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• 11. [Article] Stranding Mortality Patterns in California Sea Lions and Steller Sea Lions in Oregon and Southern Washington, 2006 to 2014

  As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts ...

  Citation × Citation Citation Abstract Copy Title: Stranding Mortality Patterns in California Sea Lions and Steller Sea Lions in Oregon and Southern Washington, 2006 to 2014 Author: Lee, Kessina Year: 2016 As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts with commercial and recreational fisheries. An analysis of strandings of California sea lions, Zalophus californianus, and Steller sea lions, Eumetopias jubatus, from 2006 to 2014, included cause of death, changing ocean conditions, and anthropogenic activity. Causes of death included disease, injury, and human interaction, such as gunshot wounds, fisheries net entanglements and boat strikes. Oregon and Washington strandings of California sea lions are primarily adult and subadult males that migrate north from California rookeries, while Steller sea lions are year-round residents and strandings are comprised of males and females of all ages. While the California sea lion population is currently at or near carrying capacity, the Eastern Pacific population of Steller sea lions was designated as Threatened under the Endangered Species Act until October 2013. Understanding impacts to these two pinniped species is vital to implementing effective management and conservation policies. Oregon and southern Washington strandings of California sea lions and Steller sea lions from 2006 to 2014 were analyzed spatially using the geographic information system (GIS), and temporally to identify possible correlations with prey availability and human interaction. Strandings were found to follow seasonal patterns from year to year: Steller sea lion strandings were highest from May to July, California sea lions peaked in September, October, and November. There was a correlation between significantly high numbers of strandings and the three largest commercial fisheries in Oregon: Chinook salmon, Coho salmon, and Dungeness crab. This analysis provides a format for continuing to monitor primary ecological and anthropogenic drivers of pinniped mortality in Oregon and southern Washington. Title: Stranding Mortality Patterns in California Sea Lions and Steller Sea Lions in Oregon and Southern Washington, 2006 to 2014 Author: Lee, Kessina Year: 2016 As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts with commercial and recreational fisheries. An analysis of strandings of California sea lions, Zalophus californianus, and Steller sea lions, Eumetopias jubatus, from 2006 to 2014, included cause of death, changing ocean conditions, and anthropogenic activity. Causes of death included disease, injury, and human interaction, such as gunshot wounds, fisheries net entanglements and boat strikes. Oregon and Washington strandings of California sea lions are primarily adult and subadult males that migrate north from California rookeries, while Steller sea lions are year-round residents and strandings are comprised of males and females of all ages. While the California sea lion population is currently at or near carrying capacity, the Eastern Pacific population of Steller sea lions was designated as Threatened under the Endangered Species Act until October 2013. Understanding impacts to these two pinniped species is vital to implementing effective management and conservation policies. Oregon and southern Washington strandings of California sea lions and Steller sea lions from 2006 to 2014 were analyzed spatially using the geographic information system (GIS), and temporally to identify possible correlations with prey availability and human interaction. Strandings were found to follow seasonal patterns from year to year: Steller sea lion strandings were highest from May to July, California sea lions peaked in September, October, and November. There was a correlation between significantly high numbers of strandings and the three largest commercial fisheries in Oregon: Chinook salmon, Coho salmon, and Dungeness crab. This analysis provides a format for continuing to monitor primary ecological and anthropogenic drivers of pinniped mortality in Oregon and southern Washington. Close

• 12. [Article] Increased Habitat Connectivity Homogenizes Freshwater Communities: Historical and Landscape Perspectives

  Increases in habitat connectivity can have consequences for taxonomic, functional, and genetic diversity of communities. Previously isolated aquatic habitats were connected with canals and pipelines in ...

  Citation × Citation Citation Abstract Copy Title: Increased Habitat Connectivity Homogenizes Freshwater Communities: Historical and Landscape Perspectives Author: Strecker, Angela L., Brittain, Jeffrey Thomas Year: 2017 Increases in habitat connectivity can have consequences for taxonomic, functional, and genetic diversity of communities. Previously isolated aquatic habitats were connected with canals and pipelines in the largest water development project in the US history, the Columbia Basin Project (CBP; eastern Washington, USA), which also altered environmental conditions; however, the ecological consequences are largely unknown. Using a historical dataset, we examined long-term patterns in zooplankton communities, water chemistry and clarity, testing the hypothesis that increased connectivity will result in taxonomic homogenization. Further, we tested contemporary drivers of communities using a comprehensive set of environmental and landscape variables. Waterbodies were sampled for zooplankton community composition as well as physical and chemical variables inside and outside the CBP using methods consistent with historical studies. We found significant declines in salinity inside the CBP, whereas changes in water clarity were prevalent across all waterbodies. Increased connectivity via canals homogenized zooplankton communities over time, as well as increasing regional richness. Other long-term changes in zooplankton communities may be related to climate change, invasive species, and land-use changes. Synthesis and applications. Though canals may offer species spatial refugia, homogenization may decrease resilience to environmental stressors. These new hybrid aquatic landscapes, or hydroscapes, should be considered carefully in future water development, including specific plans for monitoring of species and environmental conditions, as well as mitigation of undesirable conditions and/or non-native species. Title: Increased Habitat Connectivity Homogenizes Freshwater Communities: Historical and Landscape Perspectives Author: Strecker, Angela L., Brittain, Jeffrey Thomas Year: 2017 Increases in habitat connectivity can have consequences for taxonomic, functional, and genetic diversity of communities. Previously isolated aquatic habitats were connected with canals and pipelines in the largest water development project in the US history, the Columbia Basin Project (CBP; eastern Washington, USA), which also altered environmental conditions; however, the ecological consequences are largely unknown. Using a historical dataset, we examined long-term patterns in zooplankton communities, water chemistry and clarity, testing the hypothesis that increased connectivity will result in taxonomic homogenization. Further, we tested contemporary drivers of communities using a comprehensive set of environmental and landscape variables. Waterbodies were sampled for zooplankton community composition as well as physical and chemical variables inside and outside the CBP using methods consistent with historical studies. We found significant declines in salinity inside the CBP, whereas changes in water clarity were prevalent across all waterbodies. Increased connectivity via canals homogenized zooplankton communities over time, as well as increasing regional richness. Other long-term changes in zooplankton communities may be related to climate change, invasive species, and land-use changes. Synthesis and applications. Though canals may offer species spatial refugia, homogenization may decrease resilience to environmental stressors. These new hybrid aquatic landscapes, or hydroscapes, should be considered carefully in future water development, including specific plans for monitoring of species and environmental conditions, as well as mitigation of undesirable conditions and/or non-native species. Close

• 13. [Article] PrimeFish Project: Linking the Needs of the Producer, Market and Consumers

  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: PrimeFish Project: Linking the Needs of the Producer, Market and Consumers Author: Gunnlaugsson, Valur N., Stefánsson, Guðmundur 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: PrimeFish Project: Linking the Needs of the Producer, Market and Consumers Author: Gunnlaugsson, Valur N., Stefánsson, Guðmundur 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

• 14. [Article] Investigating Variation in Coral Reef Morphology with Photomosaics and Analysis of Percent Cover

  42 pages

  Citation × Citation Citation Abstract Copy Title: Investigating Variation in Coral Reef Morphology with Photomosaics and Analysis of Percent Cover Author: Culman, Justin Year: 2017 42 pages Title: Investigating Variation in Coral Reef Morphology with Photomosaics and Analysis of Percent Cover Author: Culman, Justin Year: 2017 42 pages Close

• 15. [Article] A Behavior-Based Framework for Assessing Barrier Effects to Wildlife from Vehicle Traffic Volume

  Roads, while central to the function of human society, create barriers to animal movement through collisions and habitat fragmentation. Barriers to animal movement affect the evolution and trajectory of ...

  Citation × Citation Citation Abstract Copy Title: A Behavior-Based Framework for Assessing Barrier Effects to Wildlife from Vehicle Traffic Volume Author: Jacobson, Sandra L., Bliss-Ketchum, Leslie L., de Rivera, Catherine E., Smith, Winston P. Year: 2016 Roads, while central to the function of human society, create barriers to animal movement through collisions and habitat fragmentation. Barriers to animal movement affect the evolution and trajectory of populations. Investigators have attempted to use traffic volume, the number of vehicles passing a point on a road segment, to predict effects to wildlife populations approximately linearly and along taxonomic lines; however, taxonomic groupings cannot provide sound predictions because closely related species often respond differently. We assess the role of wildlife behavioral responses to traffic volume as a tool to predict barrier effects from vehicle-caused mortality and avoidance, to provide an early warning system that recognizes traffic volume as a trigger for mitigation, and to better interpret roadkill data. We propose four categories of behavioral response based on the perceived danger to traffic: Nonresponders, Pausers, Speeders, and Avoiders. Nonresponders attempt to cross highways regardless of traffic volume. Pausers stop in the face of danger so have a low probability of successful crossing when traffic volume increases. Hence, highway barrier effects are primarily due to mortality for Nonresponders and Pausers at high traffic volumes. Speeders run away from danger but are unable to do so successfully as traffic volume increases. At moderate to high volume, Speeders are repelled by traffic danger. Avoiders face lower mortality than other categories because they begin to avoid traffic at relatively low traffic volumes. Hence, avoidance causes barrier effects more than mortality for Speeders and Avoiders even at relatively moderate traffic volumes. By considering a species’ risk-avoidance response to traffic, managers can make more appropriate and timely decisions to mitigate effects before populations decline or become locally extinct. Title: A Behavior-Based Framework for Assessing Barrier Effects to Wildlife from Vehicle Traffic Volume Author: Jacobson, Sandra L., Bliss-Ketchum, Leslie L., de Rivera, Catherine E., Smith, Winston P. Year: 2016 Roads, while central to the function of human society, create barriers to animal movement through collisions and habitat fragmentation. Barriers to animal movement affect the evolution and trajectory of populations. Investigators have attempted to use traffic volume, the number of vehicles passing a point on a road segment, to predict effects to wildlife populations approximately linearly and along taxonomic lines; however, taxonomic groupings cannot provide sound predictions because closely related species often respond differently. We assess the role of wildlife behavioral responses to traffic volume as a tool to predict barrier effects from vehicle-caused mortality and avoidance, to provide an early warning system that recognizes traffic volume as a trigger for mitigation, and to better interpret roadkill data. We propose four categories of behavioral response based on the perceived danger to traffic: Nonresponders, Pausers, Speeders, and Avoiders. Nonresponders attempt to cross highways regardless of traffic volume. Pausers stop in the face of danger so have a low probability of successful crossing when traffic volume increases. Hence, highway barrier effects are primarily due to mortality for Nonresponders and Pausers at high traffic volumes. Speeders run away from danger but are unable to do so successfully as traffic volume increases. At moderate to high volume, Speeders are repelled by traffic danger. Avoiders face lower mortality than other categories because they begin to avoid traffic at relatively low traffic volumes. Hence, avoidance causes barrier effects more than mortality for Speeders and Avoiders even at relatively moderate traffic volumes. By considering a species’ risk-avoidance response to traffic, managers can make more appropriate and timely decisions to mitigate effects before populations decline or become locally extinct. Close

• 16. [Article] Analysis of Landsat Satellite Data to Monitor Water Quality Parameters in Tenmile Lake, Oregon

  The health of North and South Tenmile Lakes in coastal Oregon has declined since the introduction of invasive species of fish and plant life in the 1920s. The lakes are now on the Federal Clean Water Act ...

  Citation × Citation Citation Abstract Copy Title: Analysis of Landsat Satellite Data to Monitor Water Quality Parameters in Tenmile Lake, Oregon Author: Waxter, Michael T. Year: 2014 The health of North and South Tenmile Lakes in coastal Oregon has declined since the introduction of invasive species of fish and plant life in the 1920s. The lakes are now on the Federal Clean Water Act list of impaired water bodies due, in part, to a lack of dissolved oxygen and Hazardous Algae Blooms (HAB) blooms that occur during June through September. In this report we discuss the possibility of detecting and monitoring these blooms using satellite measurements of water surface color. In-situ measurements obtained from the Tenmile Lakes Basin Partnership were used to calibrate reflectance from the Thematic Mapper on the Landsat 5 satellite. Results show a good linear correlation between turbidity and radiance, which are inversely related in algal dominated lakes. Additionally, a correlation between biovolume and reflectance was obtained. Spatial patterns of turbidity and biovolume are observed, with large concentrations observed in lake areas with large residence times. The comparatively lowest concentrations are observed along the probable pathway of cleaner water input by creeks into the lake. However, the ability to predict turbidity and biovolume from satellite reflectance data is currently complicated by the lack of coincident in-situ and satellite data, and the limited number of spectral bands available to separate turbidity from different species of bacteria and algae. Title: Analysis of Landsat Satellite Data to Monitor Water Quality Parameters in Tenmile Lake, Oregon Author: Waxter, Michael T. Year: 2014 The health of North and South Tenmile Lakes in coastal Oregon has declined since the introduction of invasive species of fish and plant life in the 1920s. The lakes are now on the Federal Clean Water Act list of impaired water bodies due, in part, to a lack of dissolved oxygen and Hazardous Algae Blooms (HAB) blooms that occur during June through September. In this report we discuss the possibility of detecting and monitoring these blooms using satellite measurements of water surface color. In-situ measurements obtained from the Tenmile Lakes Basin Partnership were used to calibrate reflectance from the Thematic Mapper on the Landsat 5 satellite. Results show a good linear correlation between turbidity and radiance, which are inversely related in algal dominated lakes. Additionally, a correlation between biovolume and reflectance was obtained. Spatial patterns of turbidity and biovolume are observed, with large concentrations observed in lake areas with large residence times. The comparatively lowest concentrations are observed along the probable pathway of cleaner water input by creeks into the lake. However, the ability to predict turbidity and biovolume from satellite reflectance data is currently complicated by the lack of coincident in-situ and satellite data, and the limited number of spectral bands available to separate turbidity from different species of bacteria and algae. Close

• 17. [Article] An Analysis of the Economic Value of the Endangered Species Ayumodoki - A Case Study of Kameoka City, Kyoto Prefecture in Japan

  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: An Analysis of the Economic Value of the Endangered Species Ayumodoki - A Case Study of Kameoka City, Kyoto Prefecture in Japan Author: Naito, Toyokazu, Uwasu, Michinori 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 Ann L. Shriver and Stefani J. Evers. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Title: An Analysis of the Economic Value of the Endangered Species Ayumodoki - A Case Study of Kameoka City, Kyoto Prefecture in Japan Author: Naito, Toyokazu, Uwasu, Michinori 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 Ann L. Shriver and Stefani J. Evers. International Institute of Fisheries Economics and Trade (IIFET), Corvallis, 2016. Close

• 18. [Article] Cost-Benefit Analysis of DGN Swordfish Time-Area Closure

  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: Cost-Benefit Analysis of DGN Swordfish Time-Area Closure Author: Helvey, Mark, Stohs, Stephen, Squires, Dale, Chan, Valerie, Segerson, Kathleen, Herrick, Samuel Jr., Sun, Chin-Haw, Hilger, James 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: Cost-Benefit Analysis of DGN Swordfish Time-Area Closure Author: Helvey, Mark, Stohs, Stephen, Squires, Dale, Chan, Valerie, Segerson, Kathleen, Herrick, Samuel Jr., Sun, Chin-Haw, Hilger, James 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

• 19. [Article] Quantifying Resilience of Multiple Ecosystem Services and Biodiversity in a Temperate Forest Landscape

  Resilience is increasingly being considered as a new paradigm of forest management among scientists, practitioners, and policymakers. However, metrics of resilience to environmental change are lacking. ...

  Citation × Citation Citation Abstract Copy Title: Quantifying Resilience of Multiple Ecosystem Services and Biodiversity in a Temperate Forest Landscape Author: Cantarello, Elena, Newton, Adrian C., Martin, Phillip A., Evans, Paul M., Gosal, Arjan, Lucash, Melissa S. Year: 2017 Resilience is increasingly being considered as a new paradigm of forest management among scientists, practitioners, and policymakers. However, metrics of resilience to environmental change are lacking. Faced with novel disturbances, forests may be able to sustain existing ecosystem services and biodiversity by exhibiting resilience, or alternatively these attributes may undergo either a linear or nonlinear decline. Here we provide a novel quantitative approach for assessing forest resilience that focuses on three components of resilience, namely resistance, recovery, and net change, using a spatially explicit model of forest dynamics. Under the pulse set scenarios, we explored the resilience of nine ecosystem services and four biodiversity measures following a one-off disturbance applied to an increasing percentage of forest area. Under the pulse + press set scenarios, the six disturbance intensities explored during the pulse set were followed by a continuous disturbance. We detected thresholds in net change under pulse + press scenarios for the majority of the ecosystem services and biodiversity measures, which started to decline sharply when disturbance affected >40% of the landscape. Thresholds in net change were not observed under the pulse scenarios, with the exception of timber volume and ground flora species richness. Thresholds were most pronounced for aboveground biomass, timber volume with respect to the ecosystem services, and ectomycorrhizal fungi and ground flora species richness with respect to the biodiversity measures. Synthesis and applications. The approach presented here illustrates how the multidimensionality of stability research in ecology can be addressed and how forest resilience can be estimated in practice. Managers should adopt specific management actions to support each of the three components of resilience separately, as these may respond differently to disturbance. In addition, management interventions aiming to deliver resilience should incorporate an assessment of both pulse and press disturbances to ensure detection of threshold responses to disturbance, so that appropriate management interventions can be identified. Title: Quantifying Resilience of Multiple Ecosystem Services and Biodiversity in a Temperate Forest Landscape Author: Cantarello, Elena, Newton, Adrian C., Martin, Phillip A., Evans, Paul M., Gosal, Arjan, Lucash, Melissa S. Year: 2017 Resilience is increasingly being considered as a new paradigm of forest management among scientists, practitioners, and policymakers. However, metrics of resilience to environmental change are lacking. Faced with novel disturbances, forests may be able to sustain existing ecosystem services and biodiversity by exhibiting resilience, or alternatively these attributes may undergo either a linear or nonlinear decline. Here we provide a novel quantitative approach for assessing forest resilience that focuses on three components of resilience, namely resistance, recovery, and net change, using a spatially explicit model of forest dynamics. Under the pulse set scenarios, we explored the resilience of nine ecosystem services and four biodiversity measures following a one-off disturbance applied to an increasing percentage of forest area. Under the pulse + press set scenarios, the six disturbance intensities explored during the pulse set were followed by a continuous disturbance. We detected thresholds in net change under pulse + press scenarios for the majority of the ecosystem services and biodiversity measures, which started to decline sharply when disturbance affected >40% of the landscape. Thresholds in net change were not observed under the pulse scenarios, with the exception of timber volume and ground flora species richness. Thresholds were most pronounced for aboveground biomass, timber volume with respect to the ecosystem services, and ectomycorrhizal fungi and ground flora species richness with respect to the biodiversity measures. Synthesis and applications. The approach presented here illustrates how the multidimensionality of stability research in ecology can be addressed and how forest resilience can be estimated in practice. Managers should adopt specific management actions to support each of the three components of resilience separately, as these may respond differently to disturbance. In addition, management interventions aiming to deliver resilience should incorporate an assessment of both pulse and press disturbances to ensure detection of threshold responses to disturbance, so that appropriate management interventions can be identified. Close

• 20. [Article] Phenotypic and Mutational Consequences of Mitochondrial ETC Genetic Damage

  Genetic mutation is the ultimate source of new phenotypic variation in populations. The importance of mutation cannot be understated, and constitutes a significant evolutionary force. Although single mutations ...

  Citation × Citation Citation Abstract Copy Title: Phenotypic and Mutational Consequences of Mitochondrial ETC Genetic Damage Author: Lue, Michael James Year: 2015 Genetic mutation is the ultimate source of new phenotypic variation in populations. The importance of mutation cannot be understated, and constitutes a significant evolutionary force. Although single mutations may have little to no impact on organismal performance or fitness, when multiplied across the total number of potential sites within the genome, mutation can have a large impact. Accurate measurement of the rates, molecular mechanisms, and distributions of effects of mutations are critical for many applications of evolutionary theory. Despite the importance of both deleterious and beneficial mutations, their genome-wide patterns and phenotypic consequences are poorly understood when considering the mitochondrial genome. Mitochondria are organelles that are essential for eukaryotic life. They contain their own genome and generate bioenergy (ATP) necessary to sustain life via the electron transport chain (ETC). Because of their role in eukaryotic physiology, understanding how mitochondrial genetic and phenotypic variation can impact populations and evolutionary outcomes is essential. Past studies have implicated DNA-damaging oxidative stress as a source of mutations within somatic tissue, but there is a gap in knowledge regarding its role in heritable damage within the germ line. In this thesis, I aimed to test this possibility by characterizing the phenotypic and mutational consequences of high intracellular ROS levels caused by mitochondrial ETC genetic damage. I performed experiments using Caenorhabditis elegans ETC mutant, gas-1, and mutation-accumulation (MA) lines generated from this ancestral genotype. I quantified organismal fitness (fecundity and longevity), reactive oxygen species (ROS) levels, mitochondrial membrane potential (delta psi m), and ATP levels in these lines, and compared the results to those from a set of wildtype control lines. I begin with a general introduction to the hypothesis and the C. elegans system in Chapter I. In Chapter II, I report the findings from this work. In short, I found that while gas-1 MA lines began the experiment with low lifetime fecundity in comparison to the wildtype strain, their fecundity showed no further decline as expected, and even exhibited higher fecundity levels on days 3-5 of reproduction relative to the gas-1 progenitor. The gas-1 progenitor exhibited higher rates of ROS compared to wildtype, whereas the MA lines reverted back to wildtype levels; a similar pattern was observed for delta psi m, while ATP levels were low in the gas-1 progenitor and remained low in the MA lines. I interpret these findings in light of high-throughput sequencing results from these lines showing that, while nuclear and mitochondrial DNA mutation rates were equal to wildtype in these lines, the genomic pattern of mutation was highly nonrandom and indicative of selection for beneficial or compensatory sequence changes. Because ROS levels declined to wildtype in the evolved (MA), this study was unable to address whether ROS is a major contributor to heritable mutation in this system. I hypothesize that, in addition to their putatively compensatory genetic changes, gas-1 lineages experienced physiological compensation allowing them to survive, and that this was associated with a "slow living" phenotype. In Chapter III, I summarize general conclusions and implications of this study and end by providing suggestions for further study. Title: Phenotypic and Mutational Consequences of Mitochondrial ETC Genetic Damage Author: Lue, Michael James Year: 2015 Genetic mutation is the ultimate source of new phenotypic variation in populations. The importance of mutation cannot be understated, and constitutes a significant evolutionary force. Although single mutations may have little to no impact on organismal performance or fitness, when multiplied across the total number of potential sites within the genome, mutation can have a large impact. Accurate measurement of the rates, molecular mechanisms, and distributions of effects of mutations are critical for many applications of evolutionary theory. Despite the importance of both deleterious and beneficial mutations, their genome-wide patterns and phenotypic consequences are poorly understood when considering the mitochondrial genome. Mitochondria are organelles that are essential for eukaryotic life. They contain their own genome and generate bioenergy (ATP) necessary to sustain life via the electron transport chain (ETC). Because of their role in eukaryotic physiology, understanding how mitochondrial genetic and phenotypic variation can impact populations and evolutionary outcomes is essential. Past studies have implicated DNA-damaging oxidative stress as a source of mutations within somatic tissue, but there is a gap in knowledge regarding its role in heritable damage within the germ line. In this thesis, I aimed to test this possibility by characterizing the phenotypic and mutational consequences of high intracellular ROS levels caused by mitochondrial ETC genetic damage. I performed experiments using Caenorhabditis elegans ETC mutant, gas-1, and mutation-accumulation (MA) lines generated from this ancestral genotype. I quantified organismal fitness (fecundity and longevity), reactive oxygen species (ROS) levels, mitochondrial membrane potential (delta psi m), and ATP levels in these lines, and compared the results to those from a set of wildtype control lines. I begin with a general introduction to the hypothesis and the C. elegans system in Chapter I. In Chapter II, I report the findings from this work. In short, I found that while gas-1 MA lines began the experiment with low lifetime fecundity in comparison to the wildtype strain, their fecundity showed no further decline as expected, and even exhibited higher fecundity levels on days 3-5 of reproduction relative to the gas-1 progenitor. The gas-1 progenitor exhibited higher rates of ROS compared to wildtype, whereas the MA lines reverted back to wildtype levels; a similar pattern was observed for delta psi m, while ATP levels were low in the gas-1 progenitor and remained low in the MA lines. I interpret these findings in light of high-throughput sequencing results from these lines showing that, while nuclear and mitochondrial DNA mutation rates were equal to wildtype in these lines, the genomic pattern of mutation was highly nonrandom and indicative of selection for beneficial or compensatory sequence changes. Because ROS levels declined to wildtype in the evolved (MA), this study was unable to address whether ROS is a major contributor to heritable mutation in this system. I hypothesize that, in addition to their putatively compensatory genetic changes, gas-1 lineages experienced physiological compensation allowing them to survive, and that this was associated with a "slow living" phenotype. In Chapter III, I summarize general conclusions and implications of this study and end by providing suggestions for further study. Close