A problem is that we know very little about some organisms and nothing of others. Studies that ...

  Citation × Citation Citation Abstract Copy Title: Life history variables of Dicamptodon salamanders Author: Wagner, Lisa A. It is good practice to fully understand components of an ecosystem if we hope to preserve its biodiversity. A problem is that we know very little about some organisms and nothing of others. Studies that investigate an organism’s basic biological, ecological and physiological life history variables advance our knowledge of the species of interest and also offer insight about community structure and function. In this thesis I explore courtship behaviors, metamorphic tendencies and hematological parameters in two species of Dicamptodon salamanders (D. copei and D. tenebrosus). Ecologists examine blood to assess hematological responses to a plethora of factors including hormonal changes, parasites, reproductive status and environmental stressors. While hematologic principles are fairly conserved in vertebrates, blood tissue has evolved to match the organism with its environment and there is considerable diversity in hematological parameters across taxa. Therefore, it is necessary to collect species specific baseline data for comparison. In Chapter 2, I quantified relative white blood cells and erythrocyte dry volume measurements of both D. tenebrosus and D. copei in the wild and in captivity. No prior studies have evaluated the hematological parameters of Dicamptodon salamanders. My investigation revealed similar leukocyte ratios between species and between wild and captive D. tenebrosus, while leukocyte ratios of wild and captive D. copei were significantly different. Dicamptodon species and populations vary in metamorphic tendencies though the reasons for this variation are not known. In Chapter 3 I investigated the difference in metamorphic tendencies of D. copei and D. tenebrosus. First, I tested the hypotheses that high water inhibits and thermal stress induces metamorphosis. Neither lowered water, nor increased aquatic temperatures induced metamorphosis. Secondly, I compared thermal preferences of both species and found differences in the selection tendencies between species and between sizes of both species. Lastly, I stress responses of both species to 1.66º C, 21.11 º C and 25º C water using a hematological approach. This study revealed significant differences in hematological stress indices between the two species. In Chapter 4, I explored the courtship behaviors of D. copei and D. tenebrosus and characterized each behavior and temporal pattern, using a phyloethological approach. I then compared these courtship behaviors between species and to that of the nearest salamander family, Ambystomatidae. The courtship patterns and behaviors were similar in both species, but they did not resemble the courtship patterns or behaviors of their sister taxon, Ambystoma. Title: Life history variables of Dicamptodon salamanders Author: Wagner, Lisa A. It is good practice to fully understand components of an ecosystem if we hope to preserve its biodiversity. A problem is that we know very little about some organisms and nothing of others. Studies that investigate an organism’s basic biological, ecological and physiological life history variables advance our knowledge of the species of interest and also offer insight about community structure and function. In this thesis I explore courtship behaviors, metamorphic tendencies and hematological parameters in two species of Dicamptodon salamanders (D. copei and D. tenebrosus). Ecologists examine blood to assess hematological responses to a plethora of factors including hormonal changes, parasites, reproductive status and environmental stressors. While hematologic principles are fairly conserved in vertebrates, blood tissue has evolved to match the organism with its environment and there is considerable diversity in hematological parameters across taxa. Therefore, it is necessary to collect species specific baseline data for comparison. In Chapter 2, I quantified relative white blood cells and erythrocyte dry volume measurements of both D. tenebrosus and D. copei in the wild and in captivity. No prior studies have evaluated the hematological parameters of Dicamptodon salamanders. My investigation revealed similar leukocyte ratios between species and between wild and captive D. tenebrosus, while leukocyte ratios of wild and captive D. copei were significantly different. Dicamptodon species and populations vary in metamorphic tendencies though the reasons for this variation are not known. In Chapter 3 I investigated the difference in metamorphic tendencies of D. copei and D. tenebrosus. First, I tested the hypotheses that high water inhibits and thermal stress induces metamorphosis. Neither lowered water, nor increased aquatic temperatures induced metamorphosis. Secondly, I compared thermal preferences of both species and found differences in the selection tendencies between species and between sizes of both species. Lastly, I stress responses of both species to 1.66º C, 21.11 º C and 25º C water using a hematological approach. This study revealed significant differences in hematological stress indices between the two species. In Chapter 4, I explored the courtship behaviors of D. copei and D. tenebrosus and characterized each behavior and temporal pattern, using a phyloethological approach. I then compared these courtship behaviors between species and to that of the nearest salamander family, Ambystomatidae. The courtship patterns and behaviors were similar in both species, but they did not resemble the courtship patterns or behaviors of their sister taxon, Ambystoma. Close

• 479. [Article] Onset and Breakdown of Cnidarian-Dinoflagellate Symbiosis : A Survey of the Host Transcriptomic Response and Characterization of the Sphingosine Rheostat during Symbiont Colonization and Hyperthermal Stress

  The symbiosis between cnidarians, such as corals and sea anemones, and photosynthetic dinoflagellates belonging to the genus Symbiodinium spp. is one of the most productive in the marine environment. This ...

  Citation × Citation Citation Abstract Copy Title: Onset and Breakdown of Cnidarian-Dinoflagellate Symbiosis : A Survey of the Host Transcriptomic Response and Characterization of the Sphingosine Rheostat during Symbiont Colonization and Hyperthermal Stress Author: Kitchen, Sheila Ann The symbiosis between cnidarians, such as corals and sea anemones, and photosynthetic dinoflagellates belonging to the genus Symbiodinium spp. is one of the most productive in the marine environment. This mutualistic endosymbiosis allow reef-building corals to lay down the foundation of coral reef ecosystems, which supports a highly biodiverse community of marine organisms. The relationship between the cnidarian host and algal symbiont changes over time, from the initial contact through symbiont removal. The breakdown of the partnership can be brought on by numerous environmental stressors; most notably by elevated temperatures associated with climate change. The cellular and molecular mechanisms underlying these key events in cnidarian-dinoflagellate symbiosis are still poorly understood. Lipids play a central role in symbiosis by providing cellular structure, energy storage, signaling platforms. Specifically, the signaling lipids from the sphingosine rheostat, sphingosine and sphingosine-1-phosphate (S1P), play a pivotal role in determining cell fate. Increased sphingosine drives apoptotic activity within the cell while S1P promotes cell survival. The research presented in this dissertation addresses (1) the role of signaling sphingolipids at different stages of cnidarian-dinoflagellate symbiosis and (2) the transcriptional patterns of coral larvae undergoing onset of symbiosis while exposed to elevated seawater temperatures. In Chapter 2, the proposed cnidarian sphingosine rheostat model was functionally characterized in the sea anemone Aiptasia pallida. This study identified differential response of the sphingosine rheostat with symbiont recolonization and long-term symbiont maintenance, suggesting a role in host-symbiont interactions. In Chapter 3, a heat stress experiment revealed a biphasic sphingosine rheostat response in A. pallida where acute stress inhibits rheostat expression and activity that is recovered and shifted toward cell death with longer-term heat stress. This response was not linked to symbiont loss, but has implications for a more generalized heat stress response for long-term acclimation in cnidarians. In Chapter 4, coral Acropora digitifera larvae displayed different phenotypes and transcriptional profiles with the combined stress of elevated temperature and symbiont uptake. Larval survival, symbiont colonization and algal density were highly reduced from this treatment. These transcriptional patterns indicate immune suppression, membrane reorganization and oxidative stress. Furthermore, sphingolipid signaling differed at the onset of heat stress. Overall, the work presented here indicates that the sphingosine rheostat mediates host-symbiont interactions until symbiosis dysfunction and that the determinants of symbiosis can be altered with climate-induced stress. Title: Onset and Breakdown of Cnidarian-Dinoflagellate Symbiosis : A Survey of the Host Transcriptomic Response and Characterization of the Sphingosine Rheostat during Symbiont Colonization and Hyperthermal Stress Author: Kitchen, Sheila Ann The symbiosis between cnidarians, such as corals and sea anemones, and photosynthetic dinoflagellates belonging to the genus Symbiodinium spp. is one of the most productive in the marine environment. This mutualistic endosymbiosis allow reef-building corals to lay down the foundation of coral reef ecosystems, which supports a highly biodiverse community of marine organisms. The relationship between the cnidarian host and algal symbiont changes over time, from the initial contact through symbiont removal. The breakdown of the partnership can be brought on by numerous environmental stressors; most notably by elevated temperatures associated with climate change. The cellular and molecular mechanisms underlying these key events in cnidarian-dinoflagellate symbiosis are still poorly understood. Lipids play a central role in symbiosis by providing cellular structure, energy storage, signaling platforms. Specifically, the signaling lipids from the sphingosine rheostat, sphingosine and sphingosine-1-phosphate (S1P), play a pivotal role in determining cell fate. Increased sphingosine drives apoptotic activity within the cell while S1P promotes cell survival. The research presented in this dissertation addresses (1) the role of signaling sphingolipids at different stages of cnidarian-dinoflagellate symbiosis and (2) the transcriptional patterns of coral larvae undergoing onset of symbiosis while exposed to elevated seawater temperatures. In Chapter 2, the proposed cnidarian sphingosine rheostat model was functionally characterized in the sea anemone Aiptasia pallida. This study identified differential response of the sphingosine rheostat with symbiont recolonization and long-term symbiont maintenance, suggesting a role in host-symbiont interactions. In Chapter 3, a heat stress experiment revealed a biphasic sphingosine rheostat response in A. pallida where acute stress inhibits rheostat expression and activity that is recovered and shifted toward cell death with longer-term heat stress. This response was not linked to symbiont loss, but has implications for a more generalized heat stress response for long-term acclimation in cnidarians. In Chapter 4, coral Acropora digitifera larvae displayed different phenotypes and transcriptional profiles with the combined stress of elevated temperature and symbiont uptake. Larval survival, symbiont colonization and algal density were highly reduced from this treatment. These transcriptional patterns indicate immune suppression, membrane reorganization and oxidative stress. Furthermore, sphingolipid signaling differed at the onset of heat stress. Overall, the work presented here indicates that the sphingosine rheostat mediates host-symbiont interactions until symbiosis dysfunction and that the determinants of symbiosis can be altered with climate-induced stress. Close

• 480. [Article] The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2016

  We monitored the distribution, abundance and productivity of the federally threatened Western SnowyPlover (Charadrius nivosus nivosus) along the Oregon coast from 5 April – 31 August 2016. From north to ...

  Citation × Citation Citation Abstract Copy Title: The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2016 Author: Farrar, J. Daniel, Kotaich, Adam A., Gaines, Eleanor P., Krygsman, Erica, Castelein, Kathleen A., Lauten, David J. We monitored the distribution, abundance and productivity of the federally threatened Western SnowyPlover (Charadrius nivosus nivosus) along the Oregon coast from 5 April – 31 August 2016. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North and South Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Snowy Plover Management Area, New River HRA and adjacent lands, and Floras Lake. Our objectives in 2016 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) determine nest success, 4) implement nest protection as appropriate (e.g. ropes, signs, exclosures), 5) develop and test a sampling technique to determine plover productivity, 6) monitor brood outcomes, and 7) collect general observational data about predators and use cameras to document predator activity at nests. We estimated the resident number of Snowy Plovers in Oregon at 518 individuals. The adult plover population was the highest estimate recorded since monitoring began in 1990. We monitored 694 nests in 2016. Overall apparent nest success was 25%. Nest failures were attributed to unknown depredation, unknown cause, harrier depredation, corvid depredation, mammalian depredation, gull depredation, one-egg nest, wind/weather, abandonment, overwashing and infertility. We monitored a sample of 150 of 192 known broods, and documented a minimum of 197 fledglings. Overall brood success was 71%, fledging success was 43%, but only 0.60 +/- 0.09 fledglings per male were produced. Title: The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2016 Author: Farrar, J. Daniel, Kotaich, Adam A., Gaines, Eleanor P., Krygsman, Erica, Castelein, Kathleen A., Lauten, David J. We monitored the distribution, abundance and productivity of the federally threatened Western SnowyPlover (Charadrius nivosus nivosus) along the Oregon coast from 5 April – 31 August 2016. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North and South Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Snowy Plover Management Area, New River HRA and adjacent lands, and Floras Lake. Our objectives in 2016 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) determine nest success, 4) implement nest protection as appropriate (e.g. ropes, signs, exclosures), 5) develop and test a sampling technique to determine plover productivity, 6) monitor brood outcomes, and 7) collect general observational data about predators and use cameras to document predator activity at nests. We estimated the resident number of Snowy Plovers in Oregon at 518 individuals. The adult plover population was the highest estimate recorded since monitoring began in 1990. We monitored 694 nests in 2016. Overall apparent nest success was 25%. Nest failures were attributed to unknown depredation, unknown cause, harrier depredation, corvid depredation, mammalian depredation, gull depredation, one-egg nest, wind/weather, abandonment, overwashing and infertility. We monitored a sample of 150 of 192 known broods, and documented a minimum of 197 fledglings. Overall brood success was 71%, fledging success was 43%, but only 0.60 +/- 0.09 fledglings per male were produced. Close