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• 21. [Article] Conserving avian diversity in agricultural systems : the role of isolated Oregon white oak legacy trees

  Over one third of the earth’s land surface has been modified to some extent for agricultural purposes. The large global footprint of agriculture, combined with the knowledge that existing reserve networks ...

  Citation × Citation Citation Abstract Copy Title: Conserving avian diversity in agricultural systems : the role of isolated Oregon white oak legacy trees Author: DeMars, Craig A. Over one third of the earth’s land surface has been modified to some extent for agricultural purposes. The large global footprint of agriculture, combined with the knowledge that existing reserve networks are likely insufficient for long-term conservation of native biodiversity, has necessitated that agricultural systems contribute to conservation of native biota. Current research paradigms have taken a landscape-level view of conservation in agricultural systems, assessing the relative contribution that various habitat elements make in conserving biodiversity in the agricultural matrix. Within this context, I investigated the potential role that individual Oregon white oak (Quercus garryana) trees play in conserving avian diversity in the agricultural systems of the Willamette Valley, Oregon, U.S.A. Retained by landowners primarily for cultural reasons, many of these trees pre-date Euro-American settlement of the Willamette Valley and thus are biological legacies from historic white oak habitats. I compared avian use of isolated white oak trees in three different site contexts - croplands, pastures, and oak savanna reserves - and used an information-theoretic model selection approach to determine the relative importance of site-specific and landscape-level factors thought to influence avian use of these individual trees. Specifically, I tested whether avian species presence on Oregon white oak legacy trees could best be explained by: (i) tree architecture; (ii) the distance of the tree to the nearest tree or patch; (iii) the density of trees in the surrounding landscape; or (iv) the matrix in which the tree was embedded. I evaluated species-specific responses as well as four community-level responses: (i) total bird species richness; (ii) species richness of native birds associated with oak savanna; (iii) species richness of tree foraging birds; and (iv) the combined species richness of aerial- and ground-foraging birds. I sampled 35 individual white oak trees and recorded 47 avian species using these individual trees, including a high number of oak savanna-associated species such White-breasted Nuthatch (Sitta carolinensis) and Chipping Sparrow (Spizella passerina). For the majority of these species, the frequency of use of individual oak trees was similar among crop, pasture and reserve sites. The most important factors for predicting avian use were tree size and tree density in the surrounding landscape. In general, avian use increased with increasing tree size and decreasing tree density. My findings suggest that individual white oak legacy trees have the potential to positively contribute to landscape-level conservation of a wide range of avian species within the Willamette Valley. Due to the declining abundance of white oak legacy trees on the landscape, the conservation of existing legacy trees and the recruitment of younger replacement trees should be a management priority. Title: Conserving avian diversity in agricultural systems : the role of isolated Oregon white oak legacy trees Author: DeMars, Craig A. Over one third of the earth’s land surface has been modified to some extent for agricultural purposes. The large global footprint of agriculture, combined with the knowledge that existing reserve networks are likely insufficient for long-term conservation of native biodiversity, has necessitated that agricultural systems contribute to conservation of native biota. Current research paradigms have taken a landscape-level view of conservation in agricultural systems, assessing the relative contribution that various habitat elements make in conserving biodiversity in the agricultural matrix. Within this context, I investigated the potential role that individual Oregon white oak (Quercus garryana) trees play in conserving avian diversity in the agricultural systems of the Willamette Valley, Oregon, U.S.A. Retained by landowners primarily for cultural reasons, many of these trees pre-date Euro-American settlement of the Willamette Valley and thus are biological legacies from historic white oak habitats. I compared avian use of isolated white oak trees in three different site contexts - croplands, pastures, and oak savanna reserves - and used an information-theoretic model selection approach to determine the relative importance of site-specific and landscape-level factors thought to influence avian use of these individual trees. Specifically, I tested whether avian species presence on Oregon white oak legacy trees could best be explained by: (i) tree architecture; (ii) the distance of the tree to the nearest tree or patch; (iii) the density of trees in the surrounding landscape; or (iv) the matrix in which the tree was embedded. I evaluated species-specific responses as well as four community-level responses: (i) total bird species richness; (ii) species richness of native birds associated with oak savanna; (iii) species richness of tree foraging birds; and (iv) the combined species richness of aerial- and ground-foraging birds. I sampled 35 individual white oak trees and recorded 47 avian species using these individual trees, including a high number of oak savanna-associated species such White-breasted Nuthatch (Sitta carolinensis) and Chipping Sparrow (Spizella passerina). For the majority of these species, the frequency of use of individual oak trees was similar among crop, pasture and reserve sites. The most important factors for predicting avian use were tree size and tree density in the surrounding landscape. In general, avian use increased with increasing tree size and decreasing tree density. My findings suggest that individual white oak legacy trees have the potential to positively contribute to landscape-level conservation of a wide range of avian species within the Willamette Valley. Due to the declining abundance of white oak legacy trees on the landscape, the conservation of existing legacy trees and the recruitment of younger replacement trees should be a management priority. Close

• 22. [Article] Quantifying dilution and amplification in a community of hosts for tick-borne pathogens

  Data associated with this paper have been deposited in the KNB Data Repository: https://knb.ecoinformatics.org/#view/ knb.779.2

  Citation × Citation Citation Abstract Copy Title: Quantifying dilution and amplification in a community of hosts for tick-borne pathogens Author: Ostfeld, Richard S., Keesing, Felicia, Holt, Robert D., Levi, Taal, Barfield, Michael Data associated with this paper have been deposited in the KNB Data Repository: https://knb.ecoinformatics.org/#view/ knb.779.2 Title: Quantifying dilution and amplification in a community of hosts for tick-borne pathogens Author: Ostfeld, Richard S., Keesing, Felicia, Holt, Robert D., Levi, Taal, Barfield, Michael Data associated with this paper have been deposited in the KNB Data Repository: https://knb.ecoinformatics.org/#view/ knb.779.2 Close

• 23. [Article] Headwater stream macroinvertebrates of the H.J. Andrews Experimental Forest, Oregon

  Recent studies of headwater streams have demonstrated their importance to overall watershed biodiversity, nutrient cycling, and energy flux. However, little attention has been paid to long-term effects ...

  Citation × Citation Citation Abstract Copy Title: Headwater stream macroinvertebrates of the H.J. Andrews Experimental Forest, Oregon Author: Frady, Charles H. Recent studies of headwater streams have demonstrated their importance to overall watershed biodiversity, nutrient cycling, and energy flux. However, little attention has been paid to long-term effects of forest harvest on macroinvertebrate communities in headwater streams. This study investigated headwater stream macroinvertebrate communities in the H.J. Andrews Experimental Forest, Oregon, U.S.A and used a paired-stream study design to examine the effect of prior forest harvest on stream macroinvertebrates. Concomitantly, this study examined how macroinvertebrate life-history traits were related to stream size, substrates, discharge, or water temperature. Results from this study suggest that neither richness nor densities differed between streams flowing through young growth versus old growth forests. Despite similarities among these metrics, multivariate ordination techniques helped elucidate differences in benthic community composition between paired streams when red alder was present in riparian zones of previously harvested basins. Indicator Species Analysis of community composition and abundance revealed that no taxa were exclusively indicative of either forest type. Macroinvertebrate life-history traits among headwater streams were related to stream size, stream substrates, or stream discharge. As predicted, macroinvertebrates that ingest leaf litter (shredders) decreased proportionally with increasing stream width, while macroinvertebrates that scrape off algae and biofilms from instream substrates (scrapers) increased with increasing stream width. Differences in macroinvertebrate habit-trait groups were related to differences in stream substrates or stream discharge between very small headwater streams (< 20ha basin area) and larger headwater streams (50-100ha basin size). Seasonal variation in stream discharge also influenced macroinvertebrate communities. Patterns in adult insect emergence in these streams displayed pulses of activity that varied among streams. During summer 2003, total emergence was greatest in one high elevation stream in this study. During spring 2004, total emergence began earlier in one low elevation and one mid elevation stream, but linkages with stream water temperature were tenuous; cumulative emergence remained higher in these streams than all others through early summer 2004. Though forest harvest often has immediate effects on macroinvertebrate communities, shifts in community composition may persist long-term if regrowth of riparian vegetation includes red alder (Alnus rubra). Analyses of macroinvertebrate life-history traits provided insight regarding species adaptations to environmental conditions. Among six headwater streams within a relatively small landscape (6400ha), proportions of stream macroinvertebrate communities with specific traits differed among streams relative to variability in physical stream attributes. Title: Headwater stream macroinvertebrates of the H.J. Andrews Experimental Forest, Oregon Author: Frady, Charles H. Recent studies of headwater streams have demonstrated their importance to overall watershed biodiversity, nutrient cycling, and energy flux. However, little attention has been paid to long-term effects of forest harvest on macroinvertebrate communities in headwater streams. This study investigated headwater stream macroinvertebrate communities in the H.J. Andrews Experimental Forest, Oregon, U.S.A and used a paired-stream study design to examine the effect of prior forest harvest on stream macroinvertebrates. Concomitantly, this study examined how macroinvertebrate life-history traits were related to stream size, substrates, discharge, or water temperature. Results from this study suggest that neither richness nor densities differed between streams flowing through young growth versus old growth forests. Despite similarities among these metrics, multivariate ordination techniques helped elucidate differences in benthic community composition between paired streams when red alder was present in riparian zones of previously harvested basins. Indicator Species Analysis of community composition and abundance revealed that no taxa were exclusively indicative of either forest type. Macroinvertebrate life-history traits among headwater streams were related to stream size, stream substrates, or stream discharge. As predicted, macroinvertebrates that ingest leaf litter (shredders) decreased proportionally with increasing stream width, while macroinvertebrates that scrape off algae and biofilms from instream substrates (scrapers) increased with increasing stream width. Differences in macroinvertebrate habit-trait groups were related to differences in stream substrates or stream discharge between very small headwater streams (< 20ha basin area) and larger headwater streams (50-100ha basin size). Seasonal variation in stream discharge also influenced macroinvertebrate communities. Patterns in adult insect emergence in these streams displayed pulses of activity that varied among streams. During summer 2003, total emergence was greatest in one high elevation stream in this study. During spring 2004, total emergence began earlier in one low elevation and one mid elevation stream, but linkages with stream water temperature were tenuous; cumulative emergence remained higher in these streams than all others through early summer 2004. Though forest harvest often has immediate effects on macroinvertebrate communities, shifts in community composition may persist long-term if regrowth of riparian vegetation includes red alder (Alnus rubra). Analyses of macroinvertebrate life-history traits provided insight regarding species adaptations to environmental conditions. Among six headwater streams within a relatively small landscape (6400ha), proportions of stream macroinvertebrate communities with specific traits differed among streams relative to variability in physical stream attributes. Close

• 24. [Article] Flow Management for Hydropower Extirpates Aquatic Insects, Undermining River Food Webs

  Published by Oxford University Press on behalf of American Institute of Biological Sciences 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. The published ...

  Citation × Citation Citation Abstract Copy Title: Flow Management for Hydropower Extirpates Aquatic Insects, Undermining River Food Webs Author: Lytle, David A., Baxter, Colden V., Muehlbauer, Jeffrey D., Kortenhoeven, Eric W., Yackulic, Charles B., Metcalfe, Anya N., Miller, Scott W., Dibble, Kimberly L., Kennedy, Theodore A. Published by Oxford University Press on behalf of American Institute of Biological Sciences 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. The published article can be found at: http://bioscience.oxfordjournals.org/content/66/7/561 Title: Flow Management for Hydropower Extirpates Aquatic Insects, Undermining River Food Webs Author: Lytle, David A., Baxter, Colden V., Muehlbauer, Jeffrey D., Kortenhoeven, Eric W., Yackulic, Charles B., Metcalfe, Anya N., Miller, Scott W., Dibble, Kimberly L., Kennedy, Theodore A. Published by Oxford University Press on behalf of American Institute of Biological Sciences 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. The published article can be found at: http://bioscience.oxfordjournals.org/content/66/7/561 Close

• 25. [Article] Cattle grazing in semiarid forestlands: Habitat selection during periods of drought

  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 American ...

  Citation × Citation Citation Abstract Copy Title: Cattle grazing in semiarid forestlands: Habitat selection during periods of drought Author: DelCurto, T., Rowland, M., Roever, C. L., Vavra, M., Wisdom, M. 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 American Society of Animal Science and can be found at: https://www.animalsciencepublications.org/publications/jas Title: Cattle grazing in semiarid forestlands: Habitat selection during periods of drought Author: DelCurto, T., Rowland, M., Roever, C. L., Vavra, M., Wisdom, M. 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 American Society of Animal Science and can be found at: https://www.animalsciencepublications.org/publications/jas Close

• 26. [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

• 27. [Article] Host species composition influences infection severity among amphibians in the absence of spillover transmission

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/jo...

  Citation × Citation Citation Abstract Copy Title: Host species composition influences infection severity among amphibians in the absence of spillover transmission Author: Han, Barbara A., Storfer, Andrew, Blaustein, Andrew R., Searle, Catherine L., Kerby, Jacob L. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292045-7758 Title: Host species composition influences infection severity among amphibians in the absence of spillover transmission Author: Han, Barbara A., Storfer, Andrew, Blaustein, Andrew R., Searle, Catherine L., Kerby, Jacob L. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292045-7758 Close

• 28. [Article] Amazon Rainforest Microbial Observatory Metagenomes

  79 files of metagenomic DNA sequence data, README file, OTU tables (community matrices), and metadata file for relating sequence files to original samples. NOTE: sequence data is available at http://...

  Citation × Citation Citation Abstract Copy Title: Amazon Rainforest Microbial Observatory Metagenomes Author: Bohannan, Brendan J. M., Meyer, Kyle M., Klein, Ann M., Rodrigues, Jorge L. M., Nusslein, Klaus, Tringe, Susannah G., Mirza, Babur S., Tiedje, James M. Year: 2016, 2010 79 files of metagenomic DNA sequence data, README file, OTU tables (community matrices), and metadata file for relating sequence files to original samples. NOTE: sequence data is available at http://lib-vm-rdmi.uoregon.edu/data/21993/ Title: Amazon Rainforest Microbial Observatory Metagenomes Author: Bohannan, Brendan J. M., Meyer, Kyle M., Klein, Ann M., Rodrigues, Jorge L. M., Nusslein, Klaus, Tringe, Susannah G., Mirza, Babur S., Tiedje, James M. Year: 2016, 2010 79 files of metagenomic DNA sequence data, README file, OTU tables (community matrices), and metadata file for relating sequence files to original samples. NOTE: sequence data is available at http://lib-vm-rdmi.uoregon.edu/data/21993/ Close

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

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

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