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• 101. [Article] Understanding the Links Between Cyanobacteria Physiology and Hydrodynamics may Help Find Adaption Strategies for Toxic Blooms

  Even though we are managing lakes to decrease algal blooms overall, harmful algal blooms seem to be showing up more and more frequently. Although the word “blooms” connotes dominance and rapid growth, ...

  Citation × Citation Citation Abstract Copy Title: Understanding the Links Between Cyanobacteria Physiology and Hydrodynamics may Help Find Adaption Strategies for Toxic Blooms Author: Rueter, John Year: 2016 Even though we are managing lakes to decrease algal blooms overall, harmful algal blooms seem to be showing up more and more frequently. Although the word “blooms” connotes dominance and rapid growth, dangerous accumulations of cyanobacteria can occur because of combinations of physiological advantages and particular weather and hydrodynamic conditions. I am particularly interested in specific conditions that might favor Aphanizomenon versus those that might favor Microcystis in Upper Klamath and Agency Lakes. Aphanizomenon is a nuisance and large blooms can lead to oxygen depletion and fish deaths. Microcystis can both be a nuisance and is toxic. The comparison of the physiologies of these two cyanobacterial strains could lead to an understanding of both short term adaptation and mitigation tactics as well as long term lake restoration strategies. Ideally, we would like to employ lake restoration strategies and see constant improvement leading to safer and cleaner water. However, either because of threshold effects or ineffective lake management approaches, we might have to take short-term manipulations that can reduce local accumulations of cyanobacteria to protect the health of humans and other species. These short term tactics must have three characteristics: First, we need to find mitigation techniques that might knock down or stall a bloom of algae from occurring. Second, we have to have ways to model and monitor these manipulations over relevant time and space scales. Third, any short-term techniques we employ should not substantial interfere with the long term goals of lake restoration, i.e. the quick fix shouldn’t undermine the solving the problem. I will present several potential short-term solutions based algal physiology and hydrodynamics. Then I will describe how we have used temperature datalogging (10 minute intervals) and high-resolution transects (1 meter spatial resolution) to understand impacts on accumulation processes. Then finally, I will describe a framework for supporting fast and cheap methods to adapt to cyanobacteria accumulations that don’t result in unintended consequences or interfere with lake restoration efforts. Title: Understanding the Links Between Cyanobacteria Physiology and Hydrodynamics may Help Find Adaption Strategies for Toxic Blooms Author: Rueter, John Year: 2016 Even though we are managing lakes to decrease algal blooms overall, harmful algal blooms seem to be showing up more and more frequently. Although the word “blooms” connotes dominance and rapid growth, dangerous accumulations of cyanobacteria can occur because of combinations of physiological advantages and particular weather and hydrodynamic conditions. I am particularly interested in specific conditions that might favor Aphanizomenon versus those that might favor Microcystis in Upper Klamath and Agency Lakes. Aphanizomenon is a nuisance and large blooms can lead to oxygen depletion and fish deaths. Microcystis can both be a nuisance and is toxic. The comparison of the physiologies of these two cyanobacterial strains could lead to an understanding of both short term adaptation and mitigation tactics as well as long term lake restoration strategies. Ideally, we would like to employ lake restoration strategies and see constant improvement leading to safer and cleaner water. However, either because of threshold effects or ineffective lake management approaches, we might have to take short-term manipulations that can reduce local accumulations of cyanobacteria to protect the health of humans and other species. These short term tactics must have three characteristics: First, we need to find mitigation techniques that might knock down or stall a bloom of algae from occurring. Second, we have to have ways to model and monitor these manipulations over relevant time and space scales. Third, any short-term techniques we employ should not substantial interfere with the long term goals of lake restoration, i.e. the quick fix shouldn’t undermine the solving the problem. I will present several potential short-term solutions based algal physiology and hydrodynamics. Then I will describe how we have used temperature datalogging (10 minute intervals) and high-resolution transects (1 meter spatial resolution) to understand impacts on accumulation processes. Then finally, I will describe a framework for supporting fast and cheap methods to adapt to cyanobacteria accumulations that don’t result in unintended consequences or interfere with lake restoration efforts. Close

• 102. [Article] Symbiosis with Nitrogen-fixing Rhizobia Influences Plant Defense Strategy and Plant-predator Interactions

  As sessile organisms, plants evolved a plethora of defenses against their attackers. Given the role of plants as a primary food source for many organisms, plant defense has important implications for community ...

  Citation × Citation Citation Abstract Copy Title: Symbiosis with Nitrogen-fixing Rhizobia Influences Plant Defense Strategy and Plant-predator Interactions Author: Godschalx, Adrienne Louise Year: 2017 As sessile organisms, plants evolved a plethora of defenses against their attackers. Given the role of plants as a primary food source for many organisms, plant defense has important implications for community ecology. Surprisingly, despite the potential to alter entire food webs and communities, the factors determining plant investment in defense are not well-understood, and are even less understood considering the numerous symbiotic interactions in the same plant. Legume-rhizobia symbioses engineer ecosystems by fixing nitrogen from the atmosphere in trade for plant photosynthates, yet connecting symbiotic resource exchange to food web interactions has yet to be established. Here I test how rhizobia influence plant defense and tritrophic interactions in lima bean (Fabaceae - Phaseolus lunatus L.): a model plant in chemical ecology research characterized by a broad range of different defenses. Examining suites of traits among lima bean genotypes, highly cyanogenic cultivars and wild type plants (high cyanotypes) produce more hook-shaped trichomes, as a putative combined approach of chemical and mechanical defenses, forming defense syndromes to protect against multiple feeding guilds (Chapter 2). Testing costs that may have contributed to forming tradeoffs among strategies, high cyanotypes show reduced fitness under plant-plant competition relative to low cyanotypes, but when challenged with herbivory, high cyanotypes fitness reductions are no longer evident (Chapter 3). Young leaves, not reproductive organs, are the most cyanogenic lima bean organ, and removal quantitatively decreases fitness, supporting assumptions that the most valuable tissues will be most highly defended (Chapter 4). Testing the degree to which nitrogen-fixing rhizobia contribute to cyanogenesis, high cyanotypes form more nodules than low cyanotypes. Quantitative relationships between nodule number and plant traits highlight the role symbiotic investment plays a role in plant defense and nutritive phenotype, while simultaneously, genotypically-determined levels of defense shape plant investment in symbiosis (Chapter 5). Interestingly, traits that trade off by cyanotype (i.e. high cyanogenesis but low indirect defense) reflect the patterns in plants with nitrogen-fixing rhizobia. Rhizobia-inoculated lima beans show reduced indirect defenses, recruiting fewer parasitoid wasps (Chapter 6) and predatory ants (Chapter 7). Examining plant-ant attraction in greater detail, ants prefer headspace regions above EFN droplets, corresponding with species-specific differences in suites of volatiles, indicating EFN, like floral nectar, can be scented to manipulate insect behavior (Chapter 8). Overall, understanding when investing in traits to recruit predators is more effective than investing in defensive chemistry, and how particular ecological contexts, such as symbioses can influence the outcome of defense allocation strategies remains a fascinating area of research. Determining the mechanisms underlying why rhizobia and other belowground microbial symbionts influence their host plants' aboveground interactions, whether plants traits affected by symbiotic microbes are simply a function of the costs and benefits from resource exchange, or whether symbionts can influence the success of primarily direct versus indirectly defended plants is an important question for understanding complex trophic systems and connecting to agricultural implications for more effective biological pest control. Title: Symbiosis with Nitrogen-fixing Rhizobia Influences Plant Defense Strategy and Plant-predator Interactions Author: Godschalx, Adrienne Louise Year: 2017 As sessile organisms, plants evolved a plethora of defenses against their attackers. Given the role of plants as a primary food source for many organisms, plant defense has important implications for community ecology. Surprisingly, despite the potential to alter entire food webs and communities, the factors determining plant investment in defense are not well-understood, and are even less understood considering the numerous symbiotic interactions in the same plant. Legume-rhizobia symbioses engineer ecosystems by fixing nitrogen from the atmosphere in trade for plant photosynthates, yet connecting symbiotic resource exchange to food web interactions has yet to be established. Here I test how rhizobia influence plant defense and tritrophic interactions in lima bean (Fabaceae - Phaseolus lunatus L.): a model plant in chemical ecology research characterized by a broad range of different defenses. Examining suites of traits among lima bean genotypes, highly cyanogenic cultivars and wild type plants (high cyanotypes) produce more hook-shaped trichomes, as a putative combined approach of chemical and mechanical defenses, forming defense syndromes to protect against multiple feeding guilds (Chapter 2). Testing costs that may have contributed to forming tradeoffs among strategies, high cyanotypes show reduced fitness under plant-plant competition relative to low cyanotypes, but when challenged with herbivory, high cyanotypes fitness reductions are no longer evident (Chapter 3). Young leaves, not reproductive organs, are the most cyanogenic lima bean organ, and removal quantitatively decreases fitness, supporting assumptions that the most valuable tissues will be most highly defended (Chapter 4). Testing the degree to which nitrogen-fixing rhizobia contribute to cyanogenesis, high cyanotypes form more nodules than low cyanotypes. Quantitative relationships between nodule number and plant traits highlight the role symbiotic investment plays a role in plant defense and nutritive phenotype, while simultaneously, genotypically-determined levels of defense shape plant investment in symbiosis (Chapter 5). Interestingly, traits that trade off by cyanotype (i.e. high cyanogenesis but low indirect defense) reflect the patterns in plants with nitrogen-fixing rhizobia. Rhizobia-inoculated lima beans show reduced indirect defenses, recruiting fewer parasitoid wasps (Chapter 6) and predatory ants (Chapter 7). Examining plant-ant attraction in greater detail, ants prefer headspace regions above EFN droplets, corresponding with species-specific differences in suites of volatiles, indicating EFN, like floral nectar, can be scented to manipulate insect behavior (Chapter 8). Overall, understanding when investing in traits to recruit predators is more effective than investing in defensive chemistry, and how particular ecological contexts, such as symbioses can influence the outcome of defense allocation strategies remains a fascinating area of research. Determining the mechanisms underlying why rhizobia and other belowground microbial symbionts influence their host plants' aboveground interactions, whether plants traits affected by symbiotic microbes are simply a function of the costs and benefits from resource exchange, or whether symbionts can influence the success of primarily direct versus indirectly defended plants is an important question for understanding complex trophic systems and connecting to agricultural implications for more effective biological pest control. Close

• 103. [Article] Improving the Technical and Economic Performance of Aquaculture: Perspective from Bio-Economic Model

  Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, ...

  Citation × Citation Citation Abstract Copy Title: Improving the Technical and Economic Performance of Aquaculture: Perspective from Bio-Economic Model Author: Leung, PingSun, Cai, Junning, Yuan, Xinhua, Yuan, Yongming, Luo, Yongju Year: 2016 Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, July 11-15, 2016. Compiled by Stefani J. Evers and Ann L. Shriver. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Title: Improving the Technical and Economic Performance of Aquaculture: Perspective from Bio-Economic Model Author: Leung, PingSun, Cai, Junning, Yuan, Xinhua, Yuan, Yongming, Luo, Yongju Year: 2016 Suggested Bibliographic Reference: Challenging New Frontiers in the Global Seafood Sector: Proceedings of the Eighteenth Biennial Conference of the International Institute of Fisheries Economics and Trade, July 11-15, 2016. Compiled by Stefani J. Evers and Ann L. Shriver. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Close

• 104. [Article] A Hierarchical Modeling Approach to Simulating the Geomorphic Response of River Systems to Climate Change

  Anthropogenic climate change significantly affects water resources. River flows in mountainous regions are driven by snowmelt and are therefore highly sensitive to increases in temperature resulting from ...

  Citation × Citation Citation Abstract Copy Title: A Hierarchical Modeling Approach to Simulating the Geomorphic Response of River Systems to Climate Change Author: Praskievicz, Sarah Year: 2014 Anthropogenic climate change significantly affects water resources. River flows in mountainous regions are driven by snowmelt and are therefore highly sensitive to increases in temperature resulting from climate change. Climate-driven hydrological changes are potentially significant for the fluvial geomorphology of river systems. In unchanging climatic and tectonic conditions, a river's morphology will develop in equilibrium with inputs of water and sediment, but climate change represents a potential forcing on these variables that may push the system into disequilibrium and cause significant changes in river morphology. Geomorphic factors, such as channel geometry, planform, and sediment transport, are major determinants of the value of river systems, including their suitability for threatened and endangered species and for human uses of water. This dissertation research uses a hierarchical modeling approach to investigate potential impacts of anthropogenic climate change on river morphology in the interior Pacific Northwest. The research will address the following theoretical and methodological objectives: 1) Develop downscaled climate change scenarios, based on regional climate-model output, including changes in daily minimum and maximum temperature and precipitation. 2) Estimate how climate change scenarios affect river discharge and suspended-sediment load, using a basin-scale hydrologic model. 3) Examine potential impacts of climate-driven hydrologic changes on stream power and shear stress, bedload sediment transport, and river morphology, including channel geometry and planform. The downscaling approach, based on empirically-estimated local topographic lapse rates, produces high-resolution climate grids with positive forecast skill. The hydrologic modeling results indicate that projected climate change in the study rivers will change the annual cycle of hydrology, with increased winter discharge, a decrease in the magnitude of the spring snowmelt peak, and decreased summer discharge. Geomorphic modeling results suggest that changes in reach-averaged bedload transport are highly sensitive to likely changes in the recurrence interval of the critical discharge needed to mobilize bed sediments. This dissertation research makes an original contribution to the climate-change impacts literature by linking Earth processes across a wide range of spatial scales to project changes in river systems that may be significant for management of these systems for societal and ecological benefits. This dissertation includes unpublished co-authored material. Title: A Hierarchical Modeling Approach to Simulating the Geomorphic Response of River Systems to Climate Change Author: Praskievicz, Sarah Year: 2014 Anthropogenic climate change significantly affects water resources. River flows in mountainous regions are driven by snowmelt and are therefore highly sensitive to increases in temperature resulting from climate change. Climate-driven hydrological changes are potentially significant for the fluvial geomorphology of river systems. In unchanging climatic and tectonic conditions, a river's morphology will develop in equilibrium with inputs of water and sediment, but climate change represents a potential forcing on these variables that may push the system into disequilibrium and cause significant changes in river morphology. Geomorphic factors, such as channel geometry, planform, and sediment transport, are major determinants of the value of river systems, including their suitability for threatened and endangered species and for human uses of water. This dissertation research uses a hierarchical modeling approach to investigate potential impacts of anthropogenic climate change on river morphology in the interior Pacific Northwest. The research will address the following theoretical and methodological objectives: 1) Develop downscaled climate change scenarios, based on regional climate-model output, including changes in daily minimum and maximum temperature and precipitation. 2) Estimate how climate change scenarios affect river discharge and suspended-sediment load, using a basin-scale hydrologic model. 3) Examine potential impacts of climate-driven hydrologic changes on stream power and shear stress, bedload sediment transport, and river morphology, including channel geometry and planform. The downscaling approach, based on empirically-estimated local topographic lapse rates, produces high-resolution climate grids with positive forecast skill. The hydrologic modeling results indicate that projected climate change in the study rivers will change the annual cycle of hydrology, with increased winter discharge, a decrease in the magnitude of the spring snowmelt peak, and decreased summer discharge. Geomorphic modeling results suggest that changes in reach-averaged bedload transport are highly sensitive to likely changes in the recurrence interval of the critical discharge needed to mobilize bed sediments. This dissertation research makes an original contribution to the climate-change impacts literature by linking Earth processes across a wide range of spatial scales to project changes in river systems that may be significant for management of these systems for societal and ecological benefits. This dissertation includes unpublished co-authored material. Close

• 105. [Article] The Taphonomy of Archaeological Fish Remains: Experimental Approaches to Understanding the Effects of Natural and Cultural Processes on the Presence and Identification of Cut Marks

  Despite the fact that fish are a common component of coastal and other aquatic archaeological sites, fish bone taphonomy--including bone surface modifications and the effects of burial--remains woefully ...

  Citation × Citation Citation Abstract Copy Title: The Taphonomy of Archaeological Fish Remains: Experimental Approaches to Understanding the Effects of Natural and Cultural Processes on the Presence and Identification of Cut Marks Author: Willis, Lauren Year: 2014 Despite the fact that fish are a common component of coastal and other aquatic archaeological sites, fish bone taphonomy--including bone surface modifications and the effects of burial--remains woefully understudied. Various ethnographic accounts describe fish butchering techniques for immediate consumption and drying, yet cut marks are rarely reported on archaeological fish remains. To address a significant gap in our understanding of fish taphonomy, I devised an experimental research program aimed at assessing whether butchering fish produces cut marks on fish bones and, if so, what factors might account for the discrepancy between the experimental results and the archaeological record. Chapter I provides an introduction to experimental archaeology, including the criticisms and benefits of this approach. Chapter II presents the results of my initial butchery experiment, which establishes that butchering fish can produce abundant cut marks. Chapter III evaluates the effect of the butcher's skill level on the number and distribution of cut marks produced on fish bone during butchery. The results indicate that professional butchers produce nearly 50 percent fewer cut marks than novice- and intermediate-level butchers. Chapter IV addresses the effect of post-depositional taphonomic processes on the long-term visibility of cut marks. Despite a relatively short burial period (27 months), visible cut marks decreased by up to 75 percent, depending on the species. Chapter V is a re-analysis of the fish bone from column E6 at Daisy Cave (CA-SMI-261). Appling the referential framework I acquired through the experiments, I identified 62 cut marks on bones dating from the Early to Late Holocene. A comprehensive understanding of aquatic resource use has implications for a broad range of archaeological topics, including our understanding of hominid diet and resource use; identifying butchery and processing practices among fishing peoples; distinguishing between human and natural agency in the accumulation of fish remains; and assessing questions of behavioral modernity and social complexity. As we continue to recognize the primacy of coastal adaptations throughout human history, it is increasingly critical to expand the breadth of our knowledge regarding the taphonomy of fish remains at archaeological sites. This dissertation includes previously published and unpublished co-authored material. Title: The Taphonomy of Archaeological Fish Remains: Experimental Approaches to Understanding the Effects of Natural and Cultural Processes on the Presence and Identification of Cut Marks Author: Willis, Lauren Year: 2014 Despite the fact that fish are a common component of coastal and other aquatic archaeological sites, fish bone taphonomy--including bone surface modifications and the effects of burial--remains woefully understudied. Various ethnographic accounts describe fish butchering techniques for immediate consumption and drying, yet cut marks are rarely reported on archaeological fish remains. To address a significant gap in our understanding of fish taphonomy, I devised an experimental research program aimed at assessing whether butchering fish produces cut marks on fish bones and, if so, what factors might account for the discrepancy between the experimental results and the archaeological record. Chapter I provides an introduction to experimental archaeology, including the criticisms and benefits of this approach. Chapter II presents the results of my initial butchery experiment, which establishes that butchering fish can produce abundant cut marks. Chapter III evaluates the effect of the butcher's skill level on the number and distribution of cut marks produced on fish bone during butchery. The results indicate that professional butchers produce nearly 50 percent fewer cut marks than novice- and intermediate-level butchers. Chapter IV addresses the effect of post-depositional taphonomic processes on the long-term visibility of cut marks. Despite a relatively short burial period (27 months), visible cut marks decreased by up to 75 percent, depending on the species. Chapter V is a re-analysis of the fish bone from column E6 at Daisy Cave (CA-SMI-261). Appling the referential framework I acquired through the experiments, I identified 62 cut marks on bones dating from the Early to Late Holocene. A comprehensive understanding of aquatic resource use has implications for a broad range of archaeological topics, including our understanding of hominid diet and resource use; identifying butchery and processing practices among fishing peoples; distinguishing between human and natural agency in the accumulation of fish remains; and assessing questions of behavioral modernity and social complexity. As we continue to recognize the primacy of coastal adaptations throughout human history, it is increasingly critical to expand the breadth of our knowledge regarding the taphonomy of fish remains at archaeological sites. This dissertation includes previously published and unpublished co-authored material. Close

• 106. [Article] THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON

  72 pages

  Citation × Citation Citation Abstract Copy Title: THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON Author: GUSTAFSON, ERIC PAUL Year: 2016, 1978 72 pages Title: THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON Author: GUSTAFSON, ERIC PAUL Year: 2016, 1978 72 pages Close

• 107. [Article] Physical Oceanography, Larval Dispersal, and Settlement Across Nearshore Fronts

  The larvae of coastal species interact with nearshore currents that are complex and can alter dispersal. I investigated two sites in southern Oregon with different nearshore hydrodynamics: the first site, ...

  Citation × Citation Citation Abstract Copy Title: Physical Oceanography, Larval Dispersal, and Settlement Across Nearshore Fronts Author: Jarvis, Marley Year: 2015 The larvae of coastal species interact with nearshore currents that are complex and can alter dispersal. I investigated two sites in southern Oregon with different nearshore hydrodynamics: the first site, Sunset Bay, is a small cove with a topographic front that extends across the mouth during upwelling-favorable winds. Using holey sock drogues at 1.5 m and 5.5 m depths and surface drifters at 10 cm depth, I found that, when the front was present, water at 1.5 m was retained within the bay whereas water was exchanged across the front at a depth of 5.5 m. Surface drifters indicated a surface convergence. Surface plankton tows on either side and within the frontal convergence (a shore-parallel foam line) found significantly higher concentrations of barnacle cyprids, crab megalopae and zoea, polychaete larvae, platyhelminthes juveniles, isopods, amphipods, harpacticoid copepods, and fish eggs. Crustacean nauplii (barnacle, euphausiid, and copepod) and calanoid copepods were not concentrated in the convergence, and when the front and foam line were absent, no taxa were concentrated. Plankton tows taken within the foam line as it dissipated shoreward during a wind-reversal event found that concentrations of cyprids, megalopae, and gastropod veligers remained high as the foam line moved, suggesting that it acts as a moving convergence propagating competent larvae shoreward. I measured settlement of two taxa at Sunset Bay and Shore Acres, an open-coast site <2 km away. Barnacle settlement measured every other day from June-September 2013 was significantly cross-correlated with the maximum daily tidal height at lags of -2 days at Sunset Bay and +2 and +4 days at Shore Acres. Settlement was also significantly negatively cross-correlated with wave height at a lag of -4 days at Sunset Bay. Coralline algae settlement measured during eight 48-hr periods in July-August 2013 was significantly negatively correlated with wave height (n = 8, R2 = 0.76, P = 0.0049) at Shore Acres but not at Sunset Bay. Despite the close proximity of the Sunset Bay and Shore Acres sites, settlement patterns differed between taxa, suggesting that differences in nearshore hydrodynamics might affect the supply of water and larvae to shore. This dissertation includes unpublished co-authored material. Title: Physical Oceanography, Larval Dispersal, and Settlement Across Nearshore Fronts Author: Jarvis, Marley Year: 2015 The larvae of coastal species interact with nearshore currents that are complex and can alter dispersal. I investigated two sites in southern Oregon with different nearshore hydrodynamics: the first site, Sunset Bay, is a small cove with a topographic front that extends across the mouth during upwelling-favorable winds. Using holey sock drogues at 1.5 m and 5.5 m depths and surface drifters at 10 cm depth, I found that, when the front was present, water at 1.5 m was retained within the bay whereas water was exchanged across the front at a depth of 5.5 m. Surface drifters indicated a surface convergence. Surface plankton tows on either side and within the frontal convergence (a shore-parallel foam line) found significantly higher concentrations of barnacle cyprids, crab megalopae and zoea, polychaete larvae, platyhelminthes juveniles, isopods, amphipods, harpacticoid copepods, and fish eggs. Crustacean nauplii (barnacle, euphausiid, and copepod) and calanoid copepods were not concentrated in the convergence, and when the front and foam line were absent, no taxa were concentrated. Plankton tows taken within the foam line as it dissipated shoreward during a wind-reversal event found that concentrations of cyprids, megalopae, and gastropod veligers remained high as the foam line moved, suggesting that it acts as a moving convergence propagating competent larvae shoreward. I measured settlement of two taxa at Sunset Bay and Shore Acres, an open-coast site <2 km away. Barnacle settlement measured every other day from June-September 2013 was significantly cross-correlated with the maximum daily tidal height at lags of -2 days at Sunset Bay and +2 and +4 days at Shore Acres. Settlement was also significantly negatively cross-correlated with wave height at a lag of -4 days at Sunset Bay. Coralline algae settlement measured during eight 48-hr periods in July-August 2013 was significantly negatively correlated with wave height (n = 8, R2 = 0.76, P = 0.0049) at Shore Acres but not at Sunset Bay. Despite the close proximity of the Sunset Bay and Shore Acres sites, settlement patterns differed between taxa, suggesting that differences in nearshore hydrodynamics might affect the supply of water and larvae to shore. This dissertation includes unpublished co-authored material. Close

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

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

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

• 109. [Article] THE ROLE OF CHROMODOMAIN PROTEIN 1 (CDP-1) AT NEUROSPORA CRASSA HETEROCHROMATIN

  36 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2...

  Citation × Citation Citation Abstract Copy Title: THE ROLE OF CHROMODOMAIN PROTEIN 1 (CDP-1) AT NEUROSPORA CRASSA HETEROCHROMATIN Author: Kim, Carissa Year: 2016 36 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Title: THE ROLE OF CHROMODOMAIN PROTEIN 1 (CDP-1) AT NEUROSPORA CRASSA HETEROCHROMATIN Author: Kim, Carissa Year: 2016 36 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Close