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• 451. [Article] The Uneven Geography of River Conservation In The U.S.: Insights From The Application Of The Wild And Scenic Rivers Act

  Rivers are vital for sustaining biodiversity and human development, yet globally only a small fraction of rivers enjoy protection and those with protections are often impaired or modified. Rapid rates ...

  Citation × Citation Citation Abstract Copy Title: The Uneven Geography of River Conservation In The U.S.: Insights From The Application Of The Wild And Scenic Rivers Act Author: Perry, Denielle Year: 2017 Rivers are vital for sustaining biodiversity and human development, yet globally only a small fraction of rivers enjoy protection and those with protections are often impaired or modified. Rapid rates of freshwater species’ extinctions indicate current conservation practices are failing. Despite over fifty years of scientific evidence justifying river conservation, it remains that less attention is focused on protecting ecosystems than on developing water resources for economic growth. This disparity is indicative of the ‘nature as resource’ versus ‘conservation of nature’ paradigm. Today, this paradigm is complicated by new attentions centering both on water resource development projects and conservation policy as climate change adaptation strategies. Policies protecting rivers are recommended for contending with more intense storms and flooding, increasing resilience for species, forests, and agricultural areas, and fostering some types of water security. Creating, implementing, and managing climate adaptation policies will require a strong state presence in water resource governance. We know, however, the aforementioned paradigm hinders conservation policymaking. Therefore, understanding how conservation policy has already been rationalized, implemented, and managed is critical to advancing climate adaptation policymaking. Yet, little empirical research has been conducted on federal river conservation policy creation or application across the U.S. To that end, this dissertation, presented in three discrete original research articles, examines the United States National Wild and Scenic Rivers System. Specifically, this study investigates the socio-ecological drivers behind the creation of the Wild and Scenic Rivers Act of 1968 (WSRA hereinafter) and the spatial dimensions of the policy’s application and management over time. This study is grounded empirically in extensive archival materials, interviews with federal land management agency personnel, conservation advocates, and technical experts, as well as spatial and temporal analysis of a geodatabase. Together, these methods were employed to answer the following research questions which guide this study: (1) What factors influence the temporal and spatial distribution of river segments protected under the Wild & Scenic Rivers Act? (2) What does the history of management in designated segments suggest about emerging trends and patterns in river conservation? (3) How are competing environmental values and ideologies understood and reconciled in the context of river conservation? Title: The Uneven Geography of River Conservation In The U.S.: Insights From The Application Of The Wild And Scenic Rivers Act Author: Perry, Denielle Year: 2017 Rivers are vital for sustaining biodiversity and human development, yet globally only a small fraction of rivers enjoy protection and those with protections are often impaired or modified. Rapid rates of freshwater species’ extinctions indicate current conservation practices are failing. Despite over fifty years of scientific evidence justifying river conservation, it remains that less attention is focused on protecting ecosystems than on developing water resources for economic growth. This disparity is indicative of the ‘nature as resource’ versus ‘conservation of nature’ paradigm. Today, this paradigm is complicated by new attentions centering both on water resource development projects and conservation policy as climate change adaptation strategies. Policies protecting rivers are recommended for contending with more intense storms and flooding, increasing resilience for species, forests, and agricultural areas, and fostering some types of water security. Creating, implementing, and managing climate adaptation policies will require a strong state presence in water resource governance. We know, however, the aforementioned paradigm hinders conservation policymaking. Therefore, understanding how conservation policy has already been rationalized, implemented, and managed is critical to advancing climate adaptation policymaking. Yet, little empirical research has been conducted on federal river conservation policy creation or application across the U.S. To that end, this dissertation, presented in three discrete original research articles, examines the United States National Wild and Scenic Rivers System. Specifically, this study investigates the socio-ecological drivers behind the creation of the Wild and Scenic Rivers Act of 1968 (WSRA hereinafter) and the spatial dimensions of the policy’s application and management over time. This study is grounded empirically in extensive archival materials, interviews with federal land management agency personnel, conservation advocates, and technical experts, as well as spatial and temporal analysis of a geodatabase. Together, these methods were employed to answer the following research questions which guide this study: (1) What factors influence the temporal and spatial distribution of river segments protected under the Wild & Scenic Rivers Act? (2) What does the history of management in designated segments suggest about emerging trends and patterns in river conservation? (3) How are competing environmental values and ideologies understood and reconciled in the context of river conservation? Close

• 452. [Article] Open Space as an Armature for Urban Expansion: A Future Scenarios Study to Assess the Effects of Spatial Concepts on Wildlife Populations

  Urbanization is one of the biggest threats to biodiversity. To address this problem, landscape planners have increasingly adopted landscape ecology as a theoretical basis for planning. They use spatial ...

  Citation × Citation Citation Abstract Copy Title: Open Space as an Armature for Urban Expansion: A Future Scenarios Study to Assess the Effects of Spatial Concepts on Wildlife Populations Author: Penteado, Homero Year: 2014 Urbanization is one of the biggest threats to biodiversity. To address this problem, landscape planners have increasingly adopted landscape ecology as a theoretical basis for planning. They use spatial concepts that express principles of landscape ecology in diagrammatic form to create frameworks for planning. This dissertation presents a quantitative approach to evaluate the application of spatial concepts developed to create an armature of open space in areas subject to urbanization. It focuses on the predicted urban expansion of Damascus, Oregon, as a case study. An alternative futures study was used to test three open space spatial concepts for patches, corridors and networks in combination with compact and dispersed urban development patterns. The resulting eight scenarios of land use and land cover were then modeled for the year 2060 to evaluate their effects on habitat quantity, quality and configuration and to identify tradeoffs between urban development and conservation for three focal wildlife species: Red-legged frog, Western meadowlark, and Douglas squirrel. Open space spatial concepts strongly influenced habitat quantity and quality differences among future scenarios. Development patterns showed less influence on those variables. Scenarios with no landscape ecological spatial concept provided the most land for urban development but reduced habitat quantity and quality. Greenway scenarios showed habitat increases but failed to provide sufficient habitat for Western meadowlark. Park system scenarios showed habitat increases, but high-quality habitats for Western meadowlark and Red-legged frog decreased. Network scenarios presented the best overall amount of habitats and high-quality habitats for the three species but constrained urban development options. Next, I used an individual-based wildlife model, HexSim, to simulate the effects of habitat configuration and to compare and contrast resulting wildlife population sizes among the eight future scenarios with the ca. 2010 baseline landscape. Network scenarios supported the largest number of Red-legged frog breeders. Park scenarios performed best for meadowlarks, while greenway scenarios showed the largest populations of squirrels. Four of the eight scenarios sustained viable populations of Western meadowlarks. Compact development scenarios performed best for most indicators, but dispersed development scenarios performed better for Western meadowlarks. This dissertation includes both previously published and unpublished material. Title: Open Space as an Armature for Urban Expansion: A Future Scenarios Study to Assess the Effects of Spatial Concepts on Wildlife Populations Author: Penteado, Homero Year: 2014 Urbanization is one of the biggest threats to biodiversity. To address this problem, landscape planners have increasingly adopted landscape ecology as a theoretical basis for planning. They use spatial concepts that express principles of landscape ecology in diagrammatic form to create frameworks for planning. This dissertation presents a quantitative approach to evaluate the application of spatial concepts developed to create an armature of open space in areas subject to urbanization. It focuses on the predicted urban expansion of Damascus, Oregon, as a case study. An alternative futures study was used to test three open space spatial concepts for patches, corridors and networks in combination with compact and dispersed urban development patterns. The resulting eight scenarios of land use and land cover were then modeled for the year 2060 to evaluate their effects on habitat quantity, quality and configuration and to identify tradeoffs between urban development and conservation for three focal wildlife species: Red-legged frog, Western meadowlark, and Douglas squirrel. Open space spatial concepts strongly influenced habitat quantity and quality differences among future scenarios. Development patterns showed less influence on those variables. Scenarios with no landscape ecological spatial concept provided the most land for urban development but reduced habitat quantity and quality. Greenway scenarios showed habitat increases but failed to provide sufficient habitat for Western meadowlark. Park system scenarios showed habitat increases, but high-quality habitats for Western meadowlark and Red-legged frog decreased. Network scenarios presented the best overall amount of habitats and high-quality habitats for the three species but constrained urban development options. Next, I used an individual-based wildlife model, HexSim, to simulate the effects of habitat configuration and to compare and contrast resulting wildlife population sizes among the eight future scenarios with the ca. 2010 baseline landscape. Network scenarios supported the largest number of Red-legged frog breeders. Park scenarios performed best for meadowlarks, while greenway scenarios showed the largest populations of squirrels. Four of the eight scenarios sustained viable populations of Western meadowlarks. Compact development scenarios performed best for most indicators, but dispersed development scenarios performed better for Western meadowlarks. This dissertation includes both previously published and unpublished material. Close

• 453. [Article] New Nemertean Diversity Discovered in the Northeast Pacific, Using Surveys of Both Planktonic Larvae and Benthic Adults

  This study doubles the known diversity of nemertean species in one region along the northeast Pacific coast by utilizing the often over-looked larval life-history stage. Prior to this work, the nemertean ...

  Citation × Citation Citation Abstract Copy Title: New Nemertean Diversity Discovered in the Northeast Pacific, Using Surveys of Both Planktonic Larvae and Benthic Adults Author: Hiebert, Terra Year: 2016 This study doubles the known diversity of nemertean species in one region along the northeast Pacific coast by utilizing the often over-looked larval life-history stage. Prior to this work, the nemertean fauna in this region was believed to be well described; however, previous assessments were based on adult life-history stages only and significantly underestimated the real diversity. With this dissertation, we update what is known about nemertean diversity and expand upon this “life-history” approach to describe new species, identify and describe larval forms, and speculate on the phylogenetic relevance of nemertean larvae. A considerable amount of new diversity takes the form of cryptic species complexes, where existing descriptions include characteristics of several species. Micrura alaskensis, a common intertidal nemertean and an emerging model system for developmental studies, existed as a species complex consisting of five species. In this dissertation we designate a new genus, re-describe M. alaskensis, and describe four new species in this complex. In doing so we make accurate identification possible for future comparative research. The complete development of few nemertean species was known before this project began, thus few species could be identified as larvae. We have identified over 30 nemertean larvae using both embryological and DNA barcoding approaches in this work. Intriguingly, many wild-caught larvae could not be matched to species previously reported from this region and instead contribute to previously unknown diversity. This new diversity includes species previously reported only from distant geographic regions as well as species new to science. The first record of a hubrechtid on the west coast of North America and the identification of two new species in the currently monotypic genus Riserius were revealed in larval assessments. Aside from increasing known species-level diversity, we revealed novel larval types. Barcoding larvae allowed us to place larval morphotypes into a phylogenetic context and identify potentially useful larval synapomorphies for nemertean phylogenies. Our results emphasize the importance of a life-history approach to biodiversity assessments for all species with biphasic life-cycles. This dissertation includes published and unpublished co-authored material. Title: New Nemertean Diversity Discovered in the Northeast Pacific, Using Surveys of Both Planktonic Larvae and Benthic Adults Author: Hiebert, Terra Year: 2016 This study doubles the known diversity of nemertean species in one region along the northeast Pacific coast by utilizing the often over-looked larval life-history stage. Prior to this work, the nemertean fauna in this region was believed to be well described; however, previous assessments were based on adult life-history stages only and significantly underestimated the real diversity. With this dissertation, we update what is known about nemertean diversity and expand upon this “life-history” approach to describe new species, identify and describe larval forms, and speculate on the phylogenetic relevance of nemertean larvae. A considerable amount of new diversity takes the form of cryptic species complexes, where existing descriptions include characteristics of several species. Micrura alaskensis, a common intertidal nemertean and an emerging model system for developmental studies, existed as a species complex consisting of five species. In this dissertation we designate a new genus, re-describe M. alaskensis, and describe four new species in this complex. In doing so we make accurate identification possible for future comparative research. The complete development of few nemertean species was known before this project began, thus few species could be identified as larvae. We have identified over 30 nemertean larvae using both embryological and DNA barcoding approaches in this work. Intriguingly, many wild-caught larvae could not be matched to species previously reported from this region and instead contribute to previously unknown diversity. This new diversity includes species previously reported only from distant geographic regions as well as species new to science. The first record of a hubrechtid on the west coast of North America and the identification of two new species in the currently monotypic genus Riserius were revealed in larval assessments. Aside from increasing known species-level diversity, we revealed novel larval types. Barcoding larvae allowed us to place larval morphotypes into a phylogenetic context and identify potentially useful larval synapomorphies for nemertean phylogenies. Our results emphasize the importance of a life-history approach to biodiversity assessments for all species with biphasic life-cycles. This dissertation includes published and unpublished co-authored material. Close

• 454. [Article] Work pants worn by loggers in Western Oregon, 1920-1970

  With the arrival of European settlers to Western Oregon nearly 150 years ago came new methods of forest management. Early settlers' forest practices consisted of little more than harvesting what seemed ...

  Citation × Citation Citation Abstract Copy Title: Work pants worn by loggers in Western Oregon, 1920-1970 Author: Gullickson, Mark A. With the arrival of European settlers to Western Oregon nearly 150 years ago came new methods of forest management. Early settlers' forest practices consisted of little more than harvesting what seemed an endless supply of timber. Forestry in the 20th century eventually incorporated such management concerns as re-forestation, biodiversity, wildlife sciences, recreation, and cultural resources. While forest practices in the Pacific Northwest changed dramatically during the 20th century, clothing worn by those most commonly associated with the field, the "logger," remained relatively unchanged. While much information has been published regarding the often over-romanticized life of the logger, information regarding the day to day-life and associative material culture remains almost nonexistent. As the 20th century economy in the Pacific Northwest became less dependent on the wood products industry, the culture and way of life for those whose lives centered around this once thriving industry began to disappear. My interest in this subject developed out of my personal experience working in the woods throughout the Pacific Northwest for seven years, as a forest fire fighter and park ranger for the Bureau of Land Management, and as an archaeologist for the U.S. Forest Service and Oregon State University Research Forests. In this study, I gathered collective memories from 18 individuals who logged throughout Western Oregon between 1920 and 1970. Informants were asked a series of questions pertaining to their logging careers and the clothing they wore. Often termed "old-timers," these informants served as the primary resource of information about work clothing worn by loggers in Western Oregon between 1920 and 1970. Published information describing the history of logging in the Pacific Northwest, photographs provided by informants showing them at work, the examination of catalogues from manufacturers of men's work clothing, and interviews with representatives of work clothing companies served as secondary resources. Published materials detailing work clothing worn by loggers is relatively nonexistent. Consequently, persons with first hand knowledge wearing logging work clothing are in many instances the only sources of information. Photographs furnished by subjects, showing them wearing their work clothing were collected as supportive material. While interviewing subjects for this project, additional questions beyond the scope of the project were asked. Subjects were asked related questions about other types of clothing they wore during their careers. Other areas of logging history and culture explored during interviews consisted of information about changes they observed in the technology of logging hand tools and machinery, land management and associative forest practices, and first hand experiences observing fellow workers severely injured or killed while working in the woods. With the passing of each "old-time" logger, a living connection between the present and the past, and the stories in between, are gone forever. This project helps to present a written record of some of these connections. Title: Work pants worn by loggers in Western Oregon, 1920-1970 Author: Gullickson, Mark A. With the arrival of European settlers to Western Oregon nearly 150 years ago came new methods of forest management. Early settlers' forest practices consisted of little more than harvesting what seemed an endless supply of timber. Forestry in the 20th century eventually incorporated such management concerns as re-forestation, biodiversity, wildlife sciences, recreation, and cultural resources. While forest practices in the Pacific Northwest changed dramatically during the 20th century, clothing worn by those most commonly associated with the field, the "logger," remained relatively unchanged. While much information has been published regarding the often over-romanticized life of the logger, information regarding the day to day-life and associative material culture remains almost nonexistent. As the 20th century economy in the Pacific Northwest became less dependent on the wood products industry, the culture and way of life for those whose lives centered around this once thriving industry began to disappear. My interest in this subject developed out of my personal experience working in the woods throughout the Pacific Northwest for seven years, as a forest fire fighter and park ranger for the Bureau of Land Management, and as an archaeologist for the U.S. Forest Service and Oregon State University Research Forests. In this study, I gathered collective memories from 18 individuals who logged throughout Western Oregon between 1920 and 1970. Informants were asked a series of questions pertaining to their logging careers and the clothing they wore. Often termed "old-timers," these informants served as the primary resource of information about work clothing worn by loggers in Western Oregon between 1920 and 1970. Published information describing the history of logging in the Pacific Northwest, photographs provided by informants showing them at work, the examination of catalogues from manufacturers of men's work clothing, and interviews with representatives of work clothing companies served as secondary resources. Published materials detailing work clothing worn by loggers is relatively nonexistent. Consequently, persons with first hand knowledge wearing logging work clothing are in many instances the only sources of information. Photographs furnished by subjects, showing them wearing their work clothing were collected as supportive material. While interviewing subjects for this project, additional questions beyond the scope of the project were asked. Subjects were asked related questions about other types of clothing they wore during their careers. Other areas of logging history and culture explored during interviews consisted of information about changes they observed in the technology of logging hand tools and machinery, land management and associative forest practices, and first hand experiences observing fellow workers severely injured or killed while working in the woods. With the passing of each "old-time" logger, a living connection between the present and the past, and the stories in between, are gone forever. This project helps to present a written record of some of these connections. Close

• 455. [Article] Modeling and mapping in support of the Regional conservational Strategy Framework

  Report from the Institute of Natural Resources, Portland State University

  Citation × Citation Citation Abstract Copy Title: Modeling and mapping in support of the Regional conservational Strategy Framework Author: Dimiceli, Jennifer, Noone, Matthew, Burcsu, Theresa, Albo, Tommy, Kagan, James S., Bernert, Joe Report from the Institute of Natural Resources, Portland State University Title: Modeling and mapping in support of the Regional conservational Strategy Framework Author: Dimiceli, Jennifer, Noone, Matthew, Burcsu, Theresa, Albo, Tommy, Kagan, James S., Bernert, Joe Report from the Institute of Natural Resources, Portland State University Close

• 456. [Article] The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2015

  We monitored the distribution, abundance and productivity of the federally threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast from 3 April – 11 September 2015. From north ...

  Citation × Citation Citation Abstract Copy Title: The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2015 Author: Castelein, Kathleen A., Gaines, Eleanor P., Lauten, David J., Farrar, J. Daniel, Kotaich, Adam A. We monitored the distribution, abundance and productivity of the federally threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast from 3 April – 11 September 2015. 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 2015 were to: 1) estimate the size of the adult Snowy Plover population along the Oregon coast, 2) locate plover nests, 3) determine nest success, 4) implement nest protection as appropriate (e.g. ropes, signs, exclosures), 5) determine fledging success, 6) monitor brood movements, and 7) collect general observational data about predators. We estimate the Snowy Plover breeding population in Oregon at 449 individuals; a minimum of 376 individuals were known to have nested. The adult plover population was the highest estimate recorded since monitoring began in 1990. We monitored 501 nests in 2015. Overall apparent nest success was 48%. Nest failures were attributed to unknown cause, unknown depredation, mammalian depredation, corvid depredation, abandonment, wind/weather, one-egg nests, harrier depredation, infertility, overwashing, gull depredation and human caused. We monitored 271 broods, including 32 from unknown nests, and documented a minimum of 333 fledglings. Overall brood success was 75%, fledging success was 49%, and 1.51 fledglings per male were produced. Title: The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2015 Author: Castelein, Kathleen A., Gaines, Eleanor P., Lauten, David J., Farrar, J. Daniel, Kotaich, Adam A. We monitored the distribution, abundance and productivity of the federally threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast from 3 April – 11 September 2015. 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 2015 were to: 1) estimate the size of the adult Snowy Plover population along the Oregon coast, 2) locate plover nests, 3) determine nest success, 4) implement nest protection as appropriate (e.g. ropes, signs, exclosures), 5) determine fledging success, 6) monitor brood movements, and 7) collect general observational data about predators. We estimate the Snowy Plover breeding population in Oregon at 449 individuals; a minimum of 376 individuals were known to have nested. The adult plover population was the highest estimate recorded since monitoring began in 1990. We monitored 501 nests in 2015. Overall apparent nest success was 48%. Nest failures were attributed to unknown cause, unknown depredation, mammalian depredation, corvid depredation, abandonment, wind/weather, one-egg nests, harrier depredation, infertility, overwashing, gull depredation and human caused. We monitored 271 broods, including 32 from unknown nests, and documented a minimum of 333 fledglings. Overall brood success was 75%, fledging success was 49%, and 1.51 fledglings per male were produced. Close

• 457. [Article] Historical vegetation of central southwest Oregon, based on GLO survey notes : final report to USDI Bureau of Land Management, Medford District

  Final report to USDI Bureau of Land Management. Medford District, Oregon

  Citation × Citation Citation Abstract Copy Title: Historical vegetation of central southwest Oregon, based on GLO survey notes : final report to USDI Bureau of Land Management, Medford District Author: Hickman, O. Eugene, Christy, John A., The Institute for Natural Resources Final report to USDI Bureau of Land Management. Medford District, Oregon Title: Historical vegetation of central southwest Oregon, based on GLO survey notes : final report to USDI Bureau of Land Management, Medford District Author: Hickman, O. Eugene, Christy, John A., The Institute for Natural Resources Final report to USDI Bureau of Land Management. Medford District, Oregon Close

• 458. [Article] Pine Creek Conservation Area: 2013 mapping and monitoring report

  Report from the Institute for Natural Resources, Portland State University. Pacific Northwest Landscape Assessment and Mapping Program.

  Citation × Citation Citation Abstract Copy Title: Pine Creek Conservation Area: 2013 mapping and monitoring report Author: Nielsen, Eric M., Kagan, James S., Lee, Matthew T., Noone, Matthew D. Report from the Institute for Natural Resources, Portland State University. Pacific Northwest Landscape Assessment and Mapping Program. Title: Pine Creek Conservation Area: 2013 mapping and monitoring report Author: Nielsen, Eric M., Kagan, James S., Lee, Matthew T., Noone, Matthew D. Report from the Institute for Natural Resources, Portland State University. Pacific Northwest Landscape Assessment and Mapping Program. Close

• 459. [Article] Songbird communities in burned and logged stands with variable tree retention in the Canadian Rocky Mountains

  By emulating natural disturbances such as wildfire, managers hope to maintain biodiversity in managed forests. Leaving residual (live) trees in harvested areas is key to this strategy. However, the effectiveness ...

  Citation × Citation Citation Abstract Copy Title: Songbird communities in burned and logged stands with variable tree retention in the Canadian Rocky Mountains Author: Stuart-Smith, A. Kari By emulating natural disturbances such as wildfire, managers hope to maintain biodiversity in managed forests. Leaving residual (live) trees in harvested areas is key to this strategy. However, the effectiveness of this approach is unknown. I surveyed songbirds in 176 stands in the Rocky Mountains of southeastern British Columbia, Canada, that had been logged or burned by wildfire. Stands varied in time-since-disturbance from 5-45 yr. and in residual tree density from 0-2 16 conifer overstory, 0-268 conifer understory, and 0-35 broadleaf trees/ha. In 28 of these stands, artificial and natural nests were used to examine nest predation. Logged and burned stands had similar dominant species, evenness, and diversity (Simpson's index) of birds, but logged stands had higher richness and abundance. Of 26 species analyzed, 20 had similar or greater abundance in logged stands; 6 had greater abundance in burned stands. Differences in songbird communities were likely related to differences in vegetation. As a result of non-intensive logging practices, logged stands had greater shrub cover, shrub richness, broadleaf tree basal area, and more vegetation layers, but fewer regenerating trees, snags, and down wood than burned stands. As time-since-disturbance increased, bird communities in the two disturbance types became more similar at higher elevations, but not at lower elevations. Residual broadleaf and conifer understory tree density positively influenced songbird richness and abundance. Abundance of individual bird species was positively and negatively associated with residual trees. There was no strong or consistent evidence that depredation of nests of ground- and shrub-nesting songbirds increased with residual tree density. Depredation of artificial nests increased with residual tree density in logged stands in one of two years, but not in burned stands. Depredation was higher for artificial than natural nests. Retaining residual trees in managed stands can enhance richness and abundance of songbirds without increasing nest predation. The range of densities in this study provided good habitat for most early seral songbirds, but higher densities of overstory trees and snags are needed to provide good habitat for some species. Logging practices that reduce broadleaf trees, shrub cover, or residual conifer understory trees may reduce songbird richness and abundance. Title: Songbird communities in burned and logged stands with variable tree retention in the Canadian Rocky Mountains Author: Stuart-Smith, A. Kari By emulating natural disturbances such as wildfire, managers hope to maintain biodiversity in managed forests. Leaving residual (live) trees in harvested areas is key to this strategy. However, the effectiveness of this approach is unknown. I surveyed songbirds in 176 stands in the Rocky Mountains of southeastern British Columbia, Canada, that had been logged or burned by wildfire. Stands varied in time-since-disturbance from 5-45 yr. and in residual tree density from 0-2 16 conifer overstory, 0-268 conifer understory, and 0-35 broadleaf trees/ha. In 28 of these stands, artificial and natural nests were used to examine nest predation. Logged and burned stands had similar dominant species, evenness, and diversity (Simpson's index) of birds, but logged stands had higher richness and abundance. Of 26 species analyzed, 20 had similar or greater abundance in logged stands; 6 had greater abundance in burned stands. Differences in songbird communities were likely related to differences in vegetation. As a result of non-intensive logging practices, logged stands had greater shrub cover, shrub richness, broadleaf tree basal area, and more vegetation layers, but fewer regenerating trees, snags, and down wood than burned stands. As time-since-disturbance increased, bird communities in the two disturbance types became more similar at higher elevations, but not at lower elevations. Residual broadleaf and conifer understory tree density positively influenced songbird richness and abundance. Abundance of individual bird species was positively and negatively associated with residual trees. There was no strong or consistent evidence that depredation of nests of ground- and shrub-nesting songbirds increased with residual tree density. Depredation of artificial nests increased with residual tree density in logged stands in one of two years, but not in burned stands. Depredation was higher for artificial than natural nests. Retaining residual trees in managed stands can enhance richness and abundance of songbirds without increasing nest predation. The range of densities in this study provided good habitat for most early seral songbirds, but higher densities of overstory trees and snags are needed to provide good habitat for some species. Logging practices that reduce broadleaf trees, shrub cover, or residual conifer understory trees may reduce songbird richness and abundance. Close

• 460. [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

• 461. [Article] The influence of forest management on headwater stream amphibians at multiple spatial scales

  To effectively manage for biodiversity at broad, ecosystem scales, the influences of habitat structure at multiple spatial scales on vertebrate species must be understood. There are few studies on the ...

  Citation × Citation Citation Abstract Copy Title: The influence of forest management on headwater stream amphibians at multiple spatial scales Author: Stoddard, Margo A. To effectively manage for biodiversity at broad, ecosystem scales, the influences of habitat structure at multiple spatial scales on vertebrate species must be understood. There are few studies on the broad-scale habitat requirements of stream amphibians despite their importance in streams in forest ecosystems in the Pacific Northwest (PNW) as predators and prey, and potentially as indicators of ecosystem health. In particular, studies on the influence of forest structure at landscape scales on stream amphibians are lacking. I examined stream amphibian-habitat relationships for Pacific giant salamanders (Dicamptodon tenebrosus), larval and metamorphosed tailed frogs (Ascaphus truei), and torrent salamanders (Rhyacotriton spp.) at four spatial scales (2-m sample unit, intermediate, sub-drainage, and drainage). Over two field seasons (1998 and 1999), I captured 1,568 amphibians in 702 sample units in 16 randomly chosen drainages in the Oregon Coast Range. I used an information theoretic approach of analysis to rank sets of a priori candidate models that described habitat relationships at each spatial scale. At the 2-m sample unit scale, all species of interest were negatively associated with fine sediments and were positively associated with either stream width or elevation. At the intermediate spatial scale, Pacific giant salamanders, metamorphosed tailed frogs, and torrent salamanders were positively associated with the presence of a 150-ft. forested band on each side of the stream, and larval tailed frogs were positively associated with the presence of forest >105 years old on at least one side of the stream. At the sub-drainage and drainage scales, all species were positively associated with the proportion of stream length in a sub-drainage or drainage with a 150-ft. forested band on each side of the stream. Heat load index (aspect) was also important for Pacific giant salamanders and larval tailed frogs at the intermediate and sub-drainage scales. Results at all spatial scales suggest that Pacific giant salamanders and larval tailed frogs occur lower in the drainage network, and metamorphosed tailed frogs and torrent salamanders occur higher in the drainage network. This study demonstrates the importance of examining headwater stream amphibian habitat at multiple spatial scales, provides insights on linkages between amphibian responses across spatial scales, and shows that broad-scale variables (e.g., the presence of forested bands or the percentage of stream length with forested bands) can be used to assess management approaches for stream amphibian communities. Geophysical characteristics such as stream aspect may also help identify areas that should not be harvested if protection of amphibian habitat is an objective. Title: The influence of forest management on headwater stream amphibians at multiple spatial scales Author: Stoddard, Margo A. To effectively manage for biodiversity at broad, ecosystem scales, the influences of habitat structure at multiple spatial scales on vertebrate species must be understood. There are few studies on the broad-scale habitat requirements of stream amphibians despite their importance in streams in forest ecosystems in the Pacific Northwest (PNW) as predators and prey, and potentially as indicators of ecosystem health. In particular, studies on the influence of forest structure at landscape scales on stream amphibians are lacking. I examined stream amphibian-habitat relationships for Pacific giant salamanders (Dicamptodon tenebrosus), larval and metamorphosed tailed frogs (Ascaphus truei), and torrent salamanders (Rhyacotriton spp.) at four spatial scales (2-m sample unit, intermediate, sub-drainage, and drainage). Over two field seasons (1998 and 1999), I captured 1,568 amphibians in 702 sample units in 16 randomly chosen drainages in the Oregon Coast Range. I used an information theoretic approach of analysis to rank sets of a priori candidate models that described habitat relationships at each spatial scale. At the 2-m sample unit scale, all species of interest were negatively associated with fine sediments and were positively associated with either stream width or elevation. At the intermediate spatial scale, Pacific giant salamanders, metamorphosed tailed frogs, and torrent salamanders were positively associated with the presence of a 150-ft. forested band on each side of the stream, and larval tailed frogs were positively associated with the presence of forest >105 years old on at least one side of the stream. At the sub-drainage and drainage scales, all species were positively associated with the proportion of stream length in a sub-drainage or drainage with a 150-ft. forested band on each side of the stream. Heat load index (aspect) was also important for Pacific giant salamanders and larval tailed frogs at the intermediate and sub-drainage scales. Results at all spatial scales suggest that Pacific giant salamanders and larval tailed frogs occur lower in the drainage network, and metamorphosed tailed frogs and torrent salamanders occur higher in the drainage network. This study demonstrates the importance of examining headwater stream amphibian habitat at multiple spatial scales, provides insights on linkages between amphibian responses across spatial scales, and shows that broad-scale variables (e.g., the presence of forested bands or the percentage of stream length with forested bands) can be used to assess management approaches for stream amphibian communities. Geophysical characteristics such as stream aspect may also help identify areas that should not be harvested if protection of amphibian habitat is an objective. Close

• 462. [Article] Total aboveground biomass and structure of tropical forest delineated by Projeto RADAMBRASIL in northern Rondonia, Brazil

  Tropical forests are of global importance with respect to their influence on biogeochemical cycles, climatic patterns, and as large reservoirs of biodiversity. Yet, few studies have quantified their structure, ...

  Citation × Citation Citation Abstract Copy Title: Total aboveground biomass and structure of tropical forest delineated by Projeto RADAMBRASIL in northern Rondonia, Brazil Author: Cummings, Dian Lyn Tropical forests are of global importance with respect to their influence on biogeochemical cycles, climatic patterns, and as large reservoirs of biodiversity. Yet, few studies have quantified their structure, biomass, and carbon pools; basic information necessary to better understand the global function of tropical forests. The RADAMBRASIL project was conducted in the 1970's to inventory Brazil's natural resources. Describing a relationship between total aboveground biomass (TAGB) and the RADAMBRASIL forest inventories could add to the usefulness of RADAMBRASIL data base for the estimation of TAGB and carbon pools of the Amazon Basin. Our study quantified TAGB and forest structure of 20 undisturbed primary forest stands that were a part of Projeto RADAMBRASIL. This study was located in Rondonia, Brazil; an area in which a large portion of Amazonian deforestation occurred. TAGB ranged from 533 Mg ha-1 in a dense forest site to 288 Mg ha-1 in an open forest site with a mean TAGB of 341 Mg ha-1. TAGB and structure in each stand was described by partitioning and measuring the vegetation components. Non-tree components included palm, vines, litter, rootmat, and dead vegetation. The non-tree component of TAGB was highly variable (i.e.; 12% and 41%). We tested the hypothesis that there was a high correlation between these enumerated TAGB estimates from our study and predictive models that use commercial volumes from RADAMBRASIL to estimate TAGB (Fearnside, 1992 and Brown and Lugo 1992). No significant correlation was found between the modeled TAGB and the field measured TAG B. The Brown and Lugo model underestimated the mean for dense forests by > 1 00 Mg ha-1 (28%), conversely the Fearnside model overestimated the mean for open forests by > 100Mg ha-1(35%). No correlation was found between the TAGB estimates from this study and commercial volume reported in RADAMBRASIL, therefore no model was possible for TAGB based on commercial volume. Determining relationships between classifications from forest inventories and actual biomass data could improve models of global climate change and biogeochemical cycles. Given results from this study, current estimates of TAGB for Amazonian rainforests that are lower than 290 Mg ha-1 based upon forest inventories should be viewed with caution. Title: Total aboveground biomass and structure of tropical forest delineated by Projeto RADAMBRASIL in northern Rondonia, Brazil Author: Cummings, Dian Lyn Tropical forests are of global importance with respect to their influence on biogeochemical cycles, climatic patterns, and as large reservoirs of biodiversity. Yet, few studies have quantified their structure, biomass, and carbon pools; basic information necessary to better understand the global function of tropical forests. The RADAMBRASIL project was conducted in the 1970's to inventory Brazil's natural resources. Describing a relationship between total aboveground biomass (TAGB) and the RADAMBRASIL forest inventories could add to the usefulness of RADAMBRASIL data base for the estimation of TAGB and carbon pools of the Amazon Basin. Our study quantified TAGB and forest structure of 20 undisturbed primary forest stands that were a part of Projeto RADAMBRASIL. This study was located in Rondonia, Brazil; an area in which a large portion of Amazonian deforestation occurred. TAGB ranged from 533 Mg ha-1 in a dense forest site to 288 Mg ha-1 in an open forest site with a mean TAGB of 341 Mg ha-1. TAGB and structure in each stand was described by partitioning and measuring the vegetation components. Non-tree components included palm, vines, litter, rootmat, and dead vegetation. The non-tree component of TAGB was highly variable (i.e.; 12% and 41%). We tested the hypothesis that there was a high correlation between these enumerated TAGB estimates from our study and predictive models that use commercial volumes from RADAMBRASIL to estimate TAGB (Fearnside, 1992 and Brown and Lugo 1992). No significant correlation was found between the modeled TAGB and the field measured TAG B. The Brown and Lugo model underestimated the mean for dense forests by > 1 00 Mg ha-1 (28%), conversely the Fearnside model overestimated the mean for open forests by > 100Mg ha-1(35%). No correlation was found between the TAGB estimates from this study and commercial volume reported in RADAMBRASIL, therefore no model was possible for TAGB based on commercial volume. Determining relationships between classifications from forest inventories and actual biomass data could improve models of global climate change and biogeochemical cycles. Given results from this study, current estimates of TAGB for Amazonian rainforests that are lower than 290 Mg ha-1 based upon forest inventories should be viewed with caution. Close

• 463. [Article] Comparison of stand development of a deciduous-dominated riparian forest and a coniferous-dominated riparian forest in the Oregon Coast Range

  Riparian forests in the central Oregon Coast Range vary along a coniferous-deciduous compositional continuum. Variations in structure and composition affect water quality, fish and wildlife, biodiversity, ...

  Citation × Citation Citation Abstract Copy Title: Comparison of stand development of a deciduous-dominated riparian forest and a coniferous-dominated riparian forest in the Oregon Coast Range Author: Poage, Nathan Jeremy Riparian forests in the central Oregon Coast Range vary along a coniferous-deciduous compositional continuum. Variations in structure and composition affect water quality, fish and wildlife, biodiversity, timber, and aesthetics. A retrospective approach was taken in this study in order to understand and compare the structure, pattern, and history of an unmanaged, mature, deciduous-dominated riparian forest and an unmanaged, mature, coniferous-dominated riparian forest in the central Oregon Coast Range. Information on forest structure and pattern was acquired by mapping locations of all trees and snags (DBH 5cm) within a 2.0 ha and a 2.25 ha reference stand. The history of each stand was reconstructed through analyses of stand structure and composition, tree ages, spatial patterns of trees and snags, as well as detailed field observations. The structure and composition of the two forests is very different. Non-random patterns of trees and snags were observed at multiple scales. Although it is not possible to infer directly the process(es) responsible for observed patterns, point-pattern analysis is a useful tool to detect and describe intra- and interspecific patterns. Neither forest resulted from a single, stand-replacing fire. Instead, both sites were at least partially burned about 145 years ago, possibly in the same fire(s) which spread across an estimated 500,000 acres between the Siuslaw and Siletz Rivers in the mid-1800's (Morris 1934). There is good evidence to suggest that a second fire occurred at the coniferous-dominated site. One or two other fires may have occurred at the deciduous-dominated site. Evidence of wind, herbivory, flooding, pathogens, mass movement events, and non-stand replacing fire was observed at one or both of the sites. Seed source availability as affected by disturbance history may have played a role in forest development at both sites. The seed source availability of red alder relative to Douglas-fir may have increased with successive disturbance events at the deciduous-dominated, riparian forest. A local source of western hemlock seed may have been a key factor in the development of the coniferous-dominated, riparian forest. Title: Comparison of stand development of a deciduous-dominated riparian forest and a coniferous-dominated riparian forest in the Oregon Coast Range Author: Poage, Nathan Jeremy Riparian forests in the central Oregon Coast Range vary along a coniferous-deciduous compositional continuum. Variations in structure and composition affect water quality, fish and wildlife, biodiversity, timber, and aesthetics. A retrospective approach was taken in this study in order to understand and compare the structure, pattern, and history of an unmanaged, mature, deciduous-dominated riparian forest and an unmanaged, mature, coniferous-dominated riparian forest in the central Oregon Coast Range. Information on forest structure and pattern was acquired by mapping locations of all trees and snags (DBH 5cm) within a 2.0 ha and a 2.25 ha reference stand. The history of each stand was reconstructed through analyses of stand structure and composition, tree ages, spatial patterns of trees and snags, as well as detailed field observations. The structure and composition of the two forests is very different. Non-random patterns of trees and snags were observed at multiple scales. Although it is not possible to infer directly the process(es) responsible for observed patterns, point-pattern analysis is a useful tool to detect and describe intra- and interspecific patterns. Neither forest resulted from a single, stand-replacing fire. Instead, both sites were at least partially burned about 145 years ago, possibly in the same fire(s) which spread across an estimated 500,000 acres between the Siuslaw and Siletz Rivers in the mid-1800's (Morris 1934). There is good evidence to suggest that a second fire occurred at the coniferous-dominated site. One or two other fires may have occurred at the deciduous-dominated site. Evidence of wind, herbivory, flooding, pathogens, mass movement events, and non-stand replacing fire was observed at one or both of the sites. Seed source availability as affected by disturbance history may have played a role in forest development at both sites. The seed source availability of red alder relative to Douglas-fir may have increased with successive disturbance events at the deciduous-dominated, riparian forest. A local source of western hemlock seed may have been a key factor in the development of the coniferous-dominated, riparian forest. Close

• 464. [Article] Relationship between plant and butterfly community composition on upland prairies of the Willamette Valley, Oregon

  Small remnants of 'natural' habitats exist today throughout much of the world. Upland prairies in the Willamette Valley, Oregon have been nearly eliminated by conversion to agriculture and other uses. ...

  Citation × Citation Citation Abstract Copy Title: Relationship between plant and butterfly community composition on upland prairies of the Willamette Valley, Oregon Author: York, Melissa M. Small remnants of 'natural' habitats exist today throughout much of the world. Upland prairies in the Willamette Valley, Oregon have been nearly eliminated by conversion to agriculture and other uses. As a result, very few prairies remain and at least four butterfly species that require this habitat appear to be locally uncommon. To better understand requirements for conservation and management of upland prairies and the species that depend on them, I investigated plant abundance and species richness, butterfly abundance and species richness, and prairie integrity on 17 prairie remnants. To evaluate the relationship between prairie integrity and butterfly community composition, integrity was defined by abundance and species richness of native, prairie plant species. Because little is known about the habitat requirements of prairie-dwelling organisms, I also investigated juvenile and adult food resource use and spatial patterns associated with resource use by four locally uncommon butterfly species: common checkered-skipper, Fender's blue, Anise swallowtail, and field crescent. Plant species used and not used for nectaring and oviposition and spatial relationships between the two were explored for each butterfly species. My study provides evidence that remnants, including small, degraded sites, serve as refuges for locally uncommon butterfly species. The greatest mean number of butterfly species was detected on sites of high integrity, but total butterfly abundance at all but one unique site was similar to that of low and medium integrity sites. Butterfly species richness appeared to be positively associated with remnant integrity while factors other than remnant integrity as defined here may be influential on butterfly abundance. Furthermore, I suggest that the locally uncommon butterflies studied here have specific habitat requirements and this likely contributed to their sparse distribution. Although host plant abundance did not appear to limit butterfly distributions within either site, I lacked sufficient sample sizes necessary to make strong inferences. Factors other than, or in combination, with host plant occurrence, such as presence of Composite nectar species and native plant abundance, may be important in determining their distribution within a site. Lack of large areas of habitat and incidence of uncommon species on remnants makes it imperative that we conserve biodiversity by the maintenance, improvement, and protection of some very small areas. Title: Relationship between plant and butterfly community composition on upland prairies of the Willamette Valley, Oregon Author: York, Melissa M. Small remnants of 'natural' habitats exist today throughout much of the world. Upland prairies in the Willamette Valley, Oregon have been nearly eliminated by conversion to agriculture and other uses. As a result, very few prairies remain and at least four butterfly species that require this habitat appear to be locally uncommon. To better understand requirements for conservation and management of upland prairies and the species that depend on them, I investigated plant abundance and species richness, butterfly abundance and species richness, and prairie integrity on 17 prairie remnants. To evaluate the relationship between prairie integrity and butterfly community composition, integrity was defined by abundance and species richness of native, prairie plant species. Because little is known about the habitat requirements of prairie-dwelling organisms, I also investigated juvenile and adult food resource use and spatial patterns associated with resource use by four locally uncommon butterfly species: common checkered-skipper, Fender's blue, Anise swallowtail, and field crescent. Plant species used and not used for nectaring and oviposition and spatial relationships between the two were explored for each butterfly species. My study provides evidence that remnants, including small, degraded sites, serve as refuges for locally uncommon butterfly species. The greatest mean number of butterfly species was detected on sites of high integrity, but total butterfly abundance at all but one unique site was similar to that of low and medium integrity sites. Butterfly species richness appeared to be positively associated with remnant integrity while factors other than remnant integrity as defined here may be influential on butterfly abundance. Furthermore, I suggest that the locally uncommon butterflies studied here have specific habitat requirements and this likely contributed to their sparse distribution. Although host plant abundance did not appear to limit butterfly distributions within either site, I lacked sufficient sample sizes necessary to make strong inferences. Factors other than, or in combination, with host plant occurrence, such as presence of Composite nectar species and native plant abundance, may be important in determining their distribution within a site. Lack of large areas of habitat and incidence of uncommon species on remnants makes it imperative that we conserve biodiversity by the maintenance, improvement, and protection of some very small areas. Close

• 465. [Article] Andean roots, coca, and grassroots development in the Bolivian Yungas : food sovereignty and agrarian change for native farmers

  Since the 1952 Bolivian agrarian reform, farmer unions have sought to establish themselves as producers for regional markets. Development strategies led by the World Bank and IMF have largely jeopardized ...

  Citation × Citation Citation Abstract Copy Title: Andean roots, coca, and grassroots development in the Bolivian Yungas : food sovereignty and agrarian change for native farmers Author: Piispanen, Kyle Henry Since the 1952 Bolivian agrarian reform, farmer unions have sought to establish themselves as producers for regional markets. Development strategies led by the World Bank and IMF have largely jeopardized small farmers, and challenged farmers to meet market demands. At present, a new agrarian revolution is being implemented and is conditioned by objectives, which include land redistribution, food sovereignty, and public food enterprises. This research was conducted in the Yungas region of Bolivia in isolated mountain communities that are part of the established traditional and legal area for coca growing and thus clearly integrated into the world "commodities" market via the illicit cocaine economy. Curiously, many farmers continue to grow crops for local markets, their homes, and organic coca for traditional use. Is this part of a greater movement of revolutionary agrarian policy or concern for food sovereignty in local communities? Under this context, I explore how some individual farmers and farming associations have developed a tradition of growing Andean root crops and their lived experience of their involvement in the associations. Through participant observation and ethnographic interviews with members of two Yungueño community associations and with regional technicians, this study explores how associations and individuals negotiate national and international policy, and NGO activity, in order to create specialty niche markets for native crops. This thesis argues that alternative agricultural development that has focused on coca reduction, export-oriented agriculture, and food security has, to a large extent, been a failure. Rather, local initiatives that focus on ecological coca, food sovereignty, and native crops for local markets taken together are meeting some local development goals. This study provides an opportunity for reframing development theory and expanding the literature on food sovereignty. The concept of the La Paz-El Alto food-shed is used as a tool for exploring the potential of reorienting the moral economy around food in re-creating a more sustainable food system. From the perspectives of an Andean root crop association, I explore particular challenges members face in farming in contested lands of commodity coca production. Associations begin by meeting specialty market needs for ritual uses of specialty Andean crops, and may utilize a variety of assistance programs but are determined to maintain a high level of autonomy. Associations are often cautious in searching for assistance because farmers cannot afford to lose time expanding alternative crops that could be better spent in coca production. Failure is common, and few associations achieve goals of significantly increased incomes. Rather semi-subsistence and diversification along with coca growing provide greater autonomy and sovereignty in practical terms when many of the anticipated national reforms are yet to be seen in these particular Yungueño communities. In addition, I briefly explore with farmers the environmental considerations and perspectives to climate, gardening, biodiversity loss, and the concern about the use of chemical applications. Title: Andean roots, coca, and grassroots development in the Bolivian Yungas : food sovereignty and agrarian change for native farmers Author: Piispanen, Kyle Henry Since the 1952 Bolivian agrarian reform, farmer unions have sought to establish themselves as producers for regional markets. Development strategies led by the World Bank and IMF have largely jeopardized small farmers, and challenged farmers to meet market demands. At present, a new agrarian revolution is being implemented and is conditioned by objectives, which include land redistribution, food sovereignty, and public food enterprises. This research was conducted in the Yungas region of Bolivia in isolated mountain communities that are part of the established traditional and legal area for coca growing and thus clearly integrated into the world "commodities" market via the illicit cocaine economy. Curiously, many farmers continue to grow crops for local markets, their homes, and organic coca for traditional use. Is this part of a greater movement of revolutionary agrarian policy or concern for food sovereignty in local communities? Under this context, I explore how some individual farmers and farming associations have developed a tradition of growing Andean root crops and their lived experience of their involvement in the associations. Through participant observation and ethnographic interviews with members of two Yungueño community associations and with regional technicians, this study explores how associations and individuals negotiate national and international policy, and NGO activity, in order to create specialty niche markets for native crops. This thesis argues that alternative agricultural development that has focused on coca reduction, export-oriented agriculture, and food security has, to a large extent, been a failure. Rather, local initiatives that focus on ecological coca, food sovereignty, and native crops for local markets taken together are meeting some local development goals. This study provides an opportunity for reframing development theory and expanding the literature on food sovereignty. The concept of the La Paz-El Alto food-shed is used as a tool for exploring the potential of reorienting the moral economy around food in re-creating a more sustainable food system. From the perspectives of an Andean root crop association, I explore particular challenges members face in farming in contested lands of commodity coca production. Associations begin by meeting specialty market needs for ritual uses of specialty Andean crops, and may utilize a variety of assistance programs but are determined to maintain a high level of autonomy. Associations are often cautious in searching for assistance because farmers cannot afford to lose time expanding alternative crops that could be better spent in coca production. Failure is common, and few associations achieve goals of significantly increased incomes. Rather semi-subsistence and diversification along with coca growing provide greater autonomy and sovereignty in practical terms when many of the anticipated national reforms are yet to be seen in these particular Yungueño communities. In addition, I briefly explore with farmers the environmental considerations and perspectives to climate, gardening, biodiversity loss, and the concern about the use of chemical applications. Close

• 466. [Article] A community-based approach for evaluating tradeoffs across marine ecosystem services in Oregon

  As competing uses of our coastlines increase, natural resource agencies are employing marine spatial planning (MSP) to designate areas for different uses or activities in order to reduce conflicts while ...

  Citation × Citation Citation Abstract Copy Title: A community-based approach for evaluating tradeoffs across marine ecosystem services in Oregon Author: Freeman, Peter M. As competing uses of our coastlines increase, natural resource agencies are employing marine spatial planning (MSP) to designate areas for different uses or activities in order to reduce conflicts while achieving ecological, economic and social objectives. A central challenge of implementing MSP is development of a rigorous approach for analyzing tradeoffs across the provision of ecosystem services (i.e., the benefits humans receive from nature). This study develops an operational approach to this problem that is founded on community-based methods, ecological production theory, and multi-criteria decision analysis (MCDA). The approach merges ecological models with surveys to identify marine ecosystem services for use in tradeoff analysis. The approach allows for a single set of marine ecosystem services to at once be valued by local stakeholders and measured by biologists, thus connecting social and biological monitoring efforts. To develop the approach in a real-world context, I examined ecosystem services associated with nearshore marine ecosystems in Oregon, where marine reserves are being introduced for biodiversity conservation. I worked with stakeholder focus groups in three Oregon communities to identify 24 marine ecosystem services. I then linked the ecosystem services with ecological indicators, which I then consolidated to derive 11 items for use in a survey-based tradeoff analysis exercise. I administered the survey to a nonrandom sample of stakeholders in Oregon (n=31), from which their relative preferences and preference weights for ecosystem services were derived. The weights and preference measures may then be used in MSP decision-making. Furthermore, I grouped the stakeholder survey data in three ways: by location of residence (coastal vs. non-coastal), by eight categories of affiliation (e.g., business owners, conservationists, commercial and recreational fishers, etc.), and by resource use patterns. I then analyzed the various groupings of stakeholders for within- and between-group homogeneity of preferences. Results of the analyses showed that there are statistically significant variations in preferences within and between most groupings. Capturing the variations in stakeholder preferences is important when developing policies that affect different stakeholder groups. Thus, when implementing the survey instrument, I suggest random sampling of stakeholders stratified by location, affiliation, and resource use. This study provides one of the first examples of a systems-based approach to ecosystem service valuation operationalized to inform MSP, and novel features of the approach have a number of implications for advancing marine research and management. First, by using stakeholders to identify ecosystem services, the approach allows for a tailored implementation of ecosystem-based management at the community level. Second, by integrating ecological and economic information on the provision and value of ecosystem services, the approach provides relevant data for MSP decision-making during the siting, evaluation, and monitoring stages. And third, by applying both stated-preference and MCDA methods, the approach may capture the array of values represented by diverse stakeholder groups. Title: A community-based approach for evaluating tradeoffs across marine ecosystem services in Oregon Author: Freeman, Peter M. As competing uses of our coastlines increase, natural resource agencies are employing marine spatial planning (MSP) to designate areas for different uses or activities in order to reduce conflicts while achieving ecological, economic and social objectives. A central challenge of implementing MSP is development of a rigorous approach for analyzing tradeoffs across the provision of ecosystem services (i.e., the benefits humans receive from nature). This study develops an operational approach to this problem that is founded on community-based methods, ecological production theory, and multi-criteria decision analysis (MCDA). The approach merges ecological models with surveys to identify marine ecosystem services for use in tradeoff analysis. The approach allows for a single set of marine ecosystem services to at once be valued by local stakeholders and measured by biologists, thus connecting social and biological monitoring efforts. To develop the approach in a real-world context, I examined ecosystem services associated with nearshore marine ecosystems in Oregon, where marine reserves are being introduced for biodiversity conservation. I worked with stakeholder focus groups in three Oregon communities to identify 24 marine ecosystem services. I then linked the ecosystem services with ecological indicators, which I then consolidated to derive 11 items for use in a survey-based tradeoff analysis exercise. I administered the survey to a nonrandom sample of stakeholders in Oregon (n=31), from which their relative preferences and preference weights for ecosystem services were derived. The weights and preference measures may then be used in MSP decision-making. Furthermore, I grouped the stakeholder survey data in three ways: by location of residence (coastal vs. non-coastal), by eight categories of affiliation (e.g., business owners, conservationists, commercial and recreational fishers, etc.), and by resource use patterns. I then analyzed the various groupings of stakeholders for within- and between-group homogeneity of preferences. Results of the analyses showed that there are statistically significant variations in preferences within and between most groupings. Capturing the variations in stakeholder preferences is important when developing policies that affect different stakeholder groups. Thus, when implementing the survey instrument, I suggest random sampling of stakeholders stratified by location, affiliation, and resource use. This study provides one of the first examples of a systems-based approach to ecosystem service valuation operationalized to inform MSP, and novel features of the approach have a number of implications for advancing marine research and management. First, by using stakeholders to identify ecosystem services, the approach allows for a tailored implementation of ecosystem-based management at the community level. Second, by integrating ecological and economic information on the provision and value of ecosystem services, the approach provides relevant data for MSP decision-making during the siting, evaluation, and monitoring stages. And third, by applying both stated-preference and MCDA methods, the approach may capture the array of values represented by diverse stakeholder groups. Close

• 467. [Article] Efficacy of Empirical Seed Zones: Pseudoroegneria Spicata Reproductive Phenology & Seedling Stage Traits

  Ecological restoration is needed to mitigate losses to biodiversity. Restoration success is enhanced through the use of native plant materials that are genetically diverse and locally adapted. Seed transfer ...

  Citation × Citation Citation Abstract Copy Title: Efficacy of Empirical Seed Zones: Pseudoroegneria Spicata Reproductive Phenology & Seedling Stage Traits Author: Prive, Kathryn A. Ecological restoration is needed to mitigate losses to biodiversity. Restoration success is enhanced through the use of native plant materials that are genetically diverse and locally adapted. Seed transfer zones have been developed to delineate geographic areas where native seed can be collected and distributed with reduced risk of maladaptation. Pseudoroegneria spicata (Pursh) Á. Löve is a widespread bunchgrass species with recently delineated seed zones, that is used extensively for ecological restoration in the Intermountain West. In this work, I conducted two studies of seed zone efficacy for P. spicata. In the first study, I determined if genetic differences in reproductive timing exist among P. spicata populations, and whether any such differences should be considered to avoid single-harvest stabilizing selection, which would cause inadvertent genetic loss during commercial seed production. In the second study, I determined if seedling traits differ among P. spicata populations, and if seed transfer zones developed using adult traits account for these differences. I utilized linear mixed modeling, intra-class coefficient analysis, nonmetric multi-dimensional scaling, and multi-response permutation procedures to quantify differences in the timing of anthesis, ripening, and dispersal and various seedling stage phenotypic traits for P. spicata. I found that variation in the timing of anthesis is not well explained by seed zones but that there was little difference in the mean values of this trait among populations from the same seed zone. On the other hand, genetic variation in seed ripening is captured by seed zones. For the dispersal stage, a lack of strong evidence for genetic differences among populations suggests a plastic response to environmental cues. Thus, typical single-pass seed harvest techniques are not likely to cause inadvertent selection for reproductive timing when seed transfer guidelines are followed. In the second study, I found that seed zones do not account for variation in seedling traits, meaning the use of current seed zones could risk the transfer of seeds to locations where seedling recruitment and establishment are hindered. This is important, since seedling establishment is often a limiting factor in restoration success. Although I focused these studies on P. spicata, my findings of incongruences between both reproductive timing and seedling stage phenotypic traits with respect to seed transfer zones suggests that such incongruities could be commonplace among other species used in restoration. Inadvertent selection during seed increase does not appear to be a risk in P. spicata when seed transfer guidelines are followed, but more research is needed to ensure that seedling stage traits are accounted for within future native species seed transfer guidelines. Title: Efficacy of Empirical Seed Zones: Pseudoroegneria Spicata Reproductive Phenology & Seedling Stage Traits Author: Prive, Kathryn A. Ecological restoration is needed to mitigate losses to biodiversity. Restoration success is enhanced through the use of native plant materials that are genetically diverse and locally adapted. Seed transfer zones have been developed to delineate geographic areas where native seed can be collected and distributed with reduced risk of maladaptation. Pseudoroegneria spicata (Pursh) Á. Löve is a widespread bunchgrass species with recently delineated seed zones, that is used extensively for ecological restoration in the Intermountain West. In this work, I conducted two studies of seed zone efficacy for P. spicata. In the first study, I determined if genetic differences in reproductive timing exist among P. spicata populations, and whether any such differences should be considered to avoid single-harvest stabilizing selection, which would cause inadvertent genetic loss during commercial seed production. In the second study, I determined if seedling traits differ among P. spicata populations, and if seed transfer zones developed using adult traits account for these differences. I utilized linear mixed modeling, intra-class coefficient analysis, nonmetric multi-dimensional scaling, and multi-response permutation procedures to quantify differences in the timing of anthesis, ripening, and dispersal and various seedling stage phenotypic traits for P. spicata. I found that variation in the timing of anthesis is not well explained by seed zones but that there was little difference in the mean values of this trait among populations from the same seed zone. On the other hand, genetic variation in seed ripening is captured by seed zones. For the dispersal stage, a lack of strong evidence for genetic differences among populations suggests a plastic response to environmental cues. Thus, typical single-pass seed harvest techniques are not likely to cause inadvertent selection for reproductive timing when seed transfer guidelines are followed. In the second study, I found that seed zones do not account for variation in seedling traits, meaning the use of current seed zones could risk the transfer of seeds to locations where seedling recruitment and establishment are hindered. This is important, since seedling establishment is often a limiting factor in restoration success. Although I focused these studies on P. spicata, my findings of incongruences between both reproductive timing and seedling stage phenotypic traits with respect to seed transfer zones suggests that such incongruities could be commonplace among other species used in restoration. Inadvertent selection during seed increase does not appear to be a risk in P. spicata when seed transfer guidelines are followed, but more research is needed to ensure that seedling stage traits are accounted for within future native species seed transfer guidelines. Close

• 468. [Article] Relationships of green-tree retention following timber harvest to forest growth and species composition in the western Cascade Mountains

  National Forest management in the Pacific Northwest is shifting from a focus on commodity production to ecosystem management, in which the health of the entire forest ecosystem is considered, rather than ...

  Citation × Citation Citation Abstract Copy Title: Relationships of green-tree retention following timber harvest to forest growth and species composition in the western Cascade Mountains Author: Rose, Coulter R. National Forest management in the Pacific Northwest is shifting from a focus on commodity production to ecosystem management, in which the health of the entire forest ecosystem is considered, rather than that of a few key species. Ecosystem management includes retention of some live trees following timber harvest (green-tree retention) to preserve biodiversity, imitating the natural fire regime of large, but patchy fires that leave many live trees. How ecosystem management will affect growth and species composition of future forests is an important question. This study takes a retrospective approach to this question by using past disturbance as an analogue to green-tree retention following timber harvest. Using USDA Forest Service timber inventory plot data from the Cascade Mountains of Oregon and SW Washington, 132 unmanaged stands were identified with a tree cohort of 70-110 years old (regeneration) or a tree cohort of 70-110 years old with an overstory of large trees 200+ years old (remnants). All stands were in the Tsuga heterophylla (Raf.) Sarg. zone (Franklin and Dyrness 1973). Single-aged stands represented clearcuts, while two-aged stands served as analogues to stands harvested with green-tree retention. Regeneration basal area/hectare (ba/ha) declined when remnant-tree densities exceeded about 15 remnant trees/ha (R²=0.51) in a relationship roughly described by a sigmoidal curve. Conceptually removing remnant-tree space occupancy effects decreased remnant-tree density's value as a predictor of regeneration ba/ha by about 50% at management-level remnant densities (≤45 remnant trees/ha). Thus, it appears that remnant "effects" were a result of both remnant-tree space occupancy and remnant resource use. Douglas-fir ba/ha in the regeneration also declined when remnant-tree densities exceeded about 15 remnant trees/ha (R²=0.60). Western hemlock ba/ha in the regeneration increased slightly with increasing remnant-tree densities (R²=0.19). Western redcedar ba/ha in the regeneration was apparently not related to remnant-tree density (R²=0.02). The degree of aggregation in remnant trees did not appear to affect regeneration ba/ha, but few stands contained the isolated clumps of remnant trees likely under a management scenario. Neither measured site characteristics nor regeneration density was related to regeneration ba/ha across species. Remnant-tree density was apparently unrelated to tree-species diversity in the regeneration. Total-stand ba/ha remained relatively constant across remnant densities. Title: Relationships of green-tree retention following timber harvest to forest growth and species composition in the western Cascade Mountains Author: Rose, Coulter R. National Forest management in the Pacific Northwest is shifting from a focus on commodity production to ecosystem management, in which the health of the entire forest ecosystem is considered, rather than that of a few key species. Ecosystem management includes retention of some live trees following timber harvest (green-tree retention) to preserve biodiversity, imitating the natural fire regime of large, but patchy fires that leave many live trees. How ecosystem management will affect growth and species composition of future forests is an important question. This study takes a retrospective approach to this question by using past disturbance as an analogue to green-tree retention following timber harvest. Using USDA Forest Service timber inventory plot data from the Cascade Mountains of Oregon and SW Washington, 132 unmanaged stands were identified with a tree cohort of 70-110 years old (regeneration) or a tree cohort of 70-110 years old with an overstory of large trees 200+ years old (remnants). All stands were in the Tsuga heterophylla (Raf.) Sarg. zone (Franklin and Dyrness 1973). Single-aged stands represented clearcuts, while two-aged stands served as analogues to stands harvested with green-tree retention. Regeneration basal area/hectare (ba/ha) declined when remnant-tree densities exceeded about 15 remnant trees/ha (R²=0.51) in a relationship roughly described by a sigmoidal curve. Conceptually removing remnant-tree space occupancy effects decreased remnant-tree density's value as a predictor of regeneration ba/ha by about 50% at management-level remnant densities (≤45 remnant trees/ha). Thus, it appears that remnant "effects" were a result of both remnant-tree space occupancy and remnant resource use. Douglas-fir ba/ha in the regeneration also declined when remnant-tree densities exceeded about 15 remnant trees/ha (R²=0.60). Western hemlock ba/ha in the regeneration increased slightly with increasing remnant-tree densities (R²=0.19). Western redcedar ba/ha in the regeneration was apparently not related to remnant-tree density (R²=0.02). The degree of aggregation in remnant trees did not appear to affect regeneration ba/ha, but few stands contained the isolated clumps of remnant trees likely under a management scenario. Neither measured site characteristics nor regeneration density was related to regeneration ba/ha across species. Remnant-tree density was apparently unrelated to tree-species diversity in the regeneration. Total-stand ba/ha remained relatively constant across remnant densities. Close

• 469. [Article] Effects of pesticides on amphibians with special reference to the pyrethroid insecticide, cypermethrin

  Pollution by pesticides is a ubiquitous concern for wildlife. The effects of pesticides are especially concerning in aquatic environments, which are particularly vulnerable as they have several exposure ...

  Citation × Citation Citation Abstract Copy Title: Effects of pesticides on amphibians with special reference to the pyrethroid insecticide, cypermethrin Author: Biga, Lindsay M. Pollution by pesticides is a ubiquitous concern for wildlife. The effects of pesticides are especially concerning in aquatic environments, which are particularly vulnerable as they have several exposure routes for the influx of chemicals. These effects are of particular concern as biodiversity loss reaches unprecedented rates. This includes recent declines of amphibian populations and loss of amphibian species. Pesticide exposure may contribute to some amphibian populations and extinctions. This dissertation explores the effects of pesticides on amphibians, with particular reference to the pyrethroid insecticide cypermethrin. I first synthesized acute toxicity data of pesticides for amphibians from the literature (Chapter 2). Using 96h LC50 values for amphibian larvae exposed to insecticides, herbicides, and fungicides, I determined that amphibian species cannot be systematically classified as sensitive or tolerant to pesticides. Rather, relative acute lethal toxicities varied among species and between chemicals and types of pesticides even within a species, indicating that no amphibian species from this analysis can represent anticipated toxic effects to all amphibians. I next examined the differences in sensitivity to cypermethrin among three developmental stages for three anuran (frog) species (Chapter 3). I experimentally exposed embryos, recently hatched larvae and larvae with limb buds to cypermethrin in the laboratory. Exposure to cypermethrin had lethal and sublethal effects on some species and stages, but not all. The Pacific treefrog (Pseudacris regilla) was the most sensitive species and the early larval stage was the most sensitive for these three species. Additionally, cypermethrin exposure induced abnormal behavior in response to prodding for some species and stages. These results indicate differences in sensitivity to cypermethrin among species of amphibians. To further understand differences in sensitivity to pesticides among amphibians, I compared how three populations of P. regilla responded to cypermethrin exposure (Chapter 4). I performed a time-to-death assay in the laboratory, exposing newly hatched larvae from each population to cypermethrin under identical conditions. All populations had high rates of mortality when exposed to cypermethrin compared to unexposed controls and populations varied in the time to death. Moreover, exposed individuals were smaller than unexposed controls. Interestingly, population sensitivity did not appear to be associated with proximity to agriculture, but rather with elevation gradient, indicating that an evolved tolerance to pesticide exposure is not the mechanism for the differences in sensitivity observed here. To investigate the effects of cypermethrin on amphibians within a community context, I studied exposure in mesocosms (Chapter 5). I set up semi-natural aquatic ponds in enclosures that contained zooplankton, phytoplankton, and periphyton along with amphibian larvae. I experimentally exposed these mesocosms to cypermethrin and measured the effects on the amphibians and the other members of the community. Cypermethrin affected the entire aquatic community, even at the lowest dose, indicating the direct and indirect deleterious effects of cypermethrin on both invertebrate and vertebrate species in an aquatic community. This dissertation provides needed data on the effects of the pyrethroid insecticide cypermethrin on amphibians and their communities. Understanding the toxicity of newer, commonly used pesticides to non-target organisms is important as conservation biologists and managers make efforts to combat future amphibian population declines which may be associated with chemicals in the environment. Title: Effects of pesticides on amphibians with special reference to the pyrethroid insecticide, cypermethrin Author: Biga, Lindsay M. Pollution by pesticides is a ubiquitous concern for wildlife. The effects of pesticides are especially concerning in aquatic environments, which are particularly vulnerable as they have several exposure routes for the influx of chemicals. These effects are of particular concern as biodiversity loss reaches unprecedented rates. This includes recent declines of amphibian populations and loss of amphibian species. Pesticide exposure may contribute to some amphibian populations and extinctions. This dissertation explores the effects of pesticides on amphibians, with particular reference to the pyrethroid insecticide cypermethrin. I first synthesized acute toxicity data of pesticides for amphibians from the literature (Chapter 2). Using 96h LC50 values for amphibian larvae exposed to insecticides, herbicides, and fungicides, I determined that amphibian species cannot be systematically classified as sensitive or tolerant to pesticides. Rather, relative acute lethal toxicities varied among species and between chemicals and types of pesticides even within a species, indicating that no amphibian species from this analysis can represent anticipated toxic effects to all amphibians. I next examined the differences in sensitivity to cypermethrin among three developmental stages for three anuran (frog) species (Chapter 3). I experimentally exposed embryos, recently hatched larvae and larvae with limb buds to cypermethrin in the laboratory. Exposure to cypermethrin had lethal and sublethal effects on some species and stages, but not all. The Pacific treefrog (Pseudacris regilla) was the most sensitive species and the early larval stage was the most sensitive for these three species. Additionally, cypermethrin exposure induced abnormal behavior in response to prodding for some species and stages. These results indicate differences in sensitivity to cypermethrin among species of amphibians. To further understand differences in sensitivity to pesticides among amphibians, I compared how three populations of P. regilla responded to cypermethrin exposure (Chapter 4). I performed a time-to-death assay in the laboratory, exposing newly hatched larvae from each population to cypermethrin under identical conditions. All populations had high rates of mortality when exposed to cypermethrin compared to unexposed controls and populations varied in the time to death. Moreover, exposed individuals were smaller than unexposed controls. Interestingly, population sensitivity did not appear to be associated with proximity to agriculture, but rather with elevation gradient, indicating that an evolved tolerance to pesticide exposure is not the mechanism for the differences in sensitivity observed here. To investigate the effects of cypermethrin on amphibians within a community context, I studied exposure in mesocosms (Chapter 5). I set up semi-natural aquatic ponds in enclosures that contained zooplankton, phytoplankton, and periphyton along with amphibian larvae. I experimentally exposed these mesocosms to cypermethrin and measured the effects on the amphibians and the other members of the community. Cypermethrin affected the entire aquatic community, even at the lowest dose, indicating the direct and indirect deleterious effects of cypermethrin on both invertebrate and vertebrate species in an aquatic community. This dissertation provides needed data on the effects of the pyrethroid insecticide cypermethrin on amphibians and their communities. Understanding the toxicity of newer, commonly used pesticides to non-target organisms is important as conservation biologists and managers make efforts to combat future amphibian population declines which may be associated with chemicals in the environment. Close

• 470. [Article] Evolutionary Insights into Cnidarian-Dinoflagellate Symbiosis from Natural Variation in Aiptasia Sea Anemones

  Mutualistic associations between corals and symbiotic microalgae of the genus Symbiodium power tropical reef ecosystems, hotspots of marine biodiversity that buffer coastlines, support tourism- and fisheries-based ...

  Citation × Citation Citation Abstract Copy Title: Evolutionary Insights into Cnidarian-Dinoflagellate Symbiosis from Natural Variation in Aiptasia Sea Anemones Author: Bellis, Emily S Mutualistic associations between corals and symbiotic microalgae of the genus Symbiodium power tropical reef ecosystems, hotspots of marine biodiversity that buffer coastlines, support tourism- and fisheries-based economies, and offer untapped potential for discovery of novel pharmaceutical compounds. However, reef ecosystems are declining at an alarming rate, in large part due to severe episodes of coral bleaching, or breakdown of the coral-Symbiodinium symbiosis. The sea anemone Aiptasia has emerged as a laboratory model system for understanding coral-Symbiodinium interactions at multiple biological levels. To further develop Aiptasia as an evolutionary model system, the goal of my dissertation work was to characterize natural variation in Aiptasia-Symbiodinium symbioses by (1) examining genome-wide polymorphism among global anemone lineages, (2) experimentally evaluating natural variation in bleaching response, and (3) investigating patterns of genetic variation in natural populations across diverse abiotic environments. In Chapter 2, I use low-coverage genome skimming to investigate polymorphism in well-studied laboratory strains hosting diverse Symbiodinium, revealing that higher genetic diversity exists in Aiptasia from the Western Atlantic compared to a more globally distributed lineage. I further compare polymorphisms in sliding windows across the genome to identify candidate genes under balancing and positive selection based on patterns of heterozygosity, nucleotide diversity, and Tajima’s D. In Chapter 3, I characterize bleaching of Aiptasia lab strains to different stressors and discover significant variation in responses to acute heat stress but not to cold-shock. In Chapter 4, I examine potential relationships between abiotic environmental variation and genetic variation of anemone-Symbiodinium assemblages in the wild, at four locations in Caribbean Panama where long-term environmental datasets are available. High-throughput genotyping of anemone populations revealed the presence of a closely related cryptic species, Exaiptasia brasiliensis, and striking differences in anemone abundance, distribution, and patterns of symbiont association across environments. An Aiptasia sub-population specific to the Bocas del Toro Archipelago is described, with strong differentiation compared to the global population at several loci predicted to be important for mediating interactions with Symbiodinium. Analyses further suggest that the spatial extent of clonal reproduction in natural populations could be somewhat limited. Overall, Chapters 2-4 support a widespread global Aiptasia population distributed throughout tropical and subtropical latitudes with one or more diverged lineages, diversity of both host lineages and holobiont assemblages centered in the tropical Western Atlantic, and holobiont distribution patterns that may be strongly influenced by abiotic environment. Future studies leveraging natural variation in the Aiptasia model system described here hold great promise for advancing our fundamental knowledge of the evolution of symbiotic interactions in the sea. Title: Evolutionary Insights into Cnidarian-Dinoflagellate Symbiosis from Natural Variation in Aiptasia Sea Anemones Author: Bellis, Emily S Mutualistic associations between corals and symbiotic microalgae of the genus Symbiodium power tropical reef ecosystems, hotspots of marine biodiversity that buffer coastlines, support tourism- and fisheries-based economies, and offer untapped potential for discovery of novel pharmaceutical compounds. However, reef ecosystems are declining at an alarming rate, in large part due to severe episodes of coral bleaching, or breakdown of the coral-Symbiodinium symbiosis. The sea anemone Aiptasia has emerged as a laboratory model system for understanding coral-Symbiodinium interactions at multiple biological levels. To further develop Aiptasia as an evolutionary model system, the goal of my dissertation work was to characterize natural variation in Aiptasia-Symbiodinium symbioses by (1) examining genome-wide polymorphism among global anemone lineages, (2) experimentally evaluating natural variation in bleaching response, and (3) investigating patterns of genetic variation in natural populations across diverse abiotic environments. In Chapter 2, I use low-coverage genome skimming to investigate polymorphism in well-studied laboratory strains hosting diverse Symbiodinium, revealing that higher genetic diversity exists in Aiptasia from the Western Atlantic compared to a more globally distributed lineage. I further compare polymorphisms in sliding windows across the genome to identify candidate genes under balancing and positive selection based on patterns of heterozygosity, nucleotide diversity, and Tajima’s D. In Chapter 3, I characterize bleaching of Aiptasia lab strains to different stressors and discover significant variation in responses to acute heat stress but not to cold-shock. In Chapter 4, I examine potential relationships between abiotic environmental variation and genetic variation of anemone-Symbiodinium assemblages in the wild, at four locations in Caribbean Panama where long-term environmental datasets are available. High-throughput genotyping of anemone populations revealed the presence of a closely related cryptic species, Exaiptasia brasiliensis, and striking differences in anemone abundance, distribution, and patterns of symbiont association across environments. An Aiptasia sub-population specific to the Bocas del Toro Archipelago is described, with strong differentiation compared to the global population at several loci predicted to be important for mediating interactions with Symbiodinium. Analyses further suggest that the spatial extent of clonal reproduction in natural populations could be somewhat limited. Overall, Chapters 2-4 support a widespread global Aiptasia population distributed throughout tropical and subtropical latitudes with one or more diverged lineages, diversity of both host lineages and holobiont assemblages centered in the tropical Western Atlantic, and holobiont distribution patterns that may be strongly influenced by abiotic environment. Future studies leveraging natural variation in the Aiptasia model system described here hold great promise for advancing our fundamental knowledge of the evolution of symbiotic interactions in the sea. Close

• 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

• 481. [Article] Mapping conservation opportunity areas for the Intertwine's Regional Conservation Strategy

  Draft report from the Institute for Natural Resources, Portland State University

  Citation × Citation Citation Abstract Copy Title: Mapping conservation opportunity areas for the Intertwine's Regional Conservation Strategy Author: Kagan, James S., Burcsu, Theresa Draft report from the Institute for Natural Resources, Portland State University Title: Mapping conservation opportunity areas for the Intertwine's Regional Conservation Strategy Author: Kagan, James S., Burcsu, Theresa Draft report from the Institute for Natural Resources, Portland State University Close

• 482. [Article] Vascular Plant Inventory for Lewis and Clark National Historical Park - Public Version

  Natural Resource Technical Report NPS/LEWI/NRTR—2012/603.N Research was conducted under permit # FOCL-2009-SCI-0002 for study number FOCL-00005

  Citation × Citation Citation Abstract Copy Title: Vascular Plant Inventory for Lewis and Clark National Historical Park - Public Version Author: Kagan, Jimmy, Institute for Natural Resources, Wise, Lindsey Koepke, The Oregon Biodiversity Information Center Natural Resource Technical Report NPS/LEWI/NRTR—2012/603.N Research was conducted under permit # FOCL-2009-SCI-0002 for study number FOCL-00005 Title: Vascular Plant Inventory for Lewis and Clark National Historical Park - Public Version Author: Kagan, Jimmy, Institute for Natural Resources, Wise, Lindsey Koepke, The Oregon Biodiversity Information Center Natural Resource Technical Report NPS/LEWI/NRTR—2012/603.N Research was conducted under permit # FOCL-2009-SCI-0002 for study number FOCL-00005 Close

• 483. [Article] Precipitation and winter temperature predict long-term range-scale abundance changes in Western North American birds

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by John Wiley & Sons Ltd., and can be found at: http://onlinelibrary.wiley.com/jou...

  Citation × Citation Citation Abstract Copy Title: Precipitation and winter temperature predict long-term range-scale abundance changes in Western North American birds Author: Jones, Julia A., Illán, Javier Gutiérrez, Thomas, Chris D., Shirley, Susan M., Betts, Matthew G., Wong, Weng-Keen This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by John Wiley & Sons Ltd., and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2486 Title: Precipitation and winter temperature predict long-term range-scale abundance changes in Western North American birds Author: Jones, Julia A., Illán, Javier Gutiérrez, Thomas, Chris D., Shirley, Susan M., Betts, Matthew G., Wong, Weng-Keen This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by John Wiley & Sons Ltd., and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2486 Close

• 484. [Article] The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2011

  From 6 April – 19 September 2011 we monitored the distribution, abundance and productivity of the federally Threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast. From north ...

  Citation × Citation Citation Abstract Copy Title: The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2011 Author: Institute for Natural Resources, Kotaich, Adam A., Portland State University/INR, Farrar, J. Daniel, The Oregon Biodiversity Information Center, Castelein, Kathleen A, Gaines, Eleanor P., Lauten, David J. From 6 April – 19 September 2011 we monitored the distribution, abundance and productivity of the federally Threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Beach, New River, and Floras Lake. Our objectives for the Oregon coastal population in 2011 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) continue use of mini-exclosures (MEs) to protect nests from predators when and where needed, 4) determine nest success, 5) determine fledging success, 6) monitor brood movements, 7) collect general observational data about predators, and 8) evaluate the effectiveness of predator management. We observed an estimated 247-253 adult Snowy Plovers; a minimum of 214 individuals were known to have nested. The adult plover population was the highest estimate recorded since monitoring began in 1990. We monitored 289 nests in 2011, the highest number of nests since monitoring began in 1990. Overall apparent nest success was 50%. Exclosed nests (n = 48) had a 71% apparent nest success rate, and unexclosed nests (n = 241) had a 48% apparent nest success rate. Nest failures were attributed to unknown depredation (22%), corvid depredation (20%), unknown cause (18%), one-egg nests (16%), abandonment (15%), wind/weather (3%), mammalian depredation (2%), adult plover depredation (2%), infertility (1%), and rodent depredation (1%). We monitored 148 broods, including four from unknown nests, and documented a minimum of 168 fledglings. Overall brood success was 71%, fledging success was 46%, and 1.57 fledglings per male were produced. Continued predator management, habitat improvement and maintenance, and management of recreational activities at all sites are recommended to achieve recovery goals. Title: The Distribution and Reproductive Success of the Western Snowy Plover along the Oregon Coast - 2011 Author: Institute for Natural Resources, Kotaich, Adam A., Portland State University/INR, Farrar, J. Daniel, The Oregon Biodiversity Information Center, Castelein, Kathleen A, Gaines, Eleanor P., Lauten, David J. From 6 April – 19 September 2011 we monitored the distribution, abundance and productivity of the federally Threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Beach, New River, and Floras Lake. Our objectives for the Oregon coastal population in 2011 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) continue use of mini-exclosures (MEs) to protect nests from predators when and where needed, 4) determine nest success, 5) determine fledging success, 6) monitor brood movements, 7) collect general observational data about predators, and 8) evaluate the effectiveness of predator management. We observed an estimated 247-253 adult Snowy Plovers; a minimum of 214 individuals were known to have nested. The adult plover population was the highest estimate recorded since monitoring began in 1990. We monitored 289 nests in 2011, the highest number of nests since monitoring began in 1990. Overall apparent nest success was 50%. Exclosed nests (n = 48) had a 71% apparent nest success rate, and unexclosed nests (n = 241) had a 48% apparent nest success rate. Nest failures were attributed to unknown depredation (22%), corvid depredation (20%), unknown cause (18%), one-egg nests (16%), abandonment (15%), wind/weather (3%), mammalian depredation (2%), adult plover depredation (2%), infertility (1%), and rodent depredation (1%). We monitored 148 broods, including four from unknown nests, and documented a minimum of 168 fledglings. Overall brood success was 71%, fledging success was 46%, and 1.57 fledglings per male were produced. Continued predator management, habitat improvement and maintenance, and management of recreational activities at all sites are recommended to achieve recovery goals. Close

• 485. [Article] Western juniper encroachment into aspen communities in the Northwest Great Basin

  In the Northwest Great Basin, aspen (Populus tremuloides) communities uniquely contribute to the biodiversity of a semi-arid, sagebrush-dominated landscape. In this same region, western juniper (Juniperus ...

  Citation × Citation Citation Abstract Copy Title: Western juniper encroachment into aspen communities in the Northwest Great Basin Author: Wall, Travis G. In the Northwest Great Basin, aspen (Populus tremuloides) communities uniquely contribute to the biodiversity of a semi-arid, sagebrush-dominated landscape. In this same region, western juniper (Juniperus occidentalis) is encroaching into aspen stands. This study determined the timing, extent, and some of the effects of this expansion. Aspen stands below 2,133 m elevation were sampled in northwest Nevada, northeast California, and southeast Oregon for density, canopy cover, age, stand structure, and recruitment of western juniper and aspen. Soils and tree litter from both species were collected to analyze the effects of western juniper in areas previously influenced by aspen. Additionally, two large aspen complexes in southeast Oregon were intensively aged to determine disturbance (fire) frequencies. Western juniper encroachment into aspen stands peaked from 1920 to 1939 with 77% of all juniper trees sampled establishing during this period. Five percent were greater than 100 years and none exceeded 145 years. Three-fourths of aspen stands sampled have established populations of western juniper. Twenty-three percent have a dominant canopy of western juniper. Twelve percent of aspen stands sampled were completely replaced by western juniper. Average density of western juniper was 1,573 trees per hectare of aspen. Seventy percent of aspen stands sampled had zero recruitment of new aspen. Within the study area aspen stands averaged 98 years old. Forty-eight percent of stands were greater than 100 years old. There was an inverse correlation between aspen canopy cover and western juniper canopy cover (r²=.80, p=.0001). Soils influenced by western juniper had a higher C:N ratio and pH; higher amounts of salts, lime, and sulfate; and lower amounts of magnesium, iron, copper, and manganese (p<.05). Aspen litter had a lower C:N ratio than western juniper litter (p<.05). Prior to 1870, the two major aspen complexes sampled had mean fire return intervals of 10 and 11 years. However, the most recent disturbance in either complex was 80 to 90 years ago. This lack of disturbance (fire) coupled with aspen stand decadence and low recruitment levels leaves aspen communities in the Northwest Great Basin vulnerable to western juniper encroachment and replacement. Title: Western juniper encroachment into aspen communities in the Northwest Great Basin Author: Wall, Travis G. In the Northwest Great Basin, aspen (Populus tremuloides) communities uniquely contribute to the biodiversity of a semi-arid, sagebrush-dominated landscape. In this same region, western juniper (Juniperus occidentalis) is encroaching into aspen stands. This study determined the timing, extent, and some of the effects of this expansion. Aspen stands below 2,133 m elevation were sampled in northwest Nevada, northeast California, and southeast Oregon for density, canopy cover, age, stand structure, and recruitment of western juniper and aspen. Soils and tree litter from both species were collected to analyze the effects of western juniper in areas previously influenced by aspen. Additionally, two large aspen complexes in southeast Oregon were intensively aged to determine disturbance (fire) frequencies. Western juniper encroachment into aspen stands peaked from 1920 to 1939 with 77% of all juniper trees sampled establishing during this period. Five percent were greater than 100 years and none exceeded 145 years. Three-fourths of aspen stands sampled have established populations of western juniper. Twenty-three percent have a dominant canopy of western juniper. Twelve percent of aspen stands sampled were completely replaced by western juniper. Average density of western juniper was 1,573 trees per hectare of aspen. Seventy percent of aspen stands sampled had zero recruitment of new aspen. Within the study area aspen stands averaged 98 years old. Forty-eight percent of stands were greater than 100 years old. There was an inverse correlation between aspen canopy cover and western juniper canopy cover (r²=.80, p=.0001). Soils influenced by western juniper had a higher C:N ratio and pH; higher amounts of salts, lime, and sulfate; and lower amounts of magnesium, iron, copper, and manganese (p<.05). Aspen litter had a lower C:N ratio than western juniper litter (p<.05). Prior to 1870, the two major aspen complexes sampled had mean fire return intervals of 10 and 11 years. However, the most recent disturbance in either complex was 80 to 90 years ago. This lack of disturbance (fire) coupled with aspen stand decadence and low recruitment levels leaves aspen communities in the Northwest Great Basin vulnerable to western juniper encroachment and replacement. Close

• 486. [Article] A ranunculalean liana stem from the cretaceous of British Columbia, Canada: Atli morinii gen. et sp nov.

  This is the publisher’s final pdf. The published article is copyrighted by The University of Chicago. and can be found at: http://www.jstor.org/action/showPublisher?publisherCode=ucpress&.

  Citation × Citation Citation Abstract Copy Title: A ranunculalean liana stem from the cretaceous of British Columbia, Canada: Atli morinii gen. et sp nov. Author: Burnham, Robyn J., Smith, Selena Y., Stockey, Ruth A., Little, Stefan A., Cooper, Ranessa L. This is the publisher’s final pdf. The published article is copyrighted by The University of Chicago. and can be found at: http://www.jstor.org/action/showPublisher?publisherCode=ucpress&. Title: A ranunculalean liana stem from the cretaceous of British Columbia, Canada: Atli morinii gen. et sp nov. Author: Burnham, Robyn J., Smith, Selena Y., Stockey, Ruth A., Little, Stefan A., Cooper, Ranessa L. This is the publisher’s final pdf. The published article is copyrighted by The University of Chicago. and can be found at: http://www.jstor.org/action/showPublisher?publisherCode=ucpress&. Close

• 487. [Article] Identifying factors driving sensitivity to fragmentation in forest breeding songbirds

  Habitat loss and fragmentation are the greatest threats to biodiversity worldwide. Fragmentation impacts landscape configuration, resulting in a larger number of patches that are smaller in size and further ...

  Citation × Citation Citation Abstract Copy Title: Identifying factors driving sensitivity to fragmentation in forest breeding songbirds Author: Valente, Jonathon J. Habitat loss and fragmentation are the greatest threats to biodiversity worldwide. Fragmentation impacts landscape configuration, resulting in a larger number of patches that are smaller in size and further apart from one another. Island biogeography and metapopulation theory predict populations in these remnant patches should be smaller, have higher extinction rates, and be less likely to receive immigrants from other populations. However, empirical data frequently do not conform with these theoretical predictions, leading to assertions that this model is too simplistic to describe distributions and dynamics of fragmented populations. However, others believe that landscape configuration effects have been poorly tested and modeled to date. In this dissertation, I use breeding bird data collected in a fragmented forest landscape to explore this lack of congruence between theory and reality. I first test the hypothesis that heterogeneity in the detectability of mobile species due to temporary emigration from sample sites can produce biased estimates of metapopulation rates. Next, I test for idiosyncrasies in the effects of forest loss and fragmentation on species belonging to different ecological trait groups. Lastly, I examine whether fragmentation actually reduces the functional connectivity of landscapes for species identified as fragmentation-sensitive. Dynamic occupancy models are popular for estimating metapopulation dynamic rates (colonization and extinction) from repeated presence/absence surveys of unmarked animals. This approach assumes closure among repeated samples within primary periods, allowing estimation of dynamic rates between these periods. However, the impact of temporary emigration (reversible changes in sampling availability) on dynamic rate estimates has not been tested. In Chapter 2, I use simulated data to investigate the degree to which temporary emigration could mislead researchers interested in quantifying metapopulation rates. I then compared results from three avian point count datasets to evaluate the likelihood that temporary emigration confounds estimates of dynamics for 19 species under a popular sampling protocol. Simulated experiments indicated that when secondary periods were open to temporary emigration, presence of dynamics was identified ≥ 95.1% of the time, and dynamic rate estimates were accurate. However, dynamic rates were biased when secondary periods were closed to temporary emigration. In empirical datasets, dynamic occupancy models had greater support than closed models for all species when secondary sampling periods occurred in immediate succession (i.e., 3 samples within 10 minutes); however, my results suggest that this is because these estimates were heavily influenced by temporary emigration. When counts within a primary period were separated by 24-48 hours, I found evidence of dynamics for less than half of these species. I recommend an alternative sampling approach that allows accurate estimation of dynamic rates when temporary emigration is of no interest, and introduce a novel model for estimating both processes simultaneously in rare cases where they are both of biological interest. Concern for violating the occupancy modeling closure assumption has led to widespread recommendations that samples within primary periods be conducted extremely close in time. However, these results indicate this is not the best approach when interest is in quantifying dynamic rates. While dynamic occupancy models provide estimates of ‘colonization’ and ‘extinction,’ these values do not inherently represent dynamics unless temporary emigration has been explicitly modeled or accounted for with sampling design. Naivete to this fact can result in incorrect conclusions about biological processes. While theory predicts that fragmentation should negatively influence biodiversity, empirical support of this idea is weak in terrestrial systems. However, tests of fragmentation effects are typically confounded with landscape composition and potentially obscured by imperfect detection. In Chapter 3, I used multi-species occupancy models and a mensurative experimental design to test competing hypotheses about how forest fragmentation influences distributions of breeding forest bird species and communities. During the breeding seasons of 2011-2013, we recorded over 80,000 bird detections in 202 forest fragments using a sampling design that isolated the effects of patch size per se from the effects of forest amount (2 km), edge, local vegetation, and sample area. I modeled the effects of these covariates on distributions of individual species categorized by ecological trait groups (i.e., forest, forest interior, or forest edge). Though my results indicated little effect of patch size on total species richness, increasing patch size tended to have a positive effect on interior species, and a negative effect on edge species. The effects of total forest amount were much more variable, and actually had a negative influence on many species, particularly cavity nesters. My results do not support theoretical predictions that forest patch size should positively influence bird species richness. However, composition of bird communities does shift toward edge species from interior species with decreasing patch size. Maintaining large forest patches is thus critical for supporting forest interior species, which tend to be of greater conservation concern. Maintenance of metapopulations requires movement of dispersers among resource patches. The degree to which a landscape facilitates or impedes such movements is defined as functional connectivity. Habitat fragmentation may reduce the functional connectivity of a landscape, but empirical linkages between distribution patterns and movement ability are lacking. In Chapter 4, I use experimental translocations to test whether forest fragmentation impedes movement of two species identified as fragmentation-sensitive in Chapter 3: Wood Thrush (Hylocichla mustelina) and Ovenbirds (Seiurus aurocapilla). I also tested for behavioral changes in translocated birds and evaluated whether fragmentation effects differed between behavioral modes. Over two breeding seasons, we translocated 35 Wood Thrush and 19 Ovenbirds (1-1.2 km) across landscapes spanning a fragmentation gradient and recorded their movement paths using VHF transmitters and receivers. Eighty-seven percent of individuals returned successfully, taking as long as 72.2 hours. Movement patterns of 96% of successful birds indicated two distinct behavioral modes: exploring, characterized by short, undirected movements and course reversals; and homing, characterized by large, fast steps towards their home territories. Forest composition and configuration had no effect on homing time or path straightness for either species. However, at a finer scale, I found that both preferred to take steps that minimized their exposure to non-forested gaps. My results demonstrate that movement limitation could drive or exacerbate fragmentation sensitivity for these birds. Further, while fragmentation effects did not differ between behavioral modes, my results highlight the need to link the dichotomous behaviors of translocated animals with natural movement processes. Despite this knowledge gap, results from our study suggest that maintaining contiguous habitat or corridors may improve functional connectivity for fragmentation-sensitive birds. Title: Identifying factors driving sensitivity to fragmentation in forest breeding songbirds Author: Valente, Jonathon J. Habitat loss and fragmentation are the greatest threats to biodiversity worldwide. Fragmentation impacts landscape configuration, resulting in a larger number of patches that are smaller in size and further apart from one another. Island biogeography and metapopulation theory predict populations in these remnant patches should be smaller, have higher extinction rates, and be less likely to receive immigrants from other populations. However, empirical data frequently do not conform with these theoretical predictions, leading to assertions that this model is too simplistic to describe distributions and dynamics of fragmented populations. However, others believe that landscape configuration effects have been poorly tested and modeled to date. In this dissertation, I use breeding bird data collected in a fragmented forest landscape to explore this lack of congruence between theory and reality. I first test the hypothesis that heterogeneity in the detectability of mobile species due to temporary emigration from sample sites can produce biased estimates of metapopulation rates. Next, I test for idiosyncrasies in the effects of forest loss and fragmentation on species belonging to different ecological trait groups. Lastly, I examine whether fragmentation actually reduces the functional connectivity of landscapes for species identified as fragmentation-sensitive. Dynamic occupancy models are popular for estimating metapopulation dynamic rates (colonization and extinction) from repeated presence/absence surveys of unmarked animals. This approach assumes closure among repeated samples within primary periods, allowing estimation of dynamic rates between these periods. However, the impact of temporary emigration (reversible changes in sampling availability) on dynamic rate estimates has not been tested. In Chapter 2, I use simulated data to investigate the degree to which temporary emigration could mislead researchers interested in quantifying metapopulation rates. I then compared results from three avian point count datasets to evaluate the likelihood that temporary emigration confounds estimates of dynamics for 19 species under a popular sampling protocol. Simulated experiments indicated that when secondary periods were open to temporary emigration, presence of dynamics was identified ≥ 95.1% of the time, and dynamic rate estimates were accurate. However, dynamic rates were biased when secondary periods were closed to temporary emigration. In empirical datasets, dynamic occupancy models had greater support than closed models for all species when secondary sampling periods occurred in immediate succession (i.e., 3 samples within 10 minutes); however, my results suggest that this is because these estimates were heavily influenced by temporary emigration. When counts within a primary period were separated by 24-48 hours, I found evidence of dynamics for less than half of these species. I recommend an alternative sampling approach that allows accurate estimation of dynamic rates when temporary emigration is of no interest, and introduce a novel model for estimating both processes simultaneously in rare cases where they are both of biological interest. Concern for violating the occupancy modeling closure assumption has led to widespread recommendations that samples within primary periods be conducted extremely close in time. However, these results indicate this is not the best approach when interest is in quantifying dynamic rates. While dynamic occupancy models provide estimates of ‘colonization’ and ‘extinction,’ these values do not inherently represent dynamics unless temporary emigration has been explicitly modeled or accounted for with sampling design. Naivete to this fact can result in incorrect conclusions about biological processes. While theory predicts that fragmentation should negatively influence biodiversity, empirical support of this idea is weak in terrestrial systems. However, tests of fragmentation effects are typically confounded with landscape composition and potentially obscured by imperfect detection. In Chapter 3, I used multi-species occupancy models and a mensurative experimental design to test competing hypotheses about how forest fragmentation influences distributions of breeding forest bird species and communities. During the breeding seasons of 2011-2013, we recorded over 80,000 bird detections in 202 forest fragments using a sampling design that isolated the effects of patch size per se from the effects of forest amount (2 km), edge, local vegetation, and sample area. I modeled the effects of these covariates on distributions of individual species categorized by ecological trait groups (i.e., forest, forest interior, or forest edge). Though my results indicated little effect of patch size on total species richness, increasing patch size tended to have a positive effect on interior species, and a negative effect on edge species. The effects of total forest amount were much more variable, and actually had a negative influence on many species, particularly cavity nesters. My results do not support theoretical predictions that forest patch size should positively influence bird species richness. However, composition of bird communities does shift toward edge species from interior species with decreasing patch size. Maintaining large forest patches is thus critical for supporting forest interior species, which tend to be of greater conservation concern. Maintenance of metapopulations requires movement of dispersers among resource patches. The degree to which a landscape facilitates or impedes such movements is defined as functional connectivity. Habitat fragmentation may reduce the functional connectivity of a landscape, but empirical linkages between distribution patterns and movement ability are lacking. In Chapter 4, I use experimental translocations to test whether forest fragmentation impedes movement of two species identified as fragmentation-sensitive in Chapter 3: Wood Thrush (Hylocichla mustelina) and Ovenbirds (Seiurus aurocapilla). I also tested for behavioral changes in translocated birds and evaluated whether fragmentation effects differed between behavioral modes. Over two breeding seasons, we translocated 35 Wood Thrush and 19 Ovenbirds (1-1.2 km) across landscapes spanning a fragmentation gradient and recorded their movement paths using VHF transmitters and receivers. Eighty-seven percent of individuals returned successfully, taking as long as 72.2 hours. Movement patterns of 96% of successful birds indicated two distinct behavioral modes: exploring, characterized by short, undirected movements and course reversals; and homing, characterized by large, fast steps towards their home territories. Forest composition and configuration had no effect on homing time or path straightness for either species. However, at a finer scale, I found that both preferred to take steps that minimized their exposure to non-forested gaps. My results demonstrate that movement limitation could drive or exacerbate fragmentation sensitivity for these birds. Further, while fragmentation effects did not differ between behavioral modes, my results highlight the need to link the dichotomous behaviors of translocated animals with natural movement processes. Despite this knowledge gap, results from our study suggest that maintaining contiguous habitat or corridors may improve functional connectivity for fragmentation-sensitive birds. Close

• 488. [Article] The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem

  Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of ...

  Citation × Citation Citation Abstract Copy Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Close

• 489. [Article] Investigation of Ambient Reactive Nitrogen Emissions Sources and Deposition in the Columbia River Gorge National Scenic Area

  Anthropogenic reactive nitrogen is emitted into the atmosphere from fossil fuel combustion (nitrogen oxides) and agricultural activities (nitrogen oxides and ammonia). Nitrogen oxide emissions have long ...

  Citation × Citation Citation Abstract Copy Title: Investigation of Ambient Reactive Nitrogen Emissions Sources and Deposition in the Columbia River Gorge National Scenic Area Author: Mainord, Jacinda L. Year: 2017 Anthropogenic reactive nitrogen is emitted into the atmosphere from fossil fuel combustion (nitrogen oxides) and agricultural activities (nitrogen oxides and ammonia). Nitrogen oxide emissions have long been controlled for their role in ambient air pollution and human health effects. However, reactive nitrogen deposition is less understood even though it can play a significant role in altering biodiversity, impairing ecosystem and biogeochemical function and degrading cultural artifacts. Although nitrogen deposition is a natural part of biogeochemical cycling, many ecosystems across the United States are at risk of exceeding the critical nitrogen deposition load. While nitrogen oxides are routinely measured in urban areas, far less is known in non-urban landscapes where ecosystems may be especially sensitive. Regional chemical transport models have been used to predict the impacts of ambient reactive nitrogen deposition in non-urban areas, but models have difficulty simulating reactive nitrogen due to poorly quantified emissions, especially from the agricultural sector. My research explores the speciated deposition of reactive nitrogen through monitoring and modeling in the unique field setting of the 150 mile Columbia River Gorge (CRG) located along the border of Oregon and Washington. This site is ideally suited for this investigation due to the large sources of reactive nitrogen at either end of the CRG and unique seasonally driven channel wind flow. Seasonally driven wind allowed us to look at the reactive nitrogen emissions flowing through the CRG to assess ambient the reactive nitrogen partitioning and deposition gradient. Using data collected by the United States Forest Service to control ambient haze in the CRG and our co-located nitrogen oxides (NOx) gas analyzer, we first characterized the influence of seasonal, bimodal wind distributions on the spatial distribution of reactive nitrogen. We found that during winter months with predominantly easterly winds, particulate nitrate and ammonium and gas-phase nitrogen dioxide levels create a gradient from the eastern end to the western end. Particulate nitrate and sulfate mass concentrations influence the CRG gradient during summer months with predominantly western winds. We also found that the magnitude of the impact from east is greater than the magnitude of impact from the west. When we compared our observations to regional chemistry transport models, we found that models are significantly under-predicting levels of reactive nitrogen in the CRG. This bias is not isolated to a single station within the Gorge, but throughout the whole Columbia Basin. Our results indicate that there are under-represented emissions in the region leading to this bias. Partly due to the bias in reactive N gas-phase species in the CRG, regional models have been underestimating the impact of gas-phase reactive N on dry N deposition. We conducted field studies at two sites within the CRG monitoring reactive nitrogen species (nitric oxide, nitrogen dioxide, ammonia, nitric acid, particulate nitrate, particulate ammonium, and particulate sulfate) as well as ozone and meteorological parameters. These measurements allowed us to conduct the first comprehensive analysis of reactive nitrogen partitioning and deposition in the CRG. Through our measurements, we found reactive nitrogen was higher in the spring than the summer. We found concentrations ranging from 0-15 ppbv ammonia, 0-7 ppbv nitric acid, 0-2 μg/m3 ammonium nitrate and 0-1 μg/m3 ammonium sulfate at the sites. Through the measurements of all these species, we evaluated the limiting gas-phase precursor to inorganic nitrogen particle formation. In the springtime, ammonia limits the formation of particulate reactive nitrogen; while in the summer, nitric acid and oxidized sulfur limit the formation of inorganic nitrogen particles. This suggests that there may be more sources of ammonia in the spring with fertilizer application or perhaps reactive nitrogen reservoirs are renoxified through thermal dissociation during warmer summer months. Our estimated deposition from gas and particle phase reactive nitrogen ranged from 0 – 0.14 kg N/ha per day. We also found that gas-phase reactive nitrogen plays the largest role in dry N deposition in the CRG with particle-phase contributing less than 15% of total dry N deposition. These results are important for land managers to understand the total impact of reactive nitrogen to non-urban areas. This research can inform mitigation strategies for haze formation, identify the major species and sources involved in dry N deposition and assess the potential impacts to ecosystems and cultural artifacts. Title: Investigation of Ambient Reactive Nitrogen Emissions Sources and Deposition in the Columbia River Gorge National Scenic Area Author: Mainord, Jacinda L. Year: 2017 Anthropogenic reactive nitrogen is emitted into the atmosphere from fossil fuel combustion (nitrogen oxides) and agricultural activities (nitrogen oxides and ammonia). Nitrogen oxide emissions have long been controlled for their role in ambient air pollution and human health effects. However, reactive nitrogen deposition is less understood even though it can play a significant role in altering biodiversity, impairing ecosystem and biogeochemical function and degrading cultural artifacts. Although nitrogen deposition is a natural part of biogeochemical cycling, many ecosystems across the United States are at risk of exceeding the critical nitrogen deposition load. While nitrogen oxides are routinely measured in urban areas, far less is known in non-urban landscapes where ecosystems may be especially sensitive. Regional chemical transport models have been used to predict the impacts of ambient reactive nitrogen deposition in non-urban areas, but models have difficulty simulating reactive nitrogen due to poorly quantified emissions, especially from the agricultural sector. My research explores the speciated deposition of reactive nitrogen through monitoring and modeling in the unique field setting of the 150 mile Columbia River Gorge (CRG) located along the border of Oregon and Washington. This site is ideally suited for this investigation due to the large sources of reactive nitrogen at either end of the CRG and unique seasonally driven channel wind flow. Seasonally driven wind allowed us to look at the reactive nitrogen emissions flowing through the CRG to assess ambient the reactive nitrogen partitioning and deposition gradient. Using data collected by the United States Forest Service to control ambient haze in the CRG and our co-located nitrogen oxides (NOx) gas analyzer, we first characterized the influence of seasonal, bimodal wind distributions on the spatial distribution of reactive nitrogen. We found that during winter months with predominantly easterly winds, particulate nitrate and ammonium and gas-phase nitrogen dioxide levels create a gradient from the eastern end to the western end. Particulate nitrate and sulfate mass concentrations influence the CRG gradient during summer months with predominantly western winds. We also found that the magnitude of the impact from east is greater than the magnitude of impact from the west. When we compared our observations to regional chemistry transport models, we found that models are significantly under-predicting levels of reactive nitrogen in the CRG. This bias is not isolated to a single station within the Gorge, but throughout the whole Columbia Basin. Our results indicate that there are under-represented emissions in the region leading to this bias. Partly due to the bias in reactive N gas-phase species in the CRG, regional models have been underestimating the impact of gas-phase reactive N on dry N deposition. We conducted field studies at two sites within the CRG monitoring reactive nitrogen species (nitric oxide, nitrogen dioxide, ammonia, nitric acid, particulate nitrate, particulate ammonium, and particulate sulfate) as well as ozone and meteorological parameters. These measurements allowed us to conduct the first comprehensive analysis of reactive nitrogen partitioning and deposition in the CRG. Through our measurements, we found reactive nitrogen was higher in the spring than the summer. We found concentrations ranging from 0-15 ppbv ammonia, 0-7 ppbv nitric acid, 0-2 μg/m3 ammonium nitrate and 0-1 μg/m3 ammonium sulfate at the sites. Through the measurements of all these species, we evaluated the limiting gas-phase precursor to inorganic nitrogen particle formation. In the springtime, ammonia limits the formation of particulate reactive nitrogen; while in the summer, nitric acid and oxidized sulfur limit the formation of inorganic nitrogen particles. This suggests that there may be more sources of ammonia in the spring with fertilizer application or perhaps reactive nitrogen reservoirs are renoxified through thermal dissociation during warmer summer months. Our estimated deposition from gas and particle phase reactive nitrogen ranged from 0 – 0.14 kg N/ha per day. We also found that gas-phase reactive nitrogen plays the largest role in dry N deposition in the CRG with particle-phase contributing less than 15% of total dry N deposition. These results are important for land managers to understand the total impact of reactive nitrogen to non-urban areas. This research can inform mitigation strategies for haze formation, identify the major species and sources involved in dry N deposition and assess the potential impacts to ecosystems and cultural artifacts. Close

• 490. [Article] Landscape level patterns in biodiversity : plant species and biomass structure

  In the tropics, widespread deforestation and conversion of primary forests to agricultural and pasture lands has resulted in losses of composition, structure, and functions of forest landscapes. Deforestation ...

  Citation × Citation Citation Abstract Copy Title: Landscape level patterns in biodiversity : plant species and biomass structure Author: Heider, Christopher In the tropics, widespread deforestation and conversion of primary forests to agricultural and pasture lands has resulted in losses of composition, structure, and functions of forest landscapes. Deforestation in the tropics is typically preformed via slash-and-burn practices; the byproducts from combustion have been identified as the second-highest form of anthropogenically derived 'greenhouse-gases' (such as carbon dioxide) to the atmosphere, and have been linked to the warming of the earth. Landscape-scale measures of species composition and biomass structure of primary forests are important for two reasons: (i) they provide accurate, land-based measures to predict what has been lost due to land-uses, and (ii) they aid in the discovery of key factors which explain patterns in compositional and structural diversity that are useful for defining conservation objectives. In this thesis, I enumerate the landscape-level patterns in species composition and biomass and C structure for 20-0.79 ha primary tropical forest stands within the region of "Los Tuxtlas", Veracruz, Mexico. These 20 sites were selected to capture the variability in composition and structure with respect to an array of environmental variables. These variables included a wide elevational range (15-1280 m.a.s.l.), variable slopes (Range: 3-41% slope), 3 soil-types (ash derived, lava flows, and weathered soils), a gradient of mean annual temperatures (~19.5-25.7°C), a broad precipitation range (2500 - 4000 mm year⁻¹), a rainfall frequency range (i.e. max rainfall in 24 hours; ranged 30->100 mm day⁻¹), and 3 Holdridge Life Zones (Tropical Moist Forest, Subtropical Wet Forest, and Subtropical Lower Montane Rain Forest). Species composition was highly correlated with the environmental variables, particularly elevation. In general for plants ≥10 cm dbh, site species richness declined at a rate of ~2 species per 100 m rise in elevation. Forest sites located at similar elevations were most similar in their species compositions as compared with sites separated by large elevational differences. Despite the gradual change in species richness and composition, four sub-regions, or forest environments, within Los Tuxtlas were identified that had different species compositions and distinct combinations of elevation, soil-types, and climates. These four sub-regions were described as community-types according to their geographic location: Lowland-Reserve (LR), La Perla Plateau (LP), Volcanic Upslope (VU), and Cloud Forests (CF). The LR, LP, and VU community-types were coarsely described as Tropical Evergreen Forests (TEF's; INEGI 2001). All community-types corresponded with classifications within the Holdridge Life Zone System; the LR community-type was classified as Tropical (transition to Subtropical) Moist Forest; LP and VU community-types were classified as Subtropical Wet Forest, and the Cloud Forest community-type was classified as Subtropical Lower Montane Rain Forest. These community-types and Life Zones are useful tools for conservation, as they represent unique forests that collectively capture much of the variation in the species richness and compositional diversity of the Los Tuxtlas region. Unlike species composition, the variability in forest structure among the 18 TEF sites was not associated with the environmental variables of the Los Tuxtlas landscape. On average, TEF's had a total aboveground biomass (TAGB) of 422 ± 17 Mg ha⁻¹ and 205 ± 8 Mg ha⁻¹ total aboveground carbon (C). The TAGB and C pools for Cloud Forests was ~18% lower than TEF's, and averaged 346 ± 1 and 168 ± 1 Mg ha⁻¹, respectively. The majority of this biomass difference was due to large trees within the forest structure. Cloud Forests had generally fewer trees ≥70 cm dbh, and a more even distribution of trees 30-70 cm dbh than TEF's. The biomass contribution of large trees (≥70 cm dbh) accounted for most, if not all, of the variation in TAGB and C for these tropical forests. The relatively high TAGB and C pools implicates Los Tuxtlas forests as a significant pool of aboveground biomass and C within the Neotropics. Title: Landscape level patterns in biodiversity : plant species and biomass structure Author: Heider, Christopher In the tropics, widespread deforestation and conversion of primary forests to agricultural and pasture lands has resulted in losses of composition, structure, and functions of forest landscapes. Deforestation in the tropics is typically preformed via slash-and-burn practices; the byproducts from combustion have been identified as the second-highest form of anthropogenically derived 'greenhouse-gases' (such as carbon dioxide) to the atmosphere, and have been linked to the warming of the earth. Landscape-scale measures of species composition and biomass structure of primary forests are important for two reasons: (i) they provide accurate, land-based measures to predict what has been lost due to land-uses, and (ii) they aid in the discovery of key factors which explain patterns in compositional and structural diversity that are useful for defining conservation objectives. In this thesis, I enumerate the landscape-level patterns in species composition and biomass and C structure for 20-0.79 ha primary tropical forest stands within the region of "Los Tuxtlas", Veracruz, Mexico. These 20 sites were selected to capture the variability in composition and structure with respect to an array of environmental variables. These variables included a wide elevational range (15-1280 m.a.s.l.), variable slopes (Range: 3-41% slope), 3 soil-types (ash derived, lava flows, and weathered soils), a gradient of mean annual temperatures (~19.5-25.7°C), a broad precipitation range (2500 - 4000 mm year⁻¹), a rainfall frequency range (i.e. max rainfall in 24 hours; ranged 30->100 mm day⁻¹), and 3 Holdridge Life Zones (Tropical Moist Forest, Subtropical Wet Forest, and Subtropical Lower Montane Rain Forest). Species composition was highly correlated with the environmental variables, particularly elevation. In general for plants ≥10 cm dbh, site species richness declined at a rate of ~2 species per 100 m rise in elevation. Forest sites located at similar elevations were most similar in their species compositions as compared with sites separated by large elevational differences. Despite the gradual change in species richness and composition, four sub-regions, or forest environments, within Los Tuxtlas were identified that had different species compositions and distinct combinations of elevation, soil-types, and climates. These four sub-regions were described as community-types according to their geographic location: Lowland-Reserve (LR), La Perla Plateau (LP), Volcanic Upslope (VU), and Cloud Forests (CF). The LR, LP, and VU community-types were coarsely described as Tropical Evergreen Forests (TEF's; INEGI 2001). All community-types corresponded with classifications within the Holdridge Life Zone System; the LR community-type was classified as Tropical (transition to Subtropical) Moist Forest; LP and VU community-types were classified as Subtropical Wet Forest, and the Cloud Forest community-type was classified as Subtropical Lower Montane Rain Forest. These community-types and Life Zones are useful tools for conservation, as they represent unique forests that collectively capture much of the variation in the species richness and compositional diversity of the Los Tuxtlas region. Unlike species composition, the variability in forest structure among the 18 TEF sites was not associated with the environmental variables of the Los Tuxtlas landscape. On average, TEF's had a total aboveground biomass (TAGB) of 422 ± 17 Mg ha⁻¹ and 205 ± 8 Mg ha⁻¹ total aboveground carbon (C). The TAGB and C pools for Cloud Forests was ~18% lower than TEF's, and averaged 346 ± 1 and 168 ± 1 Mg ha⁻¹, respectively. The majority of this biomass difference was due to large trees within the forest structure. Cloud Forests had generally fewer trees ≥70 cm dbh, and a more even distribution of trees 30-70 cm dbh than TEF's. The biomass contribution of large trees (≥70 cm dbh) accounted for most, if not all, of the variation in TAGB and C for these tropical forests. The relatively high TAGB and C pools implicates Los Tuxtlas forests as a significant pool of aboveground biomass and C within the Neotropics. Close

• 491. [Article] Movement and space use by the green hermit (Phaethornis guy) in a fragmented landscape in Costa Rica

  Human activities have altered Earth’s ecosystems. Most biomes have experienced a 20-50% conversion to human use. Loss of habitat has obvious effects on the persistence of species. Fragmentation, however, ...

  Citation × Citation Citation Abstract Copy Title: Movement and space use by the green hermit (Phaethornis guy) in a fragmented landscape in Costa Rica Author: Volpe, Noelia L. Human activities have altered Earth’s ecosystems. Most biomes have experienced a 20-50% conversion to human use. Loss of habitat has obvious effects on the persistence of species. Fragmentation, however, may also negatively affect biodiversity for those species that exhibit behavioral responses to changes in habitat configuration. Such behavioral changes include movement, which is influenced by subdividing and isolating habitats through which animals prefer to travel. Ecosystem services that depend on the ability of animals to move through the landscape could be affected by changes in habitat configuration. Pollination is one such process because access of pollinators to flowers is often the key determinant of plant reproductive success. Yet, relatively little is known about how forest fragmentation may influence the flow of pollen carried by forest-dwelling pollinators, such as hummingbirds. I evaluate how changes in the distribution of pollinators produced by habitat fragmentation in southern Costa Rica affects a pollination web occupied by a generalist tropical pollinator, the green hermit hummingbird (Phaethornis guy). I used radio-telemetry to measure patterns of space use by green hermits living in forested areas with different levels of fragmentation. I first characterize patterns of space use by green hermits at three scales: point, path and home range. I found that green hermits have marked preference for locations in forested areas with high density of Heliconia plants and canopy cover; prefer paths close to streams that minimize crossing large stretches of non-forested matrix; and establish their home ranges in areas with high forest amount. In addition, home range area was negatively related to the amount of forest within it and positively related to fragmentation per se. Average resource density within the home range appeared to be unrelated to the area covered by the green hermits. My observations indicate that while the presence of green hermits in an area is mainly determined by the amount of forest available, the way they move through a landscape will be strongly affected by habitat configuration. In this context, pollen transfer by green hermits will be limited by the presence of open, non-forested areas owing to matrix avoidance. In landscapes with small discontinuous patches, the total area covered by an individual green hermit is likely to be small so I hypothesize that the genetic variability of pollen it transports may be diminished. I also assess the effectiveness of a tool commonly used to study the effect of habitat fragmentation on animal movement: translocation experiments. Such experiments are purported to have important advantages of being time efficient and standardizing across individuals the ‘motivation’ to move. Yet, we lack tests of whether movement behavior of translocated birds reflects natural behavior of unmanipulated birds. I compared the routine movement behavior of green hermits to that of experimentally translocated individuals. Behaviors documented during translocation experiments reflected those observed during routine movements. Both translocated and non-translocated birds showed similar levels of preference for mature tropical forest at the point level and avoided moving across non-forested matrix while selecting streams as movement corridors at the path level. Movement rates (distance covered per unit time) were generally higher during translocation experiments. However, the negative influence of forest cover on movement rates was proportionately similar in translocation and routine movement treatments. My results show that movement behavior of birds during translocation experiments is similar to natural movement behavior of birds. Therefore, translocation experiments may be reliable tools to address effects of landscape structure on animal movement. Title: Movement and space use by the green hermit (Phaethornis guy) in a fragmented landscape in Costa Rica Author: Volpe, Noelia L. Human activities have altered Earth’s ecosystems. Most biomes have experienced a 20-50% conversion to human use. Loss of habitat has obvious effects on the persistence of species. Fragmentation, however, may also negatively affect biodiversity for those species that exhibit behavioral responses to changes in habitat configuration. Such behavioral changes include movement, which is influenced by subdividing and isolating habitats through which animals prefer to travel. Ecosystem services that depend on the ability of animals to move through the landscape could be affected by changes in habitat configuration. Pollination is one such process because access of pollinators to flowers is often the key determinant of plant reproductive success. Yet, relatively little is known about how forest fragmentation may influence the flow of pollen carried by forest-dwelling pollinators, such as hummingbirds. I evaluate how changes in the distribution of pollinators produced by habitat fragmentation in southern Costa Rica affects a pollination web occupied by a generalist tropical pollinator, the green hermit hummingbird (Phaethornis guy). I used radio-telemetry to measure patterns of space use by green hermits living in forested areas with different levels of fragmentation. I first characterize patterns of space use by green hermits at three scales: point, path and home range. I found that green hermits have marked preference for locations in forested areas with high density of Heliconia plants and canopy cover; prefer paths close to streams that minimize crossing large stretches of non-forested matrix; and establish their home ranges in areas with high forest amount. In addition, home range area was negatively related to the amount of forest within it and positively related to fragmentation per se. Average resource density within the home range appeared to be unrelated to the area covered by the green hermits. My observations indicate that while the presence of green hermits in an area is mainly determined by the amount of forest available, the way they move through a landscape will be strongly affected by habitat configuration. In this context, pollen transfer by green hermits will be limited by the presence of open, non-forested areas owing to matrix avoidance. In landscapes with small discontinuous patches, the total area covered by an individual green hermit is likely to be small so I hypothesize that the genetic variability of pollen it transports may be diminished. I also assess the effectiveness of a tool commonly used to study the effect of habitat fragmentation on animal movement: translocation experiments. Such experiments are purported to have important advantages of being time efficient and standardizing across individuals the ‘motivation’ to move. Yet, we lack tests of whether movement behavior of translocated birds reflects natural behavior of unmanipulated birds. I compared the routine movement behavior of green hermits to that of experimentally translocated individuals. Behaviors documented during translocation experiments reflected those observed during routine movements. Both translocated and non-translocated birds showed similar levels of preference for mature tropical forest at the point level and avoided moving across non-forested matrix while selecting streams as movement corridors at the path level. Movement rates (distance covered per unit time) were generally higher during translocation experiments. However, the negative influence of forest cover on movement rates was proportionately similar in translocation and routine movement treatments. My results show that movement behavior of birds during translocation experiments is similar to natural movement behavior of birds. Therefore, translocation experiments may be reliable tools to address effects of landscape structure on animal movement. Close

• 492. [Article] Using a species-centered approach to examine patterns and drivers of avian species richness in the Rogue Basin, Oregon

  The combined effects of habitat loss, degradation, and fragmentation pose a serious threat to Earth's biodiversity, imperiling even relatively common species. 'Habitat' is necessarily a species-specific ...

  Citation × Citation Citation Abstract Copy Title: Using a species-centered approach to examine patterns and drivers of avian species richness in the Rogue Basin, Oregon Author: Halstead, Katherine E. The combined effects of habitat loss, degradation, and fragmentation pose a serious threat to Earth's biodiversity, imperiling even relatively common species. 'Habitat' is necessarily a species-specific concept, and investigations of bird diversity relationships and subsequent efforts to prioritize conservation areas, are challenged by the difficulty of estimating complex habitat gradients for multiple species across broad spatial scales. Technologies such as fine-resolution remote sensing combined with enhanced species distribution modeling techniques hold promise for more accurate assessments of multi-species habitat distributions. In this research, I focused on forest bird species which utilize and/or are highly associated with threatened Oregon white oak and California black oak (Quercus garrayana and Q. kelloggii) vegetation types in the Rogue Basin of southwest Oregon. I created individual species distribution models (SDMs) for 48 bird species as a function of fine-resolution (30 x 30 m) remotely sensed land cover and other environmental variables using boosted regression tree (BRT) models. I then 'stacked' SDMs for spatially explicit regional estimates of multi-species avian richness. In my first chapter, I examined the potential for site-level species richness to be influenced by local vegetation and environmental conditions (e.g. the "local vegetation heterogeneity hypothesis") or by landscape-level dispersal potential (e.g. the "regional species pool hypothesis"). I summarized 'stacked' SDMs for indices of 1) habitat amount at a local scale relevant bird territory use and 2) habitat amount at a broad scale relevant to forest bird dispersal, and ask whether local- or landscape-scale habitat amount is relatively more important to site-level bird species richness. I hypothesized that greater importance of either habitat amount metric would indicate greater influence of local or landscape drivers to local richness. I found evidence that for a large pool of bird species with diverse habitat associations, landscape-scale habitat amount may be relatively more important to local (i.e., territory level) richness of forest birds than is local habitat amount. In contrast, for more specialized (i.e., oak-associated) guilds, local-scale habitat may be considerably more important than amount of habitat within the surrounding landscape. My results suggest the importance of local- and landscape-scale processes in structuring bird communities, supporting both 'local vegetation heterogeneity' and 'regional species pool' hypotheses. In my second chapter, I examined the relationships between landownership, oak vegetation distribution, and bird diversity, with the objective of determining which of five primary landownership types contribute most strongly to bird species habitat in the Rogue Basin. I asked whether individual bird species distributions and estimated richness are 'additive' or 'redundant' among land ownership types, hypothesizing that differences among owners will be apparent and related to the amount of oak-dominant vegetation held by each owner regionally. I found that estimated local mean species richness of oak-associated birds in private non-industrial (PNI) ownerships is approximately double that of other Rogue Basin public and private ownerships examined. This result may be driven by disproportionate PNI ownership of limited oak cover types, and/or by hypothesized variation in management goals and activities among owners which influence local vegetation structure. Relatively greater importance of territory-scale habitat to local oak-associated species richness suggests management for these species should maximize site-level habitat amount and quality. The importance of private non-industrial owners to oak-associated avian richness validates current focus on engaging private landowners in bird-focused oak conservation and restoration. Overall, my research links efforts to conserve avian habitat with efforts to understand multi-scale drivers of bird diversity, using a novel methodology that embraces the complexity of species' habitat gradients. Title: Using a species-centered approach to examine patterns and drivers of avian species richness in the Rogue Basin, Oregon Author: Halstead, Katherine E. The combined effects of habitat loss, degradation, and fragmentation pose a serious threat to Earth's biodiversity, imperiling even relatively common species. 'Habitat' is necessarily a species-specific concept, and investigations of bird diversity relationships and subsequent efforts to prioritize conservation areas, are challenged by the difficulty of estimating complex habitat gradients for multiple species across broad spatial scales. Technologies such as fine-resolution remote sensing combined with enhanced species distribution modeling techniques hold promise for more accurate assessments of multi-species habitat distributions. In this research, I focused on forest bird species which utilize and/or are highly associated with threatened Oregon white oak and California black oak (Quercus garrayana and Q. kelloggii) vegetation types in the Rogue Basin of southwest Oregon. I created individual species distribution models (SDMs) for 48 bird species as a function of fine-resolution (30 x 30 m) remotely sensed land cover and other environmental variables using boosted regression tree (BRT) models. I then 'stacked' SDMs for spatially explicit regional estimates of multi-species avian richness. In my first chapter, I examined the potential for site-level species richness to be influenced by local vegetation and environmental conditions (e.g. the "local vegetation heterogeneity hypothesis") or by landscape-level dispersal potential (e.g. the "regional species pool hypothesis"). I summarized 'stacked' SDMs for indices of 1) habitat amount at a local scale relevant bird territory use and 2) habitat amount at a broad scale relevant to forest bird dispersal, and ask whether local- or landscape-scale habitat amount is relatively more important to site-level bird species richness. I hypothesized that greater importance of either habitat amount metric would indicate greater influence of local or landscape drivers to local richness. I found evidence that for a large pool of bird species with diverse habitat associations, landscape-scale habitat amount may be relatively more important to local (i.e., territory level) richness of forest birds than is local habitat amount. In contrast, for more specialized (i.e., oak-associated) guilds, local-scale habitat may be considerably more important than amount of habitat within the surrounding landscape. My results suggest the importance of local- and landscape-scale processes in structuring bird communities, supporting both 'local vegetation heterogeneity' and 'regional species pool' hypotheses. In my second chapter, I examined the relationships between landownership, oak vegetation distribution, and bird diversity, with the objective of determining which of five primary landownership types contribute most strongly to bird species habitat in the Rogue Basin. I asked whether individual bird species distributions and estimated richness are 'additive' or 'redundant' among land ownership types, hypothesizing that differences among owners will be apparent and related to the amount of oak-dominant vegetation held by each owner regionally. I found that estimated local mean species richness of oak-associated birds in private non-industrial (PNI) ownerships is approximately double that of other Rogue Basin public and private ownerships examined. This result may be driven by disproportionate PNI ownership of limited oak cover types, and/or by hypothesized variation in management goals and activities among owners which influence local vegetation structure. Relatively greater importance of territory-scale habitat to local oak-associated species richness suggests management for these species should maximize site-level habitat amount and quality. The importance of private non-industrial owners to oak-associated avian richness validates current focus on engaging private landowners in bird-focused oak conservation and restoration. Overall, my research links efforts to conserve avian habitat with efforts to understand multi-scale drivers of bird diversity, using a novel methodology that embraces the complexity of species' habitat gradients. Close

• 493. [Article] Lichen Functional Trait Variation Along an East-West Climatic Gradient in Oregon and Among Habitats in Katmai National Park, Alaska

  Functional traits of vascular plants have been an important component of ecological studies for a number of years; however, in more recent times vascular plant ecologists have begun to formalize a set ...

  Citation × Citation Citation Abstract Copy Title: Lichen Functional Trait Variation Along an East-West Climatic Gradient in Oregon and Among Habitats in Katmai National Park, Alaska Author: Spickerman, Kaleigh Functional traits of vascular plants have been an important component of ecological studies for a number of years; however, in more recent times vascular plant ecologists have begun to formalize a set of key traits and universal system of trait measurement. Many recent studies hypothesize global generality of trait patterns, which would allow for comparison among ecosystems and biomes and provide a foundation for general rules and theories, the so-called “Holy Grail” of ecology. However, the majority of these studies focus on functional trait patterns of vascular plants, with a minority examining the patterns of cryptograms such as lichens. Lichens are an important component of many ecosystems due to their contributions to biodiversity and their key ecosystem services, such as contributions to mineral and hydrological cycles and ecosystem food webs. Lichens are also of special interest because of their reliance on atmospheric deposition for nutrients and water, which makes them particularly sensitive to air pollution. Therefore, they are often used as bioindicators of air pollution, climate change, and general ecosystem health. This thesis examines the functional trait patterns of lichens in two contrasting regions with fundamentally different kinds of data. To better understand the patterns of lichen functional traits, we examined reproductive, morphological, and chemical trait variation along precipitation and temperature gradients in Oregon. Specifically, we measured traits of 102 macrolichen species collected from 166 USDA Forest Service program for Forest Inventory and Analysis (FIA) plots. These plots were located in a more-or-less continuous swath across Oregon between 43°W and 45°W. Plots were grouped into seven regions (the Oregon Coast, Coast Range, Willamette Valley, Western Cascades, High Cascades, Eastern Cascades, and Eastern Oregon). Using multivariate analysis techniques we found strong linear and nonlinear trait patterns along precipitation and temperature gradients, and were able to characterize the seven main regions of Oregon by the relative abundance of lichen traits. The literature on what lichen traits are most common in which habitats is sparse and anecdotal; understanding trait-habitat patterns could have management implications due to lichen importance as bioindicators and animal forage. Understanding how key traits are distributed among habitats could provide insight into potential air pollution impacts on certain habitats, animal movement among habitats, etc. To examine trait-habitat patterns, we measured the reproductive, morphological, and chemical traits of 429 lichen species collected haphazardly (without a formal sampling framework) from ten distinct habitats within Katmai National Park in southwest Alaska as part of a taxonomic inventory. Using multivariate analysis techniques we grouped habitats based on the expression of lichen traits and described the relative abundance of each trait in different habitats. The second goal of this study was to examine the potential usefulness of herbarium collections in ecological studies of this type. Herbarium specimens are a large potential resource that is generally unused in ecological studies due to concerns over potential bias and noise introduced by variation in collection methods. However, recent work has suggested that herbarium specimens may yield more useful results than previously thought and could be a valid resource for ecological studies. The data for our study were collected in a haphazard manner for a floristic inventory, similar to the collection methods used for many herbarium specimens. The patterns that we observed indicates that herbarium specimens may be a good resource for future research. Title: Lichen Functional Trait Variation Along an East-West Climatic Gradient in Oregon and Among Habitats in Katmai National Park, Alaska Author: Spickerman, Kaleigh Functional traits of vascular plants have been an important component of ecological studies for a number of years; however, in more recent times vascular plant ecologists have begun to formalize a set of key traits and universal system of trait measurement. Many recent studies hypothesize global generality of trait patterns, which would allow for comparison among ecosystems and biomes and provide a foundation for general rules and theories, the so-called “Holy Grail” of ecology. However, the majority of these studies focus on functional trait patterns of vascular plants, with a minority examining the patterns of cryptograms such as lichens. Lichens are an important component of many ecosystems due to their contributions to biodiversity and their key ecosystem services, such as contributions to mineral and hydrological cycles and ecosystem food webs. Lichens are also of special interest because of their reliance on atmospheric deposition for nutrients and water, which makes them particularly sensitive to air pollution. Therefore, they are often used as bioindicators of air pollution, climate change, and general ecosystem health. This thesis examines the functional trait patterns of lichens in two contrasting regions with fundamentally different kinds of data. To better understand the patterns of lichen functional traits, we examined reproductive, morphological, and chemical trait variation along precipitation and temperature gradients in Oregon. Specifically, we measured traits of 102 macrolichen species collected from 166 USDA Forest Service program for Forest Inventory and Analysis (FIA) plots. These plots were located in a more-or-less continuous swath across Oregon between 43°W and 45°W. Plots were grouped into seven regions (the Oregon Coast, Coast Range, Willamette Valley, Western Cascades, High Cascades, Eastern Cascades, and Eastern Oregon). Using multivariate analysis techniques we found strong linear and nonlinear trait patterns along precipitation and temperature gradients, and were able to characterize the seven main regions of Oregon by the relative abundance of lichen traits. The literature on what lichen traits are most common in which habitats is sparse and anecdotal; understanding trait-habitat patterns could have management implications due to lichen importance as bioindicators and animal forage. Understanding how key traits are distributed among habitats could provide insight into potential air pollution impacts on certain habitats, animal movement among habitats, etc. To examine trait-habitat patterns, we measured the reproductive, morphological, and chemical traits of 429 lichen species collected haphazardly (without a formal sampling framework) from ten distinct habitats within Katmai National Park in southwest Alaska as part of a taxonomic inventory. Using multivariate analysis techniques we grouped habitats based on the expression of lichen traits and described the relative abundance of each trait in different habitats. The second goal of this study was to examine the potential usefulness of herbarium collections in ecological studies of this type. Herbarium specimens are a large potential resource that is generally unused in ecological studies due to concerns over potential bias and noise introduced by variation in collection methods. However, recent work has suggested that herbarium specimens may yield more useful results than previously thought and could be a valid resource for ecological studies. The data for our study were collected in a haphazard manner for a floristic inventory, similar to the collection methods used for many herbarium specimens. The patterns that we observed indicates that herbarium specimens may be a good resource for future research. Close

• 494. [Article] Leveraging Multi-Sensor Time Series Datasets to Map Short- and Long-Term Forest Disturbances and Drivers of Change in the Colombian Andes

  The spatial distribution of forest disturbance is commonly calculated using a satellite imagery-driven bi- or tri-temporal change analysis. Working in Colombia’s Cordillera de los Picachos National Natural ...

  Citation × Citation Citation Abstract Copy Title: Leveraging Multi-Sensor Time Series Datasets to Map Short- and Long-Term Forest Disturbances and Drivers of Change in the Colombian Andes Author: Murillo Sandoval, Paulo Jose The spatial distribution of forest disturbance is commonly calculated using a satellite imagery-driven bi- or tri-temporal change analysis. Working in Colombia’s Cordillera de los Picachos National Natural Park – a region of consistent cloud cover and dramatic topographic relief – a change assessment with such infrequent observations cannot capture long-term trends of vegetative decline (browning) or improvement (greening) nor the drivers associated with these changes. In recognition of the importance of spatio-temporally explicit information for assessing the effects of socio-environmental change and conservation strategy implementation, I developed a rigorous assessment of vegetation change using MODIS and Landsat time-series data and the Breaks For Additive Season and Trend (BFAST) algorithm to identify the timing, trends, and locations of change as well the associated drivers. First, I measured long-term vegetation trends from 2001-2015 using a Moderate Resolution Imaging Spectroradiometer (MODIS)-based 250m resolution Multi-Angle Implementation of Atmospheric Correction (MAIAC) time-series, and mapped short-term disturbances using all available Landsat images (149 dates from Landsat 5, 7, and 8). BFAST trends based on MAIAC data indicate a net greening in 6% of the park, with a net browning trend of 2.5% in the 10km-wide region surrounding the park. I also identified a 12,500 ha area within Picachos (4% of the park’s total area) that experienced a consecutive vegetative decline or browning during every year of study, a result corroborated with a BFAST Monitor assessment using finer 30m resolution Landsat data. With Landsat, I recorded 12,642 ha (±1440) of disturbed forest within the park at high spatial and temporal accuracy. Spatially, Landsat results had user’s and producer’s accuracies of 0.95±0.02 and 0.83±0.18, respectively. Temporally, a TimeSync-supported temporal validation assessment showed that 75% of Landsat-detected dates of disturbance events were accurate within ± 6 months. With disturbances identified, I characterized disturbances within Picachos’ southeastern foothills and associated drivers using a set of metrics related to the spectral, pattern and trend properties of disturbance patches derived from Landsat time-series data (1996-2015). A training dataset was initially developed to identify drivers of disturbances using Corine Land Cover maps and high-resolution imagery. A Random Forests classifier was used to attribute disturbances to specific drivers of forest cover change: conversion to pasture, conversion to subsistence agriculture, and non-stand replacing disturbance (i.e., thinning). Attribution of changes had high accuracy at patch and area levels with 1-5% commission and 2-14% omission errors, respectively, for regions that were converted to pasture or experienced thinning. Lower agreement was found for agricultural conversion with 43% omission and 9% commission errors. I found that conversion to pasture is the main cause of forest cover loss within Picachos at 9901 ha (±72) corresponding to 14.7% of Picachos’ foothills, and that subtle forest alteration contributed to 1327 ha (±92) of forest degradation. Recognizing the diversity of pressures facing conservation strategy implementation in the region, these results have direct relevance for anticipating future land use pressures within Colombia, as well as across similar regions in the Andes-Amazon transition area. Indeed, since these results reveal the possibility to uncover historical disturbances related to human-incursion in protected landscapes, the methods are well suited to enhancing landscape planning particularly where biodiversity richness is quickly diminishing due to anthropogenic presence. Title: Leveraging Multi-Sensor Time Series Datasets to Map Short- and Long-Term Forest Disturbances and Drivers of Change in the Colombian Andes Author: Murillo Sandoval, Paulo Jose The spatial distribution of forest disturbance is commonly calculated using a satellite imagery-driven bi- or tri-temporal change analysis. Working in Colombia’s Cordillera de los Picachos National Natural Park – a region of consistent cloud cover and dramatic topographic relief – a change assessment with such infrequent observations cannot capture long-term trends of vegetative decline (browning) or improvement (greening) nor the drivers associated with these changes. In recognition of the importance of spatio-temporally explicit information for assessing the effects of socio-environmental change and conservation strategy implementation, I developed a rigorous assessment of vegetation change using MODIS and Landsat time-series data and the Breaks For Additive Season and Trend (BFAST) algorithm to identify the timing, trends, and locations of change as well the associated drivers. First, I measured long-term vegetation trends from 2001-2015 using a Moderate Resolution Imaging Spectroradiometer (MODIS)-based 250m resolution Multi-Angle Implementation of Atmospheric Correction (MAIAC) time-series, and mapped short-term disturbances using all available Landsat images (149 dates from Landsat 5, 7, and 8). BFAST trends based on MAIAC data indicate a net greening in 6% of the park, with a net browning trend of 2.5% in the 10km-wide region surrounding the park. I also identified a 12,500 ha area within Picachos (4% of the park’s total area) that experienced a consecutive vegetative decline or browning during every year of study, a result corroborated with a BFAST Monitor assessment using finer 30m resolution Landsat data. With Landsat, I recorded 12,642 ha (±1440) of disturbed forest within the park at high spatial and temporal accuracy. Spatially, Landsat results had user’s and producer’s accuracies of 0.95±0.02 and 0.83±0.18, respectively. Temporally, a TimeSync-supported temporal validation assessment showed that 75% of Landsat-detected dates of disturbance events were accurate within ± 6 months. With disturbances identified, I characterized disturbances within Picachos’ southeastern foothills and associated drivers using a set of metrics related to the spectral, pattern and trend properties of disturbance patches derived from Landsat time-series data (1996-2015). A training dataset was initially developed to identify drivers of disturbances using Corine Land Cover maps and high-resolution imagery. A Random Forests classifier was used to attribute disturbances to specific drivers of forest cover change: conversion to pasture, conversion to subsistence agriculture, and non-stand replacing disturbance (i.e., thinning). Attribution of changes had high accuracy at patch and area levels with 1-5% commission and 2-14% omission errors, respectively, for regions that were converted to pasture or experienced thinning. Lower agreement was found for agricultural conversion with 43% omission and 9% commission errors. I found that conversion to pasture is the main cause of forest cover loss within Picachos at 9901 ha (±72) corresponding to 14.7% of Picachos’ foothills, and that subtle forest alteration contributed to 1327 ha (±92) of forest degradation. Recognizing the diversity of pressures facing conservation strategy implementation in the region, these results have direct relevance for anticipating future land use pressures within Colombia, as well as across similar regions in the Andes-Amazon transition area. Indeed, since these results reveal the possibility to uncover historical disturbances related to human-incursion in protected landscapes, the methods are well suited to enhancing landscape planning particularly where biodiversity richness is quickly diminishing due to anthropogenic presence. Close

• 495. [Article] Historical disturbance regimes as a reference for forest policy

  Using the historical range of forest conditions as a reference for managing landscapes has been proposed as a "coarse-filter" approach to biodiversity conservation. By emulating historical disturbance ...

  Citation × Citation Citation Abstract Copy Title: Historical disturbance regimes as a reference for forest policy Author: Thompson, Jonathan R. Using the historical range of forest conditions as a reference for managing landscapes has been proposed as a "coarse-filter" approach to biodiversity conservation. By emulating historical disturbance processes, it is thought that forest management can produce forest composition and structure similar to the conditions that once supported the native biota. Although several examples of disturbance-based management exist, only recently has this concept been incorporated into policy. This thesis explored hypotheses related to disturbance-based forest policy through a literature review, policy analyses, and simulation experiments. The primary objective of chapter 2 was to examine several examples disturbance-based forest management and evaluate their potential to transition into policy within North America. The review highlighted two Canadian provinces British Columbia and Ontario--that have codified disturbance-based management but used distinct methodologies. Nearly all of the forests in these provinces are government owned, which assisted policy development. In addition, both policy-structures focused on emulating stand-replacing fires that are characteristic in boreal forests; this minimized the costs and the degree of departure from conventional forest management. In much of the U.S., land tenure is complex and disturbance regimes vary widely; this presents difficult challenges for disturbance-based policy development. In the third chapter, disturbance-based policies were developed that attempted to address these challenges. Using datasets from the Coastal Landscape Analysis and Modeling Study (CLAMS) and the Landscape Management and Policy Simulation model (LAMPS), the economic costs and ecological benefits of several policy structures were explored. The policies included two variants of the current policy structure and three policies reflecting various aspects of the natural disturbance regime. The study area was the 3-million hectare Oregon Coast Range. Four owner groups were recognized--forest industry, nonindustrial private, state, and federal. The management intentions of each group guided the application of policies. Disturbance-based policies were primarily addressed to clearcutting on private lands because it constituted the preponderance of harvesting in the region. Information on the Coast Range's historical fire regime was used as a reference to develop disturbance-based policies. Fire severity was emulated with green-tree retention standards; fire frequency was emulated with annual harvestable area restrictions; and fire extent was emulated with harvest-unit size regulations. LAMPS projected landscape conditions, forest dynamics, management activities (clearcutting, thinning), and harvest volumes over the next century. Simulated disturbance-based policies produced age-class distributions more similar to the historical range than those created by the current policy structure. The proportions of early seral and young forest were within the historical range within 100 yrs; within this timeframe, older forests moved closer to but were still below historical conditions. In contrast, patch size distributions were less similar to historical conditions. This was because, even after a ten-fold increase in the average harvest size, the clearcut size limit remained well below the average historical fire size. Also, this was due to the scale of the analysis, which treated multiple proximate harvest-units as individual disturbance events. Therefore, regions with a high density of clearcuts, which were ubiquitous in the current policy scenarios, more closely resembled the large historical fire size. In the near term, annual revenue produced by the disturbance-based policies was estimated to be 20 to 60 percent lower than the current policy. However, relative costs were reduced significantly through time. This reflected the degree of departure between the modem and historical disturbance regimes. This simulation experiment suggested that policies attempting to reproduce historical conditions in the Coast Range would require federal forests to provide large patches of old forest that were conmon in the historical landscape. Employing public lands for this purpose would dampen costs to private landowners who would continue harvesting and provide young and early seral forest structure, which were also historically abundant. In addition, this experiment illustrated the difficultly of meeting regional-scale conservation goals across multiple private landowners and suggested that distributing costs and benefits equitably across large landscapes could be a significant challenge. Title: Historical disturbance regimes as a reference for forest policy Author: Thompson, Jonathan R. Using the historical range of forest conditions as a reference for managing landscapes has been proposed as a "coarse-filter" approach to biodiversity conservation. By emulating historical disturbance processes, it is thought that forest management can produce forest composition and structure similar to the conditions that once supported the native biota. Although several examples of disturbance-based management exist, only recently has this concept been incorporated into policy. This thesis explored hypotheses related to disturbance-based forest policy through a literature review, policy analyses, and simulation experiments. The primary objective of chapter 2 was to examine several examples disturbance-based forest management and evaluate their potential to transition into policy within North America. The review highlighted two Canadian provinces British Columbia and Ontario--that have codified disturbance-based management but used distinct methodologies. Nearly all of the forests in these provinces are government owned, which assisted policy development. In addition, both policy-structures focused on emulating stand-replacing fires that are characteristic in boreal forests; this minimized the costs and the degree of departure from conventional forest management. In much of the U.S., land tenure is complex and disturbance regimes vary widely; this presents difficult challenges for disturbance-based policy development. In the third chapter, disturbance-based policies were developed that attempted to address these challenges. Using datasets from the Coastal Landscape Analysis and Modeling Study (CLAMS) and the Landscape Management and Policy Simulation model (LAMPS), the economic costs and ecological benefits of several policy structures were explored. The policies included two variants of the current policy structure and three policies reflecting various aspects of the natural disturbance regime. The study area was the 3-million hectare Oregon Coast Range. Four owner groups were recognized--forest industry, nonindustrial private, state, and federal. The management intentions of each group guided the application of policies. Disturbance-based policies were primarily addressed to clearcutting on private lands because it constituted the preponderance of harvesting in the region. Information on the Coast Range's historical fire regime was used as a reference to develop disturbance-based policies. Fire severity was emulated with green-tree retention standards; fire frequency was emulated with annual harvestable area restrictions; and fire extent was emulated with harvest-unit size regulations. LAMPS projected landscape conditions, forest dynamics, management activities (clearcutting, thinning), and harvest volumes over the next century. Simulated disturbance-based policies produced age-class distributions more similar to the historical range than those created by the current policy structure. The proportions of early seral and young forest were within the historical range within 100 yrs; within this timeframe, older forests moved closer to but were still below historical conditions. In contrast, patch size distributions were less similar to historical conditions. This was because, even after a ten-fold increase in the average harvest size, the clearcut size limit remained well below the average historical fire size. Also, this was due to the scale of the analysis, which treated multiple proximate harvest-units as individual disturbance events. Therefore, regions with a high density of clearcuts, which were ubiquitous in the current policy scenarios, more closely resembled the large historical fire size. In the near term, annual revenue produced by the disturbance-based policies was estimated to be 20 to 60 percent lower than the current policy. However, relative costs were reduced significantly through time. This reflected the degree of departure between the modem and historical disturbance regimes. This simulation experiment suggested that policies attempting to reproduce historical conditions in the Coast Range would require federal forests to provide large patches of old forest that were conmon in the historical landscape. Employing public lands for this purpose would dampen costs to private landowners who would continue harvesting and provide young and early seral forest structure, which were also historically abundant. In addition, this experiment illustrated the difficultly of meeting regional-scale conservation goals across multiple private landowners and suggested that distributing costs and benefits equitably across large landscapes could be a significant challenge. Close

• 496. [Article] An evaluation of the likelihood of successful implementation of the long term coral reef monitoring program on the Commonwealth of the Northern Mariana Islands

  Coral reef ecosystems are the oceanic equivalent of tropical rainforests, in terms of biodiversity. The estimated 1,037,000 square kilometers worldwide of reef provide habitat for over one million species ...

  Citation × Citation Citation Abstract Copy Title: An evaluation of the likelihood of successful implementation of the long term coral reef monitoring program on the Commonwealth of the Northern Mariana Islands Author: Kylstra, Pam Coral reef ecosystems are the oceanic equivalent of tropical rainforests, in terms of biodiversity. The estimated 1,037,000 square kilometers worldwide of reef provide habitat for over one million species of plants and animals (Hinrichsen, 1997). Coral reefs are important to the economy of coastal nations because of the fisheries and tourism industries they support. Reef ecosystems provide a host of important natural services such as storm buffering, a protein source for islanders, breeding and nursery grounds for marine organisms, water filtration and a source of biomedically important products. Coral reef areas also have aesthetic and intrinsic value that is reason enough to protect them. Coral reefs are also among the most endangered ecosystems on Earth. Naturally occurring disturbances are compounded by the impacts of anthropogenic disturbance. Factors that threaten the health of coral reef ecosystems on a global scale include global warming, the continuing increase in coastal populations and associated impacts such as nutrient pollution, sedimentation and runoff, coral mining, ship groundings, overfishing, and recreational overuse. Globally, coastal areas accommodate about 60% of Earth's human population. A significant portion of the population lies within tropical regions. This population pressure subjects coral reef environments to effects of increased competition for coastal resources, increased coastal pollution and problems related to coastal construction. The synergistic effect of stressors has been the irreversible degradation worldwide of 10% of reefs and another 60% in critical condition leaving, only 30% as stable (Wilkinson, 1993). The coral reefs of the Commonwealth of the Northern Mariana Islands (CNMI) are a good example of how the combination of increasing human population and the associated environmental pressure has resulted in degradation of the reef ecosystem. The CNMI has undergone significant change in economic and population growth within the past decade. To accommodate the rapid and continuing development of the tourism industry, numerous golf courses and resort hotels have been constructed on Saipan. The population of Saipan has increased over 30% in the last ten years. Currently, the local/resident population is 60,000 while the visitor population is 750,000 per year. This rapid growth has had serious ecological consequences. Coral roads have been converted to four lane highways and infrastructure such as septic tank systems has not been improved to meet higher demand. More and more development projects have been proposed without adequate consideration of environmental impacts. Conflicts over the use and conservation of marine and watershed resources continue to arise. The continuing decline of reef systems globally and in specific areas like the CNMI, highlights the need for effective methods of assessing change in nearshore ecosystems. This paper explores the ways that coral reef monitoring can provide information about reef health that serves to affect positive changes in management strategies for marine systems. Using a criteria drawn from case study comparisons of ongoing, well established coral monitoring programs and evaluation framework proposed by policy analysts Using criteria drawn from case, the Long Term Marine Monitoring Program (LTMMP) on Saipan, CNMI is evaluated. The evaluation provides insight about coral monitoring plan components that are essential to the effectiveness of coral reef monitoring programs. This report is an outgrowth of an internship the author performed with the CNMI Division of Environmental Quality on the island of Saipan from June to October of 1997. The University of Oregon Micronesia and South Pacific Program and the government of the Commonwealth of the Northern Mariana Islands (CMNI) sponsored the internship project. The objectives of the internship were to assist in field data collection and continuing development of the ongoing Long Term Marine Monitoring Plan (LTMMP) Assist and instruct Marine Monitoring Team (MMT) members in basic computer skills, understanding of data applicability, management, interpretation and analysis, basic biology and resource management techniques as it relates to marine monitoring work Facilitate inter-governmental agency coordination of marine monitoring activities Assess likelihood of success and explore challenges facing Saipan in implementation of the monitoring program This report first describes functions and services provided by coral reefs and an introduction to the stresses and disturbances that compromise the health of reef systems globally. Using examples from case studies of established marine monitoring programs, this report considers how effective monitoring can reveal changes in the reef system over time, enabling conservation measures to be taken. It then turns to the island of Saipan and briefly describes the environmental and socio-economic framework within which the coral reef related provisions of the CNMI coastal management program are considered. This background information is used to evaluate the Long Term Marine Monitoring Plan currently in place on the CNMI. This evaluation provides insight into the challenges to implementation of coral reef monitoring plans and recommendations for improvements in the LTMMP on Saipan. Title: An evaluation of the likelihood of successful implementation of the long term coral reef monitoring program on the Commonwealth of the Northern Mariana Islands Author: Kylstra, Pam Coral reef ecosystems are the oceanic equivalent of tropical rainforests, in terms of biodiversity. The estimated 1,037,000 square kilometers worldwide of reef provide habitat for over one million species of plants and animals (Hinrichsen, 1997). Coral reefs are important to the economy of coastal nations because of the fisheries and tourism industries they support. Reef ecosystems provide a host of important natural services such as storm buffering, a protein source for islanders, breeding and nursery grounds for marine organisms, water filtration and a source of biomedically important products. Coral reef areas also have aesthetic and intrinsic value that is reason enough to protect them. Coral reefs are also among the most endangered ecosystems on Earth. Naturally occurring disturbances are compounded by the impacts of anthropogenic disturbance. Factors that threaten the health of coral reef ecosystems on a global scale include global warming, the continuing increase in coastal populations and associated impacts such as nutrient pollution, sedimentation and runoff, coral mining, ship groundings, overfishing, and recreational overuse. Globally, coastal areas accommodate about 60% of Earth's human population. A significant portion of the population lies within tropical regions. This population pressure subjects coral reef environments to effects of increased competition for coastal resources, increased coastal pollution and problems related to coastal construction. The synergistic effect of stressors has been the irreversible degradation worldwide of 10% of reefs and another 60% in critical condition leaving, only 30% as stable (Wilkinson, 1993). The coral reefs of the Commonwealth of the Northern Mariana Islands (CNMI) are a good example of how the combination of increasing human population and the associated environmental pressure has resulted in degradation of the reef ecosystem. The CNMI has undergone significant change in economic and population growth within the past decade. To accommodate the rapid and continuing development of the tourism industry, numerous golf courses and resort hotels have been constructed on Saipan. The population of Saipan has increased over 30% in the last ten years. Currently, the local/resident population is 60,000 while the visitor population is 750,000 per year. This rapid growth has had serious ecological consequences. Coral roads have been converted to four lane highways and infrastructure such as septic tank systems has not been improved to meet higher demand. More and more development projects have been proposed without adequate consideration of environmental impacts. Conflicts over the use and conservation of marine and watershed resources continue to arise. The continuing decline of reef systems globally and in specific areas like the CNMI, highlights the need for effective methods of assessing change in nearshore ecosystems. This paper explores the ways that coral reef monitoring can provide information about reef health that serves to affect positive changes in management strategies for marine systems. Using a criteria drawn from case study comparisons of ongoing, well established coral monitoring programs and evaluation framework proposed by policy analysts Using criteria drawn from case, the Long Term Marine Monitoring Program (LTMMP) on Saipan, CNMI is evaluated. The evaluation provides insight about coral monitoring plan components that are essential to the effectiveness of coral reef monitoring programs. This report is an outgrowth of an internship the author performed with the CNMI Division of Environmental Quality on the island of Saipan from June to October of 1997. The University of Oregon Micronesia and South Pacific Program and the government of the Commonwealth of the Northern Mariana Islands (CMNI) sponsored the internship project. The objectives of the internship were to assist in field data collection and continuing development of the ongoing Long Term Marine Monitoring Plan (LTMMP) Assist and instruct Marine Monitoring Team (MMT) members in basic computer skills, understanding of data applicability, management, interpretation and analysis, basic biology and resource management techniques as it relates to marine monitoring work Facilitate inter-governmental agency coordination of marine monitoring activities Assess likelihood of success and explore challenges facing Saipan in implementation of the monitoring program This report first describes functions and services provided by coral reefs and an introduction to the stresses and disturbances that compromise the health of reef systems globally. Using examples from case studies of established marine monitoring programs, this report considers how effective monitoring can reveal changes in the reef system over time, enabling conservation measures to be taken. It then turns to the island of Saipan and briefly describes the environmental and socio-economic framework within which the coral reef related provisions of the CNMI coastal management program are considered. This background information is used to evaluate the Long Term Marine Monitoring Plan currently in place on the CNMI. This evaluation provides insight into the challenges to implementation of coral reef monitoring plans and recommendations for improvements in the LTMMP on Saipan. Close

• 497. [Article] The importance of egg size for the diversity of salmonids

  Understanding the origin and nature of intra specific biodiversity enables us to better conserve and manage animal populations. Biological diversity is seen at different scales and for different traits ...

  Citation × Citation Citation Abstract Copy Title: The importance of egg size for the diversity of salmonids Author: Leblanc, Camille A. Understanding the origin and nature of intra specific biodiversity enables us to better conserve and manage animal populations. Biological diversity is seen at different scales and for different traits such as behavior, morphology, physiology, and life history. Behavior is especially important since behavioral changes are believed to precede changes in morphology or physiology among fishes. Salmonids display great diversity in terms of behavior, life histories and morphology within and among populations. Thus, differentiation among populations and morphs has been related to the evolution of new species. Various genetic, environmental and ecological factors have been shown to be important for segregation of morphs, including competition for food or other resources, phenotypic plasticity and sexual selection. Recently, it has been suggested that the importance of epigenetic and maternal effects for intra specific diversity have been underestimated. I studied the short- and long-term effects of egg size on development, behavior, body growth and physiology in Arctic charr Salvelinus alpinus and steelhead trout Oncorhynchus mykiss. I also examined how domestication can affect egg size. Egg size was smaller in domesticated fish populations after accounting for female body size and age. Egg size was negatively correlated with embryonic development before hatching, i.e. embryos in small eggs developed more rapidly. At emergence, egg size was positively correlated with length and weight of first feeding progeny. Juveniles coming from larger eggs tended to feed more at the surface whereas juveniles coming from smaller eggs fed more on the bottom. These relationships and effects of egg size on embryos and first feeding fish were observed in both species in laboratory conditions. In Arctic charr there was a higher energy content per egg in larger eggs in both aquaculture and wild populations, and the total energy content per egg varied among populations. Behavior of Arctic charr at first feeding was affected by egg size, social environment and their interaction. At 300 days post fertilization, fish coming from different egg sizes differed in morphology and behavior: larger fish coming from larger eggs fed more at the surface than smaller fish coming from smaller eggs. Independently of their genetic origin large and small juveniles, coming respectively from large and small eggs, differed in body shape. This was most clearly seen in head and body morphology, e.g. larger fish were overall slimmer than smaller fish. The influence of egg size on behavior and morphology of Arctic charr varied with female parentage, indicating strong maternal x genetic interactions. In steelhead trout, both origin of fish and egg size were related with body growth of yearling fish reared under laboratory conditions: hatchery juveniles coming from small eggs were larger than wild juveniles coming from small eggs. Both were in turn larger than hatchery and wild juveniles coming from large eggs. Hatchery progeny showed lower osmo-regulatory status compared to wild progeny but nevertheless preferentially chose salt water. This study presents novel findings that demonstrate that variability in egg size is an important source of phenotypic variation in fishes. My results support the hypothesis that females experiencing relatively high growth rate as juveniles produce a large number of small eggs as adults and that such a reduction in egg size happens rapidly, i.e. in only one generation in domestication. I discuss the implications of egg size for evolution of fishes and, especially how diversity created by egg size can influence diversification and speciation of fishes. Title: The importance of egg size for the diversity of salmonids Author: Leblanc, Camille A. Understanding the origin and nature of intra specific biodiversity enables us to better conserve and manage animal populations. Biological diversity is seen at different scales and for different traits such as behavior, morphology, physiology, and life history. Behavior is especially important since behavioral changes are believed to precede changes in morphology or physiology among fishes. Salmonids display great diversity in terms of behavior, life histories and morphology within and among populations. Thus, differentiation among populations and morphs has been related to the evolution of new species. Various genetic, environmental and ecological factors have been shown to be important for segregation of morphs, including competition for food or other resources, phenotypic plasticity and sexual selection. Recently, it has been suggested that the importance of epigenetic and maternal effects for intra specific diversity have been underestimated. I studied the short- and long-term effects of egg size on development, behavior, body growth and physiology in Arctic charr Salvelinus alpinus and steelhead trout Oncorhynchus mykiss. I also examined how domestication can affect egg size. Egg size was smaller in domesticated fish populations after accounting for female body size and age. Egg size was negatively correlated with embryonic development before hatching, i.e. embryos in small eggs developed more rapidly. At emergence, egg size was positively correlated with length and weight of first feeding progeny. Juveniles coming from larger eggs tended to feed more at the surface whereas juveniles coming from smaller eggs fed more on the bottom. These relationships and effects of egg size on embryos and first feeding fish were observed in both species in laboratory conditions. In Arctic charr there was a higher energy content per egg in larger eggs in both aquaculture and wild populations, and the total energy content per egg varied among populations. Behavior of Arctic charr at first feeding was affected by egg size, social environment and their interaction. At 300 days post fertilization, fish coming from different egg sizes differed in morphology and behavior: larger fish coming from larger eggs fed more at the surface than smaller fish coming from smaller eggs. Independently of their genetic origin large and small juveniles, coming respectively from large and small eggs, differed in body shape. This was most clearly seen in head and body morphology, e.g. larger fish were overall slimmer than smaller fish. The influence of egg size on behavior and morphology of Arctic charr varied with female parentage, indicating strong maternal x genetic interactions. In steelhead trout, both origin of fish and egg size were related with body growth of yearling fish reared under laboratory conditions: hatchery juveniles coming from small eggs were larger than wild juveniles coming from small eggs. Both were in turn larger than hatchery and wild juveniles coming from large eggs. Hatchery progeny showed lower osmo-regulatory status compared to wild progeny but nevertheless preferentially chose salt water. This study presents novel findings that demonstrate that variability in egg size is an important source of phenotypic variation in fishes. My results support the hypothesis that females experiencing relatively high growth rate as juveniles produce a large number of small eggs as adults and that such a reduction in egg size happens rapidly, i.e. in only one generation in domestication. I discuss the implications of egg size for evolution of fishes and, especially how diversity created by egg size can influence diversification and speciation of fishes. Close

• 498. [Article] Lichen communities and caribou habitat in Denali National Park and Preserve, Alaska, USA

  Lichens play many important roles in subarctic terrestrial ecosystems by fixing nitrogen, colonizing rock and gravel, stabilizing otherwise bare soil, adding significantly to vegetation biodiversity and ...

  Citation × Citation Citation Abstract Copy Title: Lichen communities and caribou habitat in Denali National Park and Preserve, Alaska, USA Author: Nelson, Peter, 1970- Lichens play many important roles in subarctic terrestrial ecosystems by fixing nitrogen, colonizing rock and gravel, stabilizing otherwise bare soil, adding significantly to vegetation biodiversity and serving as the primary food for caribou in the winter. In these chapters, I analyzed lichen community and ecological trait structure along environmental gradients, map lichens using some of their unique spectral properties to generate lichen maps and study caribou habitat selection patterns in relation to lichens and other habitat variables. Morphological and life history traits of lichens influence their ecological roles through physiological limitations imposed by their form and photobionts, the algal or cyanobacterial partner. In chapter 2, I analyzed the lichen traits in relationship to environmental gradients, other forms of vegetation and time since fire in Denali National Park and Preserve, Alaska. Lichens with different photobionts reached different maxima along environmental gradients, these corresponding to variable water availability or specific biotic factors thought to favor that photobiont. Green algal lichens were most abundant in the alpine whereas cyanolichens peaked where shrub cover increased. Tripartite lichens were most abundant in middle elevation, mossy areas. Lichen growthforms peaked along desiccation and water absorption gradients. Lichens with small vegetative propagules were most abundant in lowland forests. Recent fire favored simple, Cladonia-form lichens with soredia that grow on wood whereas erect branched fruticose lichens, the "reindeer lichens", had only partially recovered 20-100 years after fire. These results imply interacting forces of water regulation, dispersal and optimum conditions for photosynthesis drive lichen trait frequency and abundance. The fungal partner within the lichen symbiosis produces many unique compounds that are often brightly colored. Other studies have attempted to map lichens using their distinctive spectral properties but no study has yet to target specific lichen compounds in order to better model lichen cover. In chapter 3, I focused on one yellow lichen compound, usnic acid, as the target for modeling lichen cover using Landsat 7 ETM+ satellite data. Usnic lichen cover had non-linear relationships with the three best predictors; elevation, blue and near-infrared bandpasses. Using these three predictors, I generated an usnic lichen map for Denali, which I use in chapter 4 for analyzing caribou habitat selection. I also modeled and mapped other vegetation groups corresponding to caribou diet items used later. My results show that some lichens may be directly mapped from space by targeting this specific compound produced by the fungus. Caribou depend on lichens for up to 66% of their winter diet but other factors, such as snow, affect their access to the lichens. In chapter 4, I analyzed caribou habitat selection over 20 years in Denali using vegetation maps from chapter 3, climate data and other environmental variables. Over the two-decade period, caribou selected middle elevation, open areas with high graminoid cover and earlier snow-free dates. As each winter progressed, caribou aggregated where there was higher lichen cover and earlier snow-melt. Caribou selected habitat differently between years, which I collapsed into three different habitat/year groups: (1) years where most animals were in low elevation, flat terrain where there was low lichen and conifer cover but high graminoid and shrub cover with variable snow; (2) years caribou went to middle elevations with deeper snow and rugged terrain and moderate graminoid and lichen cover; and (3) years where caribou were dispersed west in low elevation woodlands with high lichen cover. My results show interacting factors determine caribou habitat selection at multiple spatial scales, specifically the importance of open, tussock tundra and long-term trends in snow melt at long time scales and lichen and snow-melt at shorter time scales. This research improves our understanding of the regional distribution and abundance of lichens in relation to higher plants, fire, and caribou. Title: Lichen communities and caribou habitat in Denali National Park and Preserve, Alaska, USA Author: Nelson, Peter, 1970- Lichens play many important roles in subarctic terrestrial ecosystems by fixing nitrogen, colonizing rock and gravel, stabilizing otherwise bare soil, adding significantly to vegetation biodiversity and serving as the primary food for caribou in the winter. In these chapters, I analyzed lichen community and ecological trait structure along environmental gradients, map lichens using some of their unique spectral properties to generate lichen maps and study caribou habitat selection patterns in relation to lichens and other habitat variables. Morphological and life history traits of lichens influence their ecological roles through physiological limitations imposed by their form and photobionts, the algal or cyanobacterial partner. In chapter 2, I analyzed the lichen traits in relationship to environmental gradients, other forms of vegetation and time since fire in Denali National Park and Preserve, Alaska. Lichens with different photobionts reached different maxima along environmental gradients, these corresponding to variable water availability or specific biotic factors thought to favor that photobiont. Green algal lichens were most abundant in the alpine whereas cyanolichens peaked where shrub cover increased. Tripartite lichens were most abundant in middle elevation, mossy areas. Lichen growthforms peaked along desiccation and water absorption gradients. Lichens with small vegetative propagules were most abundant in lowland forests. Recent fire favored simple, Cladonia-form lichens with soredia that grow on wood whereas erect branched fruticose lichens, the "reindeer lichens", had only partially recovered 20-100 years after fire. These results imply interacting forces of water regulation, dispersal and optimum conditions for photosynthesis drive lichen trait frequency and abundance. The fungal partner within the lichen symbiosis produces many unique compounds that are often brightly colored. Other studies have attempted to map lichens using their distinctive spectral properties but no study has yet to target specific lichen compounds in order to better model lichen cover. In chapter 3, I focused on one yellow lichen compound, usnic acid, as the target for modeling lichen cover using Landsat 7 ETM+ satellite data. Usnic lichen cover had non-linear relationships with the three best predictors; elevation, blue and near-infrared bandpasses. Using these three predictors, I generated an usnic lichen map for Denali, which I use in chapter 4 for analyzing caribou habitat selection. I also modeled and mapped other vegetation groups corresponding to caribou diet items used later. My results show that some lichens may be directly mapped from space by targeting this specific compound produced by the fungus. Caribou depend on lichens for up to 66% of their winter diet but other factors, such as snow, affect their access to the lichens. In chapter 4, I analyzed caribou habitat selection over 20 years in Denali using vegetation maps from chapter 3, climate data and other environmental variables. Over the two-decade period, caribou selected middle elevation, open areas with high graminoid cover and earlier snow-free dates. As each winter progressed, caribou aggregated where there was higher lichen cover and earlier snow-melt. Caribou selected habitat differently between years, which I collapsed into three different habitat/year groups: (1) years where most animals were in low elevation, flat terrain where there was low lichen and conifer cover but high graminoid and shrub cover with variable snow; (2) years caribou went to middle elevations with deeper snow and rugged terrain and moderate graminoid and lichen cover; and (3) years where caribou were dispersed west in low elevation woodlands with high lichen cover. My results show interacting factors determine caribou habitat selection at multiple spatial scales, specifically the importance of open, tussock tundra and long-term trends in snow melt at long time scales and lichen and snow-melt at shorter time scales. This research improves our understanding of the regional distribution and abundance of lichens in relation to higher plants, fire, and caribou. Close

• 499. [Article] Quantification of Ecological Change Using Repeat Photography and Ground Based Lidar

  Remote sensing techniques have long been useful in quantifying changes in ecosystems and the field of remote sensing is constantly evolving to better assess and describe changes, both spatially and temporally. ...

  Citation × Citation Citation Abstract Copy Title: Quantification of Ecological Change Using Repeat Photography and Ground Based Lidar Author: Batchelor, Jonathan L. Remote sensing techniques have long been useful in quantifying changes in ecosystems and the field of remote sensing is constantly evolving to better assess and describe changes, both spatially and temporally. In this thesis I explored the novel use of two remote sensing methods to quantify ecosystems; repeat photograph to describe change over time, and ground based lidar to describe change spatially. Using repeat photography, I assessed the effects of the removal of livestock in riparian systems at Hart Mountain National Antelope Refuge in southeastern Oregon, 23 years after the cessation of cattle grazing. I compared photos taken before grazing was ended with later retake photos. Two methods were used for this assessment: 1) a qualitative visual method comparing seven cover types and processes and 2) a new quantitative method of inserting digital line transects into photos. Results indicated that channel widths and eroding banks decreased in 64% and 73% of sites, respectively. I found a 90% decrease in the amount of bare soil (p<0.001) and a 63 % decrease in exposed channel (p<0.001) as, well as a significant increase in the cover of grasses/sedges/forbs (15% increase, p=0.037), rushes (389% increase, p=0.014) and willow (388% increase, P<0.001). I also assessed the accuracy of the new method of inserting digital line transects into photo pairs. An overall accuracy of 91% (kappa 83%) suggests digital line transects can be a useful tool for quantifying vegetation cover from photos. My results indicate that the removal of cattle can result in dramatic changes in riparian vegetation, even in semi-arid landscapes and without active restoration treatments. I used ground based lidar to quantify forest structure in a spatially explicit manner. The structural complexity of a forest has profound influences on its ecological functioning and overall health. The arrangement and amount of aboveground biomass are two important components of this structural complexity that influence the biodiversity in a forest ecosystem. In this paper, I explored and develop novel depth and openness metrics derived from single point ground-based lidar scans, which can quantify this complexity to a higher level of detail. Depth is a 3D, radial measure of the visible distance in all directions from a location (e.g., at the scanner origin). Openness is the percent of scan pulses in the near-omnidirectional view without a return,. To derive these metrics, I collected 243 scans at 27 forested stands in the Pacific Northwest region of the United States, representing a broad range of forest structure types. I created structural signatures using depth and openness for each stand and determined that our metrics could reliably differentiate forests. These metrics were compared to several traditional metrics: diameter at breast height (DBH), basal area, and diameter diversity index (DDI). The mean and variance in DBH of trees, basal area, and DDI of each stand were determined by generating isovists (polygons measuring visible space from a location) derived from point cloud cross sections. Interestingly, there was only weak to moderate correlation observed between depth or openness metrics when compared with the mean and variance in DBH, basal area, and DDI, suggesting that our new metrics (depth and openness) quantify a wider range of aspects of structure at the stand and plot level that are not captured by those traditional metrics. The proposed metrics can quantify forest structure at a high level of precision, reduce observer bias, and preserve a level of complexity lost in simple indices. The proposed metrics have great potential for quantifying change in forested systems, and describing habitat for organisms. Title: Quantification of Ecological Change Using Repeat Photography and Ground Based Lidar Author: Batchelor, Jonathan L. Remote sensing techniques have long been useful in quantifying changes in ecosystems and the field of remote sensing is constantly evolving to better assess and describe changes, both spatially and temporally. In this thesis I explored the novel use of two remote sensing methods to quantify ecosystems; repeat photograph to describe change over time, and ground based lidar to describe change spatially. Using repeat photography, I assessed the effects of the removal of livestock in riparian systems at Hart Mountain National Antelope Refuge in southeastern Oregon, 23 years after the cessation of cattle grazing. I compared photos taken before grazing was ended with later retake photos. Two methods were used for this assessment: 1) a qualitative visual method comparing seven cover types and processes and 2) a new quantitative method of inserting digital line transects into photos. Results indicated that channel widths and eroding banks decreased in 64% and 73% of sites, respectively. I found a 90% decrease in the amount of bare soil (p<0.001) and a 63 % decrease in exposed channel (p<0.001) as, well as a significant increase in the cover of grasses/sedges/forbs (15% increase, p=0.037), rushes (389% increase, p=0.014) and willow (388% increase, P<0.001). I also assessed the accuracy of the new method of inserting digital line transects into photo pairs. An overall accuracy of 91% (kappa 83%) suggests digital line transects can be a useful tool for quantifying vegetation cover from photos. My results indicate that the removal of cattle can result in dramatic changes in riparian vegetation, even in semi-arid landscapes and without active restoration treatments. I used ground based lidar to quantify forest structure in a spatially explicit manner. The structural complexity of a forest has profound influences on its ecological functioning and overall health. The arrangement and amount of aboveground biomass are two important components of this structural complexity that influence the biodiversity in a forest ecosystem. In this paper, I explored and develop novel depth and openness metrics derived from single point ground-based lidar scans, which can quantify this complexity to a higher level of detail. Depth is a 3D, radial measure of the visible distance in all directions from a location (e.g., at the scanner origin). Openness is the percent of scan pulses in the near-omnidirectional view without a return,. To derive these metrics, I collected 243 scans at 27 forested stands in the Pacific Northwest region of the United States, representing a broad range of forest structure types. I created structural signatures using depth and openness for each stand and determined that our metrics could reliably differentiate forests. These metrics were compared to several traditional metrics: diameter at breast height (DBH), basal area, and diameter diversity index (DDI). The mean and variance in DBH of trees, basal area, and DDI of each stand were determined by generating isovists (polygons measuring visible space from a location) derived from point cloud cross sections. Interestingly, there was only weak to moderate correlation observed between depth or openness metrics when compared with the mean and variance in DBH, basal area, and DDI, suggesting that our new metrics (depth and openness) quantify a wider range of aspects of structure at the stand and plot level that are not captured by those traditional metrics. The proposed metrics can quantify forest structure at a high level of precision, reduce observer bias, and preserve a level of complexity lost in simple indices. The proposed metrics have great potential for quantifying change in forested systems, and describing habitat for organisms. Close

• 500. [Article] Studies toward the synthesis of coibamide A and analogues

  Coibamide A is a highly methylated cyclic depsipeptide isolated from Panamanian marine filamentous cyanobacteria as part of an International Cooperative Biodiversity Groups (ICBG) program based in Panama. ...

  Citation × Citation Citation Abstract Copy Title: Studies toward the synthesis of coibamide A and analogues Author: Li, Dong Coibamide A is a highly methylated cyclic depsipeptide isolated from Panamanian marine filamentous cyanobacteria as part of an International Cooperative Biodiversity Groups (ICBG) program based in Panama. This structurally unique agent exhibits potent cancer cell toxicity with an unprecedented selectivity profile in the National Cancer Institute (NCI) 60 cell line panel, possibly through a novel mechanism as suggested by "COMPARE negative" results. Therefore, it is considered a promising lead agent in cancer drug discovery. Although field recollections have provided a few milligrams of coibamide A, the amount obtained is still insufficient for extensive biological testing. The producing strain has recently been cultured, but coibamide yields are very low and the growth rate is slow. Chemical synthesis of coibamide A is central to further biological testing and potential clinical development, and has become the major focus of my work. A macrocycle-side chain strategy was originally proposed for the synthesis of coibamide A. It was unsuccessful, however, due to the difficulties trying to couple the macrocycle and side chain together at the last step. To solve this problem, a modified macrocycle – side chain stragety was proposed. Coibamide A was disconnected into two other subunits: the N-MeLeu-macrocycle and the "tripeptide" side chain. The reason for this modification was that the secondary amine of N-MeLeu, with some distance from the bulky macrocycle, should be spatially more availalbe for the final step to couple with the side chain "tripeptide". This new strategy was able to generate "synthetic coibamide" in a moderate yield, this compound, however, was not the natural product coibamide A according to HPLC, 1H NMR and activity test. By Marfey's analysis, we found that in this synthetic coibamide A, no N,O-diMe L-Ser was detected and only its D-counterpart was present, which indicated an unusual L-to-D inversion during coupling reactions. Because it was very difficult to overcome this unexpected inversion during this strategy, a third scheme, the Y-Strategy, was proposed. For the Y-strategy, instead of building the macrocycle first, we coupled the side chain with a macrocycle tripeptide first to afford a linear heptapeptide. Then the ester bond between the hydroxy of N-MeThr and carboxy of N-MeAla (of a tetrapeptide) was built to generate the full-size "Y-structure", which is then deprotected and cyclized to produce the target molecule coibamide A. While the heptapeptide was synthesized sucessfully, the ester bond formation reaction to generate the Y-structure did not happen. Although the Y-strategy did not eventually yield coibamide, it is the most convergent and efficient strategy so far. Because the pharmacological data for coibamide A suggest a unique mechanism and no natural coibamide analogues were separated from the field collections or cultures, the synthesis of coibamide analogues is also extremely valueable for activity and mechanism studies and becomes part of our synthetic effort. The analogues should reasonably resemble the structure of coibamide A, and be easier to be achieved synthetically compared to coibamide A itself. Two families of analogues were designed: the N-desmethyl coibamide family (most or all of the N-methylated amino acid components were replaced by regular amino acids) and the N-MeSer coibamide family (the junction N-MeThr was changed to N-MeSer). Per-N-desmethyl coibamide and several other analogues from the first family were synthesized by the modified macrocycle - side chain strategy, however, none of them exhibits any activity against the testing cell lines. Attempt to per-methylate these compounds also failed due to decomposition of substrates under basic conditions. N-MeSer-coibamide was successfully synthesized through the Y-strategy and purified by HPLC. Cell toxicity has been observed in the activity test, although the potency was several hundred times lower than the natural coibamide A. The synthetic process of N-MeSer coibamide should be optimized for better yields and easier purification as the focus of next stage. Title: Studies toward the synthesis of coibamide A and analogues Author: Li, Dong Coibamide A is a highly methylated cyclic depsipeptide isolated from Panamanian marine filamentous cyanobacteria as part of an International Cooperative Biodiversity Groups (ICBG) program based in Panama. This structurally unique agent exhibits potent cancer cell toxicity with an unprecedented selectivity profile in the National Cancer Institute (NCI) 60 cell line panel, possibly through a novel mechanism as suggested by "COMPARE negative" results. Therefore, it is considered a promising lead agent in cancer drug discovery. Although field recollections have provided a few milligrams of coibamide A, the amount obtained is still insufficient for extensive biological testing. The producing strain has recently been cultured, but coibamide yields are very low and the growth rate is slow. Chemical synthesis of coibamide A is central to further biological testing and potential clinical development, and has become the major focus of my work. A macrocycle-side chain strategy was originally proposed for the synthesis of coibamide A. It was unsuccessful, however, due to the difficulties trying to couple the macrocycle and side chain together at the last step. To solve this problem, a modified macrocycle – side chain stragety was proposed. Coibamide A was disconnected into two other subunits: the N-MeLeu-macrocycle and the "tripeptide" side chain. The reason for this modification was that the secondary amine of N-MeLeu, with some distance from the bulky macrocycle, should be spatially more availalbe for the final step to couple with the side chain "tripeptide". This new strategy was able to generate "synthetic coibamide" in a moderate yield, this compound, however, was not the natural product coibamide A according to HPLC, 1H NMR and activity test. By Marfey's analysis, we found that in this synthetic coibamide A, no N,O-diMe L-Ser was detected and only its D-counterpart was present, which indicated an unusual L-to-D inversion during coupling reactions. Because it was very difficult to overcome this unexpected inversion during this strategy, a third scheme, the Y-Strategy, was proposed. For the Y-strategy, instead of building the macrocycle first, we coupled the side chain with a macrocycle tripeptide first to afford a linear heptapeptide. Then the ester bond between the hydroxy of N-MeThr and carboxy of N-MeAla (of a tetrapeptide) was built to generate the full-size "Y-structure", which is then deprotected and cyclized to produce the target molecule coibamide A. While the heptapeptide was synthesized sucessfully, the ester bond formation reaction to generate the Y-structure did not happen. Although the Y-strategy did not eventually yield coibamide, it is the most convergent and efficient strategy so far. Because the pharmacological data for coibamide A suggest a unique mechanism and no natural coibamide analogues were separated from the field collections or cultures, the synthesis of coibamide analogues is also extremely valueable for activity and mechanism studies and becomes part of our synthetic effort. The analogues should reasonably resemble the structure of coibamide A, and be easier to be achieved synthetically compared to coibamide A itself. Two families of analogues were designed: the N-desmethyl coibamide family (most or all of the N-methylated amino acid components were replaced by regular amino acids) and the N-MeSer coibamide family (the junction N-MeThr was changed to N-MeSer). Per-N-desmethyl coibamide and several other analogues from the first family were synthesized by the modified macrocycle - side chain strategy, however, none of them exhibits any activity against the testing cell lines. Attempt to per-methylate these compounds also failed due to decomposition of substrates under basic conditions. N-MeSer-coibamide was successfully synthesized through the Y-strategy and purified by HPLC. Cell toxicity has been observed in the activity test, although the potency was several hundred times lower than the natural coibamide A. The synthetic process of N-MeSer coibamide should be optimized for better yields and easier purification as the focus of next stage. Close