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• 1. [Article] Biological diversity and third world development : a study of the transformation of an ecological concept into natural resource policy

  This work examined the transformation of the concept of biodiversity into natural resource policies of the U.S. Agency for International Development and the World Bank through 1988. The study identified ...

  Citation × Citation Citation Abstract Copy Title: Biological diversity and third world development : a study of the transformation of an ecological concept into natural resource policy Author: Vincent, Robert Montgomery This work examined the transformation of the concept of biodiversity into natural resource policies of the U.S. Agency for International Development and the World Bank through 1988. The study identified several groups as playing key roles in the transformation process. These were nongovernmental environmental organizations, the scientific community, and the U.S. Congress. As a framework for analysis, a Process Model is presented which depicts the process that transforms a scientific concept into natural resource policy. As a result of this research, modifications to the original Process Model are proposed. Though this study focuses on the scientific concept of biological diversity, it is suggested that the Process Model may be more broadly applied to other resource issues which follow the model's general steps of concept formulation, value identification, legislation development, and policy formulation. Several conclusions are reached from this study. One is that though there was little agreement about the concept of biodiversity within the scientific community, three broad themes evolved. These themes are ecosystem diversity, species diversity, and genetic diversity. Second, NGEO members did not adopt scientific concepts of biodiversity, but rather developed value positions with respect to biodiversity. These positions were presented to lawmakers the result being that biodiversity legislation was narrowly focused and did not fully reflect the three major diversity themes developed within the scientific community. Finally, policies developed by agencies responsible for implementing biodiversity legislation reflected Congressional intent and were equally narrowly focused. One consequence is that only selected major biodiversity themes are dealt with in agency policy, and this is reflected in agency funded programs to conserve biological diversity. Title: Biological diversity and third world development : a study of the transformation of an ecological concept into natural resource policy Author: Vincent, Robert Montgomery This work examined the transformation of the concept of biodiversity into natural resource policies of the U.S. Agency for International Development and the World Bank through 1988. The study identified several groups as playing key roles in the transformation process. These were nongovernmental environmental organizations, the scientific community, and the U.S. Congress. As a framework for analysis, a Process Model is presented which depicts the process that transforms a scientific concept into natural resource policy. As a result of this research, modifications to the original Process Model are proposed. Though this study focuses on the scientific concept of biological diversity, it is suggested that the Process Model may be more broadly applied to other resource issues which follow the model's general steps of concept formulation, value identification, legislation development, and policy formulation. Several conclusions are reached from this study. One is that though there was little agreement about the concept of biodiversity within the scientific community, three broad themes evolved. These themes are ecosystem diversity, species diversity, and genetic diversity. Second, NGEO members did not adopt scientific concepts of biodiversity, but rather developed value positions with respect to biodiversity. These positions were presented to lawmakers the result being that biodiversity legislation was narrowly focused and did not fully reflect the three major diversity themes developed within the scientific community. Finally, policies developed by agencies responsible for implementing biodiversity legislation reflected Congressional intent and were equally narrowly focused. One consequence is that only selected major biodiversity themes are dealt with in agency policy, and this is reflected in agency funded programs to conserve biological diversity. Close

• 2. [Article] Soil Property Effects on Willamette Daisy (Erigeron decumbens) within William L. Finley National Wildlife Refuge

  Plant species diversity plays an important role in maintaining ecosystem function and the services that ecosystems provide. Diversity is threatened by habitat loss, invasive species, and global climate ...

  Citation × Citation Citation Abstract Copy Title: Soil Property Effects on Willamette Daisy (Erigeron decumbens) within William L. Finley National Wildlife Refuge Author: Day, Emily S. Plant species diversity plays an important role in maintaining ecosystem function and the services that ecosystems provide. Diversity is threatened by habitat loss, invasive species, and global climate change. Willamette Daisy (Erigeron decumbens), an endangered species, has been reintroduced at two different sites (Field 29 and 8N) within William L. Finely Wildlife refuge, but it grows better at one site (Field 29) than the other (Field 8N). The purpose of the study was to determine if the differences in growth at the two sites could be caused by differences in soil properties, and determine soil conditions conducive for growth. We grew E. decumbens in soil collected from each field in a greenhouse with sterile and unsterilized treatments and performed a soil analysis on samples from each field. Soil sterilization had a significantly negative effect on plant survivorship, suggesting soil biota improves establishment of E. decumbens. Field 29 had significantly higher TN, TC, and pH than Field 8N, which may be contributing to the observed differences. Results from this study suggest that these soil properties could benefit E. decumbens growth in the wild, and information on soil conditions could improve reintroduction site selection and recovery of this endangered species. Title: Soil Property Effects on Willamette Daisy (Erigeron decumbens) within William L. Finley National Wildlife Refuge Author: Day, Emily S. Plant species diversity plays an important role in maintaining ecosystem function and the services that ecosystems provide. Diversity is threatened by habitat loss, invasive species, and global climate change. Willamette Daisy (Erigeron decumbens), an endangered species, has been reintroduced at two different sites (Field 29 and 8N) within William L. Finely Wildlife refuge, but it grows better at one site (Field 29) than the other (Field 8N). The purpose of the study was to determine if the differences in growth at the two sites could be caused by differences in soil properties, and determine soil conditions conducive for growth. We grew E. decumbens in soil collected from each field in a greenhouse with sterile and unsterilized treatments and performed a soil analysis on samples from each field. Soil sterilization had a significantly negative effect on plant survivorship, suggesting soil biota improves establishment of E. decumbens. Field 29 had significantly higher TN, TC, and pH than Field 8N, which may be contributing to the observed differences. Results from this study suggest that these soil properties could benefit E. decumbens growth in the wild, and information on soil conditions could improve reintroduction site selection and recovery of this endangered species. Close

• 3. [Article] Human Visitation in the Rocky Intertidal and its Effects on Abundance of Algal and Invertebrate Species

  The rocky intertidal is a diverse ecosystem with a variety of species and ecological interactions. Many biotic and abiotic interactions act together to restrict the abundance and distribution of species. ...

  Citation × Citation Citation Abstract Copy Title: Human Visitation in the Rocky Intertidal and its Effects on Abundance of Algal and Invertebrate Species Author: Silbernagel, Justin J. The rocky intertidal is a diverse ecosystem with a variety of species and ecological interactions. Many biotic and abiotic interactions act together to restrict the abundance and distribution of species. Anthropogenic effects can have an important impact on species abundance and distribution as well. This study looks at how human visitation affects community structure in the rocky intertidal along the Oregon coast. Areas of high human visitation were found to have lower species richness than areas of low visitation in the lower vertical zones of the rocky intertidal. However, species richness was found to be higher in high visitation areas in the highest intertidal zone. Abundance of species differed between areas of high and low human visitation, but showed few overall significant trends. Title: Human Visitation in the Rocky Intertidal and its Effects on Abundance of Algal and Invertebrate Species Author: Silbernagel, Justin J. The rocky intertidal is a diverse ecosystem with a variety of species and ecological interactions. Many biotic and abiotic interactions act together to restrict the abundance and distribution of species. Anthropogenic effects can have an important impact on species abundance and distribution as well. This study looks at how human visitation affects community structure in the rocky intertidal along the Oregon coast. Areas of high human visitation were found to have lower species richness than areas of low visitation in the lower vertical zones of the rocky intertidal. However, species richness was found to be higher in high visitation areas in the highest intertidal zone. Abundance of species differed between areas of high and low human visitation, but showed few overall significant trends. Close

• 4. [Article] The development of a distribution- and growth-prediction model for the environmental grid

  Further development of an environmental grid for interpreting plant distribution and growth took place this last year as an attempt to solve problems associated with spatial diversity in ecosystems. Special ...

  Citation × Citation Citation Abstract Copy Title: The development of a distribution- and growth-prediction model for the environmental grid Author: Waring, Richard H., University of Washington, U.S. International Biological Program. Coniferous Forest Biome Further development of an environmental grid for interpreting plant distribution and growth took place this last year as an attempt to solve problems associated with spatial diversity in ecosystems. Special emphasis was placed on developing more universal integrated indexes to environment, ones that might permit wide extrapolation throughout the range of at least one or two of the more widely distributed forest species ... It was the task of this project to integrate these variables to more readily explain and predict plant distribution and growth. Title: The development of a distribution- and growth-prediction model for the environmental grid Author: Waring, Richard H., University of Washington, U.S. International Biological Program. Coniferous Forest Biome Further development of an environmental grid for interpreting plant distribution and growth took place this last year as an attempt to solve problems associated with spatial diversity in ecosystems. Special emphasis was placed on developing more universal integrated indexes to environment, ones that might permit wide extrapolation throughout the range of at least one or two of the more widely distributed forest species ... It was the task of this project to integrate these variables to more readily explain and predict plant distribution and growth. Close

• 5. [Article] Biodiversity Conservation: The Key Is Reducing Meat Consumption

  Access to this item has been restricted by repository administrators at the request of the publisher, Elsevier, until July 29, 2017.

  Citation × Citation Citation Abstract Copy Title: Biodiversity Conservation: The Key Is Reducing Meat Consumption Author: Machovina, Brian, Feeley, Kenneth J., Ripple, William J. Access to this item has been restricted by repository administrators at the request of the publisher, Elsevier, until July 29, 2017. Title: Biodiversity Conservation: The Key Is Reducing Meat Consumption Author: Machovina, Brian, Feeley, Kenneth J., Ripple, William J. Access to this item has been restricted by repository administrators at the request of the publisher, Elsevier, until July 29, 2017. Close

• 6. [Article] Stand Structure of Old Growth Dry Mixed Conifer Forests in the Deschutes and Ochoco National Forests.

  Old-growth dry-mixed conifer forests are valued as habitats for late seral forest species, for the ecosystem services and landscape diversity they provide, and for their aesthetic appeal. The structure ...

  Citation × Citation Citation Abstract Copy Title: Stand Structure of Old Growth Dry Mixed Conifer Forests in the Deschutes and Ochoco National Forests. Author: Merschel, Andrew G. Old-growth dry-mixed conifer forests are valued as habitats for late seral forest species, for the ecosystem services and landscape diversity they provide, and for their aesthetic appeal. The structure of these forests has been heavily altered by historic logging of overstory ponderosa pine and Douglas-fir. Additionally, changes in fire regime have altered understory density in these forests to an unknown extent. Conserving remaining stands and facilitating old-growth development in disturbed stands are objectives of the Deschutes and Ochoco National Forests. This investigation addressed these objectives with two separate analyses. The first analysis was an accuracy assessment of the GNN forest vegetation map’s ability to predict old-growth drymixed conifer structure at a site scale and at a landscape scale. This analysis determined that the GNN map is an adequate tool for identifying old-growth stands at a site scale, and was highly accurate at predicting dry-mixed conifer forest vegetation at a landscape scale. The second analysis characterized present day and historic stand structure of old-growth dry-mixed conifer forests, and described how stand structure varied across the Deschutes and Ochoco National Forests. The second analysis determined future research should investigate the growth rate of understory ponderosa pine and Douglas-fir under varying density levels. Title: Stand Structure of Old Growth Dry Mixed Conifer Forests in the Deschutes and Ochoco National Forests. Author: Merschel, Andrew G. Old-growth dry-mixed conifer forests are valued as habitats for late seral forest species, for the ecosystem services and landscape diversity they provide, and for their aesthetic appeal. The structure of these forests has been heavily altered by historic logging of overstory ponderosa pine and Douglas-fir. Additionally, changes in fire regime have altered understory density in these forests to an unknown extent. Conserving remaining stands and facilitating old-growth development in disturbed stands are objectives of the Deschutes and Ochoco National Forests. This investigation addressed these objectives with two separate analyses. The first analysis was an accuracy assessment of the GNN forest vegetation map’s ability to predict old-growth drymixed conifer structure at a site scale and at a landscape scale. This analysis determined that the GNN map is an adequate tool for identifying old-growth stands at a site scale, and was highly accurate at predicting dry-mixed conifer forest vegetation at a landscape scale. The second analysis characterized present day and historic stand structure of old-growth dry-mixed conifer forests, and described how stand structure varied across the Deschutes and Ochoco National Forests. The second analysis determined future research should investigate the growth rate of understory ponderosa pine and Douglas-fir under varying density levels. Close

• 7. [Article] Analytical phytoplankton carbon measurements spanning diverse ecosystems

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Elsevier. The published article can be found at: http://www.journals.elsevier.com/deep-sea-rese...

  Citation × Citation Citation Abstract Copy Title: Analytical phytoplankton carbon measurements spanning diverse ecosystems Author: Brown, Matthew B., Behrenfeld, Michael J., van Dongen-Vogels, Virginie, Westberry, Toby K., Milligan, Allen J., Graff, Jason R., Dall'Olmo, Giorgio, Reifel, Kristen M. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Elsevier. The published article can be found at: http://www.journals.elsevier.com/deep-sea-research-part-i-oceanographic-research-papers/ Title: Analytical phytoplankton carbon measurements spanning diverse ecosystems Author: Brown, Matthew B., Behrenfeld, Michael J., van Dongen-Vogels, Virginie, Westberry, Toby K., Milligan, Allen J., Graff, Jason R., Dall'Olmo, Giorgio, Reifel, Kristen M. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Elsevier. The published article can be found at: http://www.journals.elsevier.com/deep-sea-research-part-i-oceanographic-research-papers/ Close

• 8. [Article] Assessment of the vulnerability of Oregon and Washington's natural areas to climate change

  There are currently more than 580 natural areas in Oregon and Washington managed by 20 federal, state, local, and private agencies and organizations. The natural areas network is unparalleled in its representation ...

  Citation × Citation Citation Abstract Copy Title: Assessment of the vulnerability of Oregon and Washington's natural areas to climate change Author: Margaret, Massie H. There are currently more than 580 natural areas in Oregon and Washington managed by 20 federal, state, local, and private agencies and organizations. The natural areas network is unparalleled in its representation of diverse ecosystems found in the region and may be an excellent collection of sites for monitoring long-term ecological responses to climate change. The goal of this research was to build a framework for a climate change monitoring program for the Pacific Northwest based on natural areas. Objectives were to (1) describe strengths of the existing natural areas network for representing effects of climate change by conducting a proportionality assessment and (2) determine which subset of natural areas have the best potential to detect change over the long term. Findings show that natural areas were generally representative and proportional compared to the Pacific Northwest. Subsets of natural areas were prioritized for long-term monitoring efforts through bioclimatic modelling based on the current and projected (2020s, 2050s, 2080s) outputs from 13 future climate models from ClimateWNA and the Random Forest approach. Projection consensus showed a substantial range increase in suitable climate for warmer adapted forest types coupled with a contraction in cooler forest types. The results highlight the potential stress of climate change on ecosystems across the region and the need for management strategies to adapt to this uncertainty. Title: Assessment of the vulnerability of Oregon and Washington's natural areas to climate change Author: Margaret, Massie H. There are currently more than 580 natural areas in Oregon and Washington managed by 20 federal, state, local, and private agencies and organizations. The natural areas network is unparalleled in its representation of diverse ecosystems found in the region and may be an excellent collection of sites for monitoring long-term ecological responses to climate change. The goal of this research was to build a framework for a climate change monitoring program for the Pacific Northwest based on natural areas. Objectives were to (1) describe strengths of the existing natural areas network for representing effects of climate change by conducting a proportionality assessment and (2) determine which subset of natural areas have the best potential to detect change over the long term. Findings show that natural areas were generally representative and proportional compared to the Pacific Northwest. Subsets of natural areas were prioritized for long-term monitoring efforts through bioclimatic modelling based on the current and projected (2020s, 2050s, 2080s) outputs from 13 future climate models from ClimateWNA and the Random Forest approach. Projection consensus showed a substantial range increase in suitable climate for warmer adapted forest types coupled with a contraction in cooler forest types. The results highlight the potential stress of climate change on ecosystems across the region and the need for management strategies to adapt to this uncertainty. Close

• 9. [Article] Investigation of unique marine environments for microbial natural products

  Metagenomics has revealed that the marine microbial biosphere is immensely more diverse than originally considered, and is an almost untapped reservoir for the potential discovery of microbial natural ...

  Citation × Citation Citation Abstract Copy Title: Investigation of unique marine environments for microbial natural products Author: Thornburg, Christopher C. Metagenomics has revealed that the marine microbial biosphere is immensely more diverse than originally considered, and is an almost untapped reservoir for the potential discovery of microbial natural products. Despite numerous advances in culturing, biosynthetic engineering and genomic-based screening efforts to uncover much of this diversity in relatively accessible environments, a high rediscovery rate has resulted in the investigation of unique, relatively unexplored ecosystems harboring phylogenetically diverse communities of marine organisms. The focus of this research was to establish a culture repository of microorganisms collected from the Red Sea and from deep-sea hydrothermal vents, and to assess their biosynthetic potential for the production of new chemical scaffolds. Cultivation of marine cyanobacteria from the Red Sea has led to the identification of five new cyclic depsipeptides, apratoxin H, grassypeptolides D and E, Ibu-epidemethoxylyngbyastin 3 and leptochelin, the latter possessing a unique chemical scaffold capable of binding metals. A collection of deep-sea hydrothermal vent sediment and microbial mat samples led to the isolation of 64 unique bacterial strains, with eight assigned as members of the order Actinomycetales. Importantly, these isolates, along with a collection of deep-vent invertebrates and microbes, have led to the development of methods for the collection, culturing and biological screening of organisms from this extreme environment for future natural products research. Title: Investigation of unique marine environments for microbial natural products Author: Thornburg, Christopher C. Metagenomics has revealed that the marine microbial biosphere is immensely more diverse than originally considered, and is an almost untapped reservoir for the potential discovery of microbial natural products. Despite numerous advances in culturing, biosynthetic engineering and genomic-based screening efforts to uncover much of this diversity in relatively accessible environments, a high rediscovery rate has resulted in the investigation of unique, relatively unexplored ecosystems harboring phylogenetically diverse communities of marine organisms. The focus of this research was to establish a culture repository of microorganisms collected from the Red Sea and from deep-sea hydrothermal vents, and to assess their biosynthetic potential for the production of new chemical scaffolds. Cultivation of marine cyanobacteria from the Red Sea has led to the identification of five new cyclic depsipeptides, apratoxin H, grassypeptolides D and E, Ibu-epidemethoxylyngbyastin 3 and leptochelin, the latter possessing a unique chemical scaffold capable of binding metals. A collection of deep-sea hydrothermal vent sediment and microbial mat samples led to the isolation of 64 unique bacterial strains, with eight assigned as members of the order Actinomycetales. Importantly, these isolates, along with a collection of deep-vent invertebrates and microbes, have led to the development of methods for the collection, culturing and biological screening of organisms from this extreme environment for future natural products research. Close

• 10. [Article] Status and Ecological Effects of the World’s Largest Carnivores

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the author's version of the work. It is posted here by permission of the American ...

  Citation × Citation Citation Abstract Copy Title: Status and Ecological Effects of the World’s Largest Carnivores Author: Schmitz, Oswald J., Hebblewhite, Mark, Wilmers, Christopher C., Wallach, Arian D., Smith, Douglas W., Estes, James A., Beschta, Robert L., Nelson, Michael P., Berger, Joel, Ritchie, Euan G., Ripple, William J., Elmhagen, Bodil, Wirsing, Aaron J., Letnic, Mike To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the author's version of the work. It is posted here by permission of the American Association for the Advancement of Science for personal use, not for redistribution. The definitive version was published in Science, Vol. 343 (2014), doi:10.1126/science.1241484. The published article can be found at: http://www.sciencemag.org/. Title: Status and Ecological Effects of the World’s Largest Carnivores Author: Schmitz, Oswald J., Hebblewhite, Mark, Wilmers, Christopher C., Wallach, Arian D., Smith, Douglas W., Estes, James A., Beschta, Robert L., Nelson, Michael P., Berger, Joel, Ritchie, Euan G., Ripple, William J., Elmhagen, Bodil, Wirsing, Aaron J., Letnic, Mike To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the author's version of the work. It is posted here by permission of the American Association for the Advancement of Science for personal use, not for redistribution. The definitive version was published in Science, Vol. 343 (2014), doi:10.1126/science.1241484. The published article can be found at: http://www.sciencemag.org/. Close

• 11. [Article] Nature in chains : the effects of Thomas Jefferson’s rectangular survey on a Pacific Northwest landscape

  Understanding the impact of humans on the environment has long been a topic of scholarly interest and debate. As environmental problems mount, accounts of historic ecological conditions and the factors ...

  Citation × Citation Citation Abstract Copy Title: Nature in chains : the effects of Thomas Jefferson’s rectangular survey on a Pacific Northwest landscape Author: Schweickert, Tina K. Understanding the impact of humans on the environment has long been a topic of scholarly interest and debate. As environmental problems mount, accounts of historic ecological conditions and the factors of change become increasingly useful. This study considers competing schools of interpretation about human impacts on ecological landscapes and develops a case study of one thirty-six square mile township in Oregon’s Waldo Hills. Built on evidence from 1851 surveyor notes, maps, journals, aerial photos, interviews, and contemporary environmental and ecological data, this study demonstrates a transformation from ecologically diverse ecosystems under the management of native peoples to ecologically depressed monoculture landscapes under industrialized agriculture. This thesis argues that the fundamental beliefs of human societies (i.e., worldviews) become expressed in the landscape. The nature-as-community view of the Kalapuya Indians resulted in a complex, curvilinear mosaic of prairie, savanna, and woodland. The individualized and rationalized view of the Euroamericans resulted in a simplified landscape of squared-off fields, channelized streams, and roads aligned to the survey grid. Thomas Jefferson’s rectangular survey, built on the ‘virtuous square’, is examined as a symbolic and tangible instrument of rapid expansion and exploitation across the American West. Understanding that worldviews become expressed in physical conditions may benefit those working to create sustainable futures; i.e., long-term and widespread ecological improvements will likely succeed only if society at large shares a fundamental belief in the value of healthy ecosystems. Title: Nature in chains : the effects of Thomas Jefferson’s rectangular survey on a Pacific Northwest landscape Author: Schweickert, Tina K. Understanding the impact of humans on the environment has long been a topic of scholarly interest and debate. As environmental problems mount, accounts of historic ecological conditions and the factors of change become increasingly useful. This study considers competing schools of interpretation about human impacts on ecological landscapes and develops a case study of one thirty-six square mile township in Oregon’s Waldo Hills. Built on evidence from 1851 surveyor notes, maps, journals, aerial photos, interviews, and contemporary environmental and ecological data, this study demonstrates a transformation from ecologically diverse ecosystems under the management of native peoples to ecologically depressed monoculture landscapes under industrialized agriculture. This thesis argues that the fundamental beliefs of human societies (i.e., worldviews) become expressed in the landscape. The nature-as-community view of the Kalapuya Indians resulted in a complex, curvilinear mosaic of prairie, savanna, and woodland. The individualized and rationalized view of the Euroamericans resulted in a simplified landscape of squared-off fields, channelized streams, and roads aligned to the survey grid. Thomas Jefferson’s rectangular survey, built on the ‘virtuous square’, is examined as a symbolic and tangible instrument of rapid expansion and exploitation across the American West. Understanding that worldviews become expressed in physical conditions may benefit those working to create sustainable futures; i.e., long-term and widespread ecological improvements will likely succeed only if society at large shares a fundamental belief in the value of healthy ecosystems. Close

• 12. [Article] Synecological effects of cattle grazing riparian ecosystems

  In 1978, a ten year project was begun to examine the synecological effects of livestock grazing riparian ecosystems. A multitude of biotic arid physical factors, many which were unique to riparian ecosystems, ...

  Citation × Citation Citation Abstract Copy Title: Synecological effects of cattle grazing riparian ecosystems Author: Kauffman, John Boone In 1978, a ten year project was begun to examine the synecological effects of livestock grazing riparian ecosystems. A multitude of biotic arid physical factors, many which were unique to riparian ecosystems, interacted to form a complex and diverse riparian ecosystem. A total of 256 stands of vegetation representing 60 discrete plant communities were identified. Twenty species of mammals and 81 species of birds were sited utilizing the area from May-October. Approximately one-half of the riparian vegetation bordering Catherine Creek was excluded from livestock grazing. Ten plant communities were intensively sampled in grazed and exclosed areas during three growing seasons to determine some of the impacts a late season grazing scheme has on riparian vegetation. Three plant communities displayed significant species composition and productivity differences. These commmunities were within' the meadow and Doug1az Hawthorne (Crataegus douglasii) vegetation types and were utilized more heavily by livestock than any other communities sampled. In addition succession appeared to be retarded by grazing on gravel bars dominated by black cottonwood (Populus trichocarpa) saplings and willows (Salix spp.). Few differences were recorded in other plant communities sampled. Late season grazing had few short term impacts on avian populations censused from May-October. There was a significant decrease in small mammal populations after grazing in all communities sampled. However, by the following August small mammals had recolonized the grazed plant communities in essentially the same species composition and densities. Grazed areas had significantly greater streambank losses than areas that were not grazed. While overwinter losses accounted for much of the streambank erosion, the erosion and disturbance caused by livestock grazing and trampling was enough to create significantly greater streambank losses in grazed areas compared to ungrazed areas. Positive characteristics of a late season grazing scheme on. the riparian zone included increased late season livestock production, good plant vigor and productivity, minimal soil disturbance, and minimal short term disturbance to wildlife populations dependent on riparian ecosystems. Title: Synecological effects of cattle grazing riparian ecosystems Author: Kauffman, John Boone In 1978, a ten year project was begun to examine the synecological effects of livestock grazing riparian ecosystems. A multitude of biotic arid physical factors, many which were unique to riparian ecosystems, interacted to form a complex and diverse riparian ecosystem. A total of 256 stands of vegetation representing 60 discrete plant communities were identified. Twenty species of mammals and 81 species of birds were sited utilizing the area from May-October. Approximately one-half of the riparian vegetation bordering Catherine Creek was excluded from livestock grazing. Ten plant communities were intensively sampled in grazed and exclosed areas during three growing seasons to determine some of the impacts a late season grazing scheme has on riparian vegetation. Three plant communities displayed significant species composition and productivity differences. These commmunities were within' the meadow and Doug1az Hawthorne (Crataegus douglasii) vegetation types and were utilized more heavily by livestock than any other communities sampled. In addition succession appeared to be retarded by grazing on gravel bars dominated by black cottonwood (Populus trichocarpa) saplings and willows (Salix spp.). Few differences were recorded in other plant communities sampled. Late season grazing had few short term impacts on avian populations censused from May-October. There was a significant decrease in small mammal populations after grazing in all communities sampled. However, by the following August small mammals had recolonized the grazed plant communities in essentially the same species composition and densities. Grazed areas had significantly greater streambank losses than areas that were not grazed. While overwinter losses accounted for much of the streambank erosion, the erosion and disturbance caused by livestock grazing and trampling was enough to create significantly greater streambank losses in grazed areas compared to ungrazed areas. Positive characteristics of a late season grazing scheme on. the riparian zone included increased late season livestock production, good plant vigor and productivity, minimal soil disturbance, and minimal short term disturbance to wildlife populations dependent on riparian ecosystems. Close

• 13. [Article] Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersi...

  Citation × Citation Citation Abstract Copy Title: Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography Author: Crump, Byron C., Adams, Heather E., Kling, George W. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology. Title: Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography Author: Crump, Byron C., Adams, Heather E., Kling, George W. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology. Close

• 14. [Article] The genome of Aiptasia, a sea anemone model for coral symbiosis

  Freely available online through the PNAS open access option.

  Citation × Citation Citation Abstract Copy Title: The genome of Aiptasia, a sea anemone model for coral symbiosis Author: Weis, Virginia M., Oates, Matt E., Aranda, Manuel, Voolstra, Christian R., Liew, Yi Jin, Hambleton, Elizabeth A., Pringle, John R., Baumgarten, Sebastian, Esherick, Lisl Y., Gough, Julian, Guse, Annika, Lehnert, Erik M., Michell, Craig T., Simakov, Oleg, Li, Yong Freely available online through the PNAS open access option. Title: The genome of Aiptasia, a sea anemone model for coral symbiosis Author: Weis, Virginia M., Oates, Matt E., Aranda, Manuel, Voolstra, Christian R., Liew, Yi Jin, Hambleton, Elizabeth A., Pringle, John R., Baumgarten, Sebastian, Esherick, Lisl Y., Gough, Julian, Guse, Annika, Lehnert, Erik M., Michell, Craig T., Simakov, Oleg, Li, Yong Freely available online through the PNAS open access option. Close

• 15. [Article] Evaluating taxonomic homogenization of freshwater fish assemblages in Chile

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by SpringerOpen. The published article can be found at: http://link.springer.com/journal/40693

  Citation × Citation Citation Abstract Copy Title: Evaluating taxonomic homogenization of freshwater fish assemblages in Chile Author: Arismendi, Ivan, Gomez-Uchida, Daniel, Vargas, Pamela V. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by SpringerOpen. The published article can be found at: http://link.springer.com/journal/40693 Title: Evaluating taxonomic homogenization of freshwater fish assemblages in Chile Author: Arismendi, Ivan, Gomez-Uchida, Daniel, Vargas, Pamela V. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by SpringerOpen. The published article can be found at: http://link.springer.com/journal/40693 Close

• 16. [Article] The Schultz Fire : an interdisciplinary perspective on its history, management, and ecological effects

  This thesis examines the Schultz Fire as a case study to explain the complex history of fire suppression management in America’s forests, and to gain further understanding of how management practices have ...

  Citation × Citation Citation Abstract Copy Title: The Schultz Fire : an interdisciplinary perspective on its history, management, and ecological effects Author: Ranseen, Susanne N. This thesis examines the Schultz Fire as a case study to explain the complex history of fire suppression management in America’s forests, and to gain further understanding of how management practices have affected the increase in fire severity levels and how forests respond to such a disturbance. The thesis objectives were: (1) to analyze the causes of the fire severity of the Schultz Fire, especially: topography, fuels, or weather; (2); to examine the possible correlation between fire severity and tree density; (3) to investigate whether post-fire species richness was related to fire severity two years after the Schultz Fire; (4) to investigate whether post-fire plant species richness, plant cover, and tree regeneration was related to fire severity two years after the Schultz Fire; and (5) to interlink and convey how these factors relate to the history of fire management and policy and public perception. The history of fire related policy and management has significantly changed the dynamics of America's national parks and forests. Understanding the larger context of this history, both of national fire management and of the effects of language and perception on policy and public reaction, is part of understanding the Schultz Fire as a whole. Based on modeling, high winds combined with the presence of high surface fuel load were the main causes of the Schultz Fire's high fire severity levels. As fire severity increased there was a statistically significant increase in species richness. Severity level had little variation on percentage of cover by plants. No statistically significant relationship between tree density and fire severity levels was found. These findings underline the need for fuel treatments in southwest Ponderosa Pine forests, and effective cooperation between communities, managers, and ecologists. The Schultz Fire serves as an example in understanding the intricacies of how history affects the present and future of fire management. How fire has been managed and portrayed in the past has left an indelible mark on how fire is presently viewed. Without a clear understanding of the history of fire management and the role of fire in the ecology, future policies towards fire will be unable to account for and manage for the diversity of ecosystems and fires effects on those ecosystems across the United States. Title: The Schultz Fire : an interdisciplinary perspective on its history, management, and ecological effects Author: Ranseen, Susanne N. This thesis examines the Schultz Fire as a case study to explain the complex history of fire suppression management in America’s forests, and to gain further understanding of how management practices have affected the increase in fire severity levels and how forests respond to such a disturbance. The thesis objectives were: (1) to analyze the causes of the fire severity of the Schultz Fire, especially: topography, fuels, or weather; (2); to examine the possible correlation between fire severity and tree density; (3) to investigate whether post-fire species richness was related to fire severity two years after the Schultz Fire; (4) to investigate whether post-fire plant species richness, plant cover, and tree regeneration was related to fire severity two years after the Schultz Fire; and (5) to interlink and convey how these factors relate to the history of fire management and policy and public perception. The history of fire related policy and management has significantly changed the dynamics of America's national parks and forests. Understanding the larger context of this history, both of national fire management and of the effects of language and perception on policy and public reaction, is part of understanding the Schultz Fire as a whole. Based on modeling, high winds combined with the presence of high surface fuel load were the main causes of the Schultz Fire's high fire severity levels. As fire severity increased there was a statistically significant increase in species richness. Severity level had little variation on percentage of cover by plants. No statistically significant relationship between tree density and fire severity levels was found. These findings underline the need for fuel treatments in southwest Ponderosa Pine forests, and effective cooperation between communities, managers, and ecologists. The Schultz Fire serves as an example in understanding the intricacies of how history affects the present and future of fire management. How fire has been managed and portrayed in the past has left an indelible mark on how fire is presently viewed. Without a clear understanding of the history of fire management and the role of fire in the ecology, future policies towards fire will be unable to account for and manage for the diversity of ecosystems and fires effects on those ecosystems across the United States. Close

• 17. [Article] The effects of multiple pathogens on amphibians in the Pacific Northwest

  The earth is undergoing a “biodiversity crisis” characterized by loss of populations, species, genetic diversity, and ecosystem services. Part of this crisis consists of population declines, extinctions, ...

  Citation × Citation Citation Abstract Copy Title: The effects of multiple pathogens on amphibians in the Pacific Northwest Author: Romansic, John M. The earth is undergoing a “biodiversity crisis” characterized by loss of populations, species, genetic diversity, and ecosystem services. Part of this crisis consists of population declines, extinctions, and increased incidence of deformities in amphibians. It is unknown whether deformities contribute to these declines. Many cases of population declines in amphibians are associated with infectious disease. Water molds (Oomycota: Oomycetes: Saprolegniales) (e.g. Achlya and Saprolegnia) may contribute to amphibian population declines whereas parasitic flatworms (Ribeiroia) appear to be major causes of amphibian deformities. I found that Saprolegnia can kill larval and newly-metamorphosed juvenile amphibians. In addition, I investigated synergistic effects of Saprolegnia and the environmental contaminant nitrate on survival of amphibian larvae. No synergisms were found. However, there was a less-than-additive interaction affecting one frog species. Saprolegnia killed Rana aurora (red-legged frog) larvae, but only when nitrate was not added, consistent with nitrate preventing Saprolegnia from killing R. aurora. I also tested for possible interactions among the pathogenic water mold A. flagellata, the pathogenic fungus Batrachochytrium dendrobatidis (BD), and the parasitic trematode Ribeiroia. No between-pathogen interactions were found, however, there were main effects of Ribeiroia and BD. Ribeiroia caused mortality and increased frequency of limb deformities. There were differences in the composition of deformity types between my study and previous work, suggesting that the relative frequencies of different deformity types produced by Ribeiroia may be context-dependent. Also, there was an overall effect of delayed development in Ribeiroia-exposed individuals. In addition, individuals that did not die or display limb deformities following Ribeiroia exposure had slower development than controls not exposed to Ribeiroia. Delayed development may contribute to the effects of Ribeiroia on amphibian populations. In contrast, BD sped up development, although there was no evidence of BD infection. These results are consistent with amphibian larvae responding to the presence of BD by increasing the rate of development. Hastened metamorphosis and dispersal from larval habitats may decrease the risk of BD infection or reduce BD infection load. Mortality of post-embryonic life stages from water molds and sublethal effects of Ribeiroia and BD on amphibian development may influence how these pathogens interact with amphibian populations. Title: The effects of multiple pathogens on amphibians in the Pacific Northwest Author: Romansic, John M. The earth is undergoing a “biodiversity crisis” characterized by loss of populations, species, genetic diversity, and ecosystem services. Part of this crisis consists of population declines, extinctions, and increased incidence of deformities in amphibians. It is unknown whether deformities contribute to these declines. Many cases of population declines in amphibians are associated with infectious disease. Water molds (Oomycota: Oomycetes: Saprolegniales) (e.g. Achlya and Saprolegnia) may contribute to amphibian population declines whereas parasitic flatworms (Ribeiroia) appear to be major causes of amphibian deformities. I found that Saprolegnia can kill larval and newly-metamorphosed juvenile amphibians. In addition, I investigated synergistic effects of Saprolegnia and the environmental contaminant nitrate on survival of amphibian larvae. No synergisms were found. However, there was a less-than-additive interaction affecting one frog species. Saprolegnia killed Rana aurora (red-legged frog) larvae, but only when nitrate was not added, consistent with nitrate preventing Saprolegnia from killing R. aurora. I also tested for possible interactions among the pathogenic water mold A. flagellata, the pathogenic fungus Batrachochytrium dendrobatidis (BD), and the parasitic trematode Ribeiroia. No between-pathogen interactions were found, however, there were main effects of Ribeiroia and BD. Ribeiroia caused mortality and increased frequency of limb deformities. There were differences in the composition of deformity types between my study and previous work, suggesting that the relative frequencies of different deformity types produced by Ribeiroia may be context-dependent. Also, there was an overall effect of delayed development in Ribeiroia-exposed individuals. In addition, individuals that did not die or display limb deformities following Ribeiroia exposure had slower development than controls not exposed to Ribeiroia. Delayed development may contribute to the effects of Ribeiroia on amphibian populations. In contrast, BD sped up development, although there was no evidence of BD infection. These results are consistent with amphibian larvae responding to the presence of BD by increasing the rate of development. Hastened metamorphosis and dispersal from larval habitats may decrease the risk of BD infection or reduce BD infection load. Mortality of post-embryonic life stages from water molds and sublethal effects of Ribeiroia and BD on amphibian development may influence how these pathogens interact with amphibian populations. Close

• 18. [Article] An edaphic study of the Mt. Pisgah Arboretum water garden, Coast Fork of the Willamette River

  Wetlands are widely identified as providing important and fundamental processes valuable for maintaining ecosystem health and diversity. Located in the southern Willamette Valley, the Mt. Pisgah Arboretum ...

  Citation × Citation Citation Abstract Copy Title: An edaphic study of the Mt. Pisgah Arboretum water garden, Coast Fork of the Willamette River Author: Bergen, Cameron Francis Wetlands are widely identified as providing important and fundamental processes valuable for maintaining ecosystem health and diversity. Located in the southern Willamette Valley, the Mt. Pisgah Arboretum contains some valuable remaining wetland habitat along the Coast Fork of the Willamette River. One goal of the Mt. Pisgah Arboretum is "to promote conservation, research, and awareness of ecology". To reach this goal, the Arboretum has identified the importance of maintenance and enhancement activities for onsite native habitats, including riparian and wetland habitats. Before restoration or enhancement activities can begin, it is essential to develop an understanding of current environmental conditions. The purpose of this research was to document both the characteristics and distribution of hydric soils and the hydrology, and to provide insight into the patterns and processes associated with a floodplain wetland. In this study, transect sampling of edaphic features was used to identify the distribution of hydric soils and the hydrologic nature of the Mt. Pisgah Arboretum Water Garden. Soil morphological data for particle size, matrix colors and redox features were evaluated and compared with observations of ground water hydrology, river hydrology and precipitation. Five stratigraphic units were identified underlying the Water Garden. A basalt Bedrock unit underlies the uplands associated with Mt. Pisgah and extends at least part way beneath the floodplain. The Clay unit was formed above the Bedrock unit, with some degree of encroachment onto the floodplain. Below 153 m are floodplain sediments, cobbles at depth, then a sand layer and silty clay loam at the surface. The Cobble unit overlaps the Bedrock unit at its base and is most likely Pleistocene age alluvium. The Sand unit is of Holocene age and is found only in the abandoned thalweg, tapering off laterally in both directions across the ancient channels. Draped above this all and slightly overlapping the upland Bedrock and Clay units, is the SiCL unit. The SiCL unit represents Holocene age alluvium, fine material deposited by slow moving water and overbank deposition. The Water Garden soils reflect this mosaic of parent materials on a complex slope. Water Garden soils sometimes met saturation requirements for hydric soils, but they did not always meet hydric soil indicator requirements. The hydrological data suggest that the soils in depressional areas of the Water Garden occupy a zone where water is exchanged between saturated sediments surrounding the channel of the Coast Fork and the channel itself. The hydrology of depressional areas with both ponded surface water and near surface saturation was principally the result of hyporheic upwelling. The soils in these depressional areas tended to form redox concentrations that met hydric soil indicator criteria. Hillslope soils in concave footslope positions exhibited hydrology indicating two separate zones of saturation, one near surface, the other at depth, related to infiltration and accumulation of precipitation. Few redoximorphic features were observed in hillslope soils, and the one hydric soil indicator that was used at these locations did not require redox. Accurate and detailed delineation of hydric soils on this landscape and clear determination of dominant sources of saturation provided an improved understanding of the complex nature of the Water Garden wetland. Results of this study show that hydric soils occupy both depressional and hillslope positions within the Water Garden. Delineation of a soil as hydric or non hydric was facilitated by the use of hydric soil indicator criteria, morphology and hydrology. This analysis provides the managers of the Mt. Pisgah Arboretum with an accurate representation of where hydric soils currently exist and the respective sources of saturation. With this information, managers are better equipped to develop restoration and enhancement options that better reflect the current environmental conditions in the Water Garden. Title: An edaphic study of the Mt. Pisgah Arboretum water garden, Coast Fork of the Willamette River Author: Bergen, Cameron Francis Wetlands are widely identified as providing important and fundamental processes valuable for maintaining ecosystem health and diversity. Located in the southern Willamette Valley, the Mt. Pisgah Arboretum contains some valuable remaining wetland habitat along the Coast Fork of the Willamette River. One goal of the Mt. Pisgah Arboretum is "to promote conservation, research, and awareness of ecology". To reach this goal, the Arboretum has identified the importance of maintenance and enhancement activities for onsite native habitats, including riparian and wetland habitats. Before restoration or enhancement activities can begin, it is essential to develop an understanding of current environmental conditions. The purpose of this research was to document both the characteristics and distribution of hydric soils and the hydrology, and to provide insight into the patterns and processes associated with a floodplain wetland. In this study, transect sampling of edaphic features was used to identify the distribution of hydric soils and the hydrologic nature of the Mt. Pisgah Arboretum Water Garden. Soil morphological data for particle size, matrix colors and redox features were evaluated and compared with observations of ground water hydrology, river hydrology and precipitation. Five stratigraphic units were identified underlying the Water Garden. A basalt Bedrock unit underlies the uplands associated with Mt. Pisgah and extends at least part way beneath the floodplain. The Clay unit was formed above the Bedrock unit, with some degree of encroachment onto the floodplain. Below 153 m are floodplain sediments, cobbles at depth, then a sand layer and silty clay loam at the surface. The Cobble unit overlaps the Bedrock unit at its base and is most likely Pleistocene age alluvium. The Sand unit is of Holocene age and is found only in the abandoned thalweg, tapering off laterally in both directions across the ancient channels. Draped above this all and slightly overlapping the upland Bedrock and Clay units, is the SiCL unit. The SiCL unit represents Holocene age alluvium, fine material deposited by slow moving water and overbank deposition. The Water Garden soils reflect this mosaic of parent materials on a complex slope. Water Garden soils sometimes met saturation requirements for hydric soils, but they did not always meet hydric soil indicator requirements. The hydrological data suggest that the soils in depressional areas of the Water Garden occupy a zone where water is exchanged between saturated sediments surrounding the channel of the Coast Fork and the channel itself. The hydrology of depressional areas with both ponded surface water and near surface saturation was principally the result of hyporheic upwelling. The soils in these depressional areas tended to form redox concentrations that met hydric soil indicator criteria. Hillslope soils in concave footslope positions exhibited hydrology indicating two separate zones of saturation, one near surface, the other at depth, related to infiltration and accumulation of precipitation. Few redoximorphic features were observed in hillslope soils, and the one hydric soil indicator that was used at these locations did not require redox. Accurate and detailed delineation of hydric soils on this landscape and clear determination of dominant sources of saturation provided an improved understanding of the complex nature of the Water Garden wetland. Results of this study show that hydric soils occupy both depressional and hillslope positions within the Water Garden. Delineation of a soil as hydric or non hydric was facilitated by the use of hydric soil indicator criteria, morphology and hydrology. This analysis provides the managers of the Mt. Pisgah Arboretum with an accurate representation of where hydric soils currently exist and the respective sources of saturation. With this information, managers are better equipped to develop restoration and enhancement options that better reflect the current environmental conditions in the Water Garden. Close

• 19. [Article] What is killing the corals? Viral and bacterial interrogations using metagenomics and microscopy

  Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, ...

  Citation × Citation Citation Abstract Copy Title: What is killing the corals? Viral and bacterial interrogations using metagenomics and microscopy Author: Soffer, Nitzan Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, bacteria, protists, and viruses. Environmental stressors and disease agents can perturb the delicate balance of the coral host and its microbiota, which can lead to disease. This ultimately results in reduced fitness and/or mortality. There are over 30 described coral disease signs, but with a few exceptions, little is known about their potential etiological agents. Without knowledge on the causes of these diseases, little can be done to mitigate future outbreaks. Chapter 1 of this dissertation provides examples for studying novel diseases in difficult to study organisms with the use of metagenomic tools. Armed with these metagenomic tools and electron microscopy, this dissertation aimed to determine potential pathogens in two coral diseases, White Plague disease (WP), and Growth Anomalies (GAs). First, I set to determine whether viruses may be involved in WP disease from a 2010 outbreak in the US Virgin Islands (USVI). In chapter 2, I compared viromes from 21 Montastraea annularis samples (7= Diseased, 7= Diseased=Bleached, 5= Bleached, 2= Healthy) and surrounding seawater (n=2). After comparing the viromes, I found that small circular REP- encoding eukaryotic ssDNA viruses (SCSDv) similar to circo and nano viruses were associated with WP diseased tissue, and thus potential pathogens. Electron microscopy confirmed the presence of viral particles, and absence of bacterial infection in WP diseased tissue. Even though it was likely that viruses are involved with WP it was still important to understand the changes in bacterial community and the roles of bacteriophages during WP coral infection to characterize opportunistic microbes. These questions were addressed in Chapter 3 where I described the bacterial communities and bacteriophage consortia associated with the USVI corals. I also constructed phage-bacteria networks to understand which phages may interact with bacteria of interest (those shown to be differentially abundant in Montastraea annularis of different health states). I determined that there was a range of interaction specificity across the different phages and bacteria. Chapter 4 aimed to elucidate a potential pathogen responsible for Growth Anomalies, a chronic disease resulting in skeletal deformities, loss of symbiotic algae and reduction of fitness in Hawaiin Porites lobata. By comparing microbial and viral metagenomes across health states I was able to determine any changes in composition from healthy and diseased corals. Overall, microbial communities and viral consortia did not vary across health states. The hypothesized Porites spp. symbiont Oceanspirillales was dominant in all libraries. However, relative abundances of taxa in the orders Vibrionales and Verrucomicrobiales were elevated in diseased compared to healthy corals and healthy appearing tissue of GA infected corals. In addition, bacterial functional pathways remained stable across health states, while signatures of virulence factors were elevated in diseased viromes from healthy. Lastly, chapter 5 summarized overall trends of microbes and viruses determined through the studies. In addition, suggestions for future studies were outlined. Overall, this dissertation revealed a potential viral pathogenic group for white plague disease, explored how phages can influence bacterial opportunists in corals of different health states, and determined bacterial orders and virulence factors that are associated with Growth Anomalies. This dissertation includes the first study to find an association between a viral group and coral disease. In addition, this dissertation contains the first (to date) phage-bacterial inferred network constructed from paired phage-bacteria metagenomes. Title: What is killing the corals? Viral and bacterial interrogations using metagenomics and microscopy Author: Soffer, Nitzan Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, bacteria, protists, and viruses. Environmental stressors and disease agents can perturb the delicate balance of the coral host and its microbiota, which can lead to disease. This ultimately results in reduced fitness and/or mortality. There are over 30 described coral disease signs, but with a few exceptions, little is known about their potential etiological agents. Without knowledge on the causes of these diseases, little can be done to mitigate future outbreaks. Chapter 1 of this dissertation provides examples for studying novel diseases in difficult to study organisms with the use of metagenomic tools. Armed with these metagenomic tools and electron microscopy, this dissertation aimed to determine potential pathogens in two coral diseases, White Plague disease (WP), and Growth Anomalies (GAs). First, I set to determine whether viruses may be involved in WP disease from a 2010 outbreak in the US Virgin Islands (USVI). In chapter 2, I compared viromes from 21 Montastraea annularis samples (7= Diseased, 7= Diseased=Bleached, 5= Bleached, 2= Healthy) and surrounding seawater (n=2). After comparing the viromes, I found that small circular REP- encoding eukaryotic ssDNA viruses (SCSDv) similar to circo and nano viruses were associated with WP diseased tissue, and thus potential pathogens. Electron microscopy confirmed the presence of viral particles, and absence of bacterial infection in WP diseased tissue. Even though it was likely that viruses are involved with WP it was still important to understand the changes in bacterial community and the roles of bacteriophages during WP coral infection to characterize opportunistic microbes. These questions were addressed in Chapter 3 where I described the bacterial communities and bacteriophage consortia associated with the USVI corals. I also constructed phage-bacteria networks to understand which phages may interact with bacteria of interest (those shown to be differentially abundant in Montastraea annularis of different health states). I determined that there was a range of interaction specificity across the different phages and bacteria. Chapter 4 aimed to elucidate a potential pathogen responsible for Growth Anomalies, a chronic disease resulting in skeletal deformities, loss of symbiotic algae and reduction of fitness in Hawaiin Porites lobata. By comparing microbial and viral metagenomes across health states I was able to determine any changes in composition from healthy and diseased corals. Overall, microbial communities and viral consortia did not vary across health states. The hypothesized Porites spp. symbiont Oceanspirillales was dominant in all libraries. However, relative abundances of taxa in the orders Vibrionales and Verrucomicrobiales were elevated in diseased compared to healthy corals and healthy appearing tissue of GA infected corals. In addition, bacterial functional pathways remained stable across health states, while signatures of virulence factors were elevated in diseased viromes from healthy. Lastly, chapter 5 summarized overall trends of microbes and viruses determined through the studies. In addition, suggestions for future studies were outlined. Overall, this dissertation revealed a potential viral pathogenic group for white plague disease, explored how phages can influence bacterial opportunists in corals of different health states, and determined bacterial orders and virulence factors that are associated with Growth Anomalies. This dissertation includes the first study to find an association between a viral group and coral disease. In addition, this dissertation contains the first (to date) phage-bacterial inferred network constructed from paired phage-bacteria metagenomes. Close

• 20. [Article] Forest macro-arthropods as potential indicators of ecosystem conditions in Western Idaho : an analysis of community composition, biological diversity, and community structure

  Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new ...

  Citation × Citation Citation Abstract Copy Title: Forest macro-arthropods as potential indicators of ecosystem conditions in Western Idaho : an analysis of community composition, biological diversity, and community structure Author: Ruby, Margaret E. Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new strategies and tools to help them assess their progress in maintaining healthy, productive and biologically diverse forests. Biomonitoring of select forest macro-arthropod species can provide useful information on the effects of management on forest biodiversity and ecosystem function. The purpose of this study was threefold: (1) to inventory the macro-arthropod community and important environmental variables in the Bear Creek and Indian Creek study area within the Payette National Forest (PNF) in Western Idaho; (2) to compare measures of community composition, diversity, and structure in forest macro-arthropod communities between patches of different sizes and treatment; and (3) to assist PNF managers in their ecosystem management efforts by providing principles to guide the use of macro-arthropods as indicators of changing forest conditions. Transects with pitfall traps were used to collect macro-arthropods at 22 sites in the Bear Creek and Indian Creek study area during the summer of 1994. Five forest patch types in Abies grandis habitat types were sampled. Intact forest patches of 100 or more hectares, and large patches of 50-100 hectares, ranged in age between 50 and 250 years old with multistoried structure. Small patches up to 10 hectares were remnants or fragments of formerly intact forest isolated by logging. A plantation patch was 15 years old with patchy understory and forb cover. Clearcut patches had little or no overstory, and variable understory, and forb layers. At each transect, soil samples were collected and six environmental descriptor variables were analyzed according to patch treatment and patch size. These site descriptors were: basal area (ft²/acre); percent canopy cover for the overstory, understory; and forb layers; litter depth (cm), and percent soil moisture content. Differences detected using an ANOVA and T-tests are discussed in the Results section. Arthropod community composition, diversity, and structure were described according to relative abundance, and four measures of diversity. They were also described by membership in seventeen orders and/or super-families; ten functional groups; two disperser classes (long or short distance); and three species indicator classes. A total of 5455 macro-arthropod individuals, representing 17 orders and/or super-families and 219 species were collected in the Bear Creek and Indian Creek study area. While macro-arthropod fauna relative abundance did not vary significantly by treatment (ANOVA p<0.3), it did vary significantly by patch size (ANOVA p<0.03). Fauna relative abundance was 35% greater in clearcut patches than in large patches (T-test p<0.09). Fauna relative abundance in small patches was twice that of intact (T-test p<0.03) and large (T-test p<0.02) patches. Taxonomic diversity (number of genera/taxa) of beetle, ant, and bug taxa differed significantly according to treatment type(each ANOVA p<0.05). For the top four taxa (beetles, ants, spiders, and bugs), taxonomic diversity was highest in the plantation and clearcut patches. Ants and bugs had their highest taxonomic diversity in the plantation patch (separate T-tests p<0.05) while the taxonomic diversity of beetles was highest in clear-cut patches (T-test p<0.05). Beetle and ant taxonomic diversity varied significantly by patch size (each ANOVA p<0.05). For beetles and bugs, small patches were twice as diverse as intact patches (separate T-tests p<0.04) and 1.5 times that of large patches. Ant diversity was similarly distributed amongst the patch sizes, with significant differences between small and intact and between small and large patches (separate T-tests p<0.05). Of the four species diversity measures employed, only two, [alpha] and JK1 (both measures of richness), were found to vary significantly by patch treatment and size. Evenness (E) and the Shannon Diversity Index (H') failed to detect differences in the majority of tests. Fauna [alpha] and JK1 differed significantly by treatment type (each ANOVA p<0.05). Richness in clearcut patches was nearly twice in intact and large patches, followed by plantation and large patches. Fauna [alpha] and JKl also differed significantly by patch size (each ANOVA p <0.001), with small patch fauna twice as rich as that in large and intact patches (separate T-tests p <0.01). Of the top four functional groups, predators were the most abundant and had the highest taxonomic diversity (number of genera/functional group), followed by herbivores, fungivores and parasites. Predators and herbivores showed increasing taxonomic diversity with decreasing patch size, from intact to large to small (ANOVA p< 0.05). Similarly, predators and herbivores exhibited increasing taxonomic diversity with increasing levels of management: from intact and large to plantation and clear-cuts (ANOVA p< 0.05). Predators and herbivores were most numerous in the managed and small patches. Fungivore taxonomic diversity was also highest in the small and managed patches, though neither patch size nor treatment differences were significant (ANOVA p<0.85). Parasite taxonomic diversity differed by patch size with highest generic diversity in the small patches (ANOVA p<0.l) and by treatment type with generic diversity highest in plantations and clearcuts followed in order by large and intact patches (ANOVA p<0.l). Twice as many genera were long distance dispersers as were short distance dispersers. Relative abundance of long distance dispersers varied significantly by patch treatment and patch size (each ANOVA p<0.0l). Long distance dispersers were most numerous in clear-cut patches, followed in order by plantation, small, large, and intact patches. Relative abundance of short distance dispersers was not significantly different between treatment types (ANOVA p<0.20) but was significantly different between patch sizes (ANOVA p<0.0l). Short distance dispersers were most numerous in small patches followed by plantation, large, and intact and least numerous in clearcut patches. An indicator species analysis of 121 Bear Creek and Indian Creek genera (Dufrene and Legendre 1997), revealed sub-groups of species with 75 to 100 percent "perfect indication" or affiliation for specific patch types. When intact and large patches were pooled and analyzed against all treated patches (plantation and clearcut patches), a list of 36 genera with 75 to 100 percent "perfect affiliation" for intact or large patches was produced (MRPP p<0.05). Small patches had 42 indicators with 75 to 100 percent "perfect indication" when compared with the pooled intact and large patches (MRPP p<0.l). Conclusions Macro-arthropod community composition, diversity and structure did vary, usually significantly, by patch treatment and size. Useful measures of generic diversity include richness estimators [alpha], [beta], and JK1. Examination of taxonomic diversity was also useful, especially for the more mobile arthropods. Pitfall traps provided copious data on the structure of the community in regards to predators and herbivores. Pitfalls, however, did not provide much information about the status of fungivores and parasites in the various different patches. Another trapping method such as the berlaise funnel, would likely provide more information about those functional groups which are likely operating at a finer scale of resolution than that tested by the pitfall trap. Employing both methods would provide a much better assessment of the community of arthropods living on the forest floor. The indicator species analysis program also provided very useful lists of species which are affiliated with particular patch conditions. Taken together, these measures could be adopted for use by forest managers to allow them to assess and monitor the effects of a management regime on the structure and composition of macro-arthropod communities as part of a comprehensive adaptive management plan. Title: Forest macro-arthropods as potential indicators of ecosystem conditions in Western Idaho : an analysis of community composition, biological diversity, and community structure Author: Ruby, Margaret E. Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new strategies and tools to help them assess their progress in maintaining healthy, productive and biologically diverse forests. Biomonitoring of select forest macro-arthropod species can provide useful information on the effects of management on forest biodiversity and ecosystem function. The purpose of this study was threefold: (1) to inventory the macro-arthropod community and important environmental variables in the Bear Creek and Indian Creek study area within the Payette National Forest (PNF) in Western Idaho; (2) to compare measures of community composition, diversity, and structure in forest macro-arthropod communities between patches of different sizes and treatment; and (3) to assist PNF managers in their ecosystem management efforts by providing principles to guide the use of macro-arthropods as indicators of changing forest conditions. Transects with pitfall traps were used to collect macro-arthropods at 22 sites in the Bear Creek and Indian Creek study area during the summer of 1994. Five forest patch types in Abies grandis habitat types were sampled. Intact forest patches of 100 or more hectares, and large patches of 50-100 hectares, ranged in age between 50 and 250 years old with multistoried structure. Small patches up to 10 hectares were remnants or fragments of formerly intact forest isolated by logging. A plantation patch was 15 years old with patchy understory and forb cover. Clearcut patches had little or no overstory, and variable understory, and forb layers. At each transect, soil samples were collected and six environmental descriptor variables were analyzed according to patch treatment and patch size. These site descriptors were: basal area (ft²/acre); percent canopy cover for the overstory, understory; and forb layers; litter depth (cm), and percent soil moisture content. Differences detected using an ANOVA and T-tests are discussed in the Results section. Arthropod community composition, diversity, and structure were described according to relative abundance, and four measures of diversity. They were also described by membership in seventeen orders and/or super-families; ten functional groups; two disperser classes (long or short distance); and three species indicator classes. A total of 5455 macro-arthropod individuals, representing 17 orders and/or super-families and 219 species were collected in the Bear Creek and Indian Creek study area. While macro-arthropod fauna relative abundance did not vary significantly by treatment (ANOVA p<0.3), it did vary significantly by patch size (ANOVA p<0.03). Fauna relative abundance was 35% greater in clearcut patches than in large patches (T-test p<0.09). Fauna relative abundance in small patches was twice that of intact (T-test p<0.03) and large (T-test p<0.02) patches. Taxonomic diversity (number of genera/taxa) of beetle, ant, and bug taxa differed significantly according to treatment type(each ANOVA p<0.05). For the top four taxa (beetles, ants, spiders, and bugs), taxonomic diversity was highest in the plantation and clearcut patches. Ants and bugs had their highest taxonomic diversity in the plantation patch (separate T-tests p<0.05) while the taxonomic diversity of beetles was highest in clear-cut patches (T-test p<0.05). Beetle and ant taxonomic diversity varied significantly by patch size (each ANOVA p<0.05). For beetles and bugs, small patches were twice as diverse as intact patches (separate T-tests p<0.04) and 1.5 times that of large patches. Ant diversity was similarly distributed amongst the patch sizes, with significant differences between small and intact and between small and large patches (separate T-tests p<0.05). Of the four species diversity measures employed, only two, [alpha] and JK1 (both measures of richness), were found to vary significantly by patch treatment and size. Evenness (E) and the Shannon Diversity Index (H') failed to detect differences in the majority of tests. Fauna [alpha] and JK1 differed significantly by treatment type (each ANOVA p<0.05). Richness in clearcut patches was nearly twice in intact and large patches, followed by plantation and large patches. Fauna [alpha] and JKl also differed significantly by patch size (each ANOVA p <0.001), with small patch fauna twice as rich as that in large and intact patches (separate T-tests p <0.01). Of the top four functional groups, predators were the most abundant and had the highest taxonomic diversity (number of genera/functional group), followed by herbivores, fungivores and parasites. Predators and herbivores showed increasing taxonomic diversity with decreasing patch size, from intact to large to small (ANOVA p< 0.05). Similarly, predators and herbivores exhibited increasing taxonomic diversity with increasing levels of management: from intact and large to plantation and clear-cuts (ANOVA p< 0.05). Predators and herbivores were most numerous in the managed and small patches. Fungivore taxonomic diversity was also highest in the small and managed patches, though neither patch size nor treatment differences were significant (ANOVA p<0.85). Parasite taxonomic diversity differed by patch size with highest generic diversity in the small patches (ANOVA p<0.l) and by treatment type with generic diversity highest in plantations and clearcuts followed in order by large and intact patches (ANOVA p<0.l). Twice as many genera were long distance dispersers as were short distance dispersers. Relative abundance of long distance dispersers varied significantly by patch treatment and patch size (each ANOVA p<0.0l). Long distance dispersers were most numerous in clear-cut patches, followed in order by plantation, small, large, and intact patches. Relative abundance of short distance dispersers was not significantly different between treatment types (ANOVA p<0.20) but was significantly different between patch sizes (ANOVA p<0.0l). Short distance dispersers were most numerous in small patches followed by plantation, large, and intact and least numerous in clearcut patches. An indicator species analysis of 121 Bear Creek and Indian Creek genera (Dufrene and Legendre 1997), revealed sub-groups of species with 75 to 100 percent "perfect indication" or affiliation for specific patch types. When intact and large patches were pooled and analyzed against all treated patches (plantation and clearcut patches), a list of 36 genera with 75 to 100 percent "perfect affiliation" for intact or large patches was produced (MRPP p<0.05). Small patches had 42 indicators with 75 to 100 percent "perfect indication" when compared with the pooled intact and large patches (MRPP p<0.l). Conclusions Macro-arthropod community composition, diversity and structure did vary, usually significantly, by patch treatment and size. Useful measures of generic diversity include richness estimators [alpha], [beta], and JK1. Examination of taxonomic diversity was also useful, especially for the more mobile arthropods. Pitfall traps provided copious data on the structure of the community in regards to predators and herbivores. Pitfalls, however, did not provide much information about the status of fungivores and parasites in the various different patches. Another trapping method such as the berlaise funnel, would likely provide more information about those functional groups which are likely operating at a finer scale of resolution than that tested by the pitfall trap. Employing both methods would provide a much better assessment of the community of arthropods living on the forest floor. The indicator species analysis program also provided very useful lists of species which are affiliated with particular patch conditions. Taken together, these measures could be adopted for use by forest managers to allow them to assess and monitor the effects of a management regime on the structure and composition of macro-arthropod communities as part of a comprehensive adaptive management plan. Close

• 21. [Article] Ecological effects of post-wildfire management activities (salvage-logging and grass-seeding) on vegetation composition, diversity, biomass, and growth and survival of Pinus ponderosa and Purshia tridentata

  Salvage-logging and artificial seeding of grass following wildfire are common practices in coniferous forests of the western United States, yet few studies have quantified the ecological effects of these ...

  Citation × Citation Citation Abstract Copy Title: Ecological effects of post-wildfire management activities (salvage-logging and grass-seeding) on vegetation composition, diversity, biomass, and growth and survival of Pinus ponderosa and Purshia tridentata Author: Sexton, Timothy Ogden Salvage-logging and artificial seeding of grass following wildfire are common practices in coniferous forests of the western United States, yet few studies have quantified the ecological effects of these post-fire activities. The effects of post-wildfire salvage-logging and grass-seeding on vegetation composition, aboveground biomass, and growth and survival of Pinus ponderosa and Purshia tridentata were quantified on the area burned by the 1992 Lone Pine Fire, Winema National Forest in the Klamath Basin, Oregon. Prior to the fire, the area was dominated by uneven-aged stands of Pinus ponderosa with Purshia tridentata and Stipa occidentalis in the understory. The fire was a stand-replacement disturbance, where the majority of trees, the herbaceous component, and crowns of understory shrubs were killed. Salvage logging resulted in a significant decrease in understory biomass, species richness, species diversity, and growth and survival of P. ponderosa and P. tridentata. In addition plant community composition was shifted from native forb dominance to grass dominance. In 1993, the understory biomass of salvage-logged sites was 38% of the aboveground biomass produced on nonsalvaged sites (322 kg ha^-1 vs 843 kg ha^-1). In 1994, salvage-logged sites produced only 27% of the biomass produced on nonsalvaged sites (402 kg ha^-1 vs 1468 kg ha^-1). Salvage-logging reduced species richness, species diversity, and altered species composition. The first and second years following logging, species richness was reduced by 13% (20 versus 23), and 30% (15 versus 22), respectively. In 1993 and 1994, native forb frequency on nonsalvaged sites was 80% and 77% respectively, while salvage-logged sites recorded 68% and 31% respectively. Conversely, graminoid frequency was significantly higher on salvage-logged sites. In 1994, native graminoid frequency was 35% in nonsalvaged sites and > 61% on salvage-logged sites. During the first two years following salvage-logging, mean height growth of naturally-regenerated Pinus ponderosa was significantly lower on salvaged sites (9.4 versus 7.8 cm yr^-1) as was density of natural Purshia tridentata seedlings (313 versus 530 seedlings ha^-1). Survival in salvage-logged treatments was 22% lower for planted Purshia tridentata seedlings (57% versus 45%). Height growth in salvage-logged treatments was 16% lower for planted Pinus ponderosa (4.4 versus 3.7 cm). Total aboveground biomass on nonsalvaged burned sites (controls) averaged 843 kg ha^-1 in 1993, and 1473 kg ha^-1 in 1994. In 1993, the first year following the fire, sites seeded to Secale cereale produced = 1995 kg ha^-1 total aboveground biomass; most of the biomass was S. cereale. Those seeded sites produced 89% less native forb biomass than controls (82 versus 780 kg ha^-1), and = 80% less native forb biomass than areas seeded to the native grasses Sitanion hystrix and Festuca idahoensis. In 1994, the second post-fire year, biomass on sites seeded to S. cereale was >1653 kg ha^-1, dominated by S. cereale. In 1994, no differences in total aboveground biomass were detected between S. cereale, F idahoensis, S. hystrix, and the Control, indicating that the erosion reducing benefits of grass-seeding did not last for more than one year. Treatments seeded with S. cereale produced 58% less native forb biomass than controls (350 versus 825 kg ha^-1). Seeding S. cereale also reduced by 69% the biomass ofStipa occidentalis, the most common native grass in the area (311 kg ha^-1 on control sites versus 96 kg ha^-1 on S. cereale sites). In 1993 and 1994, fewer species were recorded on S. cereale sites than on all other sites. Grass-seeded sites exhibited no significant differences in frequency of noxious weeds in either of the two years following wildfire and seeding, rejecting the hypothesis that grass-seeding reduces noxious weeds. However, native graminoid frequency was reduced on all grass-seeded treatments. There were no significant differences between grass-seeding treatments in height and density of natural P. ponderosa and P. tridentata seedlings or growth and survival of planted P. ponderosa and P. tridentata seedlings. While salvage-logging provides an economic benefit to local communities through the extraction of commercially valuable timber, there is an ecological cost. Reduction in ecosystem structure, production, species richness, diversity and alterations in species composition are important ecological consequences of salvage logging. In addition, this study demonstrates that salvage-logging retards the re-establishment and early growth of Pinus ponderosa and Purshia tridentata, two important wildfire restoration priorities. Grass-seeding also results in significant ecological changes. Alterations in ecosystem production, species richness, diversity and species composition are important ecological consequences of grass-seeding. Managers should consider these long-term influences on ecosystem composition and structure when faced with decisions concerning post-fire rehabilitation and management. Title: Ecological effects of post-wildfire management activities (salvage-logging and grass-seeding) on vegetation composition, diversity, biomass, and growth and survival of Pinus ponderosa and Purshia tridentata Author: Sexton, Timothy Ogden Salvage-logging and artificial seeding of grass following wildfire are common practices in coniferous forests of the western United States, yet few studies have quantified the ecological effects of these post-fire activities. The effects of post-wildfire salvage-logging and grass-seeding on vegetation composition, aboveground biomass, and growth and survival of Pinus ponderosa and Purshia tridentata were quantified on the area burned by the 1992 Lone Pine Fire, Winema National Forest in the Klamath Basin, Oregon. Prior to the fire, the area was dominated by uneven-aged stands of Pinus ponderosa with Purshia tridentata and Stipa occidentalis in the understory. The fire was a stand-replacement disturbance, where the majority of trees, the herbaceous component, and crowns of understory shrubs were killed. Salvage logging resulted in a significant decrease in understory biomass, species richness, species diversity, and growth and survival of P. ponderosa and P. tridentata. In addition plant community composition was shifted from native forb dominance to grass dominance. In 1993, the understory biomass of salvage-logged sites was 38% of the aboveground biomass produced on nonsalvaged sites (322 kg ha^-1 vs 843 kg ha^-1). In 1994, salvage-logged sites produced only 27% of the biomass produced on nonsalvaged sites (402 kg ha^-1 vs 1468 kg ha^-1). Salvage-logging reduced species richness, species diversity, and altered species composition. The first and second years following logging, species richness was reduced by 13% (20 versus 23), and 30% (15 versus 22), respectively. In 1993 and 1994, native forb frequency on nonsalvaged sites was 80% and 77% respectively, while salvage-logged sites recorded 68% and 31% respectively. Conversely, graminoid frequency was significantly higher on salvage-logged sites. In 1994, native graminoid frequency was 35% in nonsalvaged sites and > 61% on salvage-logged sites. During the first two years following salvage-logging, mean height growth of naturally-regenerated Pinus ponderosa was significantly lower on salvaged sites (9.4 versus 7.8 cm yr^-1) as was density of natural Purshia tridentata seedlings (313 versus 530 seedlings ha^-1). Survival in salvage-logged treatments was 22% lower for planted Purshia tridentata seedlings (57% versus 45%). Height growth in salvage-logged treatments was 16% lower for planted Pinus ponderosa (4.4 versus 3.7 cm). Total aboveground biomass on nonsalvaged burned sites (controls) averaged 843 kg ha^-1 in 1993, and 1473 kg ha^-1 in 1994. In 1993, the first year following the fire, sites seeded to Secale cereale produced = 1995 kg ha^-1 total aboveground biomass; most of the biomass was S. cereale. Those seeded sites produced 89% less native forb biomass than controls (82 versus 780 kg ha^-1), and = 80% less native forb biomass than areas seeded to the native grasses Sitanion hystrix and Festuca idahoensis. In 1994, the second post-fire year, biomass on sites seeded to S. cereale was >1653 kg ha^-1, dominated by S. cereale. In 1994, no differences in total aboveground biomass were detected between S. cereale, F idahoensis, S. hystrix, and the Control, indicating that the erosion reducing benefits of grass-seeding did not last for more than one year. Treatments seeded with S. cereale produced 58% less native forb biomass than controls (350 versus 825 kg ha^-1). Seeding S. cereale also reduced by 69% the biomass ofStipa occidentalis, the most common native grass in the area (311 kg ha^-1 on control sites versus 96 kg ha^-1 on S. cereale sites). In 1993 and 1994, fewer species were recorded on S. cereale sites than on all other sites. Grass-seeded sites exhibited no significant differences in frequency of noxious weeds in either of the two years following wildfire and seeding, rejecting the hypothesis that grass-seeding reduces noxious weeds. However, native graminoid frequency was reduced on all grass-seeded treatments. There were no significant differences between grass-seeding treatments in height and density of natural P. ponderosa and P. tridentata seedlings or growth and survival of planted P. ponderosa and P. tridentata seedlings. While salvage-logging provides an economic benefit to local communities through the extraction of commercially valuable timber, there is an ecological cost. Reduction in ecosystem structure, production, species richness, diversity and alterations in species composition are important ecological consequences of salvage logging. In addition, this study demonstrates that salvage-logging retards the re-establishment and early growth of Pinus ponderosa and Purshia tridentata, two important wildfire restoration priorities. Grass-seeding also results in significant ecological changes. Alterations in ecosystem production, species richness, diversity and species composition are important ecological consequences of grass-seeding. Managers should consider these long-term influences on ecosystem composition and structure when faced with decisions concerning post-fire rehabilitation and management. Close

• 22. [Article] Predictability and Constraints on the Structure of Ecological Communities in the Context of Climate Change

  Ecologists must increasingly balance the need for accurate predictions about how ecosystems will be affected by climate change, against the fact that making such predictions at the ecosystem-level may ...

  Citation × Citation Citation Abstract Copy Title: Predictability and Constraints on the Structure of Ecological Communities in the Context of Climate Change Author: Barner, Allison K. Ecologists must increasingly balance the need for accurate predictions about how ecosystems will be affected by climate change, against the fact that making such predictions at the ecosystem-level may be infeasible. Although information about responses of individual species to a changing environment is increasing, scaling such information to the community level is challenging. To date, predicting responses of ecological communities to climate change is constrained by limited theoretical and empirical knowledge about the response of communities and ecosystems to change. My dissertation addresses several knowledge gaps in our understanding of community structure under climate change. This research draws from a rich experimental tradition in the species-diverse model ecosystem of the US Pacific Northwest rocky intertidal to test ecological theory. In Chapter 2, I assessed whether the response of multiple species of coralline algae to global change could be predicted from basic first principles of chemistry, physiology, and ecology. Given the rate of global change, and the time-consuming process of experimentally determining species responses to climate change, I hypothesized that species can be grouped using existing theory, either by their evolutionary relatedness or by their ecological traits, such that climate responses are similar within a group. Such a scheme would greatly reduce the number of experiments needed to characterize species climate vulnerability, requiring the characterization of the response of groups of species to climate change, rather than individual species. Using a suite of five co-occurring species of intertidal articulated coralline algae (Corallina vancouveriensis, Corallina officinalis, Bossiella plumosa, Bossiella orbiginiana, and Calliarthron tuberculosum), I applied this framework to generate ten mutually exclusive hypotheses that could explain organismal response to ocean acidification, a consequence of global climate change that threatens marine calcifying species. I found that all species had similar responses to ocean acidification, and that responses were generally predicted by the body size of the individual. Despite the power that such a framework provides in understanding group-level response to climate change, predicting community-level response requires knowledge of how organisms affect one another. In Chapter 3, I quantified species interactions in a series of removal experiments to estimate the reciprocal effects between a canopy-forming intertidal kelp (Saccharina sessilis) and a suite of understory species that persist beneath the kelp canopy. This experiment was replicated in different oceanographic conditions across a large latitudinal gradient, as a step towards understanding how interactions might change with climate change. However, the experiment demonstrated that interactions between the canopy and understory were consistent among different environmental conditions. Furthermore, the strongest effect was that of understory species, particularly articulated coralline turf algae, on the canopy species. The coralline turf algae both facilitated the recruitment of the canopy species and buffered the canopy from abiotic stress during its adult life stage. Combining experimental results and observational surveys, a hypothesized interaction network for these species was constructed, highlighting the importance of direct and indirect species interactions in promoting species coexistence. A long-standing controversy in ecology is whether or not species interactions can be inferred from observational data, as opposed to from experimental tests. Although the rocky intertidal ecosystem is unique for its ease of experimental manipulation, quantifying species interactions experimentally is often difficult or impossible. As an alternative, many have turned to statistical methods to estimate species interactions from observational data, namely, from patterns in species pairwise co-occurrences. In Chapter 4, I examined these co-occurrence methods and their potential relationship to experimentally measured species interactions. I first used a suite of different co-occurrence methods to generate a set of predicted species interactions of macrophytes and invertebrates from observational surveys conducted in the rocky intertidal zone of Oregon. I then compared the predicted species interactions to the same pairwise species interactions determined experimentally and assembled from the literature. Overall, of the seven methods tested, each generated a different set of predicted species interactions from the same data, and all methods predicted interactions that did not match those in the experimental database. Thus, predicting species interactions from patterns in occurrence remains elusive. Importantly, much work remains to be done to understand the link between species co-occurrences and their actual interactions with one another on the landscape. A key limiting frontier in climate change ecology is determining the influence of species interactions on species distributions across the landscape, and the sensitivity of such interactions to changes in climate. Finally, in Chapter 5, I used theory from the published literature and knowledge from my previous chapters to make predictions the recovery of low rocky intertidal communities after a disturbance. The process of community development after disturbance has been studied in many ways, from the successional studies of the early 1900s, to modern community assembly theory. In recent years, a focus on the unpredictability of community assembly has emerged, paying particular attention to the role of historical contingency, or priority effects, in determining the recovery trajectory of a community. Priority effects occur when the arrival of a species after a disturbance inalterably changes the composition of the developing community, driving the assembly of widely different communities at a small spatial scale. I conducted a community assembly experiment in three different low intertidal zone community "types", each characterized by different dominant macrophyte species (Saccharina sessilis, Phyllospadix spp., and algal "turfs"). Replicating this experiment at six sites along the Oregon coast, I found that both regional and local dynamics constrain the recovery of communities after disturbance. Half of the time, the community returned to the state of the nearby community type. The remaining communities were influenced by priority effects that could be predicted based on 1) regional dynamics favoring some species over others, or 2) the timing of arrival of important facilitating species. Overall, understanding the dynamic relationship between the persistence of diverse communities and a changing environment remains one of the challenges of our time. My dissertation highlights some of the challenges in predicting the future composition of communities under climate change, but also provides some ways forward. Integration of experimental, theoretical, and observational studies builds the scaffolding of prediction, whereby understanding the constraints on species physiology, the interactions among species, and community assembly can help frame the context in which predictions are made. Title: Predictability and Constraints on the Structure of Ecological Communities in the Context of Climate Change Author: Barner, Allison K. Ecologists must increasingly balance the need for accurate predictions about how ecosystems will be affected by climate change, against the fact that making such predictions at the ecosystem-level may be infeasible. Although information about responses of individual species to a changing environment is increasing, scaling such information to the community level is challenging. To date, predicting responses of ecological communities to climate change is constrained by limited theoretical and empirical knowledge about the response of communities and ecosystems to change. My dissertation addresses several knowledge gaps in our understanding of community structure under climate change. This research draws from a rich experimental tradition in the species-diverse model ecosystem of the US Pacific Northwest rocky intertidal to test ecological theory. In Chapter 2, I assessed whether the response of multiple species of coralline algae to global change could be predicted from basic first principles of chemistry, physiology, and ecology. Given the rate of global change, and the time-consuming process of experimentally determining species responses to climate change, I hypothesized that species can be grouped using existing theory, either by their evolutionary relatedness or by their ecological traits, such that climate responses are similar within a group. Such a scheme would greatly reduce the number of experiments needed to characterize species climate vulnerability, requiring the characterization of the response of groups of species to climate change, rather than individual species. Using a suite of five co-occurring species of intertidal articulated coralline algae (Corallina vancouveriensis, Corallina officinalis, Bossiella plumosa, Bossiella orbiginiana, and Calliarthron tuberculosum), I applied this framework to generate ten mutually exclusive hypotheses that could explain organismal response to ocean acidification, a consequence of global climate change that threatens marine calcifying species. I found that all species had similar responses to ocean acidification, and that responses were generally predicted by the body size of the individual. Despite the power that such a framework provides in understanding group-level response to climate change, predicting community-level response requires knowledge of how organisms affect one another. In Chapter 3, I quantified species interactions in a series of removal experiments to estimate the reciprocal effects between a canopy-forming intertidal kelp (Saccharina sessilis) and a suite of understory species that persist beneath the kelp canopy. This experiment was replicated in different oceanographic conditions across a large latitudinal gradient, as a step towards understanding how interactions might change with climate change. However, the experiment demonstrated that interactions between the canopy and understory were consistent among different environmental conditions. Furthermore, the strongest effect was that of understory species, particularly articulated coralline turf algae, on the canopy species. The coralline turf algae both facilitated the recruitment of the canopy species and buffered the canopy from abiotic stress during its adult life stage. Combining experimental results and observational surveys, a hypothesized interaction network for these species was constructed, highlighting the importance of direct and indirect species interactions in promoting species coexistence. A long-standing controversy in ecology is whether or not species interactions can be inferred from observational data, as opposed to from experimental tests. Although the rocky intertidal ecosystem is unique for its ease of experimental manipulation, quantifying species interactions experimentally is often difficult or impossible. As an alternative, many have turned to statistical methods to estimate species interactions from observational data, namely, from patterns in species pairwise co-occurrences. In Chapter 4, I examined these co-occurrence methods and their potential relationship to experimentally measured species interactions. I first used a suite of different co-occurrence methods to generate a set of predicted species interactions of macrophytes and invertebrates from observational surveys conducted in the rocky intertidal zone of Oregon. I then compared the predicted species interactions to the same pairwise species interactions determined experimentally and assembled from the literature. Overall, of the seven methods tested, each generated a different set of predicted species interactions from the same data, and all methods predicted interactions that did not match those in the experimental database. Thus, predicting species interactions from patterns in occurrence remains elusive. Importantly, much work remains to be done to understand the link between species co-occurrences and their actual interactions with one another on the landscape. A key limiting frontier in climate change ecology is determining the influence of species interactions on species distributions across the landscape, and the sensitivity of such interactions to changes in climate. Finally, in Chapter 5, I used theory from the published literature and knowledge from my previous chapters to make predictions the recovery of low rocky intertidal communities after a disturbance. The process of community development after disturbance has been studied in many ways, from the successional studies of the early 1900s, to modern community assembly theory. In recent years, a focus on the unpredictability of community assembly has emerged, paying particular attention to the role of historical contingency, or priority effects, in determining the recovery trajectory of a community. Priority effects occur when the arrival of a species after a disturbance inalterably changes the composition of the developing community, driving the assembly of widely different communities at a small spatial scale. I conducted a community assembly experiment in three different low intertidal zone community "types", each characterized by different dominant macrophyte species (Saccharina sessilis, Phyllospadix spp., and algal "turfs"). Replicating this experiment at six sites along the Oregon coast, I found that both regional and local dynamics constrain the recovery of communities after disturbance. Half of the time, the community returned to the state of the nearby community type. The remaining communities were influenced by priority effects that could be predicted based on 1) regional dynamics favoring some species over others, or 2) the timing of arrival of important facilitating species. Overall, understanding the dynamic relationship between the persistence of diverse communities and a changing environment remains one of the challenges of our time. My dissertation highlights some of the challenges in predicting the future composition of communities under climate change, but also provides some ways forward. Integration of experimental, theoretical, and observational studies builds the scaffolding of prediction, whereby understanding the constraints on species physiology, the interactions among species, and community assembly can help frame the context in which predictions are made. Close

• 23. [Article] The ecological consequences of the reduction of species diversity : experimental approaches

  The influence of loss of diversity on community dynamics and ecosystem functioning has recently received considerable attention. Although study of biodiversity has a long history within ecology, empirical ...

  Citation × Citation Citation Abstract Copy Title: The ecological consequences of the reduction of species diversity : experimental approaches Author: Allison, Gary William The influence of loss of diversity on community dynamics and ecosystem functioning has recently received considerable attention. Although study of biodiversity has a long history within ecology, empirical investigations exploring consequences of loss have been rare. Because many factors confound diversity comparisons, experimental manipulations of diversity offer the most direct way of attributing cause to diversity loss. The effects of reduction in number of species will depend on the strength and sign of species interactions affected by loss of diversity. An experiment performed on a high zone, rocky intertidal community in which macroalgal diversity was manipulated demonstrated that effects of diversity loss will be highly dependent on which species are removed. However, effects of diversity reductions were strongest at the harsh end of a stress gradient where interactions were more positive. Thus, factors that affect the strength and sign of species interactions such as the degree of physical stress may serve as a rough guide to where the effects of diversity loss will be most severe. An assessment of the influence of diversity on community response to a strong physical perturbation was performed using an experimentally-induced thermal stress. Higher diversity treatments were most strongly affected directly by the stress because such treatments had higher abundance and therefore more biomass to lose. However, those same treatments recovered more quickly from the stress. Community recovery of initially low diversity treatments was slowed by persistence of non-typical states or slow recovery of dominant species. A simulation study was performed to assess the ability of different experimental designs to detect biodiversity effects. Our ability to predict consequences of changes in diversity will be dependent on our ability to distinguish the most influential biodiversity "components" within a system. This study uncovered a phenomenon that will be common in biodiversity studies: misidentification of one biodiversity component (e. g., an effect of a keystone species) as a different component (e. g., an effect of the number of species). I call this phenomenon "aliasing." Because of the complexity of biodiversity, experiments and observational studies will be highly susceptible to aliasing and, thus, results will require careful interpretation. Title: The ecological consequences of the reduction of species diversity : experimental approaches Author: Allison, Gary William The influence of loss of diversity on community dynamics and ecosystem functioning has recently received considerable attention. Although study of biodiversity has a long history within ecology, empirical investigations exploring consequences of loss have been rare. Because many factors confound diversity comparisons, experimental manipulations of diversity offer the most direct way of attributing cause to diversity loss. The effects of reduction in number of species will depend on the strength and sign of species interactions affected by loss of diversity. An experiment performed on a high zone, rocky intertidal community in which macroalgal diversity was manipulated demonstrated that effects of diversity loss will be highly dependent on which species are removed. However, effects of diversity reductions were strongest at the harsh end of a stress gradient where interactions were more positive. Thus, factors that affect the strength and sign of species interactions such as the degree of physical stress may serve as a rough guide to where the effects of diversity loss will be most severe. An assessment of the influence of diversity on community response to a strong physical perturbation was performed using an experimentally-induced thermal stress. Higher diversity treatments were most strongly affected directly by the stress because such treatments had higher abundance and therefore more biomass to lose. However, those same treatments recovered more quickly from the stress. Community recovery of initially low diversity treatments was slowed by persistence of non-typical states or slow recovery of dominant species. A simulation study was performed to assess the ability of different experimental designs to detect biodiversity effects. Our ability to predict consequences of changes in diversity will be dependent on our ability to distinguish the most influential biodiversity "components" within a system. This study uncovered a phenomenon that will be common in biodiversity studies: misidentification of one biodiversity component (e. g., an effect of a keystone species) as a different component (e. g., an effect of the number of species). I call this phenomenon "aliasing." Because of the complexity of biodiversity, experiments and observational studies will be highly susceptible to aliasing and, thus, results will require careful interpretation. Close

• 24. [Article] Fishermen, Markets, and Population Diversity

  Fishing impacts biodiversity on multiple levels, potentially resulting in unintended feedbacks to economic performance of the fishery over time. For example, targeting observable traits within a population ...

  Citation × Citation Citation Abstract Copy Title: Fishermen, Markets, and Population Diversity Author: Sanchirico, James N., Jardine, Sunny Fishing impacts biodiversity on multiple levels, potentially resulting in unintended feedbacks to economic performance of the fishery over time. For example, targeting observable traits within a population can impact genetic diversity, targeting populations within a species can impact population diversity, and targeting valuable species can impact biodiversity at the ecosystem level. The natural science and economics literatures, however, have given little attention to the impact of fishing on population diversity, even though population diversity is directly linked ecosystem services and estimates of population extinction rates are three orders of magnitude higher than species extinction rates. Here we develop a stochastic bioeconomic model that links the harvest of multiple salmon populations by a single commercial fishery to the trajectory of population diversity in a salmon stock complex. We parameterize our model with biological and economic data from the Copper River Chinook salmon fishery. We show that markets can incentivize the degradation of population diversity, reducing infra-marginal fishery rents and increase the variability in financial returns to the fishery. Factors impacting the magnitude of our results include the level and distribution of harvesting efficiency and market conditions. We also show that second-best management can conserve population diversity and improve welfare. Furthermore, depending fishermen’s time preferences, this management strategy is potentially self-financing. Title: Fishermen, Markets, and Population Diversity Author: Sanchirico, James N., Jardine, Sunny Fishing impacts biodiversity on multiple levels, potentially resulting in unintended feedbacks to economic performance of the fishery over time. For example, targeting observable traits within a population can impact genetic diversity, targeting populations within a species can impact population diversity, and targeting valuable species can impact biodiversity at the ecosystem level. The natural science and economics literatures, however, have given little attention to the impact of fishing on population diversity, even though population diversity is directly linked ecosystem services and estimates of population extinction rates are three orders of magnitude higher than species extinction rates. Here we develop a stochastic bioeconomic model that links the harvest of multiple salmon populations by a single commercial fishery to the trajectory of population diversity in a salmon stock complex. We parameterize our model with biological and economic data from the Copper River Chinook salmon fishery. We show that markets can incentivize the degradation of population diversity, reducing infra-marginal fishery rents and increase the variability in financial returns to the fishery. Factors impacting the magnitude of our results include the level and distribution of harvesting efficiency and market conditions. We also show that second-best management can conserve population diversity and improve welfare. Furthermore, depending fishermen’s time preferences, this management strategy is potentially self-financing. Close

• 25. [Article] Native bee diversity and floral resource availability in two Willamette Valley Oregon ecosystems

  The importance of pollinators in native and managed landscapes is well known, and recent interest is directed towards investigating the role of native bees as providers of pollination ecosystem services. ...

  Citation × Citation Citation Abstract Copy Title: Native bee diversity and floral resource availability in two Willamette Valley Oregon ecosystems Author: Bergh, Jennifer E. The importance of pollinators in native and managed landscapes is well known, and recent interest is directed towards investigating the role of native bees as providers of pollination ecosystem services. Uncertainty about bee populations at global and local scales has prompted research and general interest in conservation of bee diversity. To sustain robust populations, bees need nesting habitat and quality forage resources. This thesis describes two studies related to the relationship between bee diversity and landscape floral resource availability in two Willamette Valley ecosystems: wet prairies and blueberry agroecosystems. The wetlands are florally diverse, heterogeneous, and temporally patchy in spring and summer, whereas blueberries are florally abundant during spring crop bloom with potentially fewer floral resources after berry set; the intention of these studies was to determine if the floral resources in each ecosystem were adequate to support robust native bee communities. For each site type, the bee fauna and associated melittophilous floral resources are described and characterized. In the studies, it was determined that bee diversity, and specifically bee abundance, was positively correlated with floral resources. This thesis presents the results of community analyses, floral resources that were identified as important forage sources, and a discussion of the relationship between landscape phenology and bee population dynamics in each ecosystem type. Implications and recommendations for landscape management to conserve and potentially enhance local native bee communities are discussed. Title: Native bee diversity and floral resource availability in two Willamette Valley Oregon ecosystems Author: Bergh, Jennifer E. The importance of pollinators in native and managed landscapes is well known, and recent interest is directed towards investigating the role of native bees as providers of pollination ecosystem services. Uncertainty about bee populations at global and local scales has prompted research and general interest in conservation of bee diversity. To sustain robust populations, bees need nesting habitat and quality forage resources. This thesis describes two studies related to the relationship between bee diversity and landscape floral resource availability in two Willamette Valley ecosystems: wet prairies and blueberry agroecosystems. The wetlands are florally diverse, heterogeneous, and temporally patchy in spring and summer, whereas blueberries are florally abundant during spring crop bloom with potentially fewer floral resources after berry set; the intention of these studies was to determine if the floral resources in each ecosystem were adequate to support robust native bee communities. For each site type, the bee fauna and associated melittophilous floral resources are described and characterized. In the studies, it was determined that bee diversity, and specifically bee abundance, was positively correlated with floral resources. This thesis presents the results of community analyses, floral resources that were identified as important forage sources, and a discussion of the relationship between landscape phenology and bee population dynamics in each ecosystem type. Implications and recommendations for landscape management to conserve and potentially enhance local native bee communities are discussed. Close

• 26. [Article] Evaluating tradeoffs among ecosystem services to inform marine spatial planning

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/marine-policy/.

  Citation × Citation Citation Abstract Copy Title: Evaluating tradeoffs among ecosystem services to inform marine spatial planning Author: Gaines, Steven D., Halpern, Benjamin S., Lester, Sarah E., Barth, John A., White, Crow, Costello, Christopher This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/marine-policy/. Title: Evaluating tradeoffs among ecosystem services to inform marine spatial planning Author: Gaines, Steven D., Halpern, Benjamin S., Lester, Sarah E., Barth, John A., White, Crow, Costello, Christopher This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/marine-policy/. Close

• 27. [Article] Cultural Biodiversity: Indigenous Relationships within Their Environment

  When we talk about indigenous cultural practices we are in fact talking about responsibilities that have evolved into unwritten tribal laws over millennia. These responsibilities and laws are directly ...

  Citation × Citation Citation Abstract Copy Title: Cultural Biodiversity: Indigenous Relationships within Their Environment Author: Happynook, Tom Mexsis Year: 2001 When we talk about indigenous cultural practices we are in fact talking about responsibilities that have evolved into unwritten tribal laws over millennia. These responsibilities and laws are directly tied to nature and is a product of the slow integration of cultures within their environment and the ecosystems. Thus, the environment is not a place of divisions but rather a place of relations, a place where cultural diversity and bio-diversity are not separate but in fact need each other. The most important aspects of cultural bio-diversity are those that integrate people, (the human relationship), with the ecosystems found within their environment. Some indigenous practices had cultural importance at the time they were being practiced, (arranged marriages, etc), but most indigenous practices, such as fishing, hunting and gathering have a much deeper ecological management role. These indigenous practices maintained the balance within nature, the environment and the ecosystems. I am not talking about the morality of the cultural practice, but rather the cultural practice of responsibility to bio-diversity. It is from this perspective that we begin to realize that the realm of cultural diversity and bio-diversity are not separate from the environment but rather connected through our relationships with the ecosystems. This is cultural biodiversity; a practice which has been developed and nurtured over millennia; in the Nuu-chah-nulth language “Hishuk Tsawalk”, everything is one, everything is connected. In today’s world, laws have been created around “the human relationship aspect”. Unfortunately, these laws have established a system that leaves humans outside of nature or makes us believe that we are dominant over the environment or a cancer on this earth. We have even created a set of consequences for any broken human relations within this system: fines, prisons, institutions, etc. On the other hand, indigenous peoples have lived within the “law of nature”. It is within this boundary that our indigenous systems of justice, tribal laws, societies and cultural practices developed and have turned into the indigenous rights of today. Title: Cultural Biodiversity: Indigenous Relationships within Their Environment Author: Happynook, Tom Mexsis Year: 2001 When we talk about indigenous cultural practices we are in fact talking about responsibilities that have evolved into unwritten tribal laws over millennia. These responsibilities and laws are directly tied to nature and is a product of the slow integration of cultures within their environment and the ecosystems. Thus, the environment is not a place of divisions but rather a place of relations, a place where cultural diversity and bio-diversity are not separate but in fact need each other. The most important aspects of cultural bio-diversity are those that integrate people, (the human relationship), with the ecosystems found within their environment. Some indigenous practices had cultural importance at the time they were being practiced, (arranged marriages, etc), but most indigenous practices, such as fishing, hunting and gathering have a much deeper ecological management role. These indigenous practices maintained the balance within nature, the environment and the ecosystems. I am not talking about the morality of the cultural practice, but rather the cultural practice of responsibility to bio-diversity. It is from this perspective that we begin to realize that the realm of cultural diversity and bio-diversity are not separate from the environment but rather connected through our relationships with the ecosystems. This is cultural biodiversity; a practice which has been developed and nurtured over millennia; in the Nuu-chah-nulth language “Hishuk Tsawalk”, everything is one, everything is connected. In today’s world, laws have been created around “the human relationship aspect”. Unfortunately, these laws have established a system that leaves humans outside of nature or makes us believe that we are dominant over the environment or a cancer on this earth. We have even created a set of consequences for any broken human relations within this system: fines, prisons, institutions, etc. On the other hand, indigenous peoples have lived within the “law of nature”. It is within this boundary that our indigenous systems of justice, tribal laws, societies and cultural practices developed and have turned into the indigenous rights of today. Close

• 28. [Article] Forecasting functional implications of global changes in riparian plant communities

  This is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: http://esa.org/.

  Citation × Citation Citation Abstract Copy Title: Forecasting functional implications of global changes in riparian plant communities Author: Mineau, Madeleine M., McElarney, Yvonne R., Fischer, Dylan G., Tiegs, Scott D., Canhoto, Cristina, Larranaga, Aitor, Giling, Darren P., Swan, Christopher M., Kominoski, John S., LeRoy, Carri J., Gonzalez, Eduardo, Griffiths, Natalie A., Shirley, Susan M., Follstad Shah, Jennifer J. This is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: http://esa.org/. Title: Forecasting functional implications of global changes in riparian plant communities Author: Mineau, Madeleine M., McElarney, Yvonne R., Fischer, Dylan G., Tiegs, Scott D., Canhoto, Cristina, Larranaga, Aitor, Giling, Darren P., Swan, Christopher M., Kominoski, John S., LeRoy, Carri J., Gonzalez, Eduardo, Griffiths, Natalie A., Shirley, Susan M., Follstad Shah, Jennifer J. This is the publisher’s final pdf. The published article is copyrighted by Ecological Society of America and can be found at: http://esa.org/. Close

• 29. [Article] The Human Side of the Ecosystem Approach to Fisheries Management: Preliminary Results of an FAO Expert Consultation

  Research Paper

  Citation × Citation Citation Abstract Copy Title: The Human Side of the Ecosystem Approach to Fisheries Management: Preliminary Results of an FAO Expert Consultation Author: De Young, Cassandra Research Paper Title: The Human Side of the Ecosystem Approach to Fisheries Management: Preliminary Results of an FAO Expert Consultation Author: De Young, Cassandra Research Paper Close

• 30. [Article] Convergent diversity and trait composition in temporary streams and ponds

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Ecological Society of America. The published article can be found at: http://esajournals.online...

  Citation × Citation Citation Abstract Copy Title: Convergent diversity and trait composition in temporary streams and ponds Author: Lytle, David A., Schriever, Tiffany A. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Ecological Society of America. The published article can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Title: Convergent diversity and trait composition in temporary streams and ponds Author: Lytle, David A., Schriever, Tiffany A. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Ecological Society of America. The published article can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%292150-8925/ Close

• 31. [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

• 32. [Article] Investing upstream : a social-ecological systems perspective on water utility investments in ecosystem services

  The concept of ecosystem services broadens perspectives on nature to include not only intrinsic value but also the utilitarian value it provides to society. Viewing nature through this lens informs our ...

  Citation × Citation Citation Abstract Copy Title: Investing upstream : a social-ecological systems perspective on water utility investments in ecosystem services Author: Bennett, Drew E. The concept of ecosystem services broadens perspectives on nature to include not only intrinsic value but also the utilitarian value it provides to society. Viewing nature through this lens informs our understanding of how particular ecological processes benefit different actors. In this research, I examine how water utilities in the United States are beginning to recognize the economic value of functioning ecosystems that were previously ignored or taken for granted. In an effort to protect or restore valuable ecosystem services, many utilities are now developing payments for ecosystem services (PES) programs to link water customers to conservation efforts upstream through direct financial investments. Despite the increasing number of water utility PES programs, there is a lack of information regarding how these programs work, the social and environmental conditions necessary for their emergence, and how they fit into the context of their larger social-ecological systems (SES). This research addresses this gap. To characterize the diversity of water utility PES programs, I developed a working typology highlighting similarities and differences among 37 identified programs covering source water protection, fire risk mitigation, point source pollution offsets, voluntary customer offsets, and hydropower mitigation. Results from my research also show that the concept of PES has largely been promoted as a market-like approach to conservation that emphasizes economic efficiency through reduced transaction costs, perfect information, and the minimization of the role of state actors. While this framing of PES is widely shared, I argue that it does not capture the diversity of social and environmental settings in which PES programs are embedded. Instead, I demonstrate that PES initiatives often emerge in response to a variety of institutional needs, poorly understood environmental drivers, and involve a diversity of public and private actors. As a result, I argue that PES is better viewed through a broader "collective action" lens and suggest that those developing PES initiatives should expand from a focus on the market logic of efficiency to approaches that promote social capital and the collaborative capacity of community groups in the implementation of PES programs. I also argue that a more integrative conceptualization of PES--through synthesis with the SES framework--is necessary to take into account the broader social and ecological landscapes in which PES initiatives are embedded. The SES framework can provide insight into the multitude of factors that influence PES and facilitate the integration of knowledge from diverse disciplinary perspectives by providing a common language and consistency in the variables considered in analyses. To this end, I present an initial effort in the development of a taxonomy of core variables relevant to analyzing and understanding PES. I feel this adapted SES framework will help scholars move beyond academic debates and towards a shared understanding of the potential and limitations of PES as a policy mechanism for addressing complex ecosystem service management problems in diverse SESs. Title: Investing upstream : a social-ecological systems perspective on water utility investments in ecosystem services Author: Bennett, Drew E. The concept of ecosystem services broadens perspectives on nature to include not only intrinsic value but also the utilitarian value it provides to society. Viewing nature through this lens informs our understanding of how particular ecological processes benefit different actors. In this research, I examine how water utilities in the United States are beginning to recognize the economic value of functioning ecosystems that were previously ignored or taken for granted. In an effort to protect or restore valuable ecosystem services, many utilities are now developing payments for ecosystem services (PES) programs to link water customers to conservation efforts upstream through direct financial investments. Despite the increasing number of water utility PES programs, there is a lack of information regarding how these programs work, the social and environmental conditions necessary for their emergence, and how they fit into the context of their larger social-ecological systems (SES). This research addresses this gap. To characterize the diversity of water utility PES programs, I developed a working typology highlighting similarities and differences among 37 identified programs covering source water protection, fire risk mitigation, point source pollution offsets, voluntary customer offsets, and hydropower mitigation. Results from my research also show that the concept of PES has largely been promoted as a market-like approach to conservation that emphasizes economic efficiency through reduced transaction costs, perfect information, and the minimization of the role of state actors. While this framing of PES is widely shared, I argue that it does not capture the diversity of social and environmental settings in which PES programs are embedded. Instead, I demonstrate that PES initiatives often emerge in response to a variety of institutional needs, poorly understood environmental drivers, and involve a diversity of public and private actors. As a result, I argue that PES is better viewed through a broader "collective action" lens and suggest that those developing PES initiatives should expand from a focus on the market logic of efficiency to approaches that promote social capital and the collaborative capacity of community groups in the implementation of PES programs. I also argue that a more integrative conceptualization of PES--through synthesis with the SES framework--is necessary to take into account the broader social and ecological landscapes in which PES initiatives are embedded. The SES framework can provide insight into the multitude of factors that influence PES and facilitate the integration of knowledge from diverse disciplinary perspectives by providing a common language and consistency in the variables considered in analyses. To this end, I present an initial effort in the development of a taxonomy of core variables relevant to analyzing and understanding PES. I feel this adapted SES framework will help scholars move beyond academic debates and towards a shared understanding of the potential and limitations of PES as a policy mechanism for addressing complex ecosystem service management problems in diverse SESs. Close

• 33. [Article] Eutrophication weakens stabilizing effects of diversity in natural grasslands

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the Nature ...

  Citation × Citation Citation Abstract Copy Title: Eutrophication weakens stabilizing effects of diversity in natural grasslands Author: O'Halloran, Lydia R., Hautier, Yann, Borer, Elizabeth T., et al., Seabloom, Eric W. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the Nature Publishing Group and can be found at: http://www.nature.com/nature/index.html. Title: Eutrophication weakens stabilizing effects of diversity in natural grasslands Author: O'Halloran, Lydia R., Hautier, Yann, Borer, Elizabeth T., et al., Seabloom, Eric W. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the Nature Publishing Group and can be found at: http://www.nature.com/nature/index.html. Close

• 34. [Article] A choice experiment analysis of public preferences for conservation of biological diversity in the Oregon Coast Range

  Ecosystem management has become an increasingly mainstream paradigm for natural resource management. Nowhere is this more evident than on the public and private forestland of the Pacific Northwest. While ...

  Citation × Citation Citation Abstract Copy Title: A choice experiment analysis of public preferences for conservation of biological diversity in the Oregon Coast Range Author: Garber-Yonts, Brian E. Ecosystem management has become an increasingly mainstream paradigm for natural resource management. Nowhere is this more evident than on the public and private forestland of the Pacific Northwest. While ecosystem management has become a widely accepted principle of resource management, substantial questions remain about its implementation. A case in point is the conservation of biological diversity: within both the scientific literature and the policy debate, it is unclear what are the best methods for its conservation. In addition, the public goods nature of biological diversity limits the ability of managers and policy makers to use economic information to prioritize biodiversity policy goals in making resource management decisions. This study uses a choice experiment (CE) framework to produce utility theoretic estimates of the welfare effects of changes in the level of biodiversity protection under different conservation programs. The sample frame for the study spans Oregon households, with three regional strata (Eastern, Willamette Valley, and Coastal), allowing measurement of regional preference heterogeneity. We present biodiversity policy as an amalgam of four different conservation programs: aquatic habitat conservation, forest rotation management, endangered species protection, and large-scale conservation reserves. The study results indicate substantial support for conservation programs. While WTP is positive for initial increases above baseline levels of protection, results indicate that WTP for large increases fall to zero or become negative, requiring monetary compensation for further increases, substantial increases over the current baseline would generate increased consumer surplus, though overall location of land resources to biodiversity is perceived on average as a welfare loss. The survey instrument included a dichotomous choice contingent valuation WTP elicitation for the purpose of methodological comparison to the CE approach. Results tentatively support the conclusion that the CE approach produces more conservative (lower) estimates of consumer surplus. The study also indicated a strong bias toward the management status quo, though the basis for this preference, and its importance in the context of policy analysis, remains an important subject for further research. Title: A choice experiment analysis of public preferences for conservation of biological diversity in the Oregon Coast Range Author: Garber-Yonts, Brian E. Ecosystem management has become an increasingly mainstream paradigm for natural resource management. Nowhere is this more evident than on the public and private forestland of the Pacific Northwest. While ecosystem management has become a widely accepted principle of resource management, substantial questions remain about its implementation. A case in point is the conservation of biological diversity: within both the scientific literature and the policy debate, it is unclear what are the best methods for its conservation. In addition, the public goods nature of biological diversity limits the ability of managers and policy makers to use economic information to prioritize biodiversity policy goals in making resource management decisions. This study uses a choice experiment (CE) framework to produce utility theoretic estimates of the welfare effects of changes in the level of biodiversity protection under different conservation programs. The sample frame for the study spans Oregon households, with three regional strata (Eastern, Willamette Valley, and Coastal), allowing measurement of regional preference heterogeneity. We present biodiversity policy as an amalgam of four different conservation programs: aquatic habitat conservation, forest rotation management, endangered species protection, and large-scale conservation reserves. The study results indicate substantial support for conservation programs. While WTP is positive for initial increases above baseline levels of protection, results indicate that WTP for large increases fall to zero or become negative, requiring monetary compensation for further increases, substantial increases over the current baseline would generate increased consumer surplus, though overall location of land resources to biodiversity is perceived on average as a welfare loss. The survey instrument included a dichotomous choice contingent valuation WTP elicitation for the purpose of methodological comparison to the CE approach. Results tentatively support the conclusion that the CE approach produces more conservative (lower) estimates of consumer surplus. The study also indicated a strong bias toward the management status quo, though the basis for this preference, and its importance in the context of policy analysis, remains an important subject for further research. Close

• 35. [Article] Ecosystem services markets for family foresters

  This is a report produced as part of a class led by John Bliss, Sally Duncan and James Johnston under a grant from the American Forest Foundation.

  Citation × Citation Citation Abstract Copy Title: Ecosystem services markets for family foresters Author: Butler, Greg, MacFarland, Kate, Comfort, Emily, Salas, Javier, Cummings, Ed, Institute for Natural Resources, Pfeiffer, Vera, Harrison, Jane, Eliis, Tana, Smedstad, Jill, Overdevest, Justin This is a report produced as part of a class led by John Bliss, Sally Duncan and James Johnston under a grant from the American Forest Foundation. Title: Ecosystem services markets for family foresters Author: Butler, Greg, MacFarland, Kate, Comfort, Emily, Salas, Javier, Cummings, Ed, Institute for Natural Resources, Pfeiffer, Vera, Harrison, Jane, Eliis, Tana, Smedstad, Jill, Overdevest, Justin This is a report produced as part of a class led by John Bliss, Sally Duncan and James Johnston under a grant from the American Forest Foundation. Close

• 36. [Article] Multi-scale Drivers of Spatial Variation in Old-Growth Forest Carbon Density Disentangled with Lidar and an Individual-Based Landscape Model

  This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10021. To the best of our knowledge, one or more authors of this ...

  Citation × Citation Citation Abstract Copy Title: Multi-scale Drivers of Spatial Variation in Old-Growth Forest Carbon Density Disentangled with Lidar and an Individual-Based Landscape Model Author: Pabst, Robert J., Olsen, Keith, Spies, Thomas A., Seidl, Rupert, Steel, E. Ashley, Rammer, Werner This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10021. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Title: Multi-scale Drivers of Spatial Variation in Old-Growth Forest Carbon Density Disentangled with Lidar and an Individual-Based Landscape Model Author: Pabst, Robert J., Olsen, Keith, Spies, Thomas A., Seidl, Rupert, Steel, E. Ashley, Rammer, Werner This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/10021. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Close

• 37. [Article] Hydrology shapes taxonomic and functional structure of desert stream invertebrate communities

  This is an author's peer-reviewed final manuscript, as accepted by the publisher. The article is copyrighted by The Society for Freshwater Science and published by The University of Chicago Press. It can ...

  Citation × Citation Citation Abstract Copy Title: Hydrology shapes taxonomic and functional structure of desert stream invertebrate communities Author: Lytle, David A., Olden, Julian D., Jaeger, Kristin L., Bogan, Michael T., Schriever, Tiffany A., Cañedo-Argüelles, Miguel, Boersma, Kate S. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The article is copyrighted by The Society for Freshwater Science and published by The University of Chicago Press. It can be found at: http://www.press.uchicago.edu/ucp/journals/journal/fws.html Title: Hydrology shapes taxonomic and functional structure of desert stream invertebrate communities Author: Lytle, David A., Olden, Julian D., Jaeger, Kristin L., Bogan, Michael T., Schriever, Tiffany A., Cañedo-Argüelles, Miguel, Boersma, Kate S. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The article is copyrighted by The Society for Freshwater Science and published by The University of Chicago Press. It can be found at: http://www.press.uchicago.edu/ucp/journals/journal/fws.html Close

• 38. [Article] Comparative Composition, Diversity and Trophic Ecology of Sediment Macrofauna at Vents, Seeps and Organic Falls

  This is the publisher’s final pdf. The published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action.

  Citation × Citation Citation Abstract Copy Title: Comparative Composition, Diversity and Trophic Ecology of Sediment Macrofauna at Vents, Seeps and Organic Falls Author: Smith, Craig R., Thurber, Andrew R., Levin, Lisa A., Bernardino, Angelo F. This is the publisher’s final pdf. The published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action. Title: Comparative Composition, Diversity and Trophic Ecology of Sediment Macrofauna at Vents, Seeps and Organic Falls Author: Smith, Craig R., Thurber, Andrew R., Levin, Lisa A., Bernardino, Angelo F. This is the publisher’s final pdf. The published article is copyrighted by the Public Library of Science and can be found at: http://www.plosone.org/home.action. Close

• 39. [Article] Hydroclimatic and hydrochemical controls on Plecoptera diversity and distribution in northern freshwater ecosystems

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Springer ...

  Citation × Citation Citation Abstract Copy Title: Hydroclimatic and hydrochemical controls on Plecoptera diversity and distribution in northern freshwater ecosystems Author: Soulsby, Chris, Laudon, Hjalmar, Cunjak, Richard, Carey, Sean K., Shanley, Jamie, Buttle, Jim, Seibert, Jan, Kruitbos, Laura M., McGuire, Kevin, McDonnell, Jeffrey J., Tetzlaff, Doerthe To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springer.com/?SGWID=0-102-0-0-0. Title: Hydroclimatic and hydrochemical controls on Plecoptera diversity and distribution in northern freshwater ecosystems Author: Soulsby, Chris, Laudon, Hjalmar, Cunjak, Richard, Carey, Sean K., Shanley, Jamie, Buttle, Jim, Seibert, Jan, Kruitbos, Laura M., McGuire, Kevin, McDonnell, Jeffrey J., Tetzlaff, Doerthe To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springer.com/?SGWID=0-102-0-0-0. Close

• 40. [Article] Obligations to Protect Marine Ecosystems Under International Conventions and other Legal Instruments

  Research Paper

  Citation × Citation Citation Abstract Copy Title: Obligations to Protect Marine Ecosystems Under International Conventions and other Legal Instruments Author: Aqorau, Transform Research Paper Title: Obligations to Protect Marine Ecosystems Under International Conventions and other Legal Instruments Author: Aqorau, Transform Research Paper Close

• 41. [Article] Laboratory studies of successional patterns in assemblages of attached estuarine diatoms

  Successional patterns of attached estuarine diatoms were investigated using laboratory model ecosystems. Artificial substrates of acrylic plastic were exposed to 0, 4, and 10 hours of desiccation per day. ...

  Citation × Citation Citation Abstract Copy Title: Laboratory studies of successional patterns in assemblages of attached estuarine diatoms Author: Berglund, Lisette Aline Successional patterns of attached estuarine diatoms were investigated using laboratory model ecosystems. Artificial substrates of acrylic plastic were exposed to 0, 4, and 10 hours of desiccation per day. Diatom assemblages that developed under temperatures normal for Yaquina Bay, Oregon (control ecosystem) were compared to assemblages that developed at temperatures elevated 10 C (heated ecosystem). Continuously submerged substrates were quickly invaded by solitary, motile and attached diatoms. By the end of the experiment, filamentous and tube dwelling colonial diatoms had become established with many motile and epiphytic diatoms interspersed among the colonies. However, planktonic taxa were the first to settle on the substrates exposed to 4 and 10 hours of desiccation. These taxa were gradually replaced in prominence by solitary, motile and attached taxa that had previously colonized the continuously submerged substrates and by several species that were tolerant of desiccation and high air temperatures. Again, filamentous and tube dwelling forms began to establish colonies at the end of the experiment. A total of 21,569 diatoms was counted in 42 samples, and 136 species were identified. The most abundant diatoms found in the control ecosystem included Navicula directa, Thalassiosira no. 1, Thalassionema nitzschioides, Nitzschia no. 2, and Navicula diserta. Thalassiosira no. 1, Thalassionema nitzschioides, Nitzschia aerophila, Nitzschia sigma, and Navicula no. 2 were the most abundant species in the heated ecosystem. Of these taxa, Navicula directa and Thalassionema nitzschioides were the most evenly distributed over the samples. Species diversity was higher in the heated ecosystem than in the control ecosystem. Title: Laboratory studies of successional patterns in assemblages of attached estuarine diatoms Author: Berglund, Lisette Aline Successional patterns of attached estuarine diatoms were investigated using laboratory model ecosystems. Artificial substrates of acrylic plastic were exposed to 0, 4, and 10 hours of desiccation per day. Diatom assemblages that developed under temperatures normal for Yaquina Bay, Oregon (control ecosystem) were compared to assemblages that developed at temperatures elevated 10 C (heated ecosystem). Continuously submerged substrates were quickly invaded by solitary, motile and attached diatoms. By the end of the experiment, filamentous and tube dwelling colonial diatoms had become established with many motile and epiphytic diatoms interspersed among the colonies. However, planktonic taxa were the first to settle on the substrates exposed to 4 and 10 hours of desiccation. These taxa were gradually replaced in prominence by solitary, motile and attached taxa that had previously colonized the continuously submerged substrates and by several species that were tolerant of desiccation and high air temperatures. Again, filamentous and tube dwelling forms began to establish colonies at the end of the experiment. A total of 21,569 diatoms was counted in 42 samples, and 136 species were identified. The most abundant diatoms found in the control ecosystem included Navicula directa, Thalassiosira no. 1, Thalassionema nitzschioides, Nitzschia no. 2, and Navicula diserta. Thalassiosira no. 1, Thalassionema nitzschioides, Nitzschia aerophila, Nitzschia sigma, and Navicula no. 2 were the most abundant species in the heated ecosystem. Of these taxa, Navicula directa and Thalassionema nitzschioides were the most evenly distributed over the samples. Species diversity was higher in the heated ecosystem than in the control ecosystem. Close

• 42. [Article] Environmental variability and system heterogeneity in terrestrial biogeochemical models

  Ecosystems are highly heterogeneous systems subjected to important levels of environmental variability; however, it is common in terrestrial biogeochemical models to assume homogeneous properties of the ...

  Citation × Citation Citation Abstract Copy Title: Environmental variability and system heterogeneity in terrestrial biogeochemical models Author: Sierra, Carlos Alberto Ecosystems are highly heterogeneous systems subjected to important levels of environmental variability; however, it is common in terrestrial biogeochemical models to assume homogeneous properties of the elements of the system or constant environmental conditions. For some processes, heterogeneity in these models is treated very simplistically, but there is not much information about the advantages of including more complex representations in these models. By environmental variability I refer to the continuous changes of abiotic drivers in ecosystems, mainly climatic conditions. System heterogeneity is treated here as the diversity of elements that compose an ecosystem and respond differently to biotic and abiotic drivers. In this dissertation I performed a theoretical analysis to evaluate the consequences of ignoring heterogeneity and variability on the representation of carbon and nitrogen cycling in terrestrial biogeochemical models. For this purpose I used tools from probability theory and simulation models to test the hypothesis that ignoring heterogeneity and variability excludes a variety of system properties and behaviors that cannot be obtained with simpler models. Explicit treatments of climatic variability showed that changes in temperature variance alone can modify the amounts of respiration and carbon storage in ecosystems. Additionally, changes in temperature variance can modify predictions solely based on changes in temperature averages. This behavior is strongly dependent on the degree and nature of nonlinearity in ecosystems. Effects of system heterogeneity on carbon and nitrogen cycling are also strongly influenced by nonlinearities. Extrapolations of average system behavior are only valid when the system is linear and the elements of the system are distributed homogeneously or symmetrically around an average value. In all other cases, the nonlinearity of the system and the distribution of its elements produce complex behaviors that are impossible to predict with simple models. Title: Environmental variability and system heterogeneity in terrestrial biogeochemical models Author: Sierra, Carlos Alberto Ecosystems are highly heterogeneous systems subjected to important levels of environmental variability; however, it is common in terrestrial biogeochemical models to assume homogeneous properties of the elements of the system or constant environmental conditions. For some processes, heterogeneity in these models is treated very simplistically, but there is not much information about the advantages of including more complex representations in these models. By environmental variability I refer to the continuous changes of abiotic drivers in ecosystems, mainly climatic conditions. System heterogeneity is treated here as the diversity of elements that compose an ecosystem and respond differently to biotic and abiotic drivers. In this dissertation I performed a theoretical analysis to evaluate the consequences of ignoring heterogeneity and variability on the representation of carbon and nitrogen cycling in terrestrial biogeochemical models. For this purpose I used tools from probability theory and simulation models to test the hypothesis that ignoring heterogeneity and variability excludes a variety of system properties and behaviors that cannot be obtained with simpler models. Explicit treatments of climatic variability showed that changes in temperature variance alone can modify the amounts of respiration and carbon storage in ecosystems. Additionally, changes in temperature variance can modify predictions solely based on changes in temperature averages. This behavior is strongly dependent on the degree and nature of nonlinearity in ecosystems. Effects of system heterogeneity on carbon and nitrogen cycling are also strongly influenced by nonlinearities. Extrapolations of average system behavior are only valid when the system is linear and the elements of the system are distributed homogeneously or symmetrically around an average value. In all other cases, the nonlinearity of the system and the distribution of its elements produce complex behaviors that are impossible to predict with simple models. Close

• 43. [Article] Climate Change Impacts on Marine Ecosystems

  This is the publisher’s final pdf. The published article is copyrighted by Annual Reviews and can be found at: http://www.annualreviews.org/.

  Citation × Citation Citation Abstract Copy Title: Climate Change Impacts on Marine Ecosystems Author: Ruckelshaus, Mary, English, Chad A., Chan, Francis, Grebmeier, Jacqueline M., Hollowed, Anne B., Galindo, Heather M., Barry, James P., Duffy, J. Emmett, Sydeman, William J., Knowlton, Nancy, Talley, Lynne D., Doney, Scott C., Polovina, Jeffrey, Rabalais, Nancy N. This is the publisher’s final pdf. The published article is copyrighted by Annual Reviews and can be found at: http://www.annualreviews.org/. Title: Climate Change Impacts on Marine Ecosystems Author: Ruckelshaus, Mary, English, Chad A., Chan, Francis, Grebmeier, Jacqueline M., Hollowed, Anne B., Galindo, Heather M., Barry, James P., Duffy, J. Emmett, Sydeman, William J., Knowlton, Nancy, Talley, Lynne D., Doney, Scott C., Polovina, Jeffrey, Rabalais, Nancy N. This is the publisher’s final pdf. The published article is copyrighted by Annual Reviews and can be found at: http://www.annualreviews.org/. Close

• 44. [Article] Resource waves: phenological diversity enhances foraging opportunities for mobile consumers

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the Ecological Society ...

  Citation × Citation Citation Abstract Copy Title: Resource waves: phenological diversity enhances foraging opportunities for mobile consumers Author: Takimoto, Gaku, Hayes, Matthew M., Schindler, Daniel E., Kauffman, Matthew J., Armstrong, Jonathan B. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the Ecological Society of America and published by John Wiley & Sons, Inc. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%291939-9170/ Title: Resource waves: phenological diversity enhances foraging opportunities for mobile consumers Author: Takimoto, Gaku, Hayes, Matthew M., Schindler, Daniel E., Kauffman, Matthew J., Armstrong, Jonathan B. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by the Ecological Society of America and published by John Wiley & Sons, Inc. It can be found at: http://esajournals.onlinelibrary.wiley.com/hub/journal/10.1002/%28ISSN%291939-9170/ Close

• 45. [Article] Patterns and Variation in Benthic Biodiversity in a Large Marine Ecosystem

  Supporting information can be located at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135135#sec014

  Citation × Citation Citation Abstract Copy Title: Patterns and Variation in Benthic Biodiversity in a Large Marine Ecosystem Author: Ingeman, Kurt E., Lindsley, Amy J., Piacenza, Susan E., Barner, Allison K., Reimer, Jessica N., Rowe, Jennifer C., Heppell, Selina S., Thompson, Kevin A., Boersma, Kate S., Kindinger, Tye L., Cerny-Chipman, Elizabeth B., Benkwitt, Cassandra E., Lee, Jonathan D., Thurman, Lindsey L., Shen, Chenchen Supporting information can be located at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135135#sec014 Title: Patterns and Variation in Benthic Biodiversity in a Large Marine Ecosystem Author: Ingeman, Kurt E., Lindsley, Amy J., Piacenza, Susan E., Barner, Allison K., Reimer, Jessica N., Rowe, Jennifer C., Heppell, Selina S., Thompson, Kevin A., Boersma, Kate S., Kindinger, Tye L., Cerny-Chipman, Elizabeth B., Benkwitt, Cassandra E., Lee, Jonathan D., Thurman, Lindsey L., Shen, Chenchen Supporting information can be located at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135135#sec014 Close

• 46. [Article] Determinants of moth diversity and community in a temperate mountain landscape: vegetation, topography, and seasonality

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Ecological Society of America. The published article can be found at: http://www.esajournal...

  Citation × Citation Citation Abstract Copy Title: Determinants of moth diversity and community in a temperate mountain landscape: vegetation, topography, and seasonality Author: Miller, Jeffrey C., Jones, Julia A., Highland, Steven A. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Ecological Society of America. The published article can be found at: http://www.esajournals.org/loi/ecsp. Title: Determinants of moth diversity and community in a temperate mountain landscape: vegetation, topography, and seasonality Author: Miller, Jeffrey C., Jones, Julia A., Highland, Steven A. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Ecological Society of America. The published article can be found at: http://www.esajournals.org/loi/ecsp. Close

• 47. [Article] Diversity and productivity of hypogeous fungal sporocarps in a variably thinned Douglas-fir forest

  Although ecosystem management techniques are designed to enhance species diversity in managed forests, no comprehensive study has been conducted to evaluate effects of such techniques on diversity and ...

  Citation × Citation Citation Abstract Copy Title: Diversity and productivity of hypogeous fungal sporocarps in a variably thinned Douglas-fir forest Author: Trappe, James M., Carey, Andrew B., Colgan, Wesley, Thysell, David, Molina, Randy Although ecosystem management techniques are designed to enhance species diversity in managed forests, no comprehensive study has been conducted to evaluate effects of such techniques on diversity and productivity of hypogeous fungi (truffles). During this study, truffles were collected in a 55- to 65-year-old Douglas-fir forest from March 1993 through December 1995 at approximately 6-week intervals. Half of the stands served as controls, half were assigned a variable density thinning (VDT) treatment. A VDT stand comprised a mosaic of patches thinned to different densities of standing live trees. To further evaluate the effect of harvesting impacts, this mosaic was divided into two thinning categories, lightly thinned and heavily thinned areas. Truffle standing crop varied greatly but generally was highest in spring with a smaller peak in the fall. At least some sporocarps were found year round, with winter having the lowest biomass and species richness. Overall standing crop biomass (over all seasons) was significantly lower in VDT stands compared with control stands. The abundance of Gautieria and Hysterangium species was lower in thinned stands, while Melanogaster species diversity and productivity were highest in these stands. Title: Diversity and productivity of hypogeous fungal sporocarps in a variably thinned Douglas-fir forest Author: Trappe, James M., Carey, Andrew B., Colgan, Wesley, Thysell, David, Molina, Randy Although ecosystem management techniques are designed to enhance species diversity in managed forests, no comprehensive study has been conducted to evaluate effects of such techniques on diversity and productivity of hypogeous fungi (truffles). During this study, truffles were collected in a 55- to 65-year-old Douglas-fir forest from March 1993 through December 1995 at approximately 6-week intervals. Half of the stands served as controls, half were assigned a variable density thinning (VDT) treatment. A VDT stand comprised a mosaic of patches thinned to different densities of standing live trees. To further evaluate the effect of harvesting impacts, this mosaic was divided into two thinning categories, lightly thinned and heavily thinned areas. Truffle standing crop varied greatly but generally was highest in spring with a smaller peak in the fall. At least some sporocarps were found year round, with winter having the lowest biomass and species richness. Overall standing crop biomass (over all seasons) was significantly lower in VDT stands compared with control stands. The abundance of Gautieria and Hysterangium species was lower in thinned stands, while Melanogaster species diversity and productivity were highest in these stands. Close

• 48. [Article] Multi-scale relationships between aspen and birds in the northern Yellowstone ecosystem

  I conducted a multi-scale evaluation of aspen – bird relationships in the northern ungulate winter range of the northern Yellowstone ecosystem during June 2001-03. Questions addressed were: (1) Does bird ...

  Citation × Citation Citation Abstract Copy Title: Multi-scale relationships between aspen and birds in the northern Yellowstone ecosystem Author: Hollenbeck, Jeff P., 1967- I conducted a multi-scale evaluation of aspen – bird relationships in the northern ungulate winter range of the northern Yellowstone ecosystem during June 2001-03. Questions addressed were: (1) Does bird diversity increase with conifer presence in aspen stands? (2) Given known habitat selection cues, are migrating birds passively intercepted by aspen patches oriented perpendicular to migratory direction of travel? (3) Are resident (short-distance migrant) birds passively intercepted by aspen patches? and (4) Given the dynamics of wolves, ungulates, and forage plants in the northern Yellowstone ecosystem, what is the present condition of aspen and cavity-nesting birds within Yellowstone National Park (YNP) and how will they change over the next 100+ years? Regression analyses of migratory bird diversity (species richness or Shannon-Weiner index) on measures of habitat heterogeneity (ratio of conifer to aspen canopy cover, or basal area) suggested no positive relationship with intermediate levels of conifer presence. Migratory birds were most diverse in pure aspen, and least diverse in pure conifer. I found a weak, but significant, positive relationship between most measures of habitat heterogeneity and resident bird diversity. Many residents were habitat generalists or conifer-associated species. To maximize bird diversity and aspen, managers may want to manage for pure aspen stands in a matrix that includes conifer habitat. Using model selection techniques, long-distance migratory birds did not show evidence of passive interception by aspen patches oriented against northerly or elevational direction of travel. Aspen patch area was most important for migratory birds, given the data and set of models analyzed. Resident (and short-distance migrant) birds showed a marked positive response to patch orientation relative to the elevational gradient of the northern range. Migratory birds appear not to be passively intercepted at high elevation sites such as YNP’s northern range. Short distance migrants appear to be passively intercepted. Northern range aspen stands within YNP have 10cm greater mean live and dead stem diameter, 80% more snags, and greater abundance of many cavity-nesting bird species than northern range stands outside YNP. These conditions fit a conceptual framework of interactions driven by a top-down ecosystem structure that predicts aspen and cavity-nester dynamics over several decades. Title: Multi-scale relationships between aspen and birds in the northern Yellowstone ecosystem Author: Hollenbeck, Jeff P., 1967- I conducted a multi-scale evaluation of aspen – bird relationships in the northern ungulate winter range of the northern Yellowstone ecosystem during June 2001-03. Questions addressed were: (1) Does bird diversity increase with conifer presence in aspen stands? (2) Given known habitat selection cues, are migrating birds passively intercepted by aspen patches oriented perpendicular to migratory direction of travel? (3) Are resident (short-distance migrant) birds passively intercepted by aspen patches? and (4) Given the dynamics of wolves, ungulates, and forage plants in the northern Yellowstone ecosystem, what is the present condition of aspen and cavity-nesting birds within Yellowstone National Park (YNP) and how will they change over the next 100+ years? Regression analyses of migratory bird diversity (species richness or Shannon-Weiner index) on measures of habitat heterogeneity (ratio of conifer to aspen canopy cover, or basal area) suggested no positive relationship with intermediate levels of conifer presence. Migratory birds were most diverse in pure aspen, and least diverse in pure conifer. I found a weak, but significant, positive relationship between most measures of habitat heterogeneity and resident bird diversity. Many residents were habitat generalists or conifer-associated species. To maximize bird diversity and aspen, managers may want to manage for pure aspen stands in a matrix that includes conifer habitat. Using model selection techniques, long-distance migratory birds did not show evidence of passive interception by aspen patches oriented against northerly or elevational direction of travel. Aspen patch area was most important for migratory birds, given the data and set of models analyzed. Resident (and short-distance migrant) birds showed a marked positive response to patch orientation relative to the elevational gradient of the northern range. Migratory birds appear not to be passively intercepted at high elevation sites such as YNP’s northern range. Short distance migrants appear to be passively intercepted. Northern range aspen stands within YNP have 10cm greater mean live and dead stem diameter, 80% more snags, and greater abundance of many cavity-nesting bird species than northern range stands outside YNP. These conditions fit a conceptual framework of interactions driven by a top-down ecosystem structure that predicts aspen and cavity-nester dynamics over several decades. Close

• 49. [Article] Modeling ocean ecosystems: The PARADIGM program

  THE ROLE OF THE OCEANS in Earth systems ecology, and the effects of climate variability on the ocean and its ecosystems, can be understood only by observing, describing, and ultimately predicting the state ...

  Citation × Citation Citation Abstract Copy Title: Modeling ocean ecosystems: The PARADIGM program Author: Denman, Ken, Cullen, John, Spitz, Yvette, Abbott, Mark R., Doney, Scott, Hoffman, Eileen, Chassignet, Eric, Yoder, James, Ducklow, Hugh, McGillicuddy, Dennis, Maltrud, Mathew, Karl, David, Olascoaga, M., Fennel, Katja, Rothstein, Lewis, McClain, Chuck, Haidvogel, Dale, Kindle, John, Wiggert, Jerry, Follows, Mick, Lima, Ivan THE ROLE OF THE OCEANS in Earth systems ecology, and the effects of climate variability on the ocean and its ecosystems, can be understood only by observing, describing, and ultimately predicting the state of the ocean as a physically forced ecological and biogeochemical system. This is a daunting but exciting challenge, because the ocean-atmosphere system is dynamically linked, and oceanic habitats are both diverse and complex, providing tremendous variety in environmental conditions and associated life forms. And paradoxically, as we learn more and more about ocean life, for example, through the genomics revolution (Doney et al., 2004), the number of unanswered questions increases. Models, be they conceptual, statistical, or numerical simulations, are useful and necessary tools for studying the complex interactions that influence ecosystem structure and function. Originally, a primary function of marine ecosystem models was to help in the development of understanding; also, they were applied in fisheries models to predict the abundance of specific commercial fish stocks. Now, they are being asked to do much more. On local and regional scales, there is growing recognition that management of marine resources and assessment of human perturbations must encompass the whole ecosystem, not individual species. Extending further to basin and global scales, the potential impacts of global change present an immediate challenge, nationally and globally, to define and execute responsive strategies, based to a large extent on the predictions of interdisciplinary global models that must be validated by comparison with measurements. Consequently, the ultimate objective of any comprehensive marine ecosystem modeling program must be the development and implementation of reliable forecast systems, guided by and validated with systematic observations of the sea. Title: Modeling ocean ecosystems: The PARADIGM program Author: Denman, Ken, Cullen, John, Spitz, Yvette, Abbott, Mark R., Doney, Scott, Hoffman, Eileen, Chassignet, Eric, Yoder, James, Ducklow, Hugh, McGillicuddy, Dennis, Maltrud, Mathew, Karl, David, Olascoaga, M., Fennel, Katja, Rothstein, Lewis, McClain, Chuck, Haidvogel, Dale, Kindle, John, Wiggert, Jerry, Follows, Mick, Lima, Ivan THE ROLE OF THE OCEANS in Earth systems ecology, and the effects of climate variability on the ocean and its ecosystems, can be understood only by observing, describing, and ultimately predicting the state of the ocean as a physically forced ecological and biogeochemical system. This is a daunting but exciting challenge, because the ocean-atmosphere system is dynamically linked, and oceanic habitats are both diverse and complex, providing tremendous variety in environmental conditions and associated life forms. And paradoxically, as we learn more and more about ocean life, for example, through the genomics revolution (Doney et al., 2004), the number of unanswered questions increases. Models, be they conceptual, statistical, or numerical simulations, are useful and necessary tools for studying the complex interactions that influence ecosystem structure and function. Originally, a primary function of marine ecosystem models was to help in the development of understanding; also, they were applied in fisheries models to predict the abundance of specific commercial fish stocks. Now, they are being asked to do much more. On local and regional scales, there is growing recognition that management of marine resources and assessment of human perturbations must encompass the whole ecosystem, not individual species. Extending further to basin and global scales, the potential impacts of global change present an immediate challenge, nationally and globally, to define and execute responsive strategies, based to a large extent on the predictions of interdisciplinary global models that must be validated by comparison with measurements. Consequently, the ultimate objective of any comprehensive marine ecosystem modeling program must be the development and implementation of reliable forecast systems, guided by and validated with systematic observations of the sea. Close

• 50. [Article] Grazing, nutrients, and marine benthic algae : insights into the drivers and protection of diversity

  Two of the most powerful ways in which humans have altered ecosystems are by increasing productivity and changing the densities of important consumers. The bottom-up effects of productivity and the top-down ...

  Citation × Citation Citation Abstract Copy Title: Grazing, nutrients, and marine benthic algae : insights into the drivers and protection of diversity Author: Guerry, Anne D., 1973- Two of the most powerful ways in which humans have altered ecosystems are by increasing productivity and changing the densities of important consumers. The bottom-up effects of productivity and the top-down effects of consumers have been identified as primary determinants of biological diversity, though the links between them remain unclear. Understanding how consumers and productivity act and interact to yield differences in diversity is of both conceptual and pragmatic importance. Here, I describe three experiments designed to examine the links between grazing, productivity, and diversity in rocky intertidal systems in Oregon and New Zealand. In two experiments I used fully-factorial designs in which I manipulated both grazing and nutrients. Both experiments revealed the primary importance of grazing as a structuring force of algal assemblages. In the Oregon experiment, I also document an interaction between grazing and productivity, with nutrient enrichment decreasing algal diversity at low grazer densities and increasing algal diversity at high grazer densities. This interaction was not apparent in the New Zealand experiment. In the absence of grazers, nutrient addition led to increased abundance of foliose algae at this site but had no net effect on algal diversity. In the third experiment, also conducted in New Zealand, I used natural variation in nearshore productivity as a backdrop against which I manipulated the access of grazers. In this experiment, I found that grazers had negative impacts on benthic algal diversity and abundance at sites with lower productivity and negligible impacts on benthic algal assemblages at sites with higher productivity. Overall these three studies suggest that in these intertidal grazer-dominated communities, the strong top-down effects often documented in such systems can be modified by more subtle bottom-up effects. Together, results from these experiments elucidate factors that determine algal diversity in these systems and underscore the importance of the evolutionary context in which experiments are conducted. Finally, I conclude with a synthesis of the literature in which I put these and other findings to work by exploring the ways in which basic marine ecological research can inform the management of human activities that affect the marine environment. Title: Grazing, nutrients, and marine benthic algae : insights into the drivers and protection of diversity Author: Guerry, Anne D., 1973- Two of the most powerful ways in which humans have altered ecosystems are by increasing productivity and changing the densities of important consumers. The bottom-up effects of productivity and the top-down effects of consumers have been identified as primary determinants of biological diversity, though the links between them remain unclear. Understanding how consumers and productivity act and interact to yield differences in diversity is of both conceptual and pragmatic importance. Here, I describe three experiments designed to examine the links between grazing, productivity, and diversity in rocky intertidal systems in Oregon and New Zealand. In two experiments I used fully-factorial designs in which I manipulated both grazing and nutrients. Both experiments revealed the primary importance of grazing as a structuring force of algal assemblages. In the Oregon experiment, I also document an interaction between grazing and productivity, with nutrient enrichment decreasing algal diversity at low grazer densities and increasing algal diversity at high grazer densities. This interaction was not apparent in the New Zealand experiment. In the absence of grazers, nutrient addition led to increased abundance of foliose algae at this site but had no net effect on algal diversity. In the third experiment, also conducted in New Zealand, I used natural variation in nearshore productivity as a backdrop against which I manipulated the access of grazers. In this experiment, I found that grazers had negative impacts on benthic algal diversity and abundance at sites with lower productivity and negligible impacts on benthic algal assemblages at sites with higher productivity. Overall these three studies suggest that in these intertidal grazer-dominated communities, the strong top-down effects often documented in such systems can be modified by more subtle bottom-up effects. Together, results from these experiments elucidate factors that determine algal diversity in these systems and underscore the importance of the evolutionary context in which experiments are conducted. Finally, I conclude with a synthesis of the literature in which I put these and other findings to work by exploring the ways in which basic marine ecological research can inform the management of human activities that affect the marine environment. Close