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• 1. [Article] Sex-Specific Fungal Communities of the Dioicous Moss Ceratodon purpureus

  Mosses display a number of hallmark life history traits that influence their ecology at the population and community level. The long lived separation of sexes observed in the haploid gametophyte (dioicy) ...

  Citation × Citation Citation Abstract Copy Title: Sex-Specific Fungal Communities of the Dioicous Moss Ceratodon purpureus Author: Balkan, Mehmet Ali Year: 2016 Mosses display a number of hallmark life history traits that influence their ecology at the population and community level. The long lived separation of sexes observed in the haploid gametophyte (dioicy) is one such feature of particular importance, as it is observed in the majority of bryophytes and creates intraspecific specialization of male and female individuals. The prevalence of sexually dimorphic mosses raises the possibility of sex-specific interactions with fungi as observed in some vascular plants. Here I investigated how moss sex shapes fungal communities associated with gametophytic tissues of the ubiquitous moss, Ceratodon purpureus. Using greenhouse populations of C. purpureus grown in a common garden, I examined fungal community structure and overall abundance of fungal biomass associated with male and female individuals from multiple populations. I hypothesized that individual mosses would harbor unique fungal communities based on their sex, and that overall fungal biomass associated with host tissues would differ significantly due to differences in morphological and physiological characteristics between the sexes. I found that fungal community composition and overall abundance (i.e. biomass) differ between male and female individuals of C. purpureus, and that sex-specific patterns are retained across individuals from three different populations. This work provides a first glance at how genetically based sexual systems in early land plants influence affiliated fungal community composition. Title: Sex-Specific Fungal Communities of the Dioicous Moss Ceratodon purpureus Author: Balkan, Mehmet Ali Year: 2016 Mosses display a number of hallmark life history traits that influence their ecology at the population and community level. The long lived separation of sexes observed in the haploid gametophyte (dioicy) is one such feature of particular importance, as it is observed in the majority of bryophytes and creates intraspecific specialization of male and female individuals. The prevalence of sexually dimorphic mosses raises the possibility of sex-specific interactions with fungi as observed in some vascular plants. Here I investigated how moss sex shapes fungal communities associated with gametophytic tissues of the ubiquitous moss, Ceratodon purpureus. Using greenhouse populations of C. purpureus grown in a common garden, I examined fungal community structure and overall abundance of fungal biomass associated with male and female individuals from multiple populations. I hypothesized that individual mosses would harbor unique fungal communities based on their sex, and that overall fungal biomass associated with host tissues would differ significantly due to differences in morphological and physiological characteristics between the sexes. I found that fungal community composition and overall abundance (i.e. biomass) differ between male and female individuals of C. purpureus, and that sex-specific patterns are retained across individuals from three different populations. This work provides a first glance at how genetically based sexual systems in early land plants influence affiliated fungal community composition. Close

• 2. [Article] Assessing the Potential of Land Use Modification to Mitigate Ambient NO2 and Its Consequences for Respiratory Health

  Understanding how local land use and land cover (LULC) shapes intra-urban concentrations of atmospheric pollutants—and thus human health—is a key component in designing healthier cities. Here, NO2 is modeled ...

  Citation × Citation Citation Abstract Copy Title: Assessing the Potential of Land Use Modification to Mitigate Ambient NO2 and Its Consequences for Respiratory Health Author: Rao, Meenakshi, George, Linda A., Shandas, Vivek, Rosenstiel, Todd N. Year: 2017 Understanding how local land use and land cover (LULC) shapes intra-urban concentrations of atmospheric pollutants—and thus human health—is a key component in designing healthier cities. Here, NO2 is modeled based on spatially dense summer and winter NO2 observations in Portland-Hillsboro-Vancouver (USA), and the spatial variation of NO2 with LULC investigated using random forest, an ensemble data learning technique. The NO2 random forest model, together with BenMAP, is further used to develop a better understanding of the relationship among LULC, ambient NO2 and respiratory health. The impact of land use modifications on ambient NO2, and consequently on respiratory health, is also investigated using a sensitivity analysis. We find that NO2 associated with roadways and tree-canopied areas may be affecting annual incidence rates of asthma exacerbation in 4–12 year olds by +3000 per 100,000 and -1400 per 100,000, respectively. Our model shows that increasing local tree canopy by 5% may reduce local incidences rates of asthma exacerbation by 6%, indicating that targeted local tree-planting efforts may have a substantial impact on reducing city-wide incidence of respiratory distress. Our findings demonstrate the utility of random forest modeling in evaluating LULC modifications for enhanced respiratory health. Title: Assessing the Potential of Land Use Modification to Mitigate Ambient NO2 and Its Consequences for Respiratory Health Author: Rao, Meenakshi, George, Linda A., Shandas, Vivek, Rosenstiel, Todd N. Year: 2017 Understanding how local land use and land cover (LULC) shapes intra-urban concentrations of atmospheric pollutants—and thus human health—is a key component in designing healthier cities. Here, NO2 is modeled based on spatially dense summer and winter NO2 observations in Portland-Hillsboro-Vancouver (USA), and the spatial variation of NO2 with LULC investigated using random forest, an ensemble data learning technique. The NO2 random forest model, together with BenMAP, is further used to develop a better understanding of the relationship among LULC, ambient NO2 and respiratory health. The impact of land use modifications on ambient NO2, and consequently on respiratory health, is also investigated using a sensitivity analysis. We find that NO2 associated with roadways and tree-canopied areas may be affecting annual incidence rates of asthma exacerbation in 4–12 year olds by +3000 per 100,000 and -1400 per 100,000, respectively. Our model shows that increasing local tree canopy by 5% may reduce local incidences rates of asthma exacerbation by 6%, indicating that targeted local tree-planting efforts may have a substantial impact on reducing city-wide incidence of respiratory distress. Our findings demonstrate the utility of random forest modeling in evaluating LULC modifications for enhanced respiratory health. Close

• 3. [Article] Why Do Animals Do What They Do, When They Do It? Characterizing the Role of the Hypothalamus-Pituitary-Adrenal Axis in Seasonal Life-History Transitions

  Resource availability follows seasonal cycles in environmental conditions. To align physiology and behavior with prevailing environmental conditions, seasonal animals integrate cues from the environment ...

  Citation × Citation Citation Abstract Copy Title: Why Do Animals Do What They Do, When They Do It? Characterizing the Role of the Hypothalamus-Pituitary-Adrenal Axis in Seasonal Life-History Transitions Author: Dayger Forbes, Catherine Anne Year: 2017 Resource availability follows seasonal cycles in environmental conditions. To align physiology and behavior with prevailing environmental conditions, seasonal animals integrate cues from the environment with their internal state. One of the systems animals use to integrate those cues is the hypothalamus-pituitary-adrenal (HPA) axis and its primary effector, glucocorticoid hormones. The HPA axis has wide-ranging effects on physiology and behavior and, in the context of a glucocorticoid stress response, is known to mediate tradeoffs between immediate survival and future fitness. The HPA axis also plays an important role in facilitating predictable life-history events. Variation in HPA axis activity has been reported in all vertebrates, often coordinating seasonal reproduction and possibly also transitions between life-history stages. My dissertation research used red-sided garter snakes (Thamnophis sirtalis parietalis) to examine the role of the HPA axis in regulating seasonal life-history transitions, especially in females In Chapter 2, I hypothesized that seasonal plasticity in stress responses is regulated, in part, by changes in the responsiveness of the adrenal glands to adrenocorticotropic hormone (ACTH). I found that glucocorticoid responses to ACTH challenge were smaller in males than in females during the spring, suggesting that reports of reduced stress responsiveness in males may reflect lower adrenal responsiveness to ACTH. The sex difference in mating season duration and consequently also in the timing of migration led me to hypothesize that sex differences in HPA axis activity could explain sex differences in the timing of migration. Furthermore, adrenal responsiveness to ACTH also varied seasonally in males, but not females, suggesting that female stress responses, which have not been studied, may not vary seasonally. In Chapter 3, I investigated potential seasonal variation in female stress responses, which have not previously been examined. In males, baseline glucocorticoids decrease over the course of the mating season resulting in significantly lower baseline levels in males that have begun to migrate. I hypothesized that a change in HPA axis activity occurs during spring and fall migration. Peak stress-induced glucocorticoid concentration occurred at an earlier sampling time in females during the spring compared to the fall. Peak stress-induced glucocorticoid concentrations also occurred at a later sampling time in migrating females than in pre-migratory females during the spring, suggesting that negative feedback regulation of the HPA axis changes as soon as females begin to migrate during the spring. Female red-sided garter snakes are biennial breeders that give birth approximately every other year implying that a female's recent reproductive history can influence whether or not she will reproduce in a given year. Body condition can be used as a proxy for recent reproductive history and can be related to baseline and stress-induced glucocorticoid concentrations. In Chapter 4, I hypothesized that hormonal and behavioral stress responses vary with body condition. Baseline glucocorticoids did not vary with body condition, but females in low body condition showed a significantly larger increase in plasma glucocorticoids in response to capture stress. Body condition, but not capture stress, influenced latency to copulate, suggesting that females are resistant to the behavioral effects of capture stress during the spring mating season. Only females in low body condition increased latency to copulate in response to injection of a physiological (15 µg) dose of exogenous CORT, while all females responded to a pharmacological (60 µg) dose, indicating that behavioral responses to exogenous glucocorticoids vary with female body condition. These data suggest that variation in body condition may be associated with differences in HPA axis sensitivity and/or glucocorticoid receptor (GR) density in the brain. I directly tested if there is a relationship among body condition, reproductive history and HPA axis activity in Chapter 5. I found that glucocorticoid stress responses and mating behavior did not vary with body condition, nor was body condition related to brain GR or reproductive condition (parturient vs post-parturient females). Only unreceptive females showed a significant stress-induced increase in glucocorticoids, suggesting that reduced stress responsiveness is associated with receptivity. Parturient females mated faster (were more proceptive) than post-parturient females. These data suggest that HPA axis activity influences reproductive "decisions" by modulating receptivity, while proceptivity is related primarily to recent reproductive history. Together, these chapters help characterize how HPA axis activity varies with season, sex, reproductive history and migration status. By systematically probing the HPA axis in a single, tractable system, I have gained insight into how changes in the HPA axis support and modulate transitions between life-history stages. These results highlight the HPA axis' important function in mediating the critical trade-offs all animals must navigate to be successful in a changing world. Title: Why Do Animals Do What They Do, When They Do It? Characterizing the Role of the Hypothalamus-Pituitary-Adrenal Axis in Seasonal Life-History Transitions Author: Dayger Forbes, Catherine Anne Year: 2017 Resource availability follows seasonal cycles in environmental conditions. To align physiology and behavior with prevailing environmental conditions, seasonal animals integrate cues from the environment with their internal state. One of the systems animals use to integrate those cues is the hypothalamus-pituitary-adrenal (HPA) axis and its primary effector, glucocorticoid hormones. The HPA axis has wide-ranging effects on physiology and behavior and, in the context of a glucocorticoid stress response, is known to mediate tradeoffs between immediate survival and future fitness. The HPA axis also plays an important role in facilitating predictable life-history events. Variation in HPA axis activity has been reported in all vertebrates, often coordinating seasonal reproduction and possibly also transitions between life-history stages. My dissertation research used red-sided garter snakes (Thamnophis sirtalis parietalis) to examine the role of the HPA axis in regulating seasonal life-history transitions, especially in females In Chapter 2, I hypothesized that seasonal plasticity in stress responses is regulated, in part, by changes in the responsiveness of the adrenal glands to adrenocorticotropic hormone (ACTH). I found that glucocorticoid responses to ACTH challenge were smaller in males than in females during the spring, suggesting that reports of reduced stress responsiveness in males may reflect lower adrenal responsiveness to ACTH. The sex difference in mating season duration and consequently also in the timing of migration led me to hypothesize that sex differences in HPA axis activity could explain sex differences in the timing of migration. Furthermore, adrenal responsiveness to ACTH also varied seasonally in males, but not females, suggesting that female stress responses, which have not been studied, may not vary seasonally. In Chapter 3, I investigated potential seasonal variation in female stress responses, which have not previously been examined. In males, baseline glucocorticoids decrease over the course of the mating season resulting in significantly lower baseline levels in males that have begun to migrate. I hypothesized that a change in HPA axis activity occurs during spring and fall migration. Peak stress-induced glucocorticoid concentration occurred at an earlier sampling time in females during the spring compared to the fall. Peak stress-induced glucocorticoid concentrations also occurred at a later sampling time in migrating females than in pre-migratory females during the spring, suggesting that negative feedback regulation of the HPA axis changes as soon as females begin to migrate during the spring. Female red-sided garter snakes are biennial breeders that give birth approximately every other year implying that a female's recent reproductive history can influence whether or not she will reproduce in a given year. Body condition can be used as a proxy for recent reproductive history and can be related to baseline and stress-induced glucocorticoid concentrations. In Chapter 4, I hypothesized that hormonal and behavioral stress responses vary with body condition. Baseline glucocorticoids did not vary with body condition, but females in low body condition showed a significantly larger increase in plasma glucocorticoids in response to capture stress. Body condition, but not capture stress, influenced latency to copulate, suggesting that females are resistant to the behavioral effects of capture stress during the spring mating season. Only females in low body condition increased latency to copulate in response to injection of a physiological (15 µg) dose of exogenous CORT, while all females responded to a pharmacological (60 µg) dose, indicating that behavioral responses to exogenous glucocorticoids vary with female body condition. These data suggest that variation in body condition may be associated with differences in HPA axis sensitivity and/or glucocorticoid receptor (GR) density in the brain. I directly tested if there is a relationship among body condition, reproductive history and HPA axis activity in Chapter 5. I found that glucocorticoid stress responses and mating behavior did not vary with body condition, nor was body condition related to brain GR or reproductive condition (parturient vs post-parturient females). Only unreceptive females showed a significant stress-induced increase in glucocorticoids, suggesting that reduced stress responsiveness is associated with receptivity. Parturient females mated faster (were more proceptive) than post-parturient females. These data suggest that HPA axis activity influences reproductive "decisions" by modulating receptivity, while proceptivity is related primarily to recent reproductive history. Together, these chapters help characterize how HPA axis activity varies with season, sex, reproductive history and migration status. By systematically probing the HPA axis in a single, tractable system, I have gained insight into how changes in the HPA axis support and modulate transitions between life-history stages. These results highlight the HPA axis' important function in mediating the critical trade-offs all animals must navigate to be successful in a changing world. Close

• 4. [Article] Physiological Strategies During Animal Diapause: Lessons from Brine Shrimp and Annual Killifish.

  Diapause is a programmed state of developmental arrest that typically occurs as part of the natural developmental progression of organisms that inhabit seasonal environments. The brine shrimp Artemia franciscana ...

  Citation × Citation Citation Abstract Copy Title: Physiological Strategies During Animal Diapause: Lessons from Brine Shrimp and Annual Killifish. Author: Podrabsky, Jason E., Hand, Steven C. Year: 2015 Diapause is a programmed state of developmental arrest that typically occurs as part of the natural developmental progression of organisms that inhabit seasonal environments. The brine shrimp Artemia franciscana and annual killifish Austrofundulus limnaeus share strikingly similar life histories that include embryonic diapause as a means to synchronize the growth and reproduction phases of their life history to favorable environmental conditions. In both species, respiration rate is severely depressed during diapause and thus alterations in mitochondrial physiology are a key component of the suite of characters associated with cessation of development. Here, we use these two species to illustrate the basic principles of metabolic depression at the physiological and biochemical levels. It is clear that these two species use divergent molecular mechanisms to achieve the same physiological and ecological outcomes. This pattern of convergent physiological strategies supports the importance of biochemical and physiological adaptations to cope with extreme environmental stress and suggests that inferring mechanism from transcriptomics or proteomics or metabolomics alone, without rigorous follow-up at the biochemical and physiological levels, could lead to erroneous conclusions. Title: Physiological Strategies During Animal Diapause: Lessons from Brine Shrimp and Annual Killifish. Author: Podrabsky, Jason E., Hand, Steven C. Year: 2015 Diapause is a programmed state of developmental arrest that typically occurs as part of the natural developmental progression of organisms that inhabit seasonal environments. The brine shrimp Artemia franciscana and annual killifish Austrofundulus limnaeus share strikingly similar life histories that include embryonic diapause as a means to synchronize the growth and reproduction phases of their life history to favorable environmental conditions. In both species, respiration rate is severely depressed during diapause and thus alterations in mitochondrial physiology are a key component of the suite of characters associated with cessation of development. Here, we use these two species to illustrate the basic principles of metabolic depression at the physiological and biochemical levels. It is clear that these two species use divergent molecular mechanisms to achieve the same physiological and ecological outcomes. This pattern of convergent physiological strategies supports the importance of biochemical and physiological adaptations to cope with extreme environmental stress and suggests that inferring mechanism from transcriptomics or proteomics or metabolomics alone, without rigorous follow-up at the biochemical and physiological levels, could lead to erroneous conclusions. Close

• 5. [Article] Rapid and Repeatable Shifts in Life-History Timing of <i>Rhagoletis pomonella</i> (Diptera: Tephritidae) Following Colonization of Novel Host Plants in the Pacific Northwestern United States

  Host shifts of phytophagous insect specialists to novel plants can result in divergent ecological adaptation, generating reproductive isolation and potentially new species. Rhagoletis pomonellafruit flies ...

  Citation × Citation Citation Abstract Copy Title: Rapid and Repeatable Shifts in Life-History Timing of <i>Rhagoletis pomonella</i> (Diptera: Tephritidae) Following Colonization of Novel Host Plants in the Pacific Northwestern United States Author: Mattsson, Monte, Hood, Glen R., Feder, Jeffery L., Ruedas, Luis A. Year: 2015 Host shifts of phytophagous insect specialists to novel plants can result in divergent ecological adaptation, generating reproductive isolation and potentially new species. Rhagoletis pomonellafruit flies in eastern North America underwent a host shift ~160 ya from native downy hawthorn (Crataegus mollis) to introduced, domesticated apple (Malus domestica). Divergent selection on diapause phenology related to the earlier fruiting time of apples versus downy hawthorns resulted in partial allochronic reproductive isolation between the fly races. Here, we test for how rapid and repeatable shifts in life-history timing are driving ecological divergence of R. pomonella in the Pacific Northwestern USA. The fly was introduced into the region via larval-infested apples 40–65 ya and now attacks native black hawthorn (Crataegus douglasii) and introduced ornamental hawthorn (Crataegus monogyna), in addition to early- and late-maturing apple varieties in the region. To investigate the life-history timing hypothesis, we used a field-based experiment to characterize the host-associated eclosion and flight activity patterns of adults, and the feeding times of larvae at a field site in Vancouver, Washington. We also assessed the degree to which differences in host-fruiting time generate allochronic isolation among apple-, black hawthorn-, and ornamental hawthorn-associated fly populations. We conclude that host-associated fly populations are temporally offset 24.4% to 92.6% in their seasonal distributions. Our results imply that R. pomonella possesses the capacity for rapid and repeatable shifts in diapause life history to match host-fruiting phenology, which can generate ecologically based reproductive isolation, and potentially biodiversity in the process. Title: Rapid and Repeatable Shifts in Life-History Timing of <i>Rhagoletis pomonella</i> (Diptera: Tephritidae) Following Colonization of Novel Host Plants in the Pacific Northwestern United States Author: Mattsson, Monte, Hood, Glen R., Feder, Jeffery L., Ruedas, Luis A. Year: 2015 Host shifts of phytophagous insect specialists to novel plants can result in divergent ecological adaptation, generating reproductive isolation and potentially new species. Rhagoletis pomonellafruit flies in eastern North America underwent a host shift ~160 ya from native downy hawthorn (Crataegus mollis) to introduced, domesticated apple (Malus domestica). Divergent selection on diapause phenology related to the earlier fruiting time of apples versus downy hawthorns resulted in partial allochronic reproductive isolation between the fly races. Here, we test for how rapid and repeatable shifts in life-history timing are driving ecological divergence of R. pomonella in the Pacific Northwestern USA. The fly was introduced into the region via larval-infested apples 40–65 ya and now attacks native black hawthorn (Crataegus douglasii) and introduced ornamental hawthorn (Crataegus monogyna), in addition to early- and late-maturing apple varieties in the region. To investigate the life-history timing hypothesis, we used a field-based experiment to characterize the host-associated eclosion and flight activity patterns of adults, and the feeding times of larvae at a field site in Vancouver, Washington. We also assessed the degree to which differences in host-fruiting time generate allochronic isolation among apple-, black hawthorn-, and ornamental hawthorn-associated fly populations. We conclude that host-associated fly populations are temporally offset 24.4% to 92.6% in their seasonal distributions. Our results imply that R. pomonella possesses the capacity for rapid and repeatable shifts in diapause life history to match host-fruiting phenology, which can generate ecologically based reproductive isolation, and potentially biodiversity in the process. Close

• 6. [Article] Alternate Developmental Pathways

  Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies ...

  Citation × Citation Citation Abstract Copy Title: Alternate Developmental Pathways Author: Podrabsky, Jason E., Romney, Amie L., Culpepper, Kristin M. Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Title: Alternate Developmental Pathways Author: Podrabsky, Jason E., Romney, Amie L., Culpepper, Kristin M. Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Close

• 7. [Article] Tolerance of Environmental Stress

  Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies ...

  Citation × Citation Citation Abstract Copy Title: Tolerance of Environmental Stress Author: Podrabsky, Jason E., Riggs, Claire L., Wagner, Josiah Tad Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Title: Tolerance of Environmental Stress Author: Podrabsky, Jason E., Riggs, Claire L., Wagner, Josiah Tad Year: 2015 Chapter from the book, Annual Fishes: Life History Strategy, Diversity, and Evolution -- the first comprehensive reference on current knowledge of diverse species that exhibit unique survival strategies and provide important models for basic and applied research. This work fills a void, covering the life cycle, reproductive biology, evolutionary ecology, reproductive behavior, sexual selection, genetics, speciation, and integrative and conservation strategies of annual fishes. Bringing together researchers in different areas of annual fishes to summarize previous work, overview the current research, and highlight promising areas of research, the book is organized into three sections focusing on: Diversity, life history, and reproductive biology Ecology and conservation Evolution The book provides a thorough understanding of the complexity of annual fishes and emphasizes their usefulness as a unique model organism for studies in vertebrate biology, particularly in areas such as speciation and senescence. It also notes the gaps in knowledge that challenge future research and encourages the continued expansion and development of research studies on annual fishes to address these gaps so that general vertebrate biology can be better understood. It serves as a valuable resource for scientists in a range of disciplines such as ichthyology, zoology, developmental and evolutionary biology, molecular biology and genetics, and ecology. Close

• 8. [Article] Empirical Demonstration of Environmental Sensing in Catalytic RNA: Evolution of Interpretive Behavior at the Origins of Life

  Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic ...

  Citation × Citation Citation Abstract Copy Title: Empirical Demonstration of Environmental Sensing in Catalytic RNA: Evolution of Interpretive Behavior at the Origins of Life Author: Lehman, Niles, Bernhard, Tess, Larson, Brian C., Robinson, Andrew J.N., Southgate, Christopher C.B. Year: 2014 Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically. Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. By assaying the responsiveness of two variants of the Tetrahymena ribozyme to the Ca2+ ion as a sign for the more catalytically useful Mg2+ ion, we show an empirical proof-of-principle that interpretation can be an evolvable trait in RNA, often suggested as a model system for early life. In particular we demonstrate that in vitro, the wild-type version of the Tetrahymena ribozyme is not interpretive, in that it cannot use Ca2+ as a sign for Mg2+. Yet a variant of this sequence containing five mutations that alter its ability to utilize the Ca2+ ion engenders a strong interpretive characteristic in this RNA. Conclusions: We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment. Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life’s history. Title: Empirical Demonstration of Environmental Sensing in Catalytic RNA: Evolution of Interpretive Behavior at the Origins of Life Author: Lehman, Niles, Bernhard, Tess, Larson, Brian C., Robinson, Andrew J.N., Southgate, Christopher C.B. Year: 2014 Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically. Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. By assaying the responsiveness of two variants of the Tetrahymena ribozyme to the Ca2+ ion as a sign for the more catalytically useful Mg2+ ion, we show an empirical proof-of-principle that interpretation can be an evolvable trait in RNA, often suggested as a model system for early life. In particular we demonstrate that in vitro, the wild-type version of the Tetrahymena ribozyme is not interpretive, in that it cannot use Ca2+ as a sign for Mg2+. Yet a variant of this sequence containing five mutations that alter its ability to utilize the Ca2+ ion engenders a strong interpretive characteristic in this RNA. Conclusions: We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment. Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life’s history. Close

• 9. [Article] Genomics-Informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment

  Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing ...

  Citation × Citation Citation Abstract Copy Title: Genomics-Informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment Author: Wurch, Louie, Giannone, Richard J., Belisle, Bernard S., Swift, Carolyn, Utturkar, Sagar, Hettich, Robert L., Reysenbach, Anna-Louise, Podar, Mircea Year: 2016 Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Genomic and proteomic comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea. Title: Genomics-Informed Isolation and Characterization of a Symbiotic Nanoarchaeota System from a Terrestrial Geothermal Environment Author: Wurch, Louie, Giannone, Richard J., Belisle, Bernard S., Swift, Carolyn, Utturkar, Sagar, Hettich, Robert L., Reysenbach, Anna-Louise, Podar, Mircea Year: 2016 Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Genomic and proteomic comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea. Close

• 10. [Article] Rare, Threatened and Endangered Species of Oregon

  Extinction is a natural process. Today, however, plant and animal species are disappearing world-wide at an accelerated pace. Based on current trends, half of the species on earth will be extinct within ...

  Citation × Citation Citation Abstract Copy Title: Rare, Threatened and Endangered Species of Oregon Author: Kagan, James S., Vrilakas, Sue, Christy, John A., Gaines, Eleanor P., Wise, Lindsey, Pahl, Cameron, Howell, Kathy Year: 2016 Extinction is a natural process. Today, however, plant and animal species are disappearing world-wide at an accelerated pace. Based on current trends, half of the species on earth will be extinct within the next 100 years. The major reasons for this are human caused changes to the environment, which continue to increase - in Oregon and throughout the world. Once lost, a species can never be recovered, and there is no way of knowing how useful it may have been. We do know that human beings and many of their industries depend on plant and animal products. About 50% of all pharmaceuticals have a natural component as an active ingredient, yet less than one percent of the world's species have been chemically analyzed and tested. Many insects and plants contain undescribed and highly functional compounds. Limnanthes pumila subsp. grandiflora, or wooly meadow-foam, a rare plant that grows in southwest Oregon, has been found to produce a hybrid with the more common member of the genus, Limnanthes alba. This hybrid grows well in the poorly drained soils of the Willamette Valley and produces a valuable oil used for soaps, plastic and rubber production. In addition, the new hybrid meadow-foam does not require the field burning necessary for other crops. This species, and many other Oregon natives, will be lost without intervention. The purpose of this publication is to provide land managers, owners and interested parties with a list of those species in Oregon which are in greatest jeopardy. Title: Rare, Threatened and Endangered Species of Oregon Author: Kagan, James S., Vrilakas, Sue, Christy, John A., Gaines, Eleanor P., Wise, Lindsey, Pahl, Cameron, Howell, Kathy Year: 2016 Extinction is a natural process. Today, however, plant and animal species are disappearing world-wide at an accelerated pace. Based on current trends, half of the species on earth will be extinct within the next 100 years. The major reasons for this are human caused changes to the environment, which continue to increase - in Oregon and throughout the world. Once lost, a species can never be recovered, and there is no way of knowing how useful it may have been. We do know that human beings and many of their industries depend on plant and animal products. About 50% of all pharmaceuticals have a natural component as an active ingredient, yet less than one percent of the world's species have been chemically analyzed and tested. Many insects and plants contain undescribed and highly functional compounds. Limnanthes pumila subsp. grandiflora, or wooly meadow-foam, a rare plant that grows in southwest Oregon, has been found to produce a hybrid with the more common member of the genus, Limnanthes alba. This hybrid grows well in the poorly drained soils of the Willamette Valley and produces a valuable oil used for soaps, plastic and rubber production. In addition, the new hybrid meadow-foam does not require the field burning necessary for other crops. This species, and many other Oregon natives, will be lost without intervention. The purpose of this publication is to provide land managers, owners and interested parties with a list of those species in Oregon which are in greatest jeopardy. Close