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• 21. [Article] A Survey of Small Mammals on Islands in the Columbia and Willamette Rivers

  A survey of small mammals on eight islands in the Columbia and Willamette Rivers near Portland, Oregon was conducted in 1974. The islands were Govermnent , Sand, Lemon, McGuire and Sandy Islands in the ...

  Citation × Citation Citation Abstract Copy Title: A Survey of Small Mammals on Islands in the Columbia and Willamette Rivers Author: Kirk, Gayle Year: 1976 A survey of small mammals on eight islands in the Columbia and Willamette Rivers near Portland, Oregon was conducted in 1974. The islands were Govermnent , Sand, Lemon, McGuire and Sandy Islands in the Columbia River and East, Ross and Hardtack Islands in the Willamette River. The objectives of the study were to ascertain and compare the kinds, distribution and relative densitites of small mammals . A variety of traps was used to capture the animals including Museum Special Rodent Traps , back- break mouse traps, scissor and guillotine- type stab mole traps , Sherman traps , modified Young traps and pitfalls . Most traps were set in linear transects . Trapping was conducted with the objective of sampling the major habitats on each island. Observations of scats, tracks , burrows and dead animals were also noted. One species of small marmnal , Sorex vargrans , was found on all eight islands . Microtus was found on five islands and Peromyscus maniculatus on four islands . Two islands yielded Scapanus townsendii. Glaucomvs sabrinus was found on only one island. I hoped that evidence would be found to prove or disprove that current theories of island biogeography would apply to river islands. However, data in this study were inadequate to allow calculation of precise indices of population densities . Therefore, I was unable to determine if theories of island biogeography do apply to these river islands. Title: A Survey of Small Mammals on Islands in the Columbia and Willamette Rivers Author: Kirk, Gayle Year: 1976 A survey of small mammals on eight islands in the Columbia and Willamette Rivers near Portland, Oregon was conducted in 1974. The islands were Govermnent , Sand, Lemon, McGuire and Sandy Islands in the Columbia River and East, Ross and Hardtack Islands in the Willamette River. The objectives of the study were to ascertain and compare the kinds, distribution and relative densitites of small mammals . A variety of traps was used to capture the animals including Museum Special Rodent Traps , back- break mouse traps, scissor and guillotine- type stab mole traps , Sherman traps , modified Young traps and pitfalls . Most traps were set in linear transects . Trapping was conducted with the objective of sampling the major habitats on each island. Observations of scats, tracks , burrows and dead animals were also noted. One species of small marmnal , Sorex vargrans , was found on all eight islands . Microtus was found on five islands and Peromyscus maniculatus on four islands . Two islands yielded Scapanus townsendii. Glaucomvs sabrinus was found on only one island. I hoped that evidence would be found to prove or disprove that current theories of island biogeography would apply to river islands. However, data in this study were inadequate to allow calculation of precise indices of population densities . Therefore, I was unable to determine if theories of island biogeography do apply to these river islands. Close

• 22. [Article] Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries

  The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, ...

  Citation × Citation Citation Abstract Copy Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Close

• 23. [Article] Investigations of Larval Pacific Lamprey Entosphenus tridentatus Osmotic Stress Tolerance and Occurrence in a Tidally-Influenced Estuarine Stream

  Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range ...

  Citation × Citation Citation Abstract Copy Title: Investigations of Larval Pacific Lamprey Entosphenus tridentatus Osmotic Stress Tolerance and Occurrence in a Tidally-Influenced Estuarine Stream Author: Silver, Gregory Shell Year: 2015 Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range and reductions in Pacific lamprey abundance have been observed in Western North America, and may be indicators of range-wide declines. In the face of declining populations, the U.S. Fish and Wildlife Service has partnered with tribal, state, federal, and local entities to implement a regional Pacific lamprey conservation agreement aimed at reducing threats to Pacific lamprey and improving their habitats and population status. Research needs identified in the conservation agreement include assessing larval Pacific lamprey occupancy and distribution, habitat requirements, and the limiting factors of larval distribution in the freshwater ecosystem. As part of the effort to address these knowledge gaps, we investigated the potential for larval lampreys to occur in tidally-influenced estuarine environments. Research of this type may be valuable for future conservation, management or recovery efforts of Pacific lamprey throughout its range. We employed a two-phased approach, consisting of laboratory and field components to address our aims. We first conducted a series of controlled laboratory experiments to evaluate osmotic stress tolerance and osmoregulatory status of larval Pacific lamprey exposed to a range of (1) fixed salinity in various dilutions of saltwater and (2) oscillating salinity treatments designed to simulate tidal activity. Tolerance was assessed by monitoring and comparing survival of larvae in various treatments through 96 h. Osmoregulatory status was assessed by quantifying and comparing total body water content, plasma osmolality, and plasma cation (i.e., sodium) concentrations among larvae surviving various treatments. In fixed salinity experiments, 100% survival was observed in 0‰, 6‰, 8‰ and 10‰ through 96 h, while 0% survival was observed through 48 h in 12‰, 30 h in 15‰, and 12 h in 25‰ and 35‰. In oscillating salinity experiments, on the other hand, a significant increase in survival (100%) was observed through 96 h in treatments that oscillated between 12‰ and 0‰ (freshwater) at about 6 h intervals versus fixed 12‰ salinity experiments. A significant increase in survival also occurred in oscillating 15‰ treatments (60%) versus fixed 15‰ through 96 h. Linear regression analysis indicated higher environmental salinity in laboratory experiments was significantly related to increases in plasma osmolality and plasma sodium (the most abundant osmotically active plasma cation) concentrations, and concurrent decreases in total body water content among larvae that survived various treatments. Tidal oscillations in salinity appeared to temper the desiccating effects of salinity, as changes in body water content and sodium ion concentration were less abrupt than fixed salinity treatments. These results suggest larvae cannot osmoregulate in hyperosmotic environments, but are able to tolerate some fixed and oscillating hyperosmotic salinity exposure. Consequently, larvae may be able to occur in certain areas of estuaries, such as oligohaline habitats that are characterized by low levels of salinity. Experimental results were used, in part, to guide larval sampling in a tidally-influenced habitat. Occurrence of larval Pacific lamprey and Lampetra spp. (western brook and river lampreys) was subsequently investigated across a gradient of salinity in Ellsworth Creek (Pacific County, Washington) by electrofishing. Larval Pacific and Lampetra spp. were detected within an approximately 300 m long tidally-influenced segment of the study area. Salinity monitoring was conducted in six tidally-influenced reaches where larvae were detected for up to 14 d following electrofishing. Maximum tidal cycle salinity exceeded 15 ppt during 52% to 80% of tidal cycles within tidally-influenced reaches where larvae were detected. These results suggest potential for larval lamprey to occur in certain portions of tidal estuaries. However, long-term residence of larvae in tidally-influenced habitats and whether larvae are able to subsequently survive, grow, transform, and out-migrate is not known and requires further study. Given the potential for tidally-influenced habitats to be occupied by larvae, assessments of larval occurrence in other areas, such as the lower Columbia River, may be warranted. Knowledge of larval lamprey distribution in estuarine environments may be valuable for habitat restoration, and mitigating potential impacts from dredging and other human disturbances. Title: Investigations of Larval Pacific Lamprey Entosphenus tridentatus Osmotic Stress Tolerance and Occurrence in a Tidally-Influenced Estuarine Stream Author: Silver, Gregory Shell Year: 2015 Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range and reductions in Pacific lamprey abundance have been observed in Western North America, and may be indicators of range-wide declines. In the face of declining populations, the U.S. Fish and Wildlife Service has partnered with tribal, state, federal, and local entities to implement a regional Pacific lamprey conservation agreement aimed at reducing threats to Pacific lamprey and improving their habitats and population status. Research needs identified in the conservation agreement include assessing larval Pacific lamprey occupancy and distribution, habitat requirements, and the limiting factors of larval distribution in the freshwater ecosystem. As part of the effort to address these knowledge gaps, we investigated the potential for larval lampreys to occur in tidally-influenced estuarine environments. Research of this type may be valuable for future conservation, management or recovery efforts of Pacific lamprey throughout its range. We employed a two-phased approach, consisting of laboratory and field components to address our aims. We first conducted a series of controlled laboratory experiments to evaluate osmotic stress tolerance and osmoregulatory status of larval Pacific lamprey exposed to a range of (1) fixed salinity in various dilutions of saltwater and (2) oscillating salinity treatments designed to simulate tidal activity. Tolerance was assessed by monitoring and comparing survival of larvae in various treatments through 96 h. Osmoregulatory status was assessed by quantifying and comparing total body water content, plasma osmolality, and plasma cation (i.e., sodium) concentrations among larvae surviving various treatments. In fixed salinity experiments, 100% survival was observed in 0‰, 6‰, 8‰ and 10‰ through 96 h, while 0% survival was observed through 48 h in 12‰, 30 h in 15‰, and 12 h in 25‰ and 35‰. In oscillating salinity experiments, on the other hand, a significant increase in survival (100%) was observed through 96 h in treatments that oscillated between 12‰ and 0‰ (freshwater) at about 6 h intervals versus fixed 12‰ salinity experiments. A significant increase in survival also occurred in oscillating 15‰ treatments (60%) versus fixed 15‰ through 96 h. Linear regression analysis indicated higher environmental salinity in laboratory experiments was significantly related to increases in plasma osmolality and plasma sodium (the most abundant osmotically active plasma cation) concentrations, and concurrent decreases in total body water content among larvae that survived various treatments. Tidal oscillations in salinity appeared to temper the desiccating effects of salinity, as changes in body water content and sodium ion concentration were less abrupt than fixed salinity treatments. These results suggest larvae cannot osmoregulate in hyperosmotic environments, but are able to tolerate some fixed and oscillating hyperosmotic salinity exposure. Consequently, larvae may be able to occur in certain areas of estuaries, such as oligohaline habitats that are characterized by low levels of salinity. Experimental results were used, in part, to guide larval sampling in a tidally-influenced habitat. Occurrence of larval Pacific lamprey and Lampetra spp. (western brook and river lampreys) was subsequently investigated across a gradient of salinity in Ellsworth Creek (Pacific County, Washington) by electrofishing. Larval Pacific and Lampetra spp. were detected within an approximately 300 m long tidally-influenced segment of the study area. Salinity monitoring was conducted in six tidally-influenced reaches where larvae were detected for up to 14 d following electrofishing. Maximum tidal cycle salinity exceeded 15 ppt during 52% to 80% of tidal cycles within tidally-influenced reaches where larvae were detected. These results suggest potential for larval lamprey to occur in certain portions of tidal estuaries. However, long-term residence of larvae in tidally-influenced habitats and whether larvae are able to subsequently survive, grow, transform, and out-migrate is not known and requires further study. Given the potential for tidally-influenced habitats to be occupied by larvae, assessments of larval occurrence in other areas, such as the lower Columbia River, may be warranted. Knowledge of larval lamprey distribution in estuarine environments may be valuable for habitat restoration, and mitigating potential impacts from dredging and other human disturbances. Close

• 24. [Article] Thermal Ecology and Movement in the Leopard Lizard, Gambelia Wislizeni, Baird and Girard

  Thermal ecology and movement of the Leopard Lizard, G. wistizeniwere studied at Frog Spring, adjacent to the Alvord Desert, and at various locations throughout the Alvord Basin. Seasonal activity is known ...

  Citation × Citation Citation Abstract Copy Title: Thermal Ecology and Movement in the Leopard Lizard, Gambelia Wislizeni, Baird and Girard Author: Abts, Marvin Lynn Year: 1976 Thermal ecology and movement of the Leopard Lizard, G. wistizeniwere studied at Frog Spring, adjacent to the Alvord Desert, and at various locations throughout the Alvord Basin. Seasonal activity is known to occur from early May to mid-October, but abundance. gradually decreases after late July. During favorable late spring, and summer weather lizards exhibit a bimodal pattern of diel activity with some activity occurring at all hours of the day between 0600 and 1800 H. At other times activity was unimodal. Emergence was apparently largely temperature dependent and did not occur until sand temperature approximated 21°C. Retreat appeared to be temperature independent, and was initiated by exogenous or endogenous stimuli at sand temperatures often above body temperatures acceptable for normal activity. For the period of study, juveniles exhibited diel activity patterns similar to adults, and were found during all hours in which adults were encountered. Body temperatures of field active lizards, largely affected by the immediate weather conditions, , ranged from 18.6° to 43.4°C. Because of a variety of thermoregulatory response (changes in location, posture, and orientation, color change, burrowing, shade-seeking, and panting), even during unfavorable weather conditions, most body temperatures fell within a narrower range. Nonetheless, the ability of field active lizards to precisely thermoregulate was limited, and the levels of body temperature maintained usually encompassed a broader range than those maintained in a thermal gradient. The mean body temperature of field active lizards during favorable weather conditions, and that of active lizards in a thermal gradient, did not differ significantly, and seemed to indicate a narrow range of body temperature preference. However, prevailing weather conditions were frequently unfavorable, thus limiting the extent of time during which selection of preferred body temperature could occur. Consequently, though activity depended on the attainment of certain temperature levels, G. wislizeni was forced to adapt to a broader range of body temperatures when performing most routine tasks. The necessity of precision thermoregulation is unclear, but apparently physiological efficiency was not greatly diminished over the broad range of body temperatures fiefd active lizards were often accepting. Relatively speaking, movement in G. wislizeni was extensive. Adult males occupied an average area more than twice the size of adult females and juveniles. Plotted polygons, constructed from sighting points, tended to be elongate. The extent to which lizards occupied a definite home range was uncertain. Adult males , continuously expanding the area occupied, probably lacked a home range. Adult females, demonstrating . little area expansion, perhaps maintained a home range. Territoriality by means of intraspecific display or aggression appeared negligible in G. wislizeni.Adult males did not demonstrate such behavior toward one another . Based on a limited extent of area overlap, adult females may have exhibited territoriality toward members of their sex. Movement per hour revealed results similar to area occupied, with adult males traveling an average distance of nearly three times as great as adult females and juveniles. Greatest distances frequently coincided with peak diel activity. Individual moves were frequent in adult males and juveniles, but infrequent in ~ adult females. Adult female long moves were similar in distance to adult males, but exogenous stimuli perhaps linked with home range maintenance restricted the frequency of such jaunts. Movement in G. wislizeni appeared independent of environmental thermal conditions when body temperature was within the range acceptable for normal activity. Diel movement appeared to be random in the species. Seasonal movement in juveniles, based on dispersion data, appeared directional. Title: Thermal Ecology and Movement in the Leopard Lizard, Gambelia Wislizeni, Baird and Girard Author: Abts, Marvin Lynn Year: 1976 Thermal ecology and movement of the Leopard Lizard, G. wistizeniwere studied at Frog Spring, adjacent to the Alvord Desert, and at various locations throughout the Alvord Basin. Seasonal activity is known to occur from early May to mid-October, but abundance. gradually decreases after late July. During favorable late spring, and summer weather lizards exhibit a bimodal pattern of diel activity with some activity occurring at all hours of the day between 0600 and 1800 H. At other times activity was unimodal. Emergence was apparently largely temperature dependent and did not occur until sand temperature approximated 21°C. Retreat appeared to be temperature independent, and was initiated by exogenous or endogenous stimuli at sand temperatures often above body temperatures acceptable for normal activity. For the period of study, juveniles exhibited diel activity patterns similar to adults, and were found during all hours in which adults were encountered. Body temperatures of field active lizards, largely affected by the immediate weather conditions, , ranged from 18.6° to 43.4°C. Because of a variety of thermoregulatory response (changes in location, posture, and orientation, color change, burrowing, shade-seeking, and panting), even during unfavorable weather conditions, most body temperatures fell within a narrower range. Nonetheless, the ability of field active lizards to precisely thermoregulate was limited, and the levels of body temperature maintained usually encompassed a broader range than those maintained in a thermal gradient. The mean body temperature of field active lizards during favorable weather conditions, and that of active lizards in a thermal gradient, did not differ significantly, and seemed to indicate a narrow range of body temperature preference. However, prevailing weather conditions were frequently unfavorable, thus limiting the extent of time during which selection of preferred body temperature could occur. Consequently, though activity depended on the attainment of certain temperature levels, G. wislizeni was forced to adapt to a broader range of body temperatures when performing most routine tasks. The necessity of precision thermoregulation is unclear, but apparently physiological efficiency was not greatly diminished over the broad range of body temperatures fiefd active lizards were often accepting. Relatively speaking, movement in G. wislizeni was extensive. Adult males occupied an average area more than twice the size of adult females and juveniles. Plotted polygons, constructed from sighting points, tended to be elongate. The extent to which lizards occupied a definite home range was uncertain. Adult males , continuously expanding the area occupied, probably lacked a home range. Adult females, demonstrating . little area expansion, perhaps maintained a home range. Territoriality by means of intraspecific display or aggression appeared negligible in G. wislizeni.Adult males did not demonstrate such behavior toward one another . Based on a limited extent of area overlap, adult females may have exhibited territoriality toward members of their sex. Movement per hour revealed results similar to area occupied, with adult males traveling an average distance of nearly three times as great as adult females and juveniles. Greatest distances frequently coincided with peak diel activity. Individual moves were frequent in adult males and juveniles, but infrequent in ~ adult females. Adult female long moves were similar in distance to adult males, but exogenous stimuli perhaps linked with home range maintenance restricted the frequency of such jaunts. Movement in G. wislizeni appeared independent of environmental thermal conditions when body temperature was within the range acceptable for normal activity. Diel movement appeared to be random in the species. Seasonal movement in juveniles, based on dispersion data, appeared directional. Close

• 25. [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

• 26. [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

• 27. [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