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• 1. [Article] Using Landsat TM Imagery to Monitor Vegetation Change Following Flow Restoration to the Lower Owens River, California

  Rehabilitating river corridors to restore valuable riparian habitat consumes significant resources from both governments and private companies. Given these considerable expenditures, it is important to ...

  Citation × Citation Citation Abstract Copy Title: Using Landsat TM Imagery to Monitor Vegetation Change Following Flow Restoration to the Lower Owens River, California Author: Bross, Lesley Crandell Year: 2015 Rehabilitating river corridors to restore valuable riparian habitat consumes significant resources from both governments and private companies. Given these considerable expenditures, it is important to monitor the progress of such projects. This study evaluated the utility of using Landsat Thematic Mapper remotely-sensed data from 2002 and 2009 to monitor vegetation change induced by instream flow restoration to the Lower Owens River in central California. This study compared the results of an unsupervised classification with an NDVI threshold classification to appraise the resources required and effectiveness of each analysis method. The results were inspected by creating standard remote sensing accuracy error matrices and by correlating landscape pattern metrics with bird indicator species. Both sets of classified maps show a noticeable increase in riparian vegetation in the study area following flow restoration in 2006, indicating an improvement of the quality of bird habitat. The study concluded that analyzing vegetation change using the unsupervised classification technique required more effort, expert knowledge, and supplementary data than using the NDVI threshold method. If these prerequisites are met, the output from the unsupervised classification process produces a more precise map of land cover change than the NDVI threshold method. However, if an analyst is lacking either resources or ground verification data, the NDVI threshold technique is capable of providing a generalized, but still valid evaluation of vegetation change. This conclusion is supported by higher correlations between indicator bird species under the unsupervised classification method than were found with the NDVI threshold method. Title: Using Landsat TM Imagery to Monitor Vegetation Change Following Flow Restoration to the Lower Owens River, California Author: Bross, Lesley Crandell Year: 2015 Rehabilitating river corridors to restore valuable riparian habitat consumes significant resources from both governments and private companies. Given these considerable expenditures, it is important to monitor the progress of such projects. This study evaluated the utility of using Landsat Thematic Mapper remotely-sensed data from 2002 and 2009 to monitor vegetation change induced by instream flow restoration to the Lower Owens River in central California. This study compared the results of an unsupervised classification with an NDVI threshold classification to appraise the resources required and effectiveness of each analysis method. The results were inspected by creating standard remote sensing accuracy error matrices and by correlating landscape pattern metrics with bird indicator species. Both sets of classified maps show a noticeable increase in riparian vegetation in the study area following flow restoration in 2006, indicating an improvement of the quality of bird habitat. The study concluded that analyzing vegetation change using the unsupervised classification technique required more effort, expert knowledge, and supplementary data than using the NDVI threshold method. If these prerequisites are met, the output from the unsupervised classification process produces a more precise map of land cover change than the NDVI threshold method. However, if an analyst is lacking either resources or ground verification data, the NDVI threshold technique is capable of providing a generalized, but still valid evaluation of vegetation change. This conclusion is supported by higher correlations between indicator bird species under the unsupervised classification method than were found with the NDVI threshold method. Close

• 2. [Article] Spatial and Temporal Variability of Contaminants Within Estuarine Sediments and Native Olympia Oysters: A Contrast Between a Developed and an Undeveloped Estuary

  Chemical contaminants can be introduced into estuarine and marine ecosystems from a variety of sources including wastewater, agriculture and forestry practices, point and non-point discharges, runoff from ...

  Citation × Citation Citation Abstract Copy Title: Spatial and Temporal Variability of Contaminants Within Estuarine Sediments and Native Olympia Oysters: A Contrast Between a Developed and an Undeveloped Estuary Author: Granek, Elise F., Conn, Katherine E., Nilsen, Elena B., Pillsbury, Lori, Strecker, Angela L., Rumrill, Steven S., Fish, William Year: 2016 Chemical contaminants can be introduced into estuarine and marine ecosystems from a variety of sources including wastewater, agriculture and forestry practices, point and non-point discharges, runoff from industrial, municipal, and urban lands, accidental spills, and atmospheric deposition. The diversity of potential sources contributes to the likelihood of contaminated marine waters and sediments and increases the probability of uptake by marine organisms. Despite widespread recognition of direct and indirect pathways for contaminant deposition and organismal exposure in coastal systems, spatial and temporal variability in contaminant composition, deposition, and uptake patterns are still poorly known. We investigated these patterns for a suite of persistent legacy contaminants including polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) and chemicals of emerging concern including pharmaceuticals within two Oregon coastal estuaries (Coos and Netarts Bays). In the more urbanized Coos Bay, native Olympia oyster (Ostrea lurida) tissue had approximately twice the number of PCB congeners at over seven times the total concentration, yet fewer PBDEs at one-tenth the concentration as compared to the more rural Netarts Bay. Different pharmaceutical suites were detected during each sampling season. Variability in contaminant types and concentrations across seasons and between species and media (organisms versus sediment) indicates the limitation of using indicator species and/or sampling annually to determine contaminant loads at a site or for specific species. The results indicate the prevalence of legacy contaminants and CECs in relatively undeveloped coastal environments highlighting the need to improve policy and management actions to reduce contaminant releases into estuarine and marine waters and to deal with legacy compounds that remain long after prohibition of use. Our results point to the need for better understanding of the ecological and human health risks of exposure to the diverse cocktail of pollutants and harmful compounds that will continue to leach from estuarine sediments over time. Title: Spatial and Temporal Variability of Contaminants Within Estuarine Sediments and Native Olympia Oysters: A Contrast Between a Developed and an Undeveloped Estuary Author: Granek, Elise F., Conn, Katherine E., Nilsen, Elena B., Pillsbury, Lori, Strecker, Angela L., Rumrill, Steven S., Fish, William Year: 2016 Chemical contaminants can be introduced into estuarine and marine ecosystems from a variety of sources including wastewater, agriculture and forestry practices, point and non-point discharges, runoff from industrial, municipal, and urban lands, accidental spills, and atmospheric deposition. The diversity of potential sources contributes to the likelihood of contaminated marine waters and sediments and increases the probability of uptake by marine organisms. Despite widespread recognition of direct and indirect pathways for contaminant deposition and organismal exposure in coastal systems, spatial and temporal variability in contaminant composition, deposition, and uptake patterns are still poorly known. We investigated these patterns for a suite of persistent legacy contaminants including polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) and chemicals of emerging concern including pharmaceuticals within two Oregon coastal estuaries (Coos and Netarts Bays). In the more urbanized Coos Bay, native Olympia oyster (Ostrea lurida) tissue had approximately twice the number of PCB congeners at over seven times the total concentration, yet fewer PBDEs at one-tenth the concentration as compared to the more rural Netarts Bay. Different pharmaceutical suites were detected during each sampling season. Variability in contaminant types and concentrations across seasons and between species and media (organisms versus sediment) indicates the limitation of using indicator species and/or sampling annually to determine contaminant loads at a site or for specific species. The results indicate the prevalence of legacy contaminants and CECs in relatively undeveloped coastal environments highlighting the need to improve policy and management actions to reduce contaminant releases into estuarine and marine waters and to deal with legacy compounds that remain long after prohibition of use. Our results point to the need for better understanding of the ecological and human health risks of exposure to the diverse cocktail of pollutants and harmful compounds that will continue to leach from estuarine sediments over time. Close

• 3. [Article] How Cities Can Increase Cycling Among Women An Evaluation of: Portland, OR, Washington D.C., and Vancouver B.C.

  56 pages

  Citation × Citation Citation Abstract Copy Title: How Cities Can Increase Cycling Among Women An Evaluation of: Portland, OR, Washington D.C., and Vancouver B.C. Author: Horan, Erin Year: 2016 56 pages Title: How Cities Can Increase Cycling Among Women An Evaluation of: Portland, OR, Washington D.C., and Vancouver B.C. Author: Horan, Erin Year: 2016 56 pages Close

• 4. [Article] Species Diversification in Aquaculture: a Global Assessment

  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: Species Diversification in Aquaculture: a Global Assessment Author: Zhou, Xiaowei, Yan, Xue, Cai, Junning 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: Species Diversification in Aquaculture: a Global Assessment Author: Zhou, Xiaowei, Yan, Xue, Cai, Junning 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

• 5. [Article] Resveratrol Influence on Lifespan among Caenorhabditis Elegans Genetic Variants & Implications for Personalized Medicine

  46 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, ...

  Citation × Citation Citation Abstract Copy Title: Resveratrol Influence on Lifespan among Caenorhabditis Elegans Genetic Variants & Implications for Personalized Medicine Author: Caul, Tela Amber Year: 2017 46 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Title: Resveratrol Influence on Lifespan among Caenorhabditis Elegans Genetic Variants & Implications for Personalized Medicine Author: Caul, Tela Amber Year: 2017 46 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Close

• 6. [Article] Assessing a Fluorescence Spectroscopy Method for In-Situ Microbial Drinking Water Quality

  Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial ...

  Citation × Citation Citation Abstract Copy Title: Assessing a Fluorescence Spectroscopy Method for In-Situ Microbial Drinking Water Quality Author: Sharpe, Taylor Jeffery Year: 2017 Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial pathogens in drinking water sources have important limitations, including high initial cost, 24-48 hour delays in results, high staffing and facility requirements, and training requirements which all become especially problematic in the developing nation context. A number of alternative approaches to microbial water quality testing have been proposed, with the goal of decreasing the required testing time, decreasing overall costs, leveraging appropriate technology approaches, or improving sensitivity or specificity of the water quality testing method. One approach that may offer solutions to some of these limitations involves the deployment of sensor networks using fluorescent spectroscopy to detect intrinsic protein fluorescence in water samples as a proxy for microbial activity. In recent years, a number of researchers have found significant and meaningful correlations between indicator bacteria species and the protein fluorescence of drinking water samples. Additionally, advances in the semiconductor industry could be used to drive down the cost of such sensors. This technology may also be extensible to other water quality parameters, including dissolved organic matter or the presence of fluorescent pollutants. In this thesis, a literature review describes the fundamentals of fluorescence spectroscopy, historical and recent work regarding the fluorescence of the amino acid tryptophan and associated bacterial fluorescence, possible mechanisms for this association, and potential applications of this technology for drinking water quality monitoring and waste water process control. Extensibility of the technology is also discussed. Next, experimental methodology in reproduction of similar results is described. Samples were taken from seven (7) surface water sources and tested using membrane filtration and an off-the-shelf fluorescence spectrometer to help examine the association between the presence of indicator bacteria and the tryptophan fluorescence of the water sample. The results, showing an association of R2 = 0.560, are compared to the results of recent similar experiments. Finally, two prototypes are described, including their design requirements and data from prototype testing. The results of the testing are briefly discussed, and next steps are outlined with the goal of developing a low-cost, in-situ microbial water quality sensor using fluorescence spectroscopy principles. Title: Assessing a Fluorescence Spectroscopy Method for In-Situ Microbial Drinking Water Quality Author: Sharpe, Taylor Jeffery Year: 2017 Waterborne disease is a significant contributor to the global burden of disease, in particular among high-risk populations in developing nations. State-of-the-art methods for the enumeration of microbial pathogens in drinking water sources have important limitations, including high initial cost, 24-48 hour delays in results, high staffing and facility requirements, and training requirements which all become especially problematic in the developing nation context. A number of alternative approaches to microbial water quality testing have been proposed, with the goal of decreasing the required testing time, decreasing overall costs, leveraging appropriate technology approaches, or improving sensitivity or specificity of the water quality testing method. One approach that may offer solutions to some of these limitations involves the deployment of sensor networks using fluorescent spectroscopy to detect intrinsic protein fluorescence in water samples as a proxy for microbial activity. In recent years, a number of researchers have found significant and meaningful correlations between indicator bacteria species and the protein fluorescence of drinking water samples. Additionally, advances in the semiconductor industry could be used to drive down the cost of such sensors. This technology may also be extensible to other water quality parameters, including dissolved organic matter or the presence of fluorescent pollutants. In this thesis, a literature review describes the fundamentals of fluorescence spectroscopy, historical and recent work regarding the fluorescence of the amino acid tryptophan and associated bacterial fluorescence, possible mechanisms for this association, and potential applications of this technology for drinking water quality monitoring and waste water process control. Extensibility of the technology is also discussed. Next, experimental methodology in reproduction of similar results is described. Samples were taken from seven (7) surface water sources and tested using membrane filtration and an off-the-shelf fluorescence spectrometer to help examine the association between the presence of indicator bacteria and the tryptophan fluorescence of the water sample. The results, showing an association of R2 = 0.560, are compared to the results of recent similar experiments. Finally, two prototypes are described, including their design requirements and data from prototype testing. The results of the testing are briefly discussed, and next steps are outlined with the goal of developing a low-cost, in-situ microbial water quality sensor using fluorescence spectroscopy principles. Close

• 7. [Article] Predicted Effects of Gypsy Moth Defoliation and Climate Change on Forest Carbon Dynamics in the New Jersey Pine Barrens

  Disturbance regimes within temperate forests can significantly impact carbon cycling. Additionally, projected climate change in combination with multiple, interacting disturbance effects may disrupt the ...

  Citation × Citation Citation Abstract Copy Title: Predicted Effects of Gypsy Moth Defoliation and Climate Change on Forest Carbon Dynamics in the New Jersey Pine Barrens Author: Kretchun, Alec M., Scheller, Robert M., Lucash, Melissa S., Clark, Kenneth L., Hom, John, Van Tuyl, Steve Year: 2014 Disturbance regimes within temperate forests can significantly impact carbon cycling. Additionally, projected climate change in combination with multiple, interacting disturbance effects may disrupt the capacity of forests to act as carbon sinks at large spatial and temporal scales. We used a spatially explicit forest succession and disturbance model, LANDIS-II, to model the effects of climate change, gypsy moth (Lymantria dispar L.) defoliation, and wildfire on the C dynamics of the forests of the New Jersey Pine Barrens over the next century. Climate scenarios were simulated using current climate conditions (baseline), as well as a high emissions scenario (HadCM3 A2 emissions scenario). Our results suggest that long-term changes in C cycling will be driven more by climate change than by fire or gypsy moths over the next century. We also found that simulated disturbances will affect species composition more than tree growth or C sequestration rates at the landscape level. Projected changes in tree species biomass indicate a potential increase in oaks with climate change and gypsy moth defoliation over the course of the 100-year simulation, exacerbating current successional trends towards increased oak abundance. Our research suggests that defoliation under climate change may play a critical role in increasing the variability of tree growth rates and in determining landscape species composition over the next 100 years. Title: Predicted Effects of Gypsy Moth Defoliation and Climate Change on Forest Carbon Dynamics in the New Jersey Pine Barrens Author: Kretchun, Alec M., Scheller, Robert M., Lucash, Melissa S., Clark, Kenneth L., Hom, John, Van Tuyl, Steve Year: 2014 Disturbance regimes within temperate forests can significantly impact carbon cycling. Additionally, projected climate change in combination with multiple, interacting disturbance effects may disrupt the capacity of forests to act as carbon sinks at large spatial and temporal scales. We used a spatially explicit forest succession and disturbance model, LANDIS-II, to model the effects of climate change, gypsy moth (Lymantria dispar L.) defoliation, and wildfire on the C dynamics of the forests of the New Jersey Pine Barrens over the next century. Climate scenarios were simulated using current climate conditions (baseline), as well as a high emissions scenario (HadCM3 A2 emissions scenario). Our results suggest that long-term changes in C cycling will be driven more by climate change than by fire or gypsy moths over the next century. We also found that simulated disturbances will affect species composition more than tree growth or C sequestration rates at the landscape level. Projected changes in tree species biomass indicate a potential increase in oaks with climate change and gypsy moth defoliation over the course of the 100-year simulation, exacerbating current successional trends towards increased oak abundance. Our research suggests that defoliation under climate change may play a critical role in increasing the variability of tree growth rates and in determining landscape species composition over the next 100 years. Close

• 8. [Article] Wet Meadow Plant Associations, Double O Unit, Malheur National Wildlife Refuge, Harney County, Oregon

  This report summarizes vegetation data collected in July 2015 in wet meadow and marshy habitats on the Double O Unit of Malheur National Wildlife Refuge (MNWR). Because vegetation sampled at the Double ...

  Citation × Citation Citation Abstract Copy Title: Wet Meadow Plant Associations, Double O Unit, Malheur National Wildlife Refuge, Harney County, Oregon Author: Christy, John A. Year: 2016 This report summarizes vegetation data collected in July 2015 in wet meadow and marshy habitats on the Double O Unit of Malheur National Wildlife Refuge (MNWR). Because vegetation sampled at the Double O was wetter and more alkaline than wet meadows sampled at the south end of the refuge in 2012 and 2013 (Christy 2014), data from the Double O Unit were analyzed and summarized separately. A total of 83 plots were sampled in 2015, and analysis of the data identified 14 plant associations: Alopecurus aequalis - Juncus balticus, Alopecurus pratensis - Potentilla anserina, Carex praegracilis - Juncus balticus, Cicuta douglasii - Carex nebrascensis, Distichlis spicata - Amphiscirpus nevadensis, Distichlis spicata - Nitrophila occidentalis, Eleocharis palustris - Juncus balticus, Eleocharis rostellata, Juncus balticus - Glaux maritima, Hippuris vulgaris - Triglochin maritima, Leymus triticoides - Juncus balticus, Schoenoplectus americanus, Spartina gracilis, and Triglochin maritima. Plant associations spanned a wetland gradient from seasonally moist to seasonally or perennially flooded, but surface water had left most stands at time of sampling. Mean Wetland Indicator Status scores and species composition help to place the plant associations within gradients in soil moisture and alkalinity. Seven of the 14 plant associations are listed in the International Vegetation Classification, and the remaining types are provisional Title: Wet Meadow Plant Associations, Double O Unit, Malheur National Wildlife Refuge, Harney County, Oregon Author: Christy, John A. Year: 2016 This report summarizes vegetation data collected in July 2015 in wet meadow and marshy habitats on the Double O Unit of Malheur National Wildlife Refuge (MNWR). Because vegetation sampled at the Double O was wetter and more alkaline than wet meadows sampled at the south end of the refuge in 2012 and 2013 (Christy 2014), data from the Double O Unit were analyzed and summarized separately. A total of 83 plots were sampled in 2015, and analysis of the data identified 14 plant associations: Alopecurus aequalis - Juncus balticus, Alopecurus pratensis - Potentilla anserina, Carex praegracilis - Juncus balticus, Cicuta douglasii - Carex nebrascensis, Distichlis spicata - Amphiscirpus nevadensis, Distichlis spicata - Nitrophila occidentalis, Eleocharis palustris - Juncus balticus, Eleocharis rostellata, Juncus balticus - Glaux maritima, Hippuris vulgaris - Triglochin maritima, Leymus triticoides - Juncus balticus, Schoenoplectus americanus, Spartina gracilis, and Triglochin maritima. Plant associations spanned a wetland gradient from seasonally moist to seasonally or perennially flooded, but surface water had left most stands at time of sampling. Mean Wetland Indicator Status scores and species composition help to place the plant associations within gradients in soil moisture and alkalinity. Seven of the 14 plant associations are listed in the International Vegetation Classification, and the remaining types are provisional Close

• 9. [Article] Ecosystem Recovery in Estuarine Wetlands of the Columbia River Estuary

  In the restoration of tidal wetland ecosystems, potential drivers of plant community development range from biotic controls (e.g. plant competition, seed dispersal) to abiotic controls (e.g. tidal flooding, ...

  Citation × Citation Citation Abstract Copy Title: Ecosystem Recovery in Estuarine Wetlands of the Columbia River Estuary Author: Kidd, Sarah Ann Year: 2017 In the restoration of tidal wetland ecosystems, potential drivers of plant community development range from biotic controls (e.g. plant competition, seed dispersal) to abiotic controls (e.g. tidal flooding, salinity levels). How these controls influence the success of tidal wetland restoration are only partly understood, but have important implications for wetland habitat recovery. Specifically, the extent to which the existing native and non-native seed banks in tidally reconnected wetlands interact with these controls is not clear, yet the potential success of passive restoration methods depends upon this understanding. For a 54-year chronosequence of eleven tidal wetland restoration sites in the Lower Columbia River of western Oregon, USA, it was hypothesized that native plant species and soil properties would show trends approaching reference levels within 3 to 20 years post-restoration and that lower elevation wetland areas within restored sites would exhibit a greater native species abundance and similarity to reference sites, compared with restored high elevation wetland areas. Results indicated that plant species richness, soil organic matter, bulk density, pH, and salinity conditions among the restoration sites reached reference wetland ranges within 3-6 years post-tidal reconnection. The mid-low marsh elevation zones (2.5 m) remained dominated by non-native species Phalaris arundinacea and Juncus effusus subsp. effusus. To investigate the mechanisms driving these non-native plant invasions, it was hypothesized that native and non-native wetland plant community distributions would be reflective both of their abundance in the seed bank and of their germination tolerance to wetland tidal flooding and salinity conditions. Using a factorial study design of three tidal conditions by three salinity levels, these hypotheses were tested in the greenhouse. Overall, non-native seeds were found to significantly outnumber native seeds in both seed banks. In the greenhouse, P. arundinacea and J. effusus were found to germinate more readily out of the seed bank under freshwater high-marsh flooding (1 hour a day) treatments as compared to oligohaline (3 ppt) mid-low marsh flooding (3-6 hours twice a day) treatments and to brackish salinity (10 ppt) treatments. Dominant native wetland species, Carex lyngbyei and Schoenoplectus lacustris, germination were not found to vary significantly among the treatments (p > 0.10). These results indicate that the salinity and flooding gradients within these restored marshes suppress germination of the non-native species in the low-mid marsh but not in the high marsh, where they are likely able to outcompete the native species due to their dominance in the seed bank. The implications of these results for passive tidal wetland restoration efforts are that both seed bank composition and species-specific tolerances to restored tidal flooding and salinity gradients are key mechanisms driving native and non-native plant community development and resilience. Title: Ecosystem Recovery in Estuarine Wetlands of the Columbia River Estuary Author: Kidd, Sarah Ann Year: 2017 In the restoration of tidal wetland ecosystems, potential drivers of plant community development range from biotic controls (e.g. plant competition, seed dispersal) to abiotic controls (e.g. tidal flooding, salinity levels). How these controls influence the success of tidal wetland restoration are only partly understood, but have important implications for wetland habitat recovery. Specifically, the extent to which the existing native and non-native seed banks in tidally reconnected wetlands interact with these controls is not clear, yet the potential success of passive restoration methods depends upon this understanding. For a 54-year chronosequence of eleven tidal wetland restoration sites in the Lower Columbia River of western Oregon, USA, it was hypothesized that native plant species and soil properties would show trends approaching reference levels within 3 to 20 years post-restoration and that lower elevation wetland areas within restored sites would exhibit a greater native species abundance and similarity to reference sites, compared with restored high elevation wetland areas. Results indicated that plant species richness, soil organic matter, bulk density, pH, and salinity conditions among the restoration sites reached reference wetland ranges within 3-6 years post-tidal reconnection. The mid-low marsh elevation zones (2.5 m) remained dominated by non-native species Phalaris arundinacea and Juncus effusus subsp. effusus. To investigate the mechanisms driving these non-native plant invasions, it was hypothesized that native and non-native wetland plant community distributions would be reflective both of their abundance in the seed bank and of their germination tolerance to wetland tidal flooding and salinity conditions. Using a factorial study design of three tidal conditions by three salinity levels, these hypotheses were tested in the greenhouse. Overall, non-native seeds were found to significantly outnumber native seeds in both seed banks. In the greenhouse, P. arundinacea and J. effusus were found to germinate more readily out of the seed bank under freshwater high-marsh flooding (1 hour a day) treatments as compared to oligohaline (3 ppt) mid-low marsh flooding (3-6 hours twice a day) treatments and to brackish salinity (10 ppt) treatments. Dominant native wetland species, Carex lyngbyei and Schoenoplectus lacustris, germination were not found to vary significantly among the treatments (p > 0.10). These results indicate that the salinity and flooding gradients within these restored marshes suppress germination of the non-native species in the low-mid marsh but not in the high marsh, where they are likely able to outcompete the native species due to their dominance in the seed bank. The implications of these results for passive tidal wetland restoration efforts are that both seed bank composition and species-specific tolerances to restored tidal flooding and salinity gradients are key mechanisms driving native and non-native plant community development and resilience. Close

• 10. [Article] Sablefish (Anoplopoma fimbria) Scarcity and Zooarchaeological Data Quality in Northwest Coast Archaeological Sites

  Sablefish (Anoplopoma fimbria) is a scarcely represented species in Northwest Coast archaeology, but its remains are abundant at Tse-whit-zen, a large, Lower Elwha Klallam village in modern Port Angeles, ...

  Citation × Citation Citation Abstract Copy Title: Sablefish (Anoplopoma fimbria) Scarcity and Zooarchaeological Data Quality in Northwest Coast Archaeological Sites Author: Nims, Reno Year: 2016 Sablefish (Anoplopoma fimbria) is a scarcely represented species in Northwest Coast archaeology, but its remains are abundant at Tse-whit-zen, a large, Lower Elwha Klallam village in modern Port Angeles, WA that was occupied over the past 2,800 years. Because sablefish flesh has high nutritional value and it can be easily captured from nearshore waters in its juvenile form, sablefish should have been pursued where it was available. Therefore, the scarcity of sablefish in many Northwest Coast archaeological sites could indicate this species was not abundant in past fisheries. However, current zooarchaeological reports do not contain sufficient information on taphonomic histories, sampling, or zooarchaeological methods to determine whether patterns of sablefish scarcity could actually explained by differential destruction of sablefish remains, sample size effects, screen size effects, or misidentification. In this thesis, I examine how each of these factors may have affected the abundance of sablefish remains in Northwest coast archaeological sites. I evaluate four hypotheses that attribute sablefish representation to zooarchaeological identification methods, screen size, sample size, and post-depositional destruction of fishbone. While I do not explicitly test whether social and ecological factors affect sablefish abundance, sociocultural and environmental variation can be considered likely explanations for the observed patterns of sablefish representation if the other hypotheses are rejected. I test my hypotheses using three scales of archaeological records. First, I reanalyzed six previously analyzed Salish Sea assemblages to assess whether criteria for sablefish identification exist, are valid, and have been applied consistently. Second, I synthesized fishbone data from 35 previously analyzed Northwest Coast assemblages to evaluate the effects of screen size, sample size, and post-depositional destruction on sablefish representation. Finally, I integrate previously unreported fishbone data from the analysis of Tse-whit-zen into the synthesis of previous studies. The Tse-whit-zen materials I report on here represent six discrete time periods in the 1,800-year history of one large area of the site, which encompasses part of a plankhouse, providing a unique opportunity to examine the effects of screening, sample size, and post-depositional destruction at an extremely fine scale. I also use data from the reanalysis of a portion of the Tse-whit-zen fishbone to verify the consistency of sablefish identification for this site. I reject all four hypotheses and conclude that the uneven distribution of sablefish is likely a true reflection of ecological factors, human decision-making, or both factors. Whether sablefish scarcity is related to distributions of sablefish in past environments, or whether humans chose not to pursue sablefish is not known from the current study. Connecting sablefish capture to specific seasons with body-size regression methods may reveal associations between sablefish acquisition and other seasonal fisheries and activities, and help evaluate whether they conflicted with sablefish procurement in some contexts. Although zooarchaeological identification and reporting methods do not appear to account for sablefish scarcity, zooarchaeologists need to include more information about their methods so that the validity of inter-assemblage comparisons can be assessed. Zooarchaeologists maximize the value of their contributions to anthropology, biological sciences, and human ecodynamics when they explicitly report the methods they use to identify animal remains. By reporting the methodological and analytic procedures they used in detail, zooarchaeologists enhance the reader's confidence in their conclusions and provide future researchers with the information that is required to replicate their results. Which elements were recorded, and the criteria that were used to make taxonomic attributions, fundamentally affect the primary faunal data that researchers use. This study is part of a growing interest among zooarchaeologists in data quality assurance and quality control, which constitute a critical part of every large-scale comparative analysis. Title: Sablefish (Anoplopoma fimbria) Scarcity and Zooarchaeological Data Quality in Northwest Coast Archaeological Sites Author: Nims, Reno Year: 2016 Sablefish (Anoplopoma fimbria) is a scarcely represented species in Northwest Coast archaeology, but its remains are abundant at Tse-whit-zen, a large, Lower Elwha Klallam village in modern Port Angeles, WA that was occupied over the past 2,800 years. Because sablefish flesh has high nutritional value and it can be easily captured from nearshore waters in its juvenile form, sablefish should have been pursued where it was available. Therefore, the scarcity of sablefish in many Northwest Coast archaeological sites could indicate this species was not abundant in past fisheries. However, current zooarchaeological reports do not contain sufficient information on taphonomic histories, sampling, or zooarchaeological methods to determine whether patterns of sablefish scarcity could actually explained by differential destruction of sablefish remains, sample size effects, screen size effects, or misidentification. In this thesis, I examine how each of these factors may have affected the abundance of sablefish remains in Northwest coast archaeological sites. I evaluate four hypotheses that attribute sablefish representation to zooarchaeological identification methods, screen size, sample size, and post-depositional destruction of fishbone. While I do not explicitly test whether social and ecological factors affect sablefish abundance, sociocultural and environmental variation can be considered likely explanations for the observed patterns of sablefish representation if the other hypotheses are rejected. I test my hypotheses using three scales of archaeological records. First, I reanalyzed six previously analyzed Salish Sea assemblages to assess whether criteria for sablefish identification exist, are valid, and have been applied consistently. Second, I synthesized fishbone data from 35 previously analyzed Northwest Coast assemblages to evaluate the effects of screen size, sample size, and post-depositional destruction on sablefish representation. Finally, I integrate previously unreported fishbone data from the analysis of Tse-whit-zen into the synthesis of previous studies. The Tse-whit-zen materials I report on here represent six discrete time periods in the 1,800-year history of one large area of the site, which encompasses part of a plankhouse, providing a unique opportunity to examine the effects of screening, sample size, and post-depositional destruction at an extremely fine scale. I also use data from the reanalysis of a portion of the Tse-whit-zen fishbone to verify the consistency of sablefish identification for this site. I reject all four hypotheses and conclude that the uneven distribution of sablefish is likely a true reflection of ecological factors, human decision-making, or both factors. Whether sablefish scarcity is related to distributions of sablefish in past environments, or whether humans chose not to pursue sablefish is not known from the current study. Connecting sablefish capture to specific seasons with body-size regression methods may reveal associations between sablefish acquisition and other seasonal fisheries and activities, and help evaluate whether they conflicted with sablefish procurement in some contexts. Although zooarchaeological identification and reporting methods do not appear to account for sablefish scarcity, zooarchaeologists need to include more information about their methods so that the validity of inter-assemblage comparisons can be assessed. Zooarchaeologists maximize the value of their contributions to anthropology, biological sciences, and human ecodynamics when they explicitly report the methods they use to identify animal remains. By reporting the methodological and analytic procedures they used in detail, zooarchaeologists enhance the reader's confidence in their conclusions and provide future researchers with the information that is required to replicate their results. Which elements were recorded, and the criteria that were used to make taxonomic attributions, fundamentally affect the primary faunal data that researchers use. This study is part of a growing interest among zooarchaeologists in data quality assurance and quality control, which constitute a critical part of every large-scale comparative analysis. Close

• 11. [Article] The Uneven Geography of River Conservation In The U.S.: Insights From The Application Of The Wild And Scenic Rivers Act

  Rivers are vital for sustaining biodiversity and human development, yet globally only a small fraction of rivers enjoy protection and those with protections are often impaired or modified. Rapid rates ...

  Citation × Citation Citation Abstract Copy Title: The Uneven Geography of River Conservation In The U.S.: Insights From The Application Of The Wild And Scenic Rivers Act Author: Perry, Denielle Year: 2017 Rivers are vital for sustaining biodiversity and human development, yet globally only a small fraction of rivers enjoy protection and those with protections are often impaired or modified. Rapid rates of freshwater species’ extinctions indicate current conservation practices are failing. Despite over fifty years of scientific evidence justifying river conservation, it remains that less attention is focused on protecting ecosystems than on developing water resources for economic growth. This disparity is indicative of the ‘nature as resource’ versus ‘conservation of nature’ paradigm. Today, this paradigm is complicated by new attentions centering both on water resource development projects and conservation policy as climate change adaptation strategies. Policies protecting rivers are recommended for contending with more intense storms and flooding, increasing resilience for species, forests, and agricultural areas, and fostering some types of water security. Creating, implementing, and managing climate adaptation policies will require a strong state presence in water resource governance. We know, however, the aforementioned paradigm hinders conservation policymaking. Therefore, understanding how conservation policy has already been rationalized, implemented, and managed is critical to advancing climate adaptation policymaking. Yet, little empirical research has been conducted on federal river conservation policy creation or application across the U.S. To that end, this dissertation, presented in three discrete original research articles, examines the United States National Wild and Scenic Rivers System. Specifically, this study investigates the socio-ecological drivers behind the creation of the Wild and Scenic Rivers Act of 1968 (WSRA hereinafter) and the spatial dimensions of the policy’s application and management over time. This study is grounded empirically in extensive archival materials, interviews with federal land management agency personnel, conservation advocates, and technical experts, as well as spatial and temporal analysis of a geodatabase. Together, these methods were employed to answer the following research questions which guide this study: (1) What factors influence the temporal and spatial distribution of river segments protected under the Wild & Scenic Rivers Act? (2) What does the history of management in designated segments suggest about emerging trends and patterns in river conservation? (3) How are competing environmental values and ideologies understood and reconciled in the context of river conservation? Title: The Uneven Geography of River Conservation In The U.S.: Insights From The Application Of The Wild And Scenic Rivers Act Author: Perry, Denielle Year: 2017 Rivers are vital for sustaining biodiversity and human development, yet globally only a small fraction of rivers enjoy protection and those with protections are often impaired or modified. Rapid rates of freshwater species’ extinctions indicate current conservation practices are failing. Despite over fifty years of scientific evidence justifying river conservation, it remains that less attention is focused on protecting ecosystems than on developing water resources for economic growth. This disparity is indicative of the ‘nature as resource’ versus ‘conservation of nature’ paradigm. Today, this paradigm is complicated by new attentions centering both on water resource development projects and conservation policy as climate change adaptation strategies. Policies protecting rivers are recommended for contending with more intense storms and flooding, increasing resilience for species, forests, and agricultural areas, and fostering some types of water security. Creating, implementing, and managing climate adaptation policies will require a strong state presence in water resource governance. We know, however, the aforementioned paradigm hinders conservation policymaking. Therefore, understanding how conservation policy has already been rationalized, implemented, and managed is critical to advancing climate adaptation policymaking. Yet, little empirical research has been conducted on federal river conservation policy creation or application across the U.S. To that end, this dissertation, presented in three discrete original research articles, examines the United States National Wild and Scenic Rivers System. Specifically, this study investigates the socio-ecological drivers behind the creation of the Wild and Scenic Rivers Act of 1968 (WSRA hereinafter) and the spatial dimensions of the policy’s application and management over time. This study is grounded empirically in extensive archival materials, interviews with federal land management agency personnel, conservation advocates, and technical experts, as well as spatial and temporal analysis of a geodatabase. Together, these methods were employed to answer the following research questions which guide this study: (1) What factors influence the temporal and spatial distribution of river segments protected under the Wild & Scenic Rivers Act? (2) What does the history of management in designated segments suggest about emerging trends and patterns in river conservation? (3) How are competing environmental values and ideologies understood and reconciled in the context of river conservation? Close

• 12. [Article] Supplementary Data Terrestrial Mollusk Location and Species Count

  Supporting data in csv table format.

  Citation × Citation Citation Abstract Copy Title: Supplementary Data Terrestrial Mollusk Location and Species Count Author: Emery-Wetherell, Meaghan Marie, Mathew, Christine, Church, Cameron, Dellard, Ellie, Davis, Edward Byrd, Roering, Josh Year: 2017 Supporting data in csv table format. Title: Supplementary Data Terrestrial Mollusk Location and Species Count Author: Emery-Wetherell, Meaghan Marie, Mathew, Christine, Church, Cameron, Dellard, Ellie, Davis, Edward Byrd, Roering, Josh Year: 2017 Supporting data in csv table format. Close

• 13. [Article] Fish Species Introductions Provide Novel Insights into the Patterns and Drivers of Phylogenetic Structure in Freshwaters

  Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. ...

  Citation × Citation Citation Abstract Copy Title: Fish Species Introductions Provide Novel Insights into the Patterns and Drivers of Phylogenetic Structure in Freshwaters Author: Strecker, Angela L., Olden, Julian D. Year: 2014 Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin's naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species. Title: Fish Species Introductions Provide Novel Insights into the Patterns and Drivers of Phylogenetic Structure in Freshwaters Author: Strecker, Angela L., Olden, Julian D. Year: 2014 Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin's naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species. Close

• 14. [Article] Substrate Age Influences Species Richness and Community Composition of Calicioid Lichens and Fungi on Wooden Buildings

  Identifying processes that drive epiphytic lichen diversity and succession is important for directing conservation efforts and developing forest management plans for the maintenance of biodiversity and ...

  Citation × Citation Citation Abstract Copy Title: Substrate Age Influences Species Richness and Community Composition of Calicioid Lichens and Fungi on Wooden Buildings Author: Peterson, Kate, Calabria, Lalita M., Miller, Jesse E.D., Brown-Clay, Jesse Year: 2017 Identifying processes that drive epiphytic lichen diversity and succession is important for directing conservation efforts and developing forest management plans for the maintenance of biodiversity and forest health. Stand age has been implicated as a key factor in driving epiphytic species diversity and community composition. However, understanding the influence of substrate age, independent of the many confounding variables that affect live and dead wood substrates in a forest habitat, can be difficult. To test the hypothesis that substrate age has distinct effects on lichen community assembly independent of surface area, we sampled communities of calicioid lichens and fungi growing on wooden buildings that ranged from 2 to 82 years old. We found a total of 17 species, with a strong positive correlation between species richness and substrate age. We also tested the effects of surface area on species richness and found no relationship between the two variables. Our results indicate that substrate age influenced community composition; non-lichenized calicioid species acted as early colonizers and six calicioid species were recorded only on the oldest substrate. Old-growth associate species were found on substrates of varying ages, implying that additional variables may also be responsible for the colonization of old-growth associate species. Copyright © 2017 by The American Bryological and Lichenological Society, Inc. Title: Substrate Age Influences Species Richness and Community Composition of Calicioid Lichens and Fungi on Wooden Buildings Author: Peterson, Kate, Calabria, Lalita M., Miller, Jesse E.D., Brown-Clay, Jesse Year: 2017 Identifying processes that drive epiphytic lichen diversity and succession is important for directing conservation efforts and developing forest management plans for the maintenance of biodiversity and forest health. Stand age has been implicated as a key factor in driving epiphytic species diversity and community composition. However, understanding the influence of substrate age, independent of the many confounding variables that affect live and dead wood substrates in a forest habitat, can be difficult. To test the hypothesis that substrate age has distinct effects on lichen community assembly independent of surface area, we sampled communities of calicioid lichens and fungi growing on wooden buildings that ranged from 2 to 82 years old. We found a total of 17 species, with a strong positive correlation between species richness and substrate age. We also tested the effects of surface area on species richness and found no relationship between the two variables. Our results indicate that substrate age influenced community composition; non-lichenized calicioid species acted as early colonizers and six calicioid species were recorded only on the oldest substrate. Old-growth associate species were found on substrates of varying ages, implying that additional variables may also be responsible for the colonization of old-growth associate species. Copyright © 2017 by The American Bryological and Lichenological Society, Inc. Close

• 15. [Article] The Performance of Four Native Perennial Forb Species Along a Climate Gradient in Pacific Northwest Prairies

  To determine how Pacific Northwest prairies are influenced by local site factors versus. regional climate, we studied the reproduction, plant size, and density of sixteen natural populations of four perennial ...

  Citation × Citation Citation Abstract Copy Title: The Performance of Four Native Perennial Forb Species Along a Climate Gradient in Pacific Northwest Prairies Author: Hendricks, Lauren Year: 2016 To determine how Pacific Northwest prairies are influenced by local site factors versus. regional climate, we studied the reproduction, plant size, and density of sixteen natural populations of four perennial forb species native to Pacific Northwest prairies: Ranunculus austro-oreganus, Sidalcea malviflora spp. virgata, Microseris laciniata, and Eriophyllum lanatum. These populations were distributed along a 700 kilometer latitudinal gradient from southern Oregon to Whidbey Island, Washington. We found significant differences in plant size and reproduction among populations for all species, but correlations among edaphic and climate variables and plant size and reproduction were weak. Instead, density was more strongly correlated with both edaphic and climate variables, suggesting that this is a better indicator of long-term demographic processes. Although a few factors are important across species (e.g., nutrient availability and minimum temperature), response is idiosyncratic at the individual species level in Pacific Northwest prairies. Title: The Performance of Four Native Perennial Forb Species Along a Climate Gradient in Pacific Northwest Prairies Author: Hendricks, Lauren Year: 2016 To determine how Pacific Northwest prairies are influenced by local site factors versus. regional climate, we studied the reproduction, plant size, and density of sixteen natural populations of four perennial forb species native to Pacific Northwest prairies: Ranunculus austro-oreganus, Sidalcea malviflora spp. virgata, Microseris laciniata, and Eriophyllum lanatum. These populations were distributed along a 700 kilometer latitudinal gradient from southern Oregon to Whidbey Island, Washington. We found significant differences in plant size and reproduction among populations for all species, but correlations among edaphic and climate variables and plant size and reproduction were weak. Instead, density was more strongly correlated with both edaphic and climate variables, suggesting that this is a better indicator of long-term demographic processes. Although a few factors are important across species (e.g., nutrient availability and minimum temperature), response is idiosyncratic at the individual species level in Pacific Northwest prairies. Close

• 16. [Article] Incompatibility and Speciation Within and Between Species

  60 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: Incompatibility and Speciation Within and Between Species Author: Moore, Hanna Year: 2015 60 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 2015. Title: Incompatibility and Speciation Within and Between Species Author: Moore, Hanna Year: 2015 60 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 2015. Close

• 17. [Article] OSMB Final Report, Task 4: Oregon Lake Watch

  The Oregon Lake Watch (OLW) volunteer monitoring program was resurrected after over a decade in hibernation. The new program was designed to educate the public about threats of aquatic invasive species ...

  Citation × Citation Citation Abstract Copy Title: OSMB Final Report, Task 4: Oregon Lake Watch Author: Strecker, Angela L., Miller, Rich, Morgan, Vanessa Year: 2014 The Oregon Lake Watch (OLW) volunteer monitoring program was resurrected after over a decade in hibernation. The new program was designed to educate the public about threats of aquatic invasive species (AIS), provide early detection of AIS invasions, and provide long term water quality data for the better management of Oregon’s lakes and reservoirs. Protocols were created for citizen scientists to survey for AIS, collect temperature and water clarity data, and record the data through an online data entry portal. An OLW website was developed to educate about AIS and provide survey protocols and identification materials to volunteers. AIS surveys were focused on Watch List Species which are selected AIS that have a negative impact on the beneficial uses of our waterbodies. Eighteen volunteers were trained during five sessions conducted in western and central Oregon. Fourteen of the trained volunteers collected data from sixteen waterbodies. Six Watch List species and one other AIS species were observed in four of the waterbodies. The three Watch List Species observed in Salish Pond and one in Olallie Lake were new observations. Temperature measurements indicated a wide range of thermal profiles and Secchi transparency measurement indicated a range of trophic status from oligotrophic to eutrophic. Title: OSMB Final Report, Task 4: Oregon Lake Watch Author: Strecker, Angela L., Miller, Rich, Morgan, Vanessa Year: 2014 The Oregon Lake Watch (OLW) volunteer monitoring program was resurrected after over a decade in hibernation. The new program was designed to educate the public about threats of aquatic invasive species (AIS), provide early detection of AIS invasions, and provide long term water quality data for the better management of Oregon’s lakes and reservoirs. Protocols were created for citizen scientists to survey for AIS, collect temperature and water clarity data, and record the data through an online data entry portal. An OLW website was developed to educate about AIS and provide survey protocols and identification materials to volunteers. AIS surveys were focused on Watch List Species which are selected AIS that have a negative impact on the beneficial uses of our waterbodies. Eighteen volunteers were trained during five sessions conducted in western and central Oregon. Fourteen of the trained volunteers collected data from sixteen waterbodies. Six Watch List species and one other AIS species were observed in four of the waterbodies. The three Watch List Species observed in Salish Pond and one in Olallie Lake were new observations. Temperature measurements indicated a wide range of thermal profiles and Secchi transparency measurement indicated a range of trophic status from oligotrophic to eutrophic. Close

• 18. [Article] The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats

  Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation ...

  Citation × Citation Citation Abstract Copy Title: The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats Author: McClees, Whitney, de Rivera, Catherine E. Year: 2017 Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation is limiting the spread of non-native species, while other research has indicated that it is dispersal-driven. To determine the effects of dispersal limitation and predation on the risk to surrounding habitats of being invaded by non-native species established on marina docks, we used a three-factor design, deploying seven unglazed ceramic panels per each treatment combination of 1) inside versus outside a marina in Yaquina Bay, Oregon; 2) cage keeping out predators >mesh size, no cage, or partial cage; 3) fixed near the substrata (benthic) versus floating 1m below the surface. We also moved panels of either adults or recruits from floating in the marina to any of the treatment combinations to test if they would have lower survival outside by the substrate. The community on panels suspended in the marina only minimally overlapped with panels outside of the marina near the bottom. However, there was no difference between the cage treatments, which suggests that predators excluded by the cages are not responsible for the observed differences in species richness or composition. Title: The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats Author: McClees, Whitney, de Rivera, Catherine E. Year: 2017 Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation is limiting the spread of non-native species, while other research has indicated that it is dispersal-driven. To determine the effects of dispersal limitation and predation on the risk to surrounding habitats of being invaded by non-native species established on marina docks, we used a three-factor design, deploying seven unglazed ceramic panels per each treatment combination of 1) inside versus outside a marina in Yaquina Bay, Oregon; 2) cage keeping out predators >mesh size, no cage, or partial cage; 3) fixed near the substrata (benthic) versus floating 1m below the surface. We also moved panels of either adults or recruits from floating in the marina to any of the treatment combinations to test if they would have lower survival outside by the substrate. The community on panels suspended in the marina only minimally overlapped with panels outside of the marina near the bottom. However, there was no difference between the cage treatments, which suggests that predators excluded by the cages are not responsible for the observed differences in species richness or composition. Close

• 19. [Article] Mechanisms of Adaptation in the Newly Invasive Species <i>Brachypodium sylvaticum</i> (Hudson) Beauv.

  It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should ...

  Citation × Citation Citation Abstract Copy Title: Mechanisms of Adaptation in the Newly Invasive Species <i>Brachypodium sylvaticum</i> (Hudson) Beauv. Author: Marchini, Gina Lola Year: 2015 It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) Beauv. to determine mechanisms contributing to adaptation and success in the novel habitat. The first study used simulations and experiments to test the hypothesis that genetic purging, the process where genetic load is reduced by selection against the recessive deleterious alleles expressed in the homozygous state, promotes invasive range expansion. I found that homozygous populations on B. sylvaticum's range periphery displayed lower inbreeding depression compared to heterozygous populations near introduction sites. Empirical tests with B. sylvaticum further demonstrate that purging of genetic load is a plausible scenario promoting range expansion during invasion. Next, I explored how the interaction between population genetic diversity and the environment contributed to the establishment and spread of Brachypodium sylvaticum. I found that nitrogen application increases both final size and shoot biomass for B. sylvaticum individuals from source populations with low HS levels to levels found in individuals from populations with high HS. A coefficient of relative competition intensity index (RCI) displayed reduced effects of interspecific competition on B. sylvaticum biomass in high nitrogen plots. Results show that elevated nitrogen deposition is a factor that increases establishment of introduced species with historically small effective population sizes. Thirdly, I investigated phenotypic differentiation during the establishment and range expansion of Brachypodium sylvaticum. Utilizing a novel approach, unique alleles were used to determine the genetic probability of contribution from native source regions to invasive regions. These probabilities were integrated into QST-FST comparisons to determine the influence of selection and genetic drift on twelve physiological and anatomical traits associated with drought stress. Phenotypic divergence greater than neutral expectations was found for five traits between native and invasive populations, indicating selective divergence. Results from this study show that the majority of divergence in B. sylvaticum occurred after introduction to the novel environment, but prior to invasive range expansion. The final chapter of my dissertation investigates the adaptive role of genetic differentiation and plasticity for Brachypodium sylvaticum invasion. Plasticity was measured across treatments of contrasting water availability. Linear and nonlinear selection gradients determined the effect of directional and quadratic selection on plasticity and genetic differentiation. Invasive trait divergence was a consequence of post-introduction selection leading to genetic differentiation, as there were no plastic responses to contrasting water availability for any measured traits. Genetic divergence of invasive plants was not consistently in the direction indicated by selection, suggesting limitations of selection that may be a consequence of physical constraints and/or tradeoffs between growth and abiotic tolerance. Results suggest that selection, rather than plasticity, is driving phenotypic change in the invaded environment. The combined volume of these studies contributes significantly to the field of invasion and plant biology by providing novel insights into the processes underlying range expansion, adaptation, and ultimately, evolution of introduced species. Title: Mechanisms of Adaptation in the Newly Invasive Species <i>Brachypodium sylvaticum</i> (Hudson) Beauv. Author: Marchini, Gina Lola Year: 2015 It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) Beauv. to determine mechanisms contributing to adaptation and success in the novel habitat. The first study used simulations and experiments to test the hypothesis that genetic purging, the process where genetic load is reduced by selection against the recessive deleterious alleles expressed in the homozygous state, promotes invasive range expansion. I found that homozygous populations on B. sylvaticum's range periphery displayed lower inbreeding depression compared to heterozygous populations near introduction sites. Empirical tests with B. sylvaticum further demonstrate that purging of genetic load is a plausible scenario promoting range expansion during invasion. Next, I explored how the interaction between population genetic diversity and the environment contributed to the establishment and spread of Brachypodium sylvaticum. I found that nitrogen application increases both final size and shoot biomass for B. sylvaticum individuals from source populations with low HS levels to levels found in individuals from populations with high HS. A coefficient of relative competition intensity index (RCI) displayed reduced effects of interspecific competition on B. sylvaticum biomass in high nitrogen plots. Results show that elevated nitrogen deposition is a factor that increases establishment of introduced species with historically small effective population sizes. Thirdly, I investigated phenotypic differentiation during the establishment and range expansion of Brachypodium sylvaticum. Utilizing a novel approach, unique alleles were used to determine the genetic probability of contribution from native source regions to invasive regions. These probabilities were integrated into QST-FST comparisons to determine the influence of selection and genetic drift on twelve physiological and anatomical traits associated with drought stress. Phenotypic divergence greater than neutral expectations was found for five traits between native and invasive populations, indicating selective divergence. Results from this study show that the majority of divergence in B. sylvaticum occurred after introduction to the novel environment, but prior to invasive range expansion. The final chapter of my dissertation investigates the adaptive role of genetic differentiation and plasticity for Brachypodium sylvaticum invasion. Plasticity was measured across treatments of contrasting water availability. Linear and nonlinear selection gradients determined the effect of directional and quadratic selection on plasticity and genetic differentiation. Invasive trait divergence was a consequence of post-introduction selection leading to genetic differentiation, as there were no plastic responses to contrasting water availability for any measured traits. Genetic divergence of invasive plants was not consistently in the direction indicated by selection, suggesting limitations of selection that may be a consequence of physical constraints and/or tradeoffs between growth and abiotic tolerance. Results suggest that selection, rather than plasticity, is driving phenotypic change in the invaded environment. The combined volume of these studies contributes significantly to the field of invasion and plant biology by providing novel insights into the processes underlying range expansion, adaptation, and ultimately, evolution of introduced species. Close

• 20. [Article] Live Diatoms as Indicators of Urban Stormwater Runoff

  Diatom bioassessment of streams/rivers does not distinguish between live (cells with intact chloroplasts) and dead (empty cells) individuals, even though most diatom samples collected from the field will ...

  Citation × Citation Citation Abstract Copy Title: Live Diatoms as Indicators of Urban Stormwater Runoff Author: Gillett, Nadia D., Oudsema, Maggie E., Steinman, Alan D. Year: 2017 Diatom bioassessment of streams/rivers does not distinguish between live (cells with intact chloroplasts) and dead (empty cells) individuals, even though most diatom samples collected from the field will be composed of a mixture of both. This study aimed to evaluate whether percentage of live diatoms (PLD), live diatom density and chlorophyll a, and diatom species compositions can be used as indicators of hydrologic disturbance in an urban stream. We deployed artificial substrates on a monthly basis and collected periphyton samples weekly over the course of one calendar year (n = 182) in three tributaries of urbanized Ruddiman Creek (Michigan, USA). We also collected samples before and after six major storm events (>0.5 cm rain). We found no temporal patterns in PLD (Mann-Kendall test p > 0.05) or species composition (non-metric multidimensional scaling (NMDS) ordination), which may be explained by a diatom composition already tolerant to frequent disturbance. There was no difference in PLD before and after storm events, which might partially be explained by their disturbance resistance due to different assemblage ages (1, 2, and 4 weeks old) before the storms. High flow had differential effects on diatom species; loosely attached Navicula and Nitzschia species were more easily removed compared to stalk-forming Gomphonema parvulum. The most important environmental variable that was found to affect live diatom density and chlorophyll was stream width, which has an indirect effect (as a measure of discharge) on periphyton assemblages. In conclusion, PLD was found to be unsuitable metric for assessing stormwater runoff in urban streams where periphyton may not have enough time to form mature communities. Title: Live Diatoms as Indicators of Urban Stormwater Runoff Author: Gillett, Nadia D., Oudsema, Maggie E., Steinman, Alan D. Year: 2017 Diatom bioassessment of streams/rivers does not distinguish between live (cells with intact chloroplasts) and dead (empty cells) individuals, even though most diatom samples collected from the field will be composed of a mixture of both. This study aimed to evaluate whether percentage of live diatoms (PLD), live diatom density and chlorophyll a, and diatom species compositions can be used as indicators of hydrologic disturbance in an urban stream. We deployed artificial substrates on a monthly basis and collected periphyton samples weekly over the course of one calendar year (n = 182) in three tributaries of urbanized Ruddiman Creek (Michigan, USA). We also collected samples before and after six major storm events (>0.5 cm rain). We found no temporal patterns in PLD (Mann-Kendall test p > 0.05) or species composition (non-metric multidimensional scaling (NMDS) ordination), which may be explained by a diatom composition already tolerant to frequent disturbance. There was no difference in PLD before and after storm events, which might partially be explained by their disturbance resistance due to different assemblage ages (1, 2, and 4 weeks old) before the storms. High flow had differential effects on diatom species; loosely attached Navicula and Nitzschia species were more easily removed compared to stalk-forming Gomphonema parvulum. The most important environmental variable that was found to affect live diatom density and chlorophyll was stream width, which has an indirect effect (as a measure of discharge) on periphyton assemblages. In conclusion, PLD was found to be unsuitable metric for assessing stormwater runoff in urban streams where periphyton may not have enough time to form mature communities. Close

• 21. [Article] The Wealth of Ecosystems: Valuing Natural Capital in the Context of Ecosystem Based Management

  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: The Wealth of Ecosystems: Valuing Natural Capital in the Context of Ecosystem Based Management Author: Abbott, Joshua, Hutniczak, Barbara, Seong, Do Yun, Fenichel, Eli 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: The Wealth of Ecosystems: Valuing Natural Capital in the Context of Ecosystem Based Management Author: Abbott, Joshua, Hutniczak, Barbara, Seong, Do Yun, Fenichel, Eli 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

• 22. [Article] Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality

  Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native ...

  Citation × Citation Citation Abstract Copy Title: Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality Author: Turner, Brian Christopher Year: 2017 Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native and previously established non-native predators, can prevent establishment, limit habitat use, and reduce abundance of non-native species. Management efforts by humans using methods designed to cause mass mortality (e.g., trapping, biocide applications) can reduce or eradicate non-native populations. However, the impacts of predator and human induced mortality may be mitigated by the behavior or population-level responses of a given non-native species. My dissertation examined the responses of non-native aquatic species to the risk of predation by novel (i.e., no previous exposure) predators in the recipient community and indicators of potential compensatory responses by non-native populations to increased mortality resulting from removal efforts. My dissertation addresses four primary questions. 1) Can first generation, naïve invaders recognize and defend against predators found within the region of invasion through the expression of inducible defenses? 2) Can the overcompensatory potential of a population be predicted though examinations of intraspecific interactions of individuals from the population? 3) What is the relationship between removal effort outcome (i.e., successful or unsuccessful reduction of the target population) and compensatory population responses? 4) Is there a relationship between characteristics of removal efforts that are typically available to managers (e.g., target area size, target area connectivity, removal methodology) and compensatory population responses that could indicate the relative likelihood of compensation resulting from removal efforts? An invading species should be more likely to establish if it can successfully identify and defend against predators in the recipient range, such as through the expression of inducible defenses. Inducible defenses are behavioral or physiological changes that reduce an organism's susceptibility to predation. Through a series of laboratory experiments, I tested whether inducible defenses, in the form of increased burrowing depth, may have benefited the early stage of invasion of Nuttallia obscurata (purple varnish clam), an established Northeast Pacific invader. Specimens of N. obscurata were collected from introduced populations in the Northeast Pacific and from a native population in Japan. The clams were exposed to chemical and physical cues from Northeast Pacific crab predators, including the native Metacarcinus magister (Dungeness crab), an abundant and frequent predator of N. obscurata. While introduced N. obscurata increased their burrowing depth in the physical presence of M. magister, clams collected from their native range showed no such response. This lack of increased burrowing depth by naïve clams in response to a predator native to the newly invaded range, but a significant increase in depth for clams from populations established in the range suggests that while inducible defenses likely did not contribute to the initial establishment of N. obscurata in the Northeast Pacific, they may contribute to their continued persistence and expansion in their introduced range. Some efforts to reduce invasive populations have paradoxically led to population increases. This phenomenon, referred to as overcompensation, occurs when strong negative density-dependent interactions are reduced through increased mortality within a population, resulting in an increase in the population's recruitment rate sufficient to increase the population's overall abundance. Increases in a population's recruitment rate can result from reduced cannibalism of juveniles resulting in lower mortality of new recruits, from increased adult reproductive output, which increases the number of potential recruits, or from reductions in size and/or age at maturity of the unharvested population, which increases the number of reproductive individuals. I predicted the overcompensatory potential of a population of Carcinus maenas (European green crab) in Bodega Harbor, California, using a series of laboratory and field experiments examining intraspecific pressures of adults on juveniles in the population. This measure of intraspecific pressure was used to predict the overcompensatory potential of the population in response to increased mortality from ongoing removal efforts. This prediction was then assessed using pre- and post-removal surveys of juvenile recruitment in Bodega Harbor compared to nearby populations, testing for evidence of overcompensation. While adult C. maenas in Bodega Harbor had limited negative impacts on juveniles, I concluded it was unlikely to result in overcompensation. Relative juvenile abundance did not statistically increase in removal compared to reference populations, consistent with my conclusion from the experiments. Increases in recruitment rates can occur as a result of efforts to remove non-native species. This increase in recruitment can result in overcompensation, but more commonly results in compensation, where recruitment rates increase relative to pre-removal recruitment but does not result in in the population's abundance exceeding pre-removal levels. However, a detailed and accurate prediction of the response of a population to harvest is time consuming and data intensive. This is not feasible for most efforts to eradicate non-native species, which have the greatest chance of success when enacted rapidly after detection. For my final chapter, I performed a literature review and accompanying statistical analysis to determine if typically available information related to the removal effort (site size, site connectivity, and removal technique) could be used to determine increased risk of compensation for a given effort to remove aquatic invasive species. Compensation was closely linked to unsuccessful removal efforts and was observed only among efforts utilizing physical removal methods. However, the frequency with which compensation occurred varied with the exact technique employed, occurring most frequently in removal utilizing electrofishing. Additionally, evidence of compensation was more frequent among larger removal areas with variable connectivity. While other predictors (temperature, effort, etc) might add to the predicative power, the findings of the review provide criteria for managers to determine the relative risk of compensation prior to the start of removal. Further understanding of how invasive species respond to lethal biotic interactions, including anthropogenically mediated control measures, can aid in assessing the risk of invasion for a given species and inform managers of the risk of complications resulting from removal efforts. While inducible defenses may contribute to the long-term success of an introduced species in their recipient range, my findings did not support the idea that inducible defenses triggered by predator cues contributed to their initial introduction in this case. However, research on other non-native species and offspring of previously naïve prey would allow for a clearer picture of the role of inducible defenses in the invasion process. Compensation resulting from removal efforts does not guarantee failure, and certain characteristics of removal efforts seem to indicate increased risk of compensation. Together these components help identify how biotic interactions surrounding mortality risk of an invading species help shape the trajectory of invasion. Title: Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality Author: Turner, Brian Christopher Year: 2017 Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native and previously established non-native predators, can prevent establishment, limit habitat use, and reduce abundance of non-native species. Management efforts by humans using methods designed to cause mass mortality (e.g., trapping, biocide applications) can reduce or eradicate non-native populations. However, the impacts of predator and human induced mortality may be mitigated by the behavior or population-level responses of a given non-native species. My dissertation examined the responses of non-native aquatic species to the risk of predation by novel (i.e., no previous exposure) predators in the recipient community and indicators of potential compensatory responses by non-native populations to increased mortality resulting from removal efforts. My dissertation addresses four primary questions. 1) Can first generation, naïve invaders recognize and defend against predators found within the region of invasion through the expression of inducible defenses? 2) Can the overcompensatory potential of a population be predicted though examinations of intraspecific interactions of individuals from the population? 3) What is the relationship between removal effort outcome (i.e., successful or unsuccessful reduction of the target population) and compensatory population responses? 4) Is there a relationship between characteristics of removal efforts that are typically available to managers (e.g., target area size, target area connectivity, removal methodology) and compensatory population responses that could indicate the relative likelihood of compensation resulting from removal efforts? An invading species should be more likely to establish if it can successfully identify and defend against predators in the recipient range, such as through the expression of inducible defenses. Inducible defenses are behavioral or physiological changes that reduce an organism's susceptibility to predation. Through a series of laboratory experiments, I tested whether inducible defenses, in the form of increased burrowing depth, may have benefited the early stage of invasion of Nuttallia obscurata (purple varnish clam), an established Northeast Pacific invader. Specimens of N. obscurata were collected from introduced populations in the Northeast Pacific and from a native population in Japan. The clams were exposed to chemical and physical cues from Northeast Pacific crab predators, including the native Metacarcinus magister (Dungeness crab), an abundant and frequent predator of N. obscurata. While introduced N. obscurata increased their burrowing depth in the physical presence of M. magister, clams collected from their native range showed no such response. This lack of increased burrowing depth by naïve clams in response to a predator native to the newly invaded range, but a significant increase in depth for clams from populations established in the range suggests that while inducible defenses likely did not contribute to the initial establishment of N. obscurata in the Northeast Pacific, they may contribute to their continued persistence and expansion in their introduced range. Some efforts to reduce invasive populations have paradoxically led to population increases. This phenomenon, referred to as overcompensation, occurs when strong negative density-dependent interactions are reduced through increased mortality within a population, resulting in an increase in the population's recruitment rate sufficient to increase the population's overall abundance. Increases in a population's recruitment rate can result from reduced cannibalism of juveniles resulting in lower mortality of new recruits, from increased adult reproductive output, which increases the number of potential recruits, or from reductions in size and/or age at maturity of the unharvested population, which increases the number of reproductive individuals. I predicted the overcompensatory potential of a population of Carcinus maenas (European green crab) in Bodega Harbor, California, using a series of laboratory and field experiments examining intraspecific pressures of adults on juveniles in the population. This measure of intraspecific pressure was used to predict the overcompensatory potential of the population in response to increased mortality from ongoing removal efforts. This prediction was then assessed using pre- and post-removal surveys of juvenile recruitment in Bodega Harbor compared to nearby populations, testing for evidence of overcompensation. While adult C. maenas in Bodega Harbor had limited negative impacts on juveniles, I concluded it was unlikely to result in overcompensation. Relative juvenile abundance did not statistically increase in removal compared to reference populations, consistent with my conclusion from the experiments. Increases in recruitment rates can occur as a result of efforts to remove non-native species. This increase in recruitment can result in overcompensation, but more commonly results in compensation, where recruitment rates increase relative to pre-removal recruitment but does not result in in the population's abundance exceeding pre-removal levels. However, a detailed and accurate prediction of the response of a population to harvest is time consuming and data intensive. This is not feasible for most efforts to eradicate non-native species, which have the greatest chance of success when enacted rapidly after detection. For my final chapter, I performed a literature review and accompanying statistical analysis to determine if typically available information related to the removal effort (site size, site connectivity, and removal technique) could be used to determine increased risk of compensation for a given effort to remove aquatic invasive species. Compensation was closely linked to unsuccessful removal efforts and was observed only among efforts utilizing physical removal methods. However, the frequency with which compensation occurred varied with the exact technique employed, occurring most frequently in removal utilizing electrofishing. Additionally, evidence of compensation was more frequent among larger removal areas with variable connectivity. While other predictors (temperature, effort, etc) might add to the predicative power, the findings of the review provide criteria for managers to determine the relative risk of compensation prior to the start of removal. Further understanding of how invasive species respond to lethal biotic interactions, including anthropogenically mediated control measures, can aid in assessing the risk of invasion for a given species and inform managers of the risk of complications resulting from removal efforts. While inducible defenses may contribute to the long-term success of an introduced species in their recipient range, my findings did not support the idea that inducible defenses triggered by predator cues contributed to their initial introduction in this case. However, research on other non-native species and offspring of previously naïve prey would allow for a clearer picture of the role of inducible defenses in the invasion process. Compensation resulting from removal efforts does not guarantee failure, and certain characteristics of removal efforts seem to indicate increased risk of compensation. Together these components help identify how biotic interactions surrounding mortality risk of an invading species help shape the trajectory of invasion. Close

• 23. [Article] The Oligocene Fossil Caudates of Oregon: Classification, Analysis, and Insights on the Paleoecology and Conservation Biology of Pacific Newts

  Newts, abundant worldwide, have unclear pre-Pliocene evolution and phylogenetic relationships. North America has a sporadic pre-Pliocene newt record. Several undescribed fossils can address this lack ...

  Citation × Citation Citation Abstract Copy Title: The Oligocene Fossil Caudates of Oregon: Classification, Analysis, and Insights on the Paleoecology and Conservation Biology of Pacific Newts Author: Jacisin, John Year: 2014 Newts, abundant worldwide, have unclear pre-Pliocene evolution and phylogenetic relationships. North America has a sporadic pre-Pliocene newt record. Several undescribed fossils can address this lack of information. I built a character matrix of >70 morphological characters for extant newts and two fossil species, Taricha oligocenica and Taricha lindoei. Phylogenetic analyses were used to investigate the relationships of the fossil taxa within newts. The morphology of the fossil taxa was compared with extant North American newts to redescribe the fossil specimens. The past ecology and biogeography of North American fossil newts was compared with their current ecologies and distribution to better understand their evolution and dispersal and to predict possible changes for newts in the face of environmental change. Results indicate that T. oligocenica and T. lindoei are closely-related species nested within Taricha, but their relationships with extant species are unresolved; the genus itself is rooted at least 32 Ma. Title: The Oligocene Fossil Caudates of Oregon: Classification, Analysis, and Insights on the Paleoecology and Conservation Biology of Pacific Newts Author: Jacisin, John Year: 2014 Newts, abundant worldwide, have unclear pre-Pliocene evolution and phylogenetic relationships. North America has a sporadic pre-Pliocene newt record. Several undescribed fossils can address this lack of information. I built a character matrix of >70 morphological characters for extant newts and two fossil species, Taricha oligocenica and Taricha lindoei. Phylogenetic analyses were used to investigate the relationships of the fossil taxa within newts. The morphology of the fossil taxa was compared with extant North American newts to redescribe the fossil specimens. The past ecology and biogeography of North American fossil newts was compared with their current ecologies and distribution to better understand their evolution and dispersal and to predict possible changes for newts in the face of environmental change. Results indicate that T. oligocenica and T. lindoei are closely-related species nested within Taricha, but their relationships with extant species are unresolved; the genus itself is rooted at least 32 Ma. Close

• 24. [Article] 2014 Aquatic Weed Surveys in Timothy Lake, Lake Harriet, North Fork Reservoir, Faraday Lake, and Estacada Lake

  The Clackamas River Hydroelectric Project No. 2195 (Project) is located on the Oak Grove Fork of the Clackamas River and the mainstem of the Clackamas River in Clackamas County, Oregon. Reservoirs included ...

  Citation × Citation Citation Abstract Copy Title: 2014 Aquatic Weed Surveys in Timothy Lake, Lake Harriet, North Fork Reservoir, Faraday Lake, and Estacada Lake Author: Miller, Rich, Sytsma, Mark D., Brittain, Jeffrey Thomas Year: 2014 The Clackamas River Hydroelectric Project No. 2195 (Project) is located on the Oak Grove Fork of the Clackamas River and the mainstem of the Clackamas River in Clackamas County, Oregon. Reservoirs included in the Project include Timothy Lake, Lake Harriet, North Fork Reservoir, Faraday Lake, and Estacada Lake. The operator of the Project, Portland General Electric (PGE), was issued a license on December 21, 2010 by the Federal Energy Regulatory Commission (FERC) for continued operations and maintenance. The Final Environmental Impact Statement (FEIS) for the license noted that regular surveys for invasive aquatic weed species would be conducted as part of the Project’s Vegetation Management Plan. The term “aquatic weed” is used here to refer to any non-native aquatic plant species. Information from repeated aquatic surveys will help determine native species distributions and the need for treatment of problematic aquatic weed species, particularly hydrilla (Hydrilla verticillata), Brazilian elodea (Egeria densa), and Eurasian watermilfoil (Myriophyllum spicatum). Surveys conducted for PGE by Portland State University (PSU) in Timothy Lake, Lake Harriet, and North Fork Reservoir in 2011 did not locate any problematic submerged or floating leaved aquatic weed species. Earlier surveys of Timothy Lake, and Timothy Lake and Lake Harriet, also indicated the reservoirs were free of aquatic weeds. Heaton et al. (1996) noted that the native species Bidens beckii was present and had the potential to become weedy, however, this species was not found during the 2004 or 2011 surveys. This report covers the results of follow up aquatic vegetation surveys conducted in Lake Harriet, Timothy Lake, and North Fork Reservoir between August 14 and August 21, 2014, as well as new surveys of Faraday Lake and Estacada Lake. Shoreline surveys for emergent invasive species such as yellow flag iris (Iris pseudacorus) and purple loosestrife (Lythrum salicaria) were included in surveys for the first time. Title: 2014 Aquatic Weed Surveys in Timothy Lake, Lake Harriet, North Fork Reservoir, Faraday Lake, and Estacada Lake Author: Miller, Rich, Sytsma, Mark D., Brittain, Jeffrey Thomas Year: 2014 The Clackamas River Hydroelectric Project No. 2195 (Project) is located on the Oak Grove Fork of the Clackamas River and the mainstem of the Clackamas River in Clackamas County, Oregon. Reservoirs included in the Project include Timothy Lake, Lake Harriet, North Fork Reservoir, Faraday Lake, and Estacada Lake. The operator of the Project, Portland General Electric (PGE), was issued a license on December 21, 2010 by the Federal Energy Regulatory Commission (FERC) for continued operations and maintenance. The Final Environmental Impact Statement (FEIS) for the license noted that regular surveys for invasive aquatic weed species would be conducted as part of the Project’s Vegetation Management Plan. The term “aquatic weed” is used here to refer to any non-native aquatic plant species. Information from repeated aquatic surveys will help determine native species distributions and the need for treatment of problematic aquatic weed species, particularly hydrilla (Hydrilla verticillata), Brazilian elodea (Egeria densa), and Eurasian watermilfoil (Myriophyllum spicatum). Surveys conducted for PGE by Portland State University (PSU) in Timothy Lake, Lake Harriet, and North Fork Reservoir in 2011 did not locate any problematic submerged or floating leaved aquatic weed species. Earlier surveys of Timothy Lake, and Timothy Lake and Lake Harriet, also indicated the reservoirs were free of aquatic weeds. Heaton et al. (1996) noted that the native species Bidens beckii was present and had the potential to become weedy, however, this species was not found during the 2004 or 2011 surveys. This report covers the results of follow up aquatic vegetation surveys conducted in Lake Harriet, Timothy Lake, and North Fork Reservoir between August 14 and August 21, 2014, as well as new surveys of Faraday Lake and Estacada Lake. Shoreline surveys for emergent invasive species such as yellow flag iris (Iris pseudacorus) and purple loosestrife (Lythrum salicaria) were included in surveys for the first time. Close

• 25. [Article] Phylogeography of Two Species of the Genus Apochthonius Chamberlin, 1929, in the Pacific Northwest (Arachnida, Pseudoscorpiones)

  I used mitochondrial COI sequence data from forty one individuals to investigate phylogenetic relationships among populations of two morphologically similar species of the pseudoscorpion genus Apochthonius, ...

  Citation × Citation Citation Abstract Copy Title: Phylogeography of Two Species of the Genus Apochthonius Chamberlin, 1929, in the Pacific Northwest (Arachnida, Pseudoscorpiones) Author: Welch, Brandi Lynn Year: 2016 I used mitochondrial COI sequence data from forty one individuals to investigate phylogenetic relationships among populations of two morphologically similar species of the pseudoscorpion genus Apochthonius, A. minimus and A. occidentalis, in western Washington, Oregon, and northern California. My goal was to assess whether genetic structure in the two species was congruent with geography. Many plant and animal species in the Pacific Northwestern United States have shown patterns of genetic differentiation that follow both north-south and east-west trends, indicating that geologic and climatic events in the past separated populations to the extent that they became genetically differentiated. A distinct geographic pattern emerged within A. occidentalis, with at least one northern and two southern populations. A clade containing all A. minimus sequences was recovered. However, this clade falls within the larger clade of A. occidentalis, rendering A. occidentalis paraphyletic. Furthermore, the A. minimus sequences showed north-south geographic structuring within the clade. Population genetic analyses were performed based on geographic location within the Pacific Northwest. I found high genetic differentiation coupled with low gene flow between most populations, with the exception of the Portland and North Coast Range populations. These data suggest the presence of more than two species of Apochthonius in the Pacific Northwest. Title: Phylogeography of Two Species of the Genus Apochthonius Chamberlin, 1929, in the Pacific Northwest (Arachnida, Pseudoscorpiones) Author: Welch, Brandi Lynn Year: 2016 I used mitochondrial COI sequence data from forty one individuals to investigate phylogenetic relationships among populations of two morphologically similar species of the pseudoscorpion genus Apochthonius, A. minimus and A. occidentalis, in western Washington, Oregon, and northern California. My goal was to assess whether genetic structure in the two species was congruent with geography. Many plant and animal species in the Pacific Northwestern United States have shown patterns of genetic differentiation that follow both north-south and east-west trends, indicating that geologic and climatic events in the past separated populations to the extent that they became genetically differentiated. A distinct geographic pattern emerged within A. occidentalis, with at least one northern and two southern populations. A clade containing all A. minimus sequences was recovered. However, this clade falls within the larger clade of A. occidentalis, rendering A. occidentalis paraphyletic. Furthermore, the A. minimus sequences showed north-south geographic structuring within the clade. Population genetic analyses were performed based on geographic location within the Pacific Northwest. I found high genetic differentiation coupled with low gene flow between most populations, with the exception of the Portland and North Coast Range populations. These data suggest the presence of more than two species of Apochthonius in the Pacific Northwest. Close

• 26. [Article] Climate Change Effects on Northern Great Lake (USA) Forests: A Case for Preserving Diversity

  Under business as usual (BAU) management, stresses posed by climate change may exceed the ability of Great Lake forests to adapt. Temperature and precipitation projections in the Great Lakes region are ...

  Citation × Citation Citation Abstract Copy Title: Climate Change Effects on Northern Great Lake (USA) Forests: A Case for Preserving Diversity Author: Duveneck, Matthew Joshua, Scheller, Robert M., White, Mark A., Handler, Stephen D., Ravenscroft, Catherine Year: 2014 Under business as usual (BAU) management, stresses posed by climate change may exceed the ability of Great Lake forests to adapt. Temperature and precipitation projections in the Great Lakes region are expected to change forest tree species composition and productivity. It is unknown how a change in productivity and/or tree species diversity due to climate change will affect the relationship between diversity and productivity. We assessed how forests in two landscapes (i.e., northern lower Michigan and northeastern Minnesota, USA) would respond to climate change and explored the diversityproductivity relationship under climate change. In addition, we explored how tree species diversity varied across landscapes by soil type, climate, and management. We used a spatially dynamic forest ecosystem model, LANDIS-II, to simulate BAU forest management under three climate scenarios (current climate, low emissions, and high emissions) in each landscape. We found a positive relationship between diversity and productivity only under a high emissions future as productivity declined. Within landscapes, climate change simulations resulted in the highest diversity in the coolest climate regions and lowest diversity in the warmest climate region in Minnesota and Michigan, respectively. Simulated productivity declined in both landscapes under the high emissions climate scenario as species such as balsam fir (Abies balsamea) declined in abundance. In the Great Lakes region, a high emissions future may decrease forest productivity creating a more positive relationship between diversity and productivity. Maintaining a diversity of tree species may become increasingly important to maintain the adaptive capacity of forests. Title: Climate Change Effects on Northern Great Lake (USA) Forests: A Case for Preserving Diversity Author: Duveneck, Matthew Joshua, Scheller, Robert M., White, Mark A., Handler, Stephen D., Ravenscroft, Catherine Year: 2014 Under business as usual (BAU) management, stresses posed by climate change may exceed the ability of Great Lake forests to adapt. Temperature and precipitation projections in the Great Lakes region are expected to change forest tree species composition and productivity. It is unknown how a change in productivity and/or tree species diversity due to climate change will affect the relationship between diversity and productivity. We assessed how forests in two landscapes (i.e., northern lower Michigan and northeastern Minnesota, USA) would respond to climate change and explored the diversityproductivity relationship under climate change. In addition, we explored how tree species diversity varied across landscapes by soil type, climate, and management. We used a spatially dynamic forest ecosystem model, LANDIS-II, to simulate BAU forest management under three climate scenarios (current climate, low emissions, and high emissions) in each landscape. We found a positive relationship between diversity and productivity only under a high emissions future as productivity declined. Within landscapes, climate change simulations resulted in the highest diversity in the coolest climate regions and lowest diversity in the warmest climate region in Minnesota and Michigan, respectively. Simulated productivity declined in both landscapes under the high emissions climate scenario as species such as balsam fir (Abies balsamea) declined in abundance. In the Great Lakes region, a high emissions future may decrease forest productivity creating a more positive relationship between diversity and productivity. Maintaining a diversity of tree species may become increasingly important to maintain the adaptive capacity of forests. Close

• 27. [Article] The Ecology and Demography of the Invasive Ascidian Botrylloides violaceus in the Coos Estuary

  133 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 ...

  Citation × Citation Citation Abstract Copy Title: The Ecology and Demography of the Invasive Ascidian Botrylloides violaceus in the Coos Estuary Author: Dorning, Sandra Lynn Year: 2017 133 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 2017 Title: The Ecology and Demography of the Invasive Ascidian Botrylloides violaceus in the Coos Estuary Author: Dorning, Sandra Lynn Year: 2017 133 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 2017 Close

• 28. [Article] OSMB Final Report: Task 6. Tenmile Lake Boat Wash Effectiveness Monitoring

  Public awareness of aquatic invasive species and proper boat cleaning procedures may prove to be beneficial in reducing the transport and establishment of aquatic invasive species like New Zealand mud ...

  Citation × Citation Citation Abstract Copy Title: OSMB Final Report: Task 6. Tenmile Lake Boat Wash Effectiveness Monitoring Author: Cimino, Samuel, Strecker, Angela L. Year: 2014 Public awareness of aquatic invasive species and proper boat cleaning procedures may prove to be beneficial in reducing the transport and establishment of aquatic invasive species like New Zealand mud snails and zebra and quagga mussels as well as hydrilla and Eurasian watermilfoil. The primary objectives of this research project were to observe the use and determine the efficacy of a public boat wash station as well as increase the public’s awareness of proper boat cleaning procedures and aquatic invasive species. The Tenmile Lakes Basin Partnership, Oregon State Marine Board, and the United States Forest Service (USFS) have undertaken an initiative to increase public awareness of invasive species and proper cleaning procedures by building a boat wash station at the Tenmile Lake public boat launch. In the summer of 2012, 199 qualitative human subject surveys were administered at Tenmile Lake in Lakeside, Oregon to boaters on their boating habits and knowledge of invasive species prior to building the boat wash (“pre-boat wash”). An extension of the 2012 study was conducted in the summer of 2013 on 200 boaters after the completion of the Tenmile Lake boat wash station (“post-boat wash”). Comparisons were made on the observations and answers of boaters prior to and after the boat wash installation. Of the boaters surveyed in the pre-boat wash field season, 75.9% of boaters claimed they would use a boat wash station at Tenmile Lake. The actual use of the boat wash station based on observations made by the field researcher during the post-boat wash field season indicated only 38.5% of surveyed boaters used the station. Furthermore, more than 20% of boaters could not verbally identify an invasive species in either field season when asked their awareness of aquatic invasive species. However, the majority of boaters surveyed at Tenmile Lake in the pre-boat wash field season (63.3%) and post-boat wash field season (66%) were aware of the phrase “Clean, Drain, Dry”. These results identify a disconnect in what boaters say and what boaters do and the knowledge gaps boaters have on aquatic invasive species, but these results also identify a growing awareness of proper boat cleaning procedures. Title: OSMB Final Report: Task 6. Tenmile Lake Boat Wash Effectiveness Monitoring Author: Cimino, Samuel, Strecker, Angela L. Year: 2014 Public awareness of aquatic invasive species and proper boat cleaning procedures may prove to be beneficial in reducing the transport and establishment of aquatic invasive species like New Zealand mud snails and zebra and quagga mussels as well as hydrilla and Eurasian watermilfoil. The primary objectives of this research project were to observe the use and determine the efficacy of a public boat wash station as well as increase the public’s awareness of proper boat cleaning procedures and aquatic invasive species. The Tenmile Lakes Basin Partnership, Oregon State Marine Board, and the United States Forest Service (USFS) have undertaken an initiative to increase public awareness of invasive species and proper cleaning procedures by building a boat wash station at the Tenmile Lake public boat launch. In the summer of 2012, 199 qualitative human subject surveys were administered at Tenmile Lake in Lakeside, Oregon to boaters on their boating habits and knowledge of invasive species prior to building the boat wash (“pre-boat wash”). An extension of the 2012 study was conducted in the summer of 2013 on 200 boaters after the completion of the Tenmile Lake boat wash station (“post-boat wash”). Comparisons were made on the observations and answers of boaters prior to and after the boat wash installation. Of the boaters surveyed in the pre-boat wash field season, 75.9% of boaters claimed they would use a boat wash station at Tenmile Lake. The actual use of the boat wash station based on observations made by the field researcher during the post-boat wash field season indicated only 38.5% of surveyed boaters used the station. Furthermore, more than 20% of boaters could not verbally identify an invasive species in either field season when asked their awareness of aquatic invasive species. However, the majority of boaters surveyed at Tenmile Lake in the pre-boat wash field season (63.3%) and post-boat wash field season (66%) were aware of the phrase “Clean, Drain, Dry”. These results identify a disconnect in what boaters say and what boaters do and the knowledge gaps boaters have on aquatic invasive species, but these results also identify a growing awareness of proper boat cleaning procedures. Close

• 29. [Article] Carbon Sequestration in Managed Temperate Coniferous Forests Under Climate Change

  Management of temperate forests has the potential to increase carbon sinks and mitigate climate change. However, those opportunities may be confounded by negative climate change impacts. We therefore need ...

  Citation × Citation Citation Abstract Copy Title: Carbon Sequestration in Managed Temperate Coniferous Forests Under Climate Change Author: Dymond, Caren C., Beukema, Sarah, Nitschke, Craig R., Coates, K. David, Scheller, Robert M. Year: 2016 Management of temperate forests has the potential to increase carbon sinks and mitigate climate change. However, those opportunities may be confounded by negative climate change impacts. We therefore need a better understanding of climate change alterations to temperate forest carbon dynamics before developing mitigation strategies. The purpose of this project was to investigate the interactions of species composition, fire, management, and climate change in the Copper–Pine Creek valley, a temperate coniferous forest with a wide range of growing conditions. To do so, we used the LANDIS-II modelling framework including the new Forest Carbon Succession extension to simulate forest ecosystems under four different productivity scenarios, with and without climate change effects, until 2050. Significantly, the new extension allowed us to calculate the net sector productivity, a carbon accounting metric that integrates aboveground and belowground carbon dynamics, disturbances, and the eventual fate of forest products. The model output was validated against literature values. The results implied that the species optimum growing conditions relative to current and future conditions strongly influenced future carbon dynamics. Warmer growing conditions led to increased carbon sinks and storage in the colder and wetter ecoregions but not necessarily in the others. Climate change impacts varied among species and site conditions, and this indicates that both of these components need to be taken into account when considering climate change mitigation activities and adaptive management. The introduction of a new carbon indicator, net sector productivity, promises to be useful in assessing management effectiveness and mitigation activities. Title: Carbon Sequestration in Managed Temperate Coniferous Forests Under Climate Change Author: Dymond, Caren C., Beukema, Sarah, Nitschke, Craig R., Coates, K. David, Scheller, Robert M. Year: 2016 Management of temperate forests has the potential to increase carbon sinks and mitigate climate change. However, those opportunities may be confounded by negative climate change impacts. We therefore need a better understanding of climate change alterations to temperate forest carbon dynamics before developing mitigation strategies. The purpose of this project was to investigate the interactions of species composition, fire, management, and climate change in the Copper–Pine Creek valley, a temperate coniferous forest with a wide range of growing conditions. To do so, we used the LANDIS-II modelling framework including the new Forest Carbon Succession extension to simulate forest ecosystems under four different productivity scenarios, with and without climate change effects, until 2050. Significantly, the new extension allowed us to calculate the net sector productivity, a carbon accounting metric that integrates aboveground and belowground carbon dynamics, disturbances, and the eventual fate of forest products. The model output was validated against literature values. The results implied that the species optimum growing conditions relative to current and future conditions strongly influenced future carbon dynamics. Warmer growing conditions led to increased carbon sinks and storage in the colder and wetter ecoregions but not necessarily in the others. Climate change impacts varied among species and site conditions, and this indicates that both of these components need to be taken into account when considering climate change mitigation activities and adaptive management. The introduction of a new carbon indicator, net sector productivity, promises to be useful in assessing management effectiveness and mitigation activities. Close

• 30. [Article] Riparian Vegetation Assemblages and Associated Landscape Factors Across an Urbanizing Metropolitan Area

  While diverse, native riparian vegetation provides important functions, it remains unclear to what extent these assemblages can persist in urban areas, and under what conditions. We characterized forested ...

  Citation × Citation Citation Abstract Copy Title: Riparian Vegetation Assemblages and Associated Landscape Factors Across an Urbanizing Metropolitan Area Author: Von Behren, Christa, Dietrich, Andrew Evans, Yeakley, J. Alan Year: 2014 While diverse, native riparian vegetation provides important functions, it remains unclear to what extent these assemblages can persist in urban areas, and under what conditions. We characterized forested riparian vegetation communities across an urbanizing metropolitan area and examined their relationships with surrounding land cover. We hypothesized that native and hydrophilic species assemblages would correlate with forest cover in the landscape. For each of 30 sites in the Portland–Vancouver metro area, we recorded vegetation at 1-cm intervals along 3 transects using the line-intercept method. Land cover was characterized at 2 scales: within 500 m of each site and across the entire watershed. Multivariate analyses were used to evaluate relationships between species composition and land cover patterns. A classification tree was created to determine landscape predictors of riparian community type. Results indicated a strong relationship between watershed land cover and vegetation diversity and structural complexity. Our hypothesis of native species association with landscape forest cover in urban riparian areas was supported, but we found no clear relationship between land cover and wetland indicator status. Our results suggest that high watershed forest cover (at least 15%) may enable the persistence of functionally diverse, native riparian vegetation communities in urban landscapes. Keywords: Pacific Northwest, plant diversity, plant ecology, riparian forest, urban ecology, urban watersheds. Title: Riparian Vegetation Assemblages and Associated Landscape Factors Across an Urbanizing Metropolitan Area Author: Von Behren, Christa, Dietrich, Andrew Evans, Yeakley, J. Alan Year: 2014 While diverse, native riparian vegetation provides important functions, it remains unclear to what extent these assemblages can persist in urban areas, and under what conditions. We characterized forested riparian vegetation communities across an urbanizing metropolitan area and examined their relationships with surrounding land cover. We hypothesized that native and hydrophilic species assemblages would correlate with forest cover in the landscape. For each of 30 sites in the Portland–Vancouver metro area, we recorded vegetation at 1-cm intervals along 3 transects using the line-intercept method. Land cover was characterized at 2 scales: within 500 m of each site and across the entire watershed. Multivariate analyses were used to evaluate relationships between species composition and land cover patterns. A classification tree was created to determine landscape predictors of riparian community type. Results indicated a strong relationship between watershed land cover and vegetation diversity and structural complexity. Our hypothesis of native species association with landscape forest cover in urban riparian areas was supported, but we found no clear relationship between land cover and wetland indicator status. Our results suggest that high watershed forest cover (at least 15%) may enable the persistence of functionally diverse, native riparian vegetation communities in urban landscapes. Keywords: Pacific Northwest, plant diversity, plant ecology, riparian forest, urban ecology, urban watersheds. Close

• 31. [Article] An Investigation of Invasion: Boater Knowledge Concerning Aquatic Invasive Species and the Influence of the New Zealand Mud Snail on Benthic Food Webs

  Invasive species are second only to habitat loss as a leading cause of native species displacement and the management of invasive species costs hundreds of billions annually. Invasion is often conceptualized ...

  Citation × Citation Citation Abstract Copy Title: An Investigation of Invasion: Boater Knowledge Concerning Aquatic Invasive Species and the Influence of the New Zealand Mud Snail on Benthic Food Webs Author: Cimino, Samuel Anthony Year: 2016 Invasive species are second only to habitat loss as a leading cause of native species displacement and the management of invasive species costs hundreds of billions annually. Invasion is often conceptualized as a series of stages (Transport, Introduction, Establishment, and Spread), which encourages ecologists to isolate factors that might enable a species to pass from one stage to another and therefore guide prevention or impact management. This thesis addresses each stage of invasion and attempts to determine where management might succeed in preventing invasion or minimizing impacts. The transport and introduction of aquatic invasive species (AIS) was analyzed by conducting a three tier human subjects survey at Tenmile Lake, Oregon over a two year period in which a public boat wash station was built and installed. Assessing boater knowledge of AIS and understanding proper boat cleaning procedure is useful in determining the threat of transport and introduction as overland boater movements is a major vector of AIS. The comparison between pre- and post- boat wash surveys indicate that there is a disconnect between what boaters say they will do and how they actually behave. While 75.9% of boaters from the pre-survey claimed they would use a boat wash station at Tenmile Lake, only 38.5% of post-survey boaters were observed using the station. Furthermore, the surveys identified knowledge gaps of boaters' awareness of AIS. More than 20.0% of boaters surveyed could not verbally name any AIS. To better understand the establishment and spread stages of invasion, I examined the influence of a specific AIS, the New Zealand mud snail (Potamopyrgus antipodarum; NZMS), on benthic food webs throughout three very different aquatic ecosystems (lakes, rivers, and estuaries). Samples of benthic lake, river, and estuarine invertebrates were collected, identified, and counted, and stable isotope analyses (SIA) were conducted on several components of the food web. NZMS densities were found to be dynamic, with population densities fluctuating over time and between locations. A significant negative relationship between NZMS density and community diversity across all ecosystems was found. However, the densities of specific feeding groups had varying positive (omnivores) and negative (herbivores) correlations with NZMS densities. Furthermore, SIA indicated that NZMS don't appear to be competing with native macroinvertebrates for the same food source. NZMS were found to have different influences on each invaded ecosystem, thus management of this particular AIS is difficult once established and spreading. The results of this thesis suggest that prevention of the transport and introduction of NZMS needs to be the focus for future management. Preventative management should include public outreach regarding AIS and proper boat cleaning procedure, and management should also emphasize the need for regional policies and regulations on the transport of AIS rather than site or state specific policies and regulations. Title: An Investigation of Invasion: Boater Knowledge Concerning Aquatic Invasive Species and the Influence of the New Zealand Mud Snail on Benthic Food Webs Author: Cimino, Samuel Anthony Year: 2016 Invasive species are second only to habitat loss as a leading cause of native species displacement and the management of invasive species costs hundreds of billions annually. Invasion is often conceptualized as a series of stages (Transport, Introduction, Establishment, and Spread), which encourages ecologists to isolate factors that might enable a species to pass from one stage to another and therefore guide prevention or impact management. This thesis addresses each stage of invasion and attempts to determine where management might succeed in preventing invasion or minimizing impacts. The transport and introduction of aquatic invasive species (AIS) was analyzed by conducting a three tier human subjects survey at Tenmile Lake, Oregon over a two year period in which a public boat wash station was built and installed. Assessing boater knowledge of AIS and understanding proper boat cleaning procedure is useful in determining the threat of transport and introduction as overland boater movements is a major vector of AIS. The comparison between pre- and post- boat wash surveys indicate that there is a disconnect between what boaters say they will do and how they actually behave. While 75.9% of boaters from the pre-survey claimed they would use a boat wash station at Tenmile Lake, only 38.5% of post-survey boaters were observed using the station. Furthermore, the surveys identified knowledge gaps of boaters' awareness of AIS. More than 20.0% of boaters surveyed could not verbally name any AIS. To better understand the establishment and spread stages of invasion, I examined the influence of a specific AIS, the New Zealand mud snail (Potamopyrgus antipodarum; NZMS), on benthic food webs throughout three very different aquatic ecosystems (lakes, rivers, and estuaries). Samples of benthic lake, river, and estuarine invertebrates were collected, identified, and counted, and stable isotope analyses (SIA) were conducted on several components of the food web. NZMS densities were found to be dynamic, with population densities fluctuating over time and between locations. A significant negative relationship between NZMS density and community diversity across all ecosystems was found. However, the densities of specific feeding groups had varying positive (omnivores) and negative (herbivores) correlations with NZMS densities. Furthermore, SIA indicated that NZMS don't appear to be competing with native macroinvertebrates for the same food source. NZMS were found to have different influences on each invaded ecosystem, thus management of this particular AIS is difficult once established and spreading. The results of this thesis suggest that prevention of the transport and introduction of NZMS needs to be the focus for future management. Preventative management should include public outreach regarding AIS and proper boat cleaning procedure, and management should also emphasize the need for regional policies and regulations on the transport of AIS rather than site or state specific policies and regulations. Close

• 32. [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

• 33. [Article] Riparian Wetland Plant Response to Livestock Exclusion in the Lower Columbia River Basin

  The purpose of this study was to examine the characteristics of riparian plant communities along a gradient of livestock exclusion in the Lower Columbia River Basin (LCRB) located in the Pacific Northwest ...

  Citation × Citation Citation Abstract Copy Title: Riparian Wetland Plant Response to Livestock Exclusion in the Lower Columbia River Basin Author: Kidd, S. A., Yeakley, J. Alan Year: 2015 The purpose of this study was to examine the characteristics of riparian plant communities along a gradient of livestock exclusion in the Lower Columbia River Basin (LCRB) located in the Pacific Northwest region of the United States. Livestock exclusion from riparian wetlands is a common passive restoration technique. Few studies, however, have focused on the effects of livestock grazing or the exclusion of livestock grazing on these ecosystems. Vegetation community composition was examined in two passive restoration sites, three and 13 years since livestock exclusion, and in a reference site with continued livestock grazing. We hypothesized native plant species richness would be lower in the excluded wetlands than in the grazed wetland due to the competitive exclusion from an increase in non-native plant dominance in the absence of grazing. The grazed wetland had significantly (P < 0.02) greater mean total species richness (23.3 ± 1.6; mean ± 1 standard error), native (10.2 ± 0.5), and non-native (12 ± 1.5) species richness than both the excluded wetlands. Mean total species richness did not differ significantly (P = 0.088) between the three-year (12 ± 1.4) and 13-year (5.5 ± 2.3) excluded wetlands. Mean native and non-native species richness also did not differ significantly (native P = 0.088. non-native P = 0.064) between the three-year (native 6.3 ± 0.6, non-native 5 ± 2.3) and 13-year (native 2.8 ± 1.3, non-native 2.7 ± 1.1) excluded wetlands. However, native species abundance as indicated by percent cover was significantly (P < 0.02) lower in the 13-year excluded wetland (4.2 ± 2.0%) than both the three-year excluded (51.5 ± 3.9%) and grazed (23.2 ± 3.3%) wetlands. The invasive grass, Phalaris arundinacea (reed canarygrass), was found to be the dominant vegetation cover in all three wetlands, with average relative cover ranging from 95.2 ± 2.0% at the 13-year exclusion site to 52.8 ± 4.1% at the grazing site, and 43.0 ± 4.0% cover at the three-year exclusion site. These observations suggest that livestock exclusion alone may be an ineffective strategy for restoring riparian plant communities in regions such as LCRB where invasive species like reed canarygrass are abundant. More effective management alternatives might include short-term livestock exclusion and reintroduced targeted grazing to both reduce livestock impacts and control reed canarygrass dominance. Title: Riparian Wetland Plant Response to Livestock Exclusion in the Lower Columbia River Basin Author: Kidd, S. A., Yeakley, J. Alan Year: 2015 The purpose of this study was to examine the characteristics of riparian plant communities along a gradient of livestock exclusion in the Lower Columbia River Basin (LCRB) located in the Pacific Northwest region of the United States. Livestock exclusion from riparian wetlands is a common passive restoration technique. Few studies, however, have focused on the effects of livestock grazing or the exclusion of livestock grazing on these ecosystems. Vegetation community composition was examined in two passive restoration sites, three and 13 years since livestock exclusion, and in a reference site with continued livestock grazing. We hypothesized native plant species richness would be lower in the excluded wetlands than in the grazed wetland due to the competitive exclusion from an increase in non-native plant dominance in the absence of grazing. The grazed wetland had significantly (P < 0.02) greater mean total species richness (23.3 ± 1.6; mean ± 1 standard error), native (10.2 ± 0.5), and non-native (12 ± 1.5) species richness than both the excluded wetlands. Mean total species richness did not differ significantly (P = 0.088) between the three-year (12 ± 1.4) and 13-year (5.5 ± 2.3) excluded wetlands. Mean native and non-native species richness also did not differ significantly (native P = 0.088. non-native P = 0.064) between the three-year (native 6.3 ± 0.6, non-native 5 ± 2.3) and 13-year (native 2.8 ± 1.3, non-native 2.7 ± 1.1) excluded wetlands. However, native species abundance as indicated by percent cover was significantly (P < 0.02) lower in the 13-year excluded wetland (4.2 ± 2.0%) than both the three-year excluded (51.5 ± 3.9%) and grazed (23.2 ± 3.3%) wetlands. The invasive grass, Phalaris arundinacea (reed canarygrass), was found to be the dominant vegetation cover in all three wetlands, with average relative cover ranging from 95.2 ± 2.0% at the 13-year exclusion site to 52.8 ± 4.1% at the grazing site, and 43.0 ± 4.0% cover at the three-year exclusion site. These observations suggest that livestock exclusion alone may be an ineffective strategy for restoring riparian plant communities in regions such as LCRB where invasive species like reed canarygrass are abundant. More effective management alternatives might include short-term livestock exclusion and reintroduced targeted grazing to both reduce livestock impacts and control reed canarygrass dominance. Close

• 34. [Article] Empirical Evidence for the Scale Dependence of Biotic Interactions

  Aim: Although it is recognized that ecological patterns are scale dependent, the exact scales over which specific ecological processes operate are still a matter of controversy. In particular, understanding ...

  Citation × Citation Citation Abstract Copy Title: Empirical Evidence for the Scale Dependence of Biotic Interactions Author: Belmaker, Jonathan, Zarnetske, Phoebe, Zonneveld, Sara, Record, Sydne, Strecker, Angela L., Beaudrot, Lydia Year: 2015 Aim: Although it is recognized that ecological patterns are scale dependent, the exact scales over which specific ecological processes operate are still a matter of controversy. In particular, understanding the scales over which biotic interactions operate is critical for predicting changes in species distributions in the face of the ongoing biodiversity crisis. It has been hypothesized that biotic interactions operate predominately at fine grains, yet this conjecture has received relatively little empirical scrutiny. We use US woodpeckers as a model system to assess the relative importance of biotic interactions, environmental suitability and geographic proximity to other intraspecific occurrence sites, across scales. Methods: We combined species occurrence data from the North American Breeding Bird Survey (BBS) with a large pair-wise interaction matrix describing known interactions among woodpeckers and other bird species. Using a logistic mixed modelling framework we then established the relative importance of biotic interactions as predictors of woodpecker occurrences in relation to environment and geographic proximity to intraspecific occurrence sites. Results: We found that geographic proximity becomes a stronger predictor of woodpecker occurrence as grain becomes coarser, while environment is grain-invariant. As opposed to environment and geographic proximity, we found that when the focal species experienced positive biotic interactions, the importance of interactions decreased with increased grain. However, positive interactions remained important up to a grain size of entire BBS routes (c. 40 km), which is much coarser than the grain size used by most species distribution models. In contrast, when the focal species experienced negative interactions we did not find clear grain dependence. Main conclusions: Biotic interactions (both positive and negative) are important predictors of species occurrences. While these interactions are strongest at fine grains, they can remain important even at coarse grains, and are thus critical for predicting distributional changes in the face of the ongoing biodiversity crisis. Title: Empirical Evidence for the Scale Dependence of Biotic Interactions Author: Belmaker, Jonathan, Zarnetske, Phoebe, Zonneveld, Sara, Record, Sydne, Strecker, Angela L., Beaudrot, Lydia Year: 2015 Aim: Although it is recognized that ecological patterns are scale dependent, the exact scales over which specific ecological processes operate are still a matter of controversy. In particular, understanding the scales over which biotic interactions operate is critical for predicting changes in species distributions in the face of the ongoing biodiversity crisis. It has been hypothesized that biotic interactions operate predominately at fine grains, yet this conjecture has received relatively little empirical scrutiny. We use US woodpeckers as a model system to assess the relative importance of biotic interactions, environmental suitability and geographic proximity to other intraspecific occurrence sites, across scales. Methods: We combined species occurrence data from the North American Breeding Bird Survey (BBS) with a large pair-wise interaction matrix describing known interactions among woodpeckers and other bird species. Using a logistic mixed modelling framework we then established the relative importance of biotic interactions as predictors of woodpecker occurrences in relation to environment and geographic proximity to intraspecific occurrence sites. Results: We found that geographic proximity becomes a stronger predictor of woodpecker occurrence as grain becomes coarser, while environment is grain-invariant. As opposed to environment and geographic proximity, we found that when the focal species experienced positive biotic interactions, the importance of interactions decreased with increased grain. However, positive interactions remained important up to a grain size of entire BBS routes (c. 40 km), which is much coarser than the grain size used by most species distribution models. In contrast, when the focal species experienced negative interactions we did not find clear grain dependence. Main conclusions: Biotic interactions (both positive and negative) are important predictors of species occurrences. While these interactions are strongest at fine grains, they can remain important even at coarse grains, and are thus critical for predicting distributional changes in the face of the ongoing biodiversity crisis. Close

• 35. [Article] Effects of Antibiotic Mixtures across Marine Intertidal Trophic Levels: Examining Environmentally-Relevant Contaminant Concentrations

  Approximately 48% of Americans use prescription drugs within each 30-day period, and there are signs this trend is increasing. Although many studies track pharmaceuticals’ fates in contaminating waterways, ...

  Citation × Citation Citation Abstract Copy Title: Effects of Antibiotic Mixtures across Marine Intertidal Trophic Levels: Examining Environmentally-Relevant Contaminant Concentrations Author: Teixeira, Jaclyn Rebecca Year: 2016 Approximately 48% of Americans use prescription drugs within each 30-day period, and there are signs this trend is increasing. Although many studies track pharmaceuticals’ fates in contaminating waterways, only fairly recent efforts have examined the potential impacts of these drugs on non-target organisms. The antibiotics sulfamethoxazole and trimethoprim, often prescribed together to treat bacterial infections, have been detected worldwide in marine and estuarine environments at concentrations up to 700-800 ng/L each. Toxic effects of these drugs have been identified in freshwater organisms, with synergistic effects observed in short-term studies of mixtures of the two; however, little research has examined possible sub-lethal and longer-term effects of antibiotics in environmentally-relevant mixture concentrations on marine organisms. I examined the long-term effects of mixtures of these two antibiotics in species of a marine system: marine microalgal species, and marine mussels, to determine whether the levels currently present in waterways affect organism health and reproduction. Microalgal species may be among the most sensitive organisms to pharmaceutical contaminants based on ecotoxicity research. I exposed three species of marine microalgae (Isochrysis galbana, Chaetoceros neogracile, and Nannochloropsis oculata) to environmentally-relevant mixtures of sulfamethoxazole and trimethoprim and examined their three-week growth rates. I found that for each species, the antibiotic treatments significantly suppressed algal growth. Specifically, I found that sulfamethoxazole was a driving factor in suppression of C. neogracile and I. galbana growth, while N. oculata responded more sensitively to a broader range of treatment mixture levels, which also included trimethoprim-only treatment groups and mixtures. These results on marine microalgae address critical data gaps, and identify the impacts of pharmaceuticals on marine primary producers, which could have direct ecosystem implications to higher trophic levels. Antibiotic pharmaceuticals can also affect marine mussel health, based on previous study of sub-cellular endpoints. I hypothesized that the important benthic foundational species, the Mytilus californianus mussel, would be significantly impacted by long-term 12-week exposure to environmentally-relevant concentrations and mixtures of sulfamethoxazole and trimethoprim. Specifically, I measured growth rate, feeding rate, condition index, and gonando-somatic index as indicators of whole-organism and reproductive health. Sulfamethoxazole concentrations, in particular, and trimethoprim to a lesser extent, suppressed mussel growth and significantly affected condition index and gonandosomatic index over time. The results of this study offer an understanding of how an intertidal system responds to chronic presence of antibiotic mixtures in the water, and a more complete picture of the environmental consequences of pharmaceutical contaminants released into marine ecosystems at ever-growing rates. Title: Effects of Antibiotic Mixtures across Marine Intertidal Trophic Levels: Examining Environmentally-Relevant Contaminant Concentrations Author: Teixeira, Jaclyn Rebecca Year: 2016 Approximately 48% of Americans use prescription drugs within each 30-day period, and there are signs this trend is increasing. Although many studies track pharmaceuticals’ fates in contaminating waterways, only fairly recent efforts have examined the potential impacts of these drugs on non-target organisms. The antibiotics sulfamethoxazole and trimethoprim, often prescribed together to treat bacterial infections, have been detected worldwide in marine and estuarine environments at concentrations up to 700-800 ng/L each. Toxic effects of these drugs have been identified in freshwater organisms, with synergistic effects observed in short-term studies of mixtures of the two; however, little research has examined possible sub-lethal and longer-term effects of antibiotics in environmentally-relevant mixture concentrations on marine organisms. I examined the long-term effects of mixtures of these two antibiotics in species of a marine system: marine microalgal species, and marine mussels, to determine whether the levels currently present in waterways affect organism health and reproduction. Microalgal species may be among the most sensitive organisms to pharmaceutical contaminants based on ecotoxicity research. I exposed three species of marine microalgae (Isochrysis galbana, Chaetoceros neogracile, and Nannochloropsis oculata) to environmentally-relevant mixtures of sulfamethoxazole and trimethoprim and examined their three-week growth rates. I found that for each species, the antibiotic treatments significantly suppressed algal growth. Specifically, I found that sulfamethoxazole was a driving factor in suppression of C. neogracile and I. galbana growth, while N. oculata responded more sensitively to a broader range of treatment mixture levels, which also included trimethoprim-only treatment groups and mixtures. These results on marine microalgae address critical data gaps, and identify the impacts of pharmaceuticals on marine primary producers, which could have direct ecosystem implications to higher trophic levels. Antibiotic pharmaceuticals can also affect marine mussel health, based on previous study of sub-cellular endpoints. I hypothesized that the important benthic foundational species, the Mytilus californianus mussel, would be significantly impacted by long-term 12-week exposure to environmentally-relevant concentrations and mixtures of sulfamethoxazole and trimethoprim. Specifically, I measured growth rate, feeding rate, condition index, and gonando-somatic index as indicators of whole-organism and reproductive health. Sulfamethoxazole concentrations, in particular, and trimethoprim to a lesser extent, suppressed mussel growth and significantly affected condition index and gonandosomatic index over time. The results of this study offer an understanding of how an intertidal system responds to chronic presence of antibiotic mixtures in the water, and a more complete picture of the environmental consequences of pharmaceutical contaminants released into marine ecosystems at ever-growing rates. Close

• 36. [Article] Competition for the Resource: Management Issues in French Mediterranean Fisheries

  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: Competition for the Resource: Management Issues in French Mediterranean Fisheries Author: Saraux, C., Jadaud, A., Gourguet, Sophie, Macher, Claire, Daures, F. 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: Competition for the Resource: Management Issues in French Mediterranean Fisheries Author: Saraux, C., Jadaud, A., Gourguet, Sophie, Macher, Claire, Daures, F. 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

• 37. [Article] SMILODONICHTHYS RASTROSUS A NEW PLIOCENE SALMONID FISH FROM WESTERN UNITED STATES

  52 pages

  Citation × Citation Citation Abstract Copy Title: SMILODONICHTHYS RASTROSUS A NEW PLIOCENE SALMONID FISH FROM WESTERN UNITED STATES Author: CAVENDER, TED M., MILLER, ROBERT RUSH Year: 2016, 1972 52 pages Title: SMILODONICHTHYS RASTROSUS A NEW PLIOCENE SALMONID FISH FROM WESTERN UNITED STATES Author: CAVENDER, TED M., MILLER, ROBERT RUSH Year: 2016, 1972 52 pages Close

• 38. [Article] The Biology of Eastern Kingbirds at Malheur National Wildlife Refuge: Survival, Reproduction, and Testosterone Secretion

  This dissertation presents the results of a study that I undertook to better understand the breeding biology of Eastern Kingbirds (hereafter, kingbirds) at Malheur National Wildlife Refuge in southeastern ...

  Citation × Citation Citation Abstract Copy Title: The Biology of Eastern Kingbirds at Malheur National Wildlife Refuge: Survival, Reproduction, and Testosterone Secretion Author: Redmond, Lucas J. Year: 2015 This dissertation presents the results of a study that I undertook to better understand the breeding biology of Eastern Kingbirds (hereafter, kingbirds) at Malheur National Wildlife Refuge in southeastern Oregon from 2003 to 2009. Kingbirds are long-distance migratory songbirds that breed across much of North America. This species is socially monogamous but, via frequent extra-pair copulations, is genetically polygamous. Kingbirds exhibit relatively high breeding site fidelity, often returning to the same tree to nest in subsequent years. Both members of a pair provide parental care, but there are often specific duties performed by both male and female kingbirds. For example, males typically perform much of the vigilant nest defense that this species is well known for and contribute, to an extent, to the feeding of nestlings. Females, on the other hand, are entirely responsible for incubating and brooding. Beginning in 2002, most adults within the population of kingbirds at Malheur had been banded with a unique combination of three colored plastic leg bands and an aluminum USFWS band. Also, as many nests were located in each year as possible, and any young that survived to fledging age were banded with a unique combination of leg bands. Considerable effort was then spent each year to locate as many banded individuals as possible, which allowed me to document adult and juvenile survival. Annual survival rates of adult male and female kingbirds in the population at Malheur did not differ and were relatively high at approximately 0.65. Juvenile survival rate was approximately 0.29, indicating that slightly less than one-third of nestlings survive the interval between fledging and their first potential breeding season. Resighting probability was high for both sexes, although higher for adult males (0.94) than for adult female (0.84). The latter finding is consistent with the higher site fidelity of males than of females. Resighting probabilities for juveniles were much lower at 0.68 and 0.40 for males and females, respectively. Again, this was expected because natal site fidelity is typically much lower than breeding site fidelity. Compared to most other reports, resighting probability and return rates of juvenile kingbirds was high, presumably because the riparian habitats where kingbirds breed at Malheur function as an ecological island surrounded by, for kingbirds, unsuitable high desert habitat. Thus, unless they disperse very long distances, the only option for juvenile kingbirds is to begin nesting on the refuge. The collection of blood samples from birds has become an increasingly common practice in ornithology. The data that can be gained from these samples allow a number of interesting questions to be asked such as understanding the genetic mating system of a species, patterns of hormone secretion, and discerning migratory pathways via stable isotope analysis. The volume of blood collected is usually small and was assumed to cause no long-term negative effects on sampled individuals. However, few studies have rigorously examined the effect of blood sampling on survival. I used a multistate mark-recapture analysis to assess the effect blood sampling on annual survival of kingbirds by combining the annual survival data described above with whether or not individuals were subjected to blood sample collection. The results of this analysis indicated that blood sampling had no effect on annual survival rates of kingbirds. Whether or not this is the case for other species remains to be seen. However, my results support the assumption that when done correctly, blood sampling has little to no long-term negative effects on birds. Comparative analyses of many bird species show that testosterone secretion exhibits fairly predictable patterns among breeding birds of different mating systems. Monogamous species reach a peak during mate attraction and the period of female fertility which is then followed by a sharp decline when young are in the nest. By contrast, males of polygynous species tend to maintain higher levels of testosterone throughout the breeding season to, presumably, maximize opportunities for acquiring additional mates. Kingbirds are socially monogamous but cryptically polygamous. However, because of high rates of extra-pair paternity, variation in reproductive success among males is much higher than what is expected for a monogamous species, and, instead, is similar to what has been reported for polygynous species. Therefore from 2005 to 2009 I measured testosterone concentrations from the blood samples collected from male kingbirds to determine the breeding season profile of testosterone secretion in kingbirds and to understand the factors that influence testosterone variation among individuals. Contrary to expected for a monogamous species, the testosterone profile of kingbirds did not exhibit the brief peak in testosterone followed by a precipitous decline. Testosterone peaked early in the season, but declined very slowly as the nest cycle progressed. I attributed this gradual decline in testosterone to the cryptically polygynous nature of the kingbird extra-pair mating system. I also found substantial variation in testosterone concentration among male kingbirds and was able to identify several factors contributing to this variation. As expected, testosterone declined as the breeding season progressed (independent of stage in nest cycle) and nest density increased, while increases in testosterone were correlated with the number of fertile females within the population. This suggests that male kingbirds were capable of modulating testosterone concentrations to both cope with an increase in conspecific density, but also to ready themselves for times when extra-pair copulations were more likely. Title: The Biology of Eastern Kingbirds at Malheur National Wildlife Refuge: Survival, Reproduction, and Testosterone Secretion Author: Redmond, Lucas J. Year: 2015 This dissertation presents the results of a study that I undertook to better understand the breeding biology of Eastern Kingbirds (hereafter, kingbirds) at Malheur National Wildlife Refuge in southeastern Oregon from 2003 to 2009. Kingbirds are long-distance migratory songbirds that breed across much of North America. This species is socially monogamous but, via frequent extra-pair copulations, is genetically polygamous. Kingbirds exhibit relatively high breeding site fidelity, often returning to the same tree to nest in subsequent years. Both members of a pair provide parental care, but there are often specific duties performed by both male and female kingbirds. For example, males typically perform much of the vigilant nest defense that this species is well known for and contribute, to an extent, to the feeding of nestlings. Females, on the other hand, are entirely responsible for incubating and brooding. Beginning in 2002, most adults within the population of kingbirds at Malheur had been banded with a unique combination of three colored plastic leg bands and an aluminum USFWS band. Also, as many nests were located in each year as possible, and any young that survived to fledging age were banded with a unique combination of leg bands. Considerable effort was then spent each year to locate as many banded individuals as possible, which allowed me to document adult and juvenile survival. Annual survival rates of adult male and female kingbirds in the population at Malheur did not differ and were relatively high at approximately 0.65. Juvenile survival rate was approximately 0.29, indicating that slightly less than one-third of nestlings survive the interval between fledging and their first potential breeding season. Resighting probability was high for both sexes, although higher for adult males (0.94) than for adult female (0.84). The latter finding is consistent with the higher site fidelity of males than of females. Resighting probabilities for juveniles were much lower at 0.68 and 0.40 for males and females, respectively. Again, this was expected because natal site fidelity is typically much lower than breeding site fidelity. Compared to most other reports, resighting probability and return rates of juvenile kingbirds was high, presumably because the riparian habitats where kingbirds breed at Malheur function as an ecological island surrounded by, for kingbirds, unsuitable high desert habitat. Thus, unless they disperse very long distances, the only option for juvenile kingbirds is to begin nesting on the refuge. The collection of blood samples from birds has become an increasingly common practice in ornithology. The data that can be gained from these samples allow a number of interesting questions to be asked such as understanding the genetic mating system of a species, patterns of hormone secretion, and discerning migratory pathways via stable isotope analysis. The volume of blood collected is usually small and was assumed to cause no long-term negative effects on sampled individuals. However, few studies have rigorously examined the effect of blood sampling on survival. I used a multistate mark-recapture analysis to assess the effect blood sampling on annual survival of kingbirds by combining the annual survival data described above with whether or not individuals were subjected to blood sample collection. The results of this analysis indicated that blood sampling had no effect on annual survival rates of kingbirds. Whether or not this is the case for other species remains to be seen. However, my results support the assumption that when done correctly, blood sampling has little to no long-term negative effects on birds. Comparative analyses of many bird species show that testosterone secretion exhibits fairly predictable patterns among breeding birds of different mating systems. Monogamous species reach a peak during mate attraction and the period of female fertility which is then followed by a sharp decline when young are in the nest. By contrast, males of polygynous species tend to maintain higher levels of testosterone throughout the breeding season to, presumably, maximize opportunities for acquiring additional mates. Kingbirds are socially monogamous but cryptically polygamous. However, because of high rates of extra-pair paternity, variation in reproductive success among males is much higher than what is expected for a monogamous species, and, instead, is similar to what has been reported for polygynous species. Therefore from 2005 to 2009 I measured testosterone concentrations from the blood samples collected from male kingbirds to determine the breeding season profile of testosterone secretion in kingbirds and to understand the factors that influence testosterone variation among individuals. Contrary to expected for a monogamous species, the testosterone profile of kingbirds did not exhibit the brief peak in testosterone followed by a precipitous decline. Testosterone peaked early in the season, but declined very slowly as the nest cycle progressed. I attributed this gradual decline in testosterone to the cryptically polygynous nature of the kingbird extra-pair mating system. I also found substantial variation in testosterone concentration among male kingbirds and was able to identify several factors contributing to this variation. As expected, testosterone declined as the breeding season progressed (independent of stage in nest cycle) and nest density increased, while increases in testosterone were correlated with the number of fertile females within the population. This suggests that male kingbirds were capable of modulating testosterone concentrations to both cope with an increase in conspecific density, but also to ready themselves for times when extra-pair copulations were more likely. Close

• 39. [Article] Dendrochronology and Middle Miocene Petrified Oak: Modern Counterparts and Interpretation

  This study reports the first successful statistical crossdating among many ring width time series from petrified wood, thus providing a replicable continuous annual resolution window into tree growth and ...

  Citation × Citation Citation Abstract Copy Title: Dendrochronology and Middle Miocene Petrified Oak: Modern Counterparts and Interpretation Author: Wright, William E., Streck, Martin J., Baisan, Christopher, Wright, W. Walton, Szejner, Paul Year: 2015 This study reports the first successful statistical crossdating among many ring width time series from petrified wood, thus providing a replicable continuous annual resolution window into tree growth and environmental influences during the middle Miocene. The petrified samples, of the genus Quercus, originated at the Stinking Water (SW) locality in Oregon, a Miocene-aged exposure associated with the Columbia River Basalts. 40AR/39AR dating on pillow basalt from the locality yielded a weighted Plateau Age of 13.79 ±0.09 Ma placing the death of the trees at the end of the Langhian Stage of the Middle Miocene (15.97±0.05 to 13.65±0.05 Ma), during the middle Miocene Climate Transition (MMCT). Ring width time series from 26 radii, 17 different trees, show significant intercorrelation. A Modified Coexistence Approach was applied to determine the likely climate range when the SW trees were growing. The modified approach included regression of site-mean ring width time series statistic values on estimated soil moisture for the site locations, using site-mean data from 126 modern Quercus sites from across the United States. Identification of highly significant linearities indicated strong relationships between ring width intercorrelation and soil moisture and ring width variability and soil moisture. Comparison of individual modern site-mean statistical values with values calculated for the SW locality suggests a mesic growing environment for the SW Quercus, with moderate temperatures. Geographic placement of modern Quercus sites with site-mean statistics similar to the SW values indicates a modern analogue in the eastern United States. Modern distributions of mesic species in the genera present at the SW locality suggest similarities with the central and southern Appalachian Mountains and the Ozark/Ouachita Mountains, indicating a mean annual temperature range of between ring width intercorrelation and soil moisture and ring width variability and soil moisture. Comparison of individual modern site-mean statistical values with values calculated for the SW locality suggests a mesic growing environment for the SW Quercus, with moderate temperatures. Geographic placement of modern Quercus sites with site-mean statistics similar to the SW values indicates a modern analogue in the eastern United States. Modern distributions of mesic species in the genera present at the SW locality suggest similarities with the central and southern Appalachian Mountains and the Ozark/Ouachita Mountains, indicating a mean annual temperature range of ≅10 ˚C to ≅ 15 ˚C and a mean annual precipitation range of ≅750 mm to ≅1200 mm when the SW Quercus were growing. Title: Dendrochronology and Middle Miocene Petrified Oak: Modern Counterparts and Interpretation Author: Wright, William E., Streck, Martin J., Baisan, Christopher, Wright, W. Walton, Szejner, Paul Year: 2015 This study reports the first successful statistical crossdating among many ring width time series from petrified wood, thus providing a replicable continuous annual resolution window into tree growth and environmental influences during the middle Miocene. The petrified samples, of the genus Quercus, originated at the Stinking Water (SW) locality in Oregon, a Miocene-aged exposure associated with the Columbia River Basalts. 40AR/39AR dating on pillow basalt from the locality yielded a weighted Plateau Age of 13.79 ±0.09 Ma placing the death of the trees at the end of the Langhian Stage of the Middle Miocene (15.97±0.05 to 13.65±0.05 Ma), during the middle Miocene Climate Transition (MMCT). Ring width time series from 26 radii, 17 different trees, show significant intercorrelation. A Modified Coexistence Approach was applied to determine the likely climate range when the SW trees were growing. The modified approach included regression of site-mean ring width time series statistic values on estimated soil moisture for the site locations, using site-mean data from 126 modern Quercus sites from across the United States. Identification of highly significant linearities indicated strong relationships between ring width intercorrelation and soil moisture and ring width variability and soil moisture. Comparison of individual modern site-mean statistical values with values calculated for the SW locality suggests a mesic growing environment for the SW Quercus, with moderate temperatures. Geographic placement of modern Quercus sites with site-mean statistics similar to the SW values indicates a modern analogue in the eastern United States. Modern distributions of mesic species in the genera present at the SW locality suggest similarities with the central and southern Appalachian Mountains and the Ozark/Ouachita Mountains, indicating a mean annual temperature range of between ring width intercorrelation and soil moisture and ring width variability and soil moisture. Comparison of individual modern site-mean statistical values with values calculated for the SW locality suggests a mesic growing environment for the SW Quercus, with moderate temperatures. Geographic placement of modern Quercus sites with site-mean statistics similar to the SW values indicates a modern analogue in the eastern United States. Modern distributions of mesic species in the genera present at the SW locality suggest similarities with the central and southern Appalachian Mountains and the Ozark/Ouachita Mountains, indicating a mean annual temperature range of ≅10 ˚C to ≅ 15 ˚C and a mean annual precipitation range of ≅750 mm to ≅1200 mm when the SW Quercus were growing. Close

• 40. [Article] Effects of Pharmaceuticals and Personal Care Products on Marine Organisms: From Single-Species Studies to an Ecosystem-Based Approach

  Pharmaceuticals and personal care products (PPCPs) are contaminants of emerging concern that are increasing in use and have demonstrated negative effects on aquatic organisms. There is a growing body of ...

  Citation × Citation Citation Abstract Copy Title: Effects of Pharmaceuticals and Personal Care Products on Marine Organisms: From Single-Species Studies to an Ecosystem-Based Approach Author: Prichard, Emma C, Granek, Elise F. Year: 2016 Pharmaceuticals and personal care products (PPCPs) are contaminants of emerging concern that are increasing in use and have demonstrated negative effects on aquatic organisms. There is a growing body of literature reporting the effects of PPCPs on freshwater organisms, but studies on the effects of PPCPs to marine and estuarine organisms are limited. Among effect studies, the vast majority examines subcellular or cellular effects, with far fewer studies examining organismal- and community-level effects. We reviewed the current published literature on marine and estuarine algae, invertebrates, fish, and mammals exposed to PPCPs, in order to expand upon current reviews. This paper builds on previous reviews of PPCP contamination in marine environments, filling prior literature gaps and adding consideration of ecosystem function and level of knowledge across marine habitat types. Finally, we reviewed and compiled data gaps suggested by current researchers and reviewers and propose a multi-level model to expand the focus of current PPCP research beyond laboratory studies. This model includes examination of direct ecological effects including food web and disease dynamics, biodiversity, community composition, and other ecosystem-level indicators of contaminant-driven change. Title: Effects of Pharmaceuticals and Personal Care Products on Marine Organisms: From Single-Species Studies to an Ecosystem-Based Approach Author: Prichard, Emma C, Granek, Elise F. Year: 2016 Pharmaceuticals and personal care products (PPCPs) are contaminants of emerging concern that are increasing in use and have demonstrated negative effects on aquatic organisms. There is a growing body of literature reporting the effects of PPCPs on freshwater organisms, but studies on the effects of PPCPs to marine and estuarine organisms are limited. Among effect studies, the vast majority examines subcellular or cellular effects, with far fewer studies examining organismal- and community-level effects. We reviewed the current published literature on marine and estuarine algae, invertebrates, fish, and mammals exposed to PPCPs, in order to expand upon current reviews. This paper builds on previous reviews of PPCP contamination in marine environments, filling prior literature gaps and adding consideration of ecosystem function and level of knowledge across marine habitat types. Finally, we reviewed and compiled data gaps suggested by current researchers and reviewers and propose a multi-level model to expand the focus of current PPCP research beyond laboratory studies. This model includes examination of direct ecological effects including food web and disease dynamics, biodiversity, community composition, and other ecosystem-level indicators of contaminant-driven change. Close

• 41. [Article] Agricultural Management Decisions Impact Isoprene Emission and Physiology of Arundo donax, an Emerging Bioenergy Crop

  Arundo donax (Giant Reed) is quickly being developed as a rapidly-growing, robust, and highly productive bioenergy crop, with large scale cultivation of this species planned for the Columbia River basin ...

  Citation × Citation Citation Abstract Copy Title: Agricultural Management Decisions Impact Isoprene Emission and Physiology of Arundo donax, an Emerging Bioenergy Crop Author: Maxfield, Jason Charles Year: 2014 Arundo donax (Giant Reed) is quickly being developed as a rapidly-growing, robust, and highly productive bioenergy crop, with large scale cultivation of this species planned for the Columbia River basin of the Pacific Northwest (USA). Despite its potential as a next generation biomass crop, relatively few studies have examined the physiological performance of A. donax under agricultural conditions. Unlike traditional crops, A. donax is known to be a high-emitter of the volatile compound isoprene, which may significantly impact regional air quality, but it has not been widely cultivated in North America and little is known about how this species will perform in the Pacific Northwest. Over two field seasons, we measured isoprene fluxes from A. donax plants in both greenhouse conditions and in an agricultural field setting under a variety of conditions and fertilizer treatments. We also measured several other attributes of A. donax productivity and leaf physiology including chlorophyll content, photosynthesis rate, stomatal conductance, specific leaf mass, water use efficiency and gas exchange. We found that A. donax physiologically performs well under cultivation in the Columbia River basin, but that it also emits isoprene at significantly higher rates than previous reports indicate. We also found that both isoprene emission and leaf physiology were highly affected by agricultural management decisions, including nitrogen and irrigation management. Our findings indicate that crop management strategies can be developed that simultaneously seek to minimize isoprene emission while maximizing biomass production in this newly emerging bioenergy crop. Title: Agricultural Management Decisions Impact Isoprene Emission and Physiology of Arundo donax, an Emerging Bioenergy Crop Author: Maxfield, Jason Charles Year: 2014 Arundo donax (Giant Reed) is quickly being developed as a rapidly-growing, robust, and highly productive bioenergy crop, with large scale cultivation of this species planned for the Columbia River basin of the Pacific Northwest (USA). Despite its potential as a next generation biomass crop, relatively few studies have examined the physiological performance of A. donax under agricultural conditions. Unlike traditional crops, A. donax is known to be a high-emitter of the volatile compound isoprene, which may significantly impact regional air quality, but it has not been widely cultivated in North America and little is known about how this species will perform in the Pacific Northwest. Over two field seasons, we measured isoprene fluxes from A. donax plants in both greenhouse conditions and in an agricultural field setting under a variety of conditions and fertilizer treatments. We also measured several other attributes of A. donax productivity and leaf physiology including chlorophyll content, photosynthesis rate, stomatal conductance, specific leaf mass, water use efficiency and gas exchange. We found that A. donax physiologically performs well under cultivation in the Columbia River basin, but that it also emits isoprene at significantly higher rates than previous reports indicate. We also found that both isoprene emission and leaf physiology were highly affected by agricultural management decisions, including nitrogen and irrigation management. Our findings indicate that crop management strategies can be developed that simultaneously seek to minimize isoprene emission while maximizing biomass production in this newly emerging bioenergy crop. Close

• 42. [Article] Long-term Ecological Research in Forest Park: Tracking Urban Impacts to Forest Structure and Productivity

  Current and historic land use practices as well as exposure to an urban environment can impact forest structure and function. Past and ongoing research in Forest Park, a large urban forest in Portland, ...

  Citation × Citation Citation Abstract Copy Title: Long-term Ecological Research in Forest Park: Tracking Urban Impacts to Forest Structure and Productivity Author: Addessi, Andrew, Dresner, Marion Year: 2017 Current and historic land use practices as well as exposure to an urban environment can impact forest structure and function. Past and ongoing research in Forest Park, a large urban forest in Portland, Oregon, suggests that mature Douglas-fir (Psuedotsuga meziesii) dominated conifer stands in the more urban end of the park are not developing certain late successional features. Notably, they lack a shade-tolerant conifer understory composed of western hemlock (Tsuga heterophylla) and western red-cedar (Thuja plicata). Here, I present three lines of investigation taken from several 1-hectare permanent long-term ecological research (LTER) plots in Forest Park. First, I investigated whether plot-level differences in the intensity of past-land use, namely clearcut logging and fire, has created legacy effect on soil health, as measured by soil organic matter, soil pH, and depth of organic horizon. Second, I present 5-year growth and mortality data to characterize productivity patterns in these plots. Last, I analyzed light detection and ranging (LiDAR) data covering Forest Park to determine if canopy structural features diverged across urban and rural sections of the park. Overall, the results indicate some legacy of soil impact to urban areas most effected by past intensive logging. However, forest productivity, mortality, and structural patterns were generally consistent with stand age, and did not show strong patterns related to urban proximity. These results indicate that the lack of shade tolerant species might be most limited by ground level impacts. These results help inform park managers that regeneration of late successional tree species may require active restoration practices that focus on establishing more optimal growing sites. Title: Long-term Ecological Research in Forest Park: Tracking Urban Impacts to Forest Structure and Productivity Author: Addessi, Andrew, Dresner, Marion Year: 2017 Current and historic land use practices as well as exposure to an urban environment can impact forest structure and function. Past and ongoing research in Forest Park, a large urban forest in Portland, Oregon, suggests that mature Douglas-fir (Psuedotsuga meziesii) dominated conifer stands in the more urban end of the park are not developing certain late successional features. Notably, they lack a shade-tolerant conifer understory composed of western hemlock (Tsuga heterophylla) and western red-cedar (Thuja plicata). Here, I present three lines of investigation taken from several 1-hectare permanent long-term ecological research (LTER) plots in Forest Park. First, I investigated whether plot-level differences in the intensity of past-land use, namely clearcut logging and fire, has created legacy effect on soil health, as measured by soil organic matter, soil pH, and depth of organic horizon. Second, I present 5-year growth and mortality data to characterize productivity patterns in these plots. Last, I analyzed light detection and ranging (LiDAR) data covering Forest Park to determine if canopy structural features diverged across urban and rural sections of the park. Overall, the results indicate some legacy of soil impact to urban areas most effected by past intensive logging. However, forest productivity, mortality, and structural patterns were generally consistent with stand age, and did not show strong patterns related to urban proximity. These results indicate that the lack of shade tolerant species might be most limited by ground level impacts. These results help inform park managers that regeneration of late successional tree species may require active restoration practices that focus on establishing more optimal growing sites. Close

• 43. [Article] SITE FIDELITY AND HOMING BEHAVIOR OF THE INTERTIDAL STICHAEIDAE, XIPHISTER ATROPURPUREUS (BLACK PRICKLEBACK)

  31 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, Fall 201...

  Citation × Citation Citation Abstract Copy Title: SITE FIDELITY AND HOMING BEHAVIOR OF THE INTERTIDAL STICHAEIDAE, XIPHISTER ATROPURPUREUS (BLACK PRICKLEBACK) Author: Nelson, Ashley Kim Year: 2014, 2013 31 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, Fall 2013. Title: SITE FIDELITY AND HOMING BEHAVIOR OF THE INTERTIDAL STICHAEIDAE, XIPHISTER ATROPURPUREUS (BLACK PRICKLEBACK) Author: Nelson, Ashley Kim Year: 2014, 2013 31 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, Fall 2013. Close

• 44. [Article] Prospectus for Future Research: Temperature Effects on Green Macroalgae

  Research on temperature change has received attention from scientists. Not only has temperature change attracted scientists who study the Earth’s weather and climate, but also those who study plants and ...

  Citation × Citation Citation Abstract Copy Title: Prospectus for Future Research: Temperature Effects on Green Macroalgae Author: Gonzalez Pelayo, Ana Year: 2016 Research on temperature change has received attention from scientists. Not only has temperature change attracted scientists who study the Earth’s weather and climate, but also those who study plants and animals on land and in oceans. The research being conducted looks at how these temperature changes affect the anatomy and physiology of organisms, but other research also studies how terrestrial and aquatic ecosystems have changed and the types of responses that have occurred as a result. For many years, research in terrestrial ecosystems has dominated research in aquatic ecosystems. Limited research has been conducted in aquatic ecosystems involving green macroalgae, which are primary producers and an essential part of these ecosystems. Within the last fifteen years, research regarding the effects of temperature change on green macroalgae has shown that temperature affects photosynthesis and biochemistry. Overall, photosynthesis is almost completely inhibited after sufficient exposure due to damage in Photosystem II. There is also a substantial change in the production of chemical molecules known as reactive oxygen species that caused physical damage to the algal cells as well as a change in structure for proteins that is essential for function. I reviewed the literature within the past fifteen years, regarding the effects of temperature on a variety of green macroalgae species. The results indicated that after sufficient exposure, the photosynthetic rate of macroalgae is reduced significantly and that the change in chemistry lead to alterations in the physiology of green macroalgae. In this thesis, I propose two possible directions for algae research that involves genetic sequencing of a model species to identify a possible temperature tolerance gene, as well as the potential use of green macroalgae in photobioreactors as a source of renewable energy. Title: Prospectus for Future Research: Temperature Effects on Green Macroalgae Author: Gonzalez Pelayo, Ana Year: 2016 Research on temperature change has received attention from scientists. Not only has temperature change attracted scientists who study the Earth’s weather and climate, but also those who study plants and animals on land and in oceans. The research being conducted looks at how these temperature changes affect the anatomy and physiology of organisms, but other research also studies how terrestrial and aquatic ecosystems have changed and the types of responses that have occurred as a result. For many years, research in terrestrial ecosystems has dominated research in aquatic ecosystems. Limited research has been conducted in aquatic ecosystems involving green macroalgae, which are primary producers and an essential part of these ecosystems. Within the last fifteen years, research regarding the effects of temperature change on green macroalgae has shown that temperature affects photosynthesis and biochemistry. Overall, photosynthesis is almost completely inhibited after sufficient exposure due to damage in Photosystem II. There is also a substantial change in the production of chemical molecules known as reactive oxygen species that caused physical damage to the algal cells as well as a change in structure for proteins that is essential for function. I reviewed the literature within the past fifteen years, regarding the effects of temperature on a variety of green macroalgae species. The results indicated that after sufficient exposure, the photosynthetic rate of macroalgae is reduced significantly and that the change in chemistry lead to alterations in the physiology of green macroalgae. In this thesis, I propose two possible directions for algae research that involves genetic sequencing of a model species to identify a possible temperature tolerance gene, as well as the potential use of green macroalgae in photobioreactors as a source of renewable energy. Close

• 45. [Article] The Importance of Urban Habitat Connectivity and Influence on Native Avian Species and Community Science

  In what ways do small-scale urban backyards contribute to local bird abundance and biodiversity? In what ways might these yards serve as an ‘extension’ of neighboring native forest areas? This project ...

  Citation × Citation Citation Abstract Copy Title: The Importance of Urban Habitat Connectivity and Influence on Native Avian Species and Community Science Author: Gulick, Kristen S. Year: 2017 In what ways do small-scale urban backyards contribute to local bird abundance and biodiversity? In what ways might these yards serve as an ‘extension’ of neighboring native forest areas? This project investigates the contribution that a group of backyards, certified through the Backyard Habitat Certification Program, have in the suburb of Hillsdale, Oregon, which is adjacent to the natural area of Keller Woodland. Backyard owners functioning as citizen or community scientists assisted with conducting residential bird point-counts once a week in each backyard and the natural area. Counts were done for a total of 8 weeks during nesting season to better understand how backyard habitat restoration might affect their habitat especially when in close proximity to a natural area. The goal of the project was to help better understand the beneficial effects of urban gardening using native plants and diverse vegetation structure as this relates to bird species richness, and to explore the importance of community scientist contributions. Although the sample size was small, no significant trends were found, but the involvement of community scientists indicated increased skill, depth of understanding, and increased motivation for all participating backyard habitat owners. More backyards are needed for future research and extension into lower-income neighborhoods would be very beneficial to increase awareness of urban habitat connectivity and the diversity seen in backyard environmental characteristics and yard owner backyard habitat knowledge. A larger sample size could reveal correlations and provide a greater significance in data findings for bird abundance and diversity. A logical extension of this project would be to investigate food-web effects, specifically avian prey species, and smaller green-spaces that are often present in urban neighborhoods in addition to the large green-spaces. Authors: Kristen S. Gulick, Marion Dresner, Nikkie West Presenter: Kristen S. Gulick Title: The Importance of Urban Habitat Connectivity and Influence on Native Avian Species and Community Science Author: Gulick, Kristen S. Year: 2017 In what ways do small-scale urban backyards contribute to local bird abundance and biodiversity? In what ways might these yards serve as an ‘extension’ of neighboring native forest areas? This project investigates the contribution that a group of backyards, certified through the Backyard Habitat Certification Program, have in the suburb of Hillsdale, Oregon, which is adjacent to the natural area of Keller Woodland. Backyard owners functioning as citizen or community scientists assisted with conducting residential bird point-counts once a week in each backyard and the natural area. Counts were done for a total of 8 weeks during nesting season to better understand how backyard habitat restoration might affect their habitat especially when in close proximity to a natural area. The goal of the project was to help better understand the beneficial effects of urban gardening using native plants and diverse vegetation structure as this relates to bird species richness, and to explore the importance of community scientist contributions. Although the sample size was small, no significant trends were found, but the involvement of community scientists indicated increased skill, depth of understanding, and increased motivation for all participating backyard habitat owners. More backyards are needed for future research and extension into lower-income neighborhoods would be very beneficial to increase awareness of urban habitat connectivity and the diversity seen in backyard environmental characteristics and yard owner backyard habitat knowledge. A larger sample size could reveal correlations and provide a greater significance in data findings for bird abundance and diversity. A logical extension of this project would be to investigate food-web effects, specifically avian prey species, and smaller green-spaces that are often present in urban neighborhoods in addition to the large green-spaces. Authors: Kristen S. Gulick, Marion Dresner, Nikkie West Presenter: Kristen S. Gulick Close

• 46. [Article] Community Science and the Ecological Merits of Backyard Habitat Patches and Adjacent Green-Spaces for Urban Avian Species

  In what ways do small-scale urban backyards contribute to local bird abundance and biodiversity? In what ways might these yards serve as an ‘extension’ of neighboring native forest areas? This project ...

  Citation × Citation Citation Abstract Copy Title: Community Science and the Ecological Merits of Backyard Habitat Patches and Adjacent Green-Spaces for Urban Avian Species Author: Gulick, Kristen S., West, Nikkie, Dresner, Marion Year: 2017 In what ways do small-scale urban backyards contribute to local bird abundance and biodiversity? In what ways might these yards serve as an ‘extension’ of neighboring native forest areas? This project investigates the contribution that a group of backyards, certified through the Backyard Habitat Certification Program, have in the suburb of Hillsdale, Oregon, which is adjacent to the natural area of Keller Woodland. Backyard owners functioning as citizen or community scientists assisted with conducting residential bird point-counts once a week in each backyard and the natural area. Counts were done for a total of 8 weeks during nesting season to better understand how backyard habitat restoration might affect their habitat especially when in close proximity to a natural area. The goal of the project was to help better understand the beneficial effects of urban gardening using native plants and diverse vegetation structure as this relates to bird species richness, and to explore the importance of community scientist contributions. Although the sample size was small, no significant trends were found, but the involvement of community scientists indicated increased skill, depth of understanding, and increased motivation for all participating backyard habitat owners. More backyards are needed for future research and extension into lower-income neighborhoods would be very beneficial to increase awareness of urban habitat connectivity and the diversity seen in backyard environmental characteristics and yard owner backyard habitat knowledge. A larger sample size could reveal correlations and provide a greater significance in data findings for bird abundance and diversity. A logical extension of this project would be to investigate food-web effects, specifically avian prey species, and smaller green-spaces that are often present in urban neighborhoods in addition to the large green-spaces. Title: Community Science and the Ecological Merits of Backyard Habitat Patches and Adjacent Green-Spaces for Urban Avian Species Author: Gulick, Kristen S., West, Nikkie, Dresner, Marion Year: 2017 In what ways do small-scale urban backyards contribute to local bird abundance and biodiversity? In what ways might these yards serve as an ‘extension’ of neighboring native forest areas? This project investigates the contribution that a group of backyards, certified through the Backyard Habitat Certification Program, have in the suburb of Hillsdale, Oregon, which is adjacent to the natural area of Keller Woodland. Backyard owners functioning as citizen or community scientists assisted with conducting residential bird point-counts once a week in each backyard and the natural area. Counts were done for a total of 8 weeks during nesting season to better understand how backyard habitat restoration might affect their habitat especially when in close proximity to a natural area. The goal of the project was to help better understand the beneficial effects of urban gardening using native plants and diverse vegetation structure as this relates to bird species richness, and to explore the importance of community scientist contributions. Although the sample size was small, no significant trends were found, but the involvement of community scientists indicated increased skill, depth of understanding, and increased motivation for all participating backyard habitat owners. More backyards are needed for future research and extension into lower-income neighborhoods would be very beneficial to increase awareness of urban habitat connectivity and the diversity seen in backyard environmental characteristics and yard owner backyard habitat knowledge. A larger sample size could reveal correlations and provide a greater significance in data findings for bird abundance and diversity. A logical extension of this project would be to investigate food-web effects, specifically avian prey species, and smaller green-spaces that are often present in urban neighborhoods in addition to the large green-spaces. Close

• 47. [Article] Investigating an adaptive explanation for nonprogressor immune responses to SIV

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

  Citation × Citation Citation Abstract Copy Title: Investigating an adaptive explanation for nonprogressor immune responses to SIV Author: McVeety, Kelsie Year: 2015 62 pages. A thesis presented to the Department of Anthropology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2015. Title: Investigating an adaptive explanation for nonprogressor immune responses to SIV Author: McVeety, Kelsie Year: 2015 62 pages. A thesis presented to the Department of Anthropology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2015. Close

• 48. [Article] THE OLIGOCENE MARINE MOLLUSCAN FAUNA OF THE EUGENE FORMATION IN OREGON

  124 pages

  Citation × Citation Citation Abstract Copy Title: THE OLIGOCENE MARINE MOLLUSCAN FAUNA OF THE EUGENE FORMATION IN OREGON Author: STENTZ HICKMAN, CAROLE JEAN Year: 2016, 1969 124 pages Title: THE OLIGOCENE MARINE MOLLUSCAN FAUNA OF THE EUGENE FORMATION IN OREGON Author: STENTZ HICKMAN, CAROLE JEAN Year: 2016, 1969 124 pages Close

• 49. [Article] The Relationship between Plankton and Water Mass Properties in High Arctic (Svalbard) Fjords

  43 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, Fall 201...

  Citation × Citation Citation Abstract Copy Title: The Relationship between Plankton and Water Mass Properties in High Arctic (Svalbard) Fjords Author: Poje, Alexandra Merritt Year: 2017, 2016 43 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, Fall 2016 Title: The Relationship between Plankton and Water Mass Properties in High Arctic (Svalbard) Fjords Author: Poje, Alexandra Merritt Year: 2017, 2016 43 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, Fall 2016 Close

• 50. [Article] The Relationship between Plankton and Water Mass Properties in High Arctic (Svalbard) Fjords

  43 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, Fall 201...

  Citation × Citation Citation Abstract Copy Title: The Relationship between Plankton and Water Mass Properties in High Arctic (Svalbard) Fjords Author: Poje, Alexandra Year: 2017, 2016 43 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, Fall 2016. Title: The Relationship between Plankton and Water Mass Properties in High Arctic (Svalbard) Fjords Author: Poje, Alexandra Year: 2017, 2016 43 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, Fall 2016. Close

• 51. [Article] Controlling an Invasive Species through Consumption: The Case of Lionfish as an Impure Public Good

  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: Controlling an Invasive Species through Consumption: The Case of Lionfish as an Impure Public Good Author: Morgan, Ash, McEvoy, Dave, Huth, Bill 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: Controlling an Invasive Species through Consumption: The Case of Lionfish as an Impure Public Good Author: Morgan, Ash, McEvoy, Dave, Huth, Bill 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

• 52. [Article] Interactions Among Fuel Management, Species Composition, Bark Beetles, and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin

  Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their ...

  Citation × Citation Citation Abstract Copy Title: Interactions Among Fuel Management, Species Composition, Bark Beetles, and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin Author: Scheller, Robert M., Kretchun, Alec M., Loudermilk, E. Louise, Hurteau, Matthew D., Weisberg, Peter J., Skinner, Carl Year: 2017 Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their long-term interactions with future climate change are poorly understood. Droughts and the associated moisture deficit contribute to the onset of bark beetle outbreaks although outbreak extent and severity is dependent upon the density of host trees, wildfire, and forest management. Our objective was to estimate the effects of climate change and bark beetle outbreaks on ecosystem carbon dynamics over the next century in a western US forest. Specifically, we hypothesized that (a) bark beetle outbreaks under climate change would reduce net ecosystem carbon balance (NECB) and increase uncertainty and (b) these effects could be ameliorated by fuels management. We also examined the specific tree species dynamics—competition and release—that determined NECB response to bark beetle outbreaks. Our study area was the Lake Tahoe Basin (LTB), CA and NV, USA, an area of diverse forest types encompassing steep elevation and climatic gradients and representative of mixed-conifer forests throughout the western United States. We simulated climate change, bark beetles, wildfire, and fuels management using a landscape-scale stochastic model of disturbance and succession. We simulated the period 2010–2100 using downscaled climate projections. Recurring droughts generated conditions conducive to large-scale outbreaks; the resulting large and sustained outbreaks significantly increased the probability of LTB forests becoming C sources over decadal time scales, with slower-than-anticipated landscape-scale recovery. Tree species composition was substantially altered with a reduction in functional redundancy and productivity. Results indicate heightened uncertainty due to the synergistic influences of climate change and interacting disturbances. Our results further indicate that current fuel management practices will not be effective at reducing landscape-scale outbreak mortality. Our results provide critical insights into the interaction of drivers (bark beetles, wildfire, fuel management) that increase the risk of C loss and shifting community composition if bark beetle outbreaks become more frequent. Title: Interactions Among Fuel Management, Species Composition, Bark Beetles, and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin Author: Scheller, Robert M., Kretchun, Alec M., Loudermilk, E. Louise, Hurteau, Matthew D., Weisberg, Peter J., Skinner, Carl Year: 2017 Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their long-term interactions with future climate change are poorly understood. Droughts and the associated moisture deficit contribute to the onset of bark beetle outbreaks although outbreak extent and severity is dependent upon the density of host trees, wildfire, and forest management. Our objective was to estimate the effects of climate change and bark beetle outbreaks on ecosystem carbon dynamics over the next century in a western US forest. Specifically, we hypothesized that (a) bark beetle outbreaks under climate change would reduce net ecosystem carbon balance (NECB) and increase uncertainty and (b) these effects could be ameliorated by fuels management. We also examined the specific tree species dynamics—competition and release—that determined NECB response to bark beetle outbreaks. Our study area was the Lake Tahoe Basin (LTB), CA and NV, USA, an area of diverse forest types encompassing steep elevation and climatic gradients and representative of mixed-conifer forests throughout the western United States. We simulated climate change, bark beetles, wildfire, and fuels management using a landscape-scale stochastic model of disturbance and succession. We simulated the period 2010–2100 using downscaled climate projections. Recurring droughts generated conditions conducive to large-scale outbreaks; the resulting large and sustained outbreaks significantly increased the probability of LTB forests becoming C sources over decadal time scales, with slower-than-anticipated landscape-scale recovery. Tree species composition was substantially altered with a reduction in functional redundancy and productivity. Results indicate heightened uncertainty due to the synergistic influences of climate change and interacting disturbances. Our results further indicate that current fuel management practices will not be effective at reducing landscape-scale outbreak mortality. Our results provide critical insights into the interaction of drivers (bark beetles, wildfire, fuel management) that increase the risk of C loss and shifting community composition if bark beetle outbreaks become more frequent. Close

• 53. [Article] Community level impacts associated with the invasion of English ivy (Hedera spp.) in Forest Park: a look at the impacts of ivy on community composition and soil moisture.

  Invasive species degrade ecosystems by altering natural processes and decreasing the abundance and diversity of native flora. Communities with major fluctuations in resource supply allow invasive species ...

  Citation × Citation Citation Abstract Copy Title: Community level impacts associated with the invasion of English ivy (Hedera spp.) in Forest Park: a look at the impacts of ivy on community composition and soil moisture. Author: Copp, Sara Rose Year: 2014 Invasive species degrade ecosystems by altering natural processes and decreasing the abundance and diversity of native flora. Communities with major fluctuations in resource supply allow invasive species to exploit limiting resources making the community prone to invasion. In the Pacific Northwest, urban forests characterized with limited light and seasonally limited soil moisture are being dominated by nonnative English ivy (Hedera spp). Three observational studies were conducted in the Southern end of Forest Park within the Balch Creek Subwatershed in Portland, Oregon in order to understand 1) how English ivy changes over three growing seasons, 2) how the native understory composition responds to English ivy, 3) if the dominance of English ivy reduces soil moisture to neighboring plants, 4) how English ivy and two co-occurring native herbs (Hydrophyllum tenuipes and Vancouveria hexandra) physiologically respond to seasonal changes in soil moisture. Percent cover of the understory community was collected in both 2010 and 2013 growing seasons in 54 plots in order to understand the change in cover over time. Community response and the relationship with soil moisture was analyzed using percent cover of the understory community and associated environmental variables including soil moisture collected in 128 plots during the 2013 field season. Finally, 15 plots with co-occurring Hedera spp, H. tenuipes and V. hexandra were sampled for stomatal conductance, leaf water potential, and associated environmental variables. Results show ivy cover increases on average 14% between 2010 and 2013 while native understory cover increased on average < 1%. Once ivy forms dense cover over 44% there is a reduction of native richness, diversity and herb cover while also an increase in available soil moisture and deciduous canopy cover. There were disparate impacts to different functional groups and between species. As functional group, the herbaceous community was the most impacted by ivy invasion. The shrubs and fern community had a variable response to ivy invasion. Many of the fern and shrub species least impacted by ivy also had associations with high soil moisture and deciduous canopy cover. Finally, data suggests that ivy does not take advantage of seasonally limiting soil moisture to invade the understory community. This study indicates that English ivy is both efficient at water use and may have the ability to obtain water from distant locations throughout the forest. Once established, ivy has the ability to alter the community composition. Ivy removal and habitat restoration are essential in order to maintain and enhance biodiversity in Forest Park. Title: Community level impacts associated with the invasion of English ivy (Hedera spp.) in Forest Park: a look at the impacts of ivy on community composition and soil moisture. Author: Copp, Sara Rose Year: 2014 Invasive species degrade ecosystems by altering natural processes and decreasing the abundance and diversity of native flora. Communities with major fluctuations in resource supply allow invasive species to exploit limiting resources making the community prone to invasion. In the Pacific Northwest, urban forests characterized with limited light and seasonally limited soil moisture are being dominated by nonnative English ivy (Hedera spp). Three observational studies were conducted in the Southern end of Forest Park within the Balch Creek Subwatershed in Portland, Oregon in order to understand 1) how English ivy changes over three growing seasons, 2) how the native understory composition responds to English ivy, 3) if the dominance of English ivy reduces soil moisture to neighboring plants, 4) how English ivy and two co-occurring native herbs (Hydrophyllum tenuipes and Vancouveria hexandra) physiologically respond to seasonal changes in soil moisture. Percent cover of the understory community was collected in both 2010 and 2013 growing seasons in 54 plots in order to understand the change in cover over time. Community response and the relationship with soil moisture was analyzed using percent cover of the understory community and associated environmental variables including soil moisture collected in 128 plots during the 2013 field season. Finally, 15 plots with co-occurring Hedera spp, H. tenuipes and V. hexandra were sampled for stomatal conductance, leaf water potential, and associated environmental variables. Results show ivy cover increases on average 14% between 2010 and 2013 while native understory cover increased on average < 1%. Once ivy forms dense cover over 44% there is a reduction of native richness, diversity and herb cover while also an increase in available soil moisture and deciduous canopy cover. There were disparate impacts to different functional groups and between species. As functional group, the herbaceous community was the most impacted by ivy invasion. The shrubs and fern community had a variable response to ivy invasion. Many of the fern and shrub species least impacted by ivy also had associations with high soil moisture and deciduous canopy cover. Finally, data suggests that ivy does not take advantage of seasonally limiting soil moisture to invade the understory community. This study indicates that English ivy is both efficient at water use and may have the ability to obtain water from distant locations throughout the forest. Once established, ivy has the ability to alter the community composition. Ivy removal and habitat restoration are essential in order to maintain and enhance biodiversity in Forest Park. Close

• 54. [Article] Community assembly of benthic invertebrates on island-like marine hard substrata

  Most of the seafloor is soft sediment, so hard substrata are isolated and island-like. In this dissertation, I explore how species distribution patterns on isolated marine hard substrata resemble terrestrial ...

  Citation × Citation Citation Abstract Copy Title: Community assembly of benthic invertebrates on island-like marine hard substrata Author: Meyer, Kirstin Year: 2016 Most of the seafloor is soft sediment, so hard substrata are isolated and island-like. In this dissertation, I explore how species distribution patterns on isolated marine hard substrata resemble terrestrial island communities, drawing on classical island biogeography theory and assembly rules, and describe how benthic invertebrate communities assemble in these island-like habitats. Higher species richness occurred on larger substrata (dropstones and shipwrecks), paralleling terrestrial island communities. However, while larger islands have greater habitat diversity and primary productivity, marine hard substrata are simpler habitats. Greater elevation in the benthic boundary layer may expose fauna to faster current, higher food supply and larval flux. Substrata located closer together had more similar communities, another pattern that resembles terrestrial islands. Dropstone fauna had a clumped distribution, indicating that larvae may disperse among substrata located close together, resulting in similar communities. In Svalbard fjords, benthic megafaunal communities were significantly different between Arctic- and Atlantic-influenced fjords. Depth and temperature had the greatest influence, with the highest diversity occurring in cold Rijpfjorden and on the north Svalbard shelf. Recruitment in Svalbard fjords was spatially and temporally variable, with lower recruitment in Rijpfjorden than in Atlantic-influenced fjords and lower recruitment at greater depth. Most of the recruits in Svalbard fjords were fast-growing, poor-competitive opportunists. On shipwrecks, communities showed two mechanisms of colonization: mobile fauna with long-dispersing planktotrophic larvae, and encrusting fauna with lecithotrophic larvae. Encrusting species reproduce asexually to cover the wreck surface, and philopatry may build up dense populations, leading to uneven communities. On terrestrial islands, non-random co-occurrence is attributed to interspecific competition, but for marine substrata, there may not be a relationship. Fauna were distributed randomly on settlement plates in Svalbard fjords, even when interspecific competition was observed. On dropstones, some morphotypes co-occurred non-randomly in the absence of overgrowth competition. Non-random co-occurrence on isolated marine hard substrata may be a result of restricted larval dispersal (for pairs co-occurring less than by chance) or epibiontism (for pairs co-occurring more often than by chance). While species distribution patterns on island-like marine hard substrata resemble terrestrial islands, the mechanisms are not necessarily the same. Title: Community assembly of benthic invertebrates on island-like marine hard substrata Author: Meyer, Kirstin Year: 2016 Most of the seafloor is soft sediment, so hard substrata are isolated and island-like. In this dissertation, I explore how species distribution patterns on isolated marine hard substrata resemble terrestrial island communities, drawing on classical island biogeography theory and assembly rules, and describe how benthic invertebrate communities assemble in these island-like habitats. Higher species richness occurred on larger substrata (dropstones and shipwrecks), paralleling terrestrial island communities. However, while larger islands have greater habitat diversity and primary productivity, marine hard substrata are simpler habitats. Greater elevation in the benthic boundary layer may expose fauna to faster current, higher food supply and larval flux. Substrata located closer together had more similar communities, another pattern that resembles terrestrial islands. Dropstone fauna had a clumped distribution, indicating that larvae may disperse among substrata located close together, resulting in similar communities. In Svalbard fjords, benthic megafaunal communities were significantly different between Arctic- and Atlantic-influenced fjords. Depth and temperature had the greatest influence, with the highest diversity occurring in cold Rijpfjorden and on the north Svalbard shelf. Recruitment in Svalbard fjords was spatially and temporally variable, with lower recruitment in Rijpfjorden than in Atlantic-influenced fjords and lower recruitment at greater depth. Most of the recruits in Svalbard fjords were fast-growing, poor-competitive opportunists. On shipwrecks, communities showed two mechanisms of colonization: mobile fauna with long-dispersing planktotrophic larvae, and encrusting fauna with lecithotrophic larvae. Encrusting species reproduce asexually to cover the wreck surface, and philopatry may build up dense populations, leading to uneven communities. On terrestrial islands, non-random co-occurrence is attributed to interspecific competition, but for marine substrata, there may not be a relationship. Fauna were distributed randomly on settlement plates in Svalbard fjords, even when interspecific competition was observed. On dropstones, some morphotypes co-occurred non-randomly in the absence of overgrowth competition. Non-random co-occurrence on isolated marine hard substrata may be a result of restricted larval dispersal (for pairs co-occurring less than by chance) or epibiontism (for pairs co-occurring more often than by chance). While species distribution patterns on island-like marine hard substrata resemble terrestrial islands, the mechanisms are not necessarily the same. Close

• 55. [Article] Measuring and Managing Resistance and Resilience Under Climate Change in Northern Great Lake Forests (USA)

  Context: Climate change will have diverse and interacting effects on forests over the next century. One of the most pronounced effects may be a decline in resistance to chronic change and resilience to ...

  Citation × Citation Citation Abstract Copy Title: Measuring and Managing Resistance and Resilience Under Climate Change in Northern Great Lake Forests (USA) Author: Duveneck, Matthew Joshua, Scheller, Robert M. Year: 2016 Context: Climate change will have diverse and interacting effects on forests over the next century. One of the most pronounced effects may be a decline in resistance to chronic change and resilience to acute disturbances. The capacity for forests to persist and/or adapt to climate change remains largely unknown, in part because there is not broad agreement how to measure and apply resilience concepts. Objectives: We assessed the interactions of climate change, resistance, resilience, diversity, and alternative management of northern Great Lake forests. Methods: We simulated two landscapes (northern Minnesota and northern lower Michigan), three climate futures (current climate, a low emissions trajectory, and a high emissions trajectory), and four management regimes [business as usual, expanded forest reserves, modified silviculture, and climate suitable planting (CSP)]. We simulated each scenario with a forest landscape simulation model. We assessed resistance as the change in species composition over time. We assessed resilience and calculated an index of resilience that incorporated both recovery of pre-fire tree species composition and aboveground biomass within simulated burned areas. Results: Results indicate a positive relationship between diversity and resistance within low diversity areas. Simulations of the high emission climate future resulted in a decline in both resistance and resilience. Conclusions: Of the management regimes, the CSP regime resulted in some of the greatest resilience under climate change although our results suggest that differences in forest management are largely outweighed by the effects of climate change. Our results provide a framework for assessing resistance and resilience relevant and valuable to a broad array of ecological systems. Title: Measuring and Managing Resistance and Resilience Under Climate Change in Northern Great Lake Forests (USA) Author: Duveneck, Matthew Joshua, Scheller, Robert M. Year: 2016 Context: Climate change will have diverse and interacting effects on forests over the next century. One of the most pronounced effects may be a decline in resistance to chronic change and resilience to acute disturbances. The capacity for forests to persist and/or adapt to climate change remains largely unknown, in part because there is not broad agreement how to measure and apply resilience concepts. Objectives: We assessed the interactions of climate change, resistance, resilience, diversity, and alternative management of northern Great Lake forests. Methods: We simulated two landscapes (northern Minnesota and northern lower Michigan), three climate futures (current climate, a low emissions trajectory, and a high emissions trajectory), and four management regimes [business as usual, expanded forest reserves, modified silviculture, and climate suitable planting (CSP)]. We simulated each scenario with a forest landscape simulation model. We assessed resistance as the change in species composition over time. We assessed resilience and calculated an index of resilience that incorporated both recovery of pre-fire tree species composition and aboveground biomass within simulated burned areas. Results: Results indicate a positive relationship between diversity and resistance within low diversity areas. Simulations of the high emission climate future resulted in a decline in both resistance and resilience. Conclusions: Of the management regimes, the CSP regime resulted in some of the greatest resilience under climate change although our results suggest that differences in forest management are largely outweighed by the effects of climate change. Our results provide a framework for assessing resistance and resilience relevant and valuable to a broad array of ecological systems. Close

• 56. [Article] Interactive Physiological Responses of Nile Tilapia to Salinity- and Temperature-induced Stress: Quantifying the Regulation of Apoptosis and Cell Cycle Arrest in Oreochromis Niloticus

  Nile tilapia provide an ideal model to study the accumulation of climate change-induced stressors due to their habitat in tropical freshwater systems that are susceptible to salt water invasion and temperature ...

  Citation × Citation Citation Abstract Copy Title: Interactive Physiological Responses of Nile Tilapia to Salinity- and Temperature-induced Stress: Quantifying the Regulation of Apoptosis and Cell Cycle Arrest in Oreochromis Niloticus Author: McGuire, Charlee Year: 2017 Nile tilapia provide an ideal model to study the accumulation of climate change-induced stressors due to their habitat in tropical freshwater systems that are susceptible to salt water invasion and temperature fluctuation due to sea level rise. This study investigates the physiological responses of Nile tilapia to salinity- and temperature-induced stress to identify the interactive effects of simultaneous stressors on the cell cycle. Proteins indicative of cell cycle activity and arrest were quantified in the tissues of Nile tilapia exposed to various environmental conditions varying by temperature and salinity. Dot Blotting was utilized to measure Gadd45 while Western Blotting was used to confirm the identity of the protein. Results from previous investigations in the Buckley lab were also utilized to compare the expression patterns of Gadd45 to relevant cell activity proteins p53 and PCNA. Of the three proteins under scrutiny, a significant change in expression of p53 was observed for the interaction of salinity- and temperature- induced stress, while full strength saltwater treatment alone was found to have a significant impact on the expression of p53, Gadd45 and PCNA. These findings can be used in collaboration with existing studies to describe the coordination of apoptotic pathways in Nile tilapia and other non-mammalian species, as well as to create policy on how to conserve this important species effectively both in the wild and in fisheries for aquaculture, commercial and public health initiatives in response to global climate change. Title: Interactive Physiological Responses of Nile Tilapia to Salinity- and Temperature-induced Stress: Quantifying the Regulation of Apoptosis and Cell Cycle Arrest in Oreochromis Niloticus Author: McGuire, Charlee Year: 2017 Nile tilapia provide an ideal model to study the accumulation of climate change-induced stressors due to their habitat in tropical freshwater systems that are susceptible to salt water invasion and temperature fluctuation due to sea level rise. This study investigates the physiological responses of Nile tilapia to salinity- and temperature-induced stress to identify the interactive effects of simultaneous stressors on the cell cycle. Proteins indicative of cell cycle activity and arrest were quantified in the tissues of Nile tilapia exposed to various environmental conditions varying by temperature and salinity. Dot Blotting was utilized to measure Gadd45 while Western Blotting was used to confirm the identity of the protein. Results from previous investigations in the Buckley lab were also utilized to compare the expression patterns of Gadd45 to relevant cell activity proteins p53 and PCNA. Of the three proteins under scrutiny, a significant change in expression of p53 was observed for the interaction of salinity- and temperature- induced stress, while full strength saltwater treatment alone was found to have a significant impact on the expression of p53, Gadd45 and PCNA. These findings can be used in collaboration with existing studies to describe the coordination of apoptotic pathways in Nile tilapia and other non-mammalian species, as well as to create policy on how to conserve this important species effectively both in the wild and in fisheries for aquaculture, commercial and public health initiatives in response to global climate change. Close

• 57. [Article] The Dynamics of a Fishery When Faced with the Aquaculture Dilemma

  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: The Dynamics of a Fishery When Faced with the Aquaculture Dilemma Author: Asche, Frank, Cojocaru, Andreea L. 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: The Dynamics of a Fishery When Faced with the Aquaculture Dilemma Author: Asche, Frank, Cojocaru, Andreea L. 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

• 58. [Article] Design and Synthesis of Novel Chloroquine-based Antimalarials

  Malaria is an infectious, often fatal disease that afflicts nearly 200 million people every year. The disease, characterized by recurring and extreme flu-like symptoms, is caused by the protozoan parasite ...

  Citation × Citation Citation Abstract Copy Title: Design and Synthesis of Novel Chloroquine-based Antimalarials Author: Murphy, Kevin Vincent Year: 2015 Malaria is an infectious, often fatal disease that afflicts nearly 200 million people every year. The disease, characterized by recurring and extreme flu-like symptoms, is caused by the protozoan parasite Plasmodium falciparum. Victims usually contract the disease through a mosquito vector. Chloroquine is a chemotherapeutic that was introduced in the 1940s. For many years the drug was the foremost treatment of malaria, being effective and producing few side effects. Unfortunately, tolerance to chloroquine developed when the parasite evolved a resistance mechanism. Newer drugs have been developed and implemented, but these medicines also show a decreasing effect with continued administration. It is imperative that a new pipeline of drugs be developed in order to combat the disease and anticipated resistance. Reversed chloroquines are a new class of multiple-ligand compounds that are active against chloroquine-sensitive and chloroquine-resistance malaria species. This thesis describes research targeted at the modification of lead reversed chloroquine molecules to discover new and effective moieties, as well as to improve pharmacokinetic-related properties. An especial emphasis of this project is the addition of a sulfonamide functional group to a reversed chloroquine. Preliminary evidence indicates that this is a promising direction for this line of research. Brief discussions of some reversed chloroquine characterization studies are included in appendices. Title: Design and Synthesis of Novel Chloroquine-based Antimalarials Author: Murphy, Kevin Vincent Year: 2015 Malaria is an infectious, often fatal disease that afflicts nearly 200 million people every year. The disease, characterized by recurring and extreme flu-like symptoms, is caused by the protozoan parasite Plasmodium falciparum. Victims usually contract the disease through a mosquito vector. Chloroquine is a chemotherapeutic that was introduced in the 1940s. For many years the drug was the foremost treatment of malaria, being effective and producing few side effects. Unfortunately, tolerance to chloroquine developed when the parasite evolved a resistance mechanism. Newer drugs have been developed and implemented, but these medicines also show a decreasing effect with continued administration. It is imperative that a new pipeline of drugs be developed in order to combat the disease and anticipated resistance. Reversed chloroquines are a new class of multiple-ligand compounds that are active against chloroquine-sensitive and chloroquine-resistance malaria species. This thesis describes research targeted at the modification of lead reversed chloroquine molecules to discover new and effective moieties, as well as to improve pharmacokinetic-related properties. An especial emphasis of this project is the addition of a sulfonamide functional group to a reversed chloroquine. Preliminary evidence indicates that this is a promising direction for this line of research. Brief discussions of some reversed chloroquine characterization studies are included in appendices. Close

• 59. [Article] Mimicking the Bioactivation of the Antitubercular Agent Ethionamide using Peracetic Acid

  Tuberculosis still affects a large number of the world’s population and drug resistance is becoming an increasing problem. Second line of defense antitubercular agents such as ethionamide (ETD) are thus ...

  Citation × Citation Citation Abstract Copy Title: Mimicking the Bioactivation of the Antitubercular Agent Ethionamide using Peracetic Acid Author: Logan, Isabelle E. Year: 2016 Tuberculosis still affects a large number of the world’s population and drug resistance is becoming an increasing problem. Second line of defense antitubercular agents such as ethionamide (ETD) are thus becoming increasingly important. Since ethionamide is a prodrug, its metabolization through oxidation by a monooxygenase was successfully mimicked using peracetic acid. The reaction was found to be biphasic, with a fast initial oxidation to yield ethionamide sulfoxide (ETD-SO), which was relatively stable and was successfully isolated. We derived a bimolecular rate constant of 3.08 ± 0.72 × 102 M-1 s-1 for this initial phase of the reaction. In the slow second phase, further oxidation yielded 2-ethylisonicotinamide, where zero order kinetics were observed. Electrospray ionization mass spectroscopy (ESI-MS) was used to determine the identities of the products. No sulfinic nor sulfonic acids were detected, indicating that the sulfur-carbon bond was cleaved at the sulfenic acid stage, resulting in the release of an unstable sulfur monoxide species, which dimerized in solution to form dithionite. Title: Mimicking the Bioactivation of the Antitubercular Agent Ethionamide using Peracetic Acid Author: Logan, Isabelle E. Year: 2016 Tuberculosis still affects a large number of the world’s population and drug resistance is becoming an increasing problem. Second line of defense antitubercular agents such as ethionamide (ETD) are thus becoming increasingly important. Since ethionamide is a prodrug, its metabolization through oxidation by a monooxygenase was successfully mimicked using peracetic acid. The reaction was found to be biphasic, with a fast initial oxidation to yield ethionamide sulfoxide (ETD-SO), which was relatively stable and was successfully isolated. We derived a bimolecular rate constant of 3.08 ± 0.72 × 102 M-1 s-1 for this initial phase of the reaction. In the slow second phase, further oxidation yielded 2-ethylisonicotinamide, where zero order kinetics were observed. Electrospray ionization mass spectroscopy (ESI-MS) was used to determine the identities of the products. No sulfinic nor sulfonic acids were detected, indicating that the sulfur-carbon bond was cleaved at the sulfenic acid stage, resulting in the release of an unstable sulfur monoxide species, which dimerized in solution to form dithionite. Close

• 60. [Article] Novel Application of Simple Molybdates: Catalytic Hydrolysis of an Organophosphate Neurotoxin Under Mild Aqueous Conditions

  A novel protocol for hydrolyzing phosphonothioate neurotoxins has been developed that uses a readily available, inexpensive and non-toxic molybdate (MoO42−). The target organophosphate is O,S-diethylphenyl ...

  Citation × Citation Citation Abstract Copy Title: Novel Application of Simple Molybdates: Catalytic Hydrolysis of an Organophosphate Neurotoxin Under Mild Aqueous Conditions Author: Kuo, Louis Y., Dill, Kristina M., Shari'ati, Yusef A., Bright, Emily K., McCormick, Theresa Year: 2017 A novel protocol for hydrolyzing phosphonothioate neurotoxins has been developed that uses a readily available, inexpensive and non-toxic molybdate (MoO42−). The target organophosphate is O,S-diethylphenyl phosphonothioate (1), a model compound that has served as an analog of the chemical warfare agent VX. Molybdate-mediated hydrolysis of 1 proceeds at room temperature (pH ∼ 7.5) and yields a relatively safe phosphonate product through P-S specific scission. This is the first report of utilizing the molybdate, MoO42−, to degrade an organophosphate neurotoxin with turnover. A ΔS‡ of −81.5 J/mol·K (−19.5 cal/mol·K) indicates a bimolecular process, and 18O-labeling studies show no oxygen exchange of 1 throughout the hydrolysis by MoO42−(aq). We hypothesize primarily the monomeric molybdate is the active species at pH 7.5 where a SN2(P) mechanism takes place. Density functional theory methods suggest the molybdate oxoanion serves as the nucleophile to attack phosphonothioate 1 to form a molybdate-phosphonate anhydride that subsequently hydrolyzes to the starting molybdate and phenylethyl phosphonate. Title: Novel Application of Simple Molybdates: Catalytic Hydrolysis of an Organophosphate Neurotoxin Under Mild Aqueous Conditions Author: Kuo, Louis Y., Dill, Kristina M., Shari'ati, Yusef A., Bright, Emily K., McCormick, Theresa Year: 2017 A novel protocol for hydrolyzing phosphonothioate neurotoxins has been developed that uses a readily available, inexpensive and non-toxic molybdate (MoO42−). The target organophosphate is O,S-diethylphenyl phosphonothioate (1), a model compound that has served as an analog of the chemical warfare agent VX. Molybdate-mediated hydrolysis of 1 proceeds at room temperature (pH ∼ 7.5) and yields a relatively safe phosphonate product through P-S specific scission. This is the first report of utilizing the molybdate, MoO42−, to degrade an organophosphate neurotoxin with turnover. A ΔS‡ of −81.5 J/mol·K (−19.5 cal/mol·K) indicates a bimolecular process, and 18O-labeling studies show no oxygen exchange of 1 throughout the hydrolysis by MoO42−(aq). We hypothesize primarily the monomeric molybdate is the active species at pH 7.5 where a SN2(P) mechanism takes place. Density functional theory methods suggest the molybdate oxoanion serves as the nucleophile to attack phosphonothioate 1 to form a molybdate-phosphonate anhydride that subsequently hydrolyzes to the starting molybdate and phenylethyl phosphonate. Close

• 61. [Article] Green Roofs Support a Wide Diversity of Collembola in Urban Portland, Oregon

  Green roofs can help address habitat loss in urban areas by supporting plant and animal communities. To determine whether green roofs can support collembola biodiversity, we collected pitfall samples from ...

  Citation × Citation Citation Abstract Copy Title: Green Roofs Support a Wide Diversity of Collembola in Urban Portland, Oregon Author: Miziolek, Konrad Year: 2015 Green roofs can help address habitat loss in urban areas by supporting plant and animal communities. To determine whether green roofs can support collembola biodiversity, we collected pitfall samples from April-June 2015 on two extensive and two intensive green roofs in urban Portland, Oregon. Twenty morphospecies were found across the roofs, indicating that green roofs support a diversity of collembola taxa. The intensive roofs were more biodiverse than the extensive, though roof type may not be the most significant factor affecting collembolan biodiversity. Each of the four green roofs were characterized by a different and unique most dominant morphospecies, and, indeed, each roof possessed a different set of top-three abundant collembola taxa. While green roofs support moderate collembola diversity, preserving natural habitat is important to maintain species richness. Title: Green Roofs Support a Wide Diversity of Collembola in Urban Portland, Oregon Author: Miziolek, Konrad Year: 2015 Green roofs can help address habitat loss in urban areas by supporting plant and animal communities. To determine whether green roofs can support collembola biodiversity, we collected pitfall samples from April-June 2015 on two extensive and two intensive green roofs in urban Portland, Oregon. Twenty morphospecies were found across the roofs, indicating that green roofs support a diversity of collembola taxa. The intensive roofs were more biodiverse than the extensive, though roof type may not be the most significant factor affecting collembolan biodiversity. Each of the four green roofs were characterized by a different and unique most dominant morphospecies, and, indeed, each roof possessed a different set of top-three abundant collembola taxa. While green roofs support moderate collembola diversity, preserving natural habitat is important to maintain species richness. Close

• 62. [Article] A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick

  Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern ...

  Citation × Citation Citation Abstract Copy Title: A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick Author: Smith, Todd A., Driscoll, Timothy, Gillespie, Joseph J., Raghavan, Rahul Year: 2015 Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern tick-associated rash illness. Blood-feeding insects (Class Insecta) depend on bacterial endosymbionts to provide vitamins and cofactors that are scarce in blood. It is unclear how this deficiency is compensated in ticks (Class Arachnida) that feed exclusively on mammalian blood. A bacterium related to Coxiella burnetii, the agent of humanQfever,has been observedpreviously within cells of A. americanum. Eliminating this bacterium (CLEAA, Coxiella-like endosymbiont of A. americanum) with antibiotics reduced tick fecundity, indicating that it is an essential endosymbiont. In an effort to determine its role within this symbiosis, we sequenced the CLEAA genome. While highly reduced (656,901 bp) compared with C. burnetii (1,995,281 bp), the CLEAA genome encodes most major vitamin and cofactor biosynthesis pathways, implicatingCLEAAas a vitamin provisioningendosymbiont. In contrast,CLEAAlacks any recognizable virulencegenes, indicating that it is not a pathogen despite its presence in tick salivary glands. As both C. burnetii and numerous “Coxiella-like bacteria” have been reported from several species of ticks,we determined the evolutionary relationship between the two bacteria. Phylogeny estimation revealed that CLEAA is a close relative of C. burnetii,but was not derived from it. Our results are important for strategies geared toward controlling A. americanum and the pathogens it vectors, and also contribute novel information regarding the metabolic interdependencies of ticks and their nutrient-provisioning endosymbionts. Title: A Coxiella-Like Endosymbiont Is a PotentialVitamin Source for the Lone Star Tick Author: Smith, Todd A., Driscoll, Timothy, Gillespie, Joseph J., Raghavan, Rahul Year: 2015 Amblyomma americanum (Lone star tick) is an important disease vector in the United States. It transmits several human pathogens, including the agents of human monocytic ehrlichiosis, tularemia, and southern tick-associated rash illness. Blood-feeding insects (Class Insecta) depend on bacterial endosymbionts to provide vitamins and cofactors that are scarce in blood. It is unclear how this deficiency is compensated in ticks (Class Arachnida) that feed exclusively on mammalian blood. A bacterium related to Coxiella burnetii, the agent of humanQfever,has been observedpreviously within cells of A. americanum. Eliminating this bacterium (CLEAA, Coxiella-like endosymbiont of A. americanum) with antibiotics reduced tick fecundity, indicating that it is an essential endosymbiont. In an effort to determine its role within this symbiosis, we sequenced the CLEAA genome. While highly reduced (656,901 bp) compared with C. burnetii (1,995,281 bp), the CLEAA genome encodes most major vitamin and cofactor biosynthesis pathways, implicatingCLEAAas a vitamin provisioningendosymbiont. In contrast,CLEAAlacks any recognizable virulencegenes, indicating that it is not a pathogen despite its presence in tick salivary glands. As both C. burnetii and numerous “Coxiella-like bacteria” have been reported from several species of ticks,we determined the evolutionary relationship between the two bacteria. Phylogeny estimation revealed that CLEAA is a close relative of C. burnetii,but was not derived from it. Our results are important for strategies geared toward controlling A. americanum and the pathogens it vectors, and also contribute novel information regarding the metabolic interdependencies of ticks and their nutrient-provisioning endosymbionts. Close

• 63. [Article] Price Transmission in Indian Shrimp Exports

  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: Price Transmission in Indian Shrimp Exports Author: Achoth, Lalith, Krishnan, Dr. Mahadeva, Qureshi, Neha 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: Price Transmission in Indian Shrimp Exports Author: Achoth, Lalith, Krishnan, Dr. Mahadeva, Qureshi, Neha 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

• 64. [Article] Sex Determination in Zebrafish: Genetics of Sex and wnt4a

  Effective reproduction is essential for species survival. Sexual reproduction depends upon functional gonads and reproductive ducts. Zebrafish (Danio rerio) is a popular model organism, but the genetic ...

  Citation × Citation Citation Abstract Copy Title: Sex Determination in Zebrafish: Genetics of Sex and wnt4a Author: High, Samantha Year: 2016 Effective reproduction is essential for species survival. Sexual reproduction depends upon functional gonads and reproductive ducts. Zebrafish (Danio rerio) is a popular model organism, but the genetic basis of zebrafish sex determination, gonad development, and reproductive tract development are not fully understood, and understanding this basis could inform about the evolutionary conservation of these genes and the use of zebrafish to investigate and treat reproductive diseases. In chapter I, I give a overview of sex determination systems, gonad development, and reproductive duct development in mammals and fish, and ask how sex is determined and how reproductive ducts develop in zebrafish. In chapter II, I used genome wide association studies (GWAS) to investigate if the genetic basis of sex determination in a variety of zebrafish strains -- two ‘wild-type’ strains cultured for about 30 years in the lab, and four ‘natural’ strains, wild-type strains isolated directly or recently from nature in India -- and identified a sex-associated region on zebrafish chromosome 4 in natural zebrafish strains that was lacking in the lab strains. In chapter III, I investigated whether or not wnt4a is important for zebrafish ovarian development, and found that wnt4a is expressed in the early bipotential gonad and that loss of wnt4a results in male-biased sex ratios, indicating that wnt4a is important for zebrafish ovarian development. In chapter IV, I investigated whether or not wnt4a is important for male reproductive duct development, and found that loss of wnt4a slows the formation of male reproductive ducts and prevents the male fused ducti deferens from connecting to the genital orifice in zebrafish males. Results further showed that wnt4a is expressed in tissue around the site where this connection should occur before and after the connection is formed, revealing a novel wnt4a phenotype in zebrafish that hasn’t been seen thus far, and indicating that wnt4a is necessary for proper male reproductive duct development in zebrafish. This dissertation contains both published and unpublished co-authored material. Title: Sex Determination in Zebrafish: Genetics of Sex and wnt4a Author: High, Samantha Year: 2016 Effective reproduction is essential for species survival. Sexual reproduction depends upon functional gonads and reproductive ducts. Zebrafish (Danio rerio) is a popular model organism, but the genetic basis of zebrafish sex determination, gonad development, and reproductive tract development are not fully understood, and understanding this basis could inform about the evolutionary conservation of these genes and the use of zebrafish to investigate and treat reproductive diseases. In chapter I, I give a overview of sex determination systems, gonad development, and reproductive duct development in mammals and fish, and ask how sex is determined and how reproductive ducts develop in zebrafish. In chapter II, I used genome wide association studies (GWAS) to investigate if the genetic basis of sex determination in a variety of zebrafish strains -- two ‘wild-type’ strains cultured for about 30 years in the lab, and four ‘natural’ strains, wild-type strains isolated directly or recently from nature in India -- and identified a sex-associated region on zebrafish chromosome 4 in natural zebrafish strains that was lacking in the lab strains. In chapter III, I investigated whether or not wnt4a is important for zebrafish ovarian development, and found that wnt4a is expressed in the early bipotential gonad and that loss of wnt4a results in male-biased sex ratios, indicating that wnt4a is important for zebrafish ovarian development. In chapter IV, I investigated whether or not wnt4a is important for male reproductive duct development, and found that loss of wnt4a slows the formation of male reproductive ducts and prevents the male fused ducti deferens from connecting to the genital orifice in zebrafish males. Results further showed that wnt4a is expressed in tissue around the site where this connection should occur before and after the connection is formed, revealing a novel wnt4a phenotype in zebrafish that hasn’t been seen thus far, and indicating that wnt4a is necessary for proper male reproductive duct development in zebrafish. This dissertation contains both published and unpublished co-authored material. Close

• 65. [Article] Effectiveness of Fuel Treatments for Mitigating Wildfire Risk and Sequestering Forest Carbon: A Case Study in the Lake Tahoe Basin

  Fuel-reduction treatments are used extensively to reduce wildfire risk and restore forest diversity and function. In the near future, increasing regulation of carbon (C) emissions may force forest managers ...

  Citation × Citation Citation Abstract Copy Title: Effectiveness of Fuel Treatments for Mitigating Wildfire Risk and Sequestering Forest Carbon: A Case Study in the Lake Tahoe Basin Author: Loudermilk, E. Louise, Stanton, Alison, Scheller, Robert M., Dilts, Thomas E., Weisberg, Peter J., Skinner, Carl, Yang, Jian Year: 2014 Fuel-reduction treatments are used extensively to reduce wildfire risk and restore forest diversity and function. In the near future, increasing regulation of carbon (C) emissions may force forest managers to balance the use of fuel treatments for reducing wildfire risk against an alternative goal of C sequestration. The objective of this study was to evaluate how long-term fuel treatments mitigate wildfires and affect forest C. For the Lake Tahoe Basin in the central Sierra Nevada, USA, fuel treatment efficiency was explored with a landscape-scale simulation model, LANDIS-II, using five fuel treatment scenarios and two (contemporary and potential future) fire regimes. Treatment scenarios included applying a combination of light (hand) and moderate (mechanical) forest thinning continuously through time and transitioning from these prescriptions to a more mid-seral thinning prescription, both on a 15 and 30 year rotation interval. In the last scenario, fuel treatments were isolated to around the lake shore (nearby urban settlement) to simulate a low investment alternative were future resources may be limited. Results indicated that the forest will remain a C sink regardless of treatment or fire regime simulated, due to the landscape legacy of historic logging. Achievement of a net C gain required decades with intensive treatment and depended on wildfire activity: Fuel treatments were more effective in a more active fire environment, where the interface between wildfires and treatment areas increased and caused net C gain earlier than as compared to our scenarios with less wildfire activity. Fuel treatments were most effective when continuously applied and strategically placed in high ignition areas. Treatment type and re-application interval were less influential at the landscape scale, but had notable effects on species dynamics within management units. Treatments created more diverse forest conditions by shifting dominance patterns to a more mixed conifer system, with a higher proportion of fire-tolerant species. We demonstrated that a small amount of wildfire on the landscape resulted in significant changes in the C pool, and that strategically placed fuel treatments substantially reduced wildfire risk, increased fire resiliency of the forest, and is beneficial for long-term C management. Implications for landscape management included consideration for prioritization of treatment areas and creating ideal re-entry schedules that meet logistic, safety, and conservation goals. In forests with a concentrated wildland urban interface, fuel treatments may be vital for ensuring human welfare and enhancing forest integrity in a fire-prone future. Title: Effectiveness of Fuel Treatments for Mitigating Wildfire Risk and Sequestering Forest Carbon: A Case Study in the Lake Tahoe Basin Author: Loudermilk, E. Louise, Stanton, Alison, Scheller, Robert M., Dilts, Thomas E., Weisberg, Peter J., Skinner, Carl, Yang, Jian Year: 2014 Fuel-reduction treatments are used extensively to reduce wildfire risk and restore forest diversity and function. In the near future, increasing regulation of carbon (C) emissions may force forest managers to balance the use of fuel treatments for reducing wildfire risk against an alternative goal of C sequestration. The objective of this study was to evaluate how long-term fuel treatments mitigate wildfires and affect forest C. For the Lake Tahoe Basin in the central Sierra Nevada, USA, fuel treatment efficiency was explored with a landscape-scale simulation model, LANDIS-II, using five fuel treatment scenarios and two (contemporary and potential future) fire regimes. Treatment scenarios included applying a combination of light (hand) and moderate (mechanical) forest thinning continuously through time and transitioning from these prescriptions to a more mid-seral thinning prescription, both on a 15 and 30 year rotation interval. In the last scenario, fuel treatments were isolated to around the lake shore (nearby urban settlement) to simulate a low investment alternative were future resources may be limited. Results indicated that the forest will remain a C sink regardless of treatment or fire regime simulated, due to the landscape legacy of historic logging. Achievement of a net C gain required decades with intensive treatment and depended on wildfire activity: Fuel treatments were more effective in a more active fire environment, where the interface between wildfires and treatment areas increased and caused net C gain earlier than as compared to our scenarios with less wildfire activity. Fuel treatments were most effective when continuously applied and strategically placed in high ignition areas. Treatment type and re-application interval were less influential at the landscape scale, but had notable effects on species dynamics within management units. Treatments created more diverse forest conditions by shifting dominance patterns to a more mixed conifer system, with a higher proportion of fire-tolerant species. We demonstrated that a small amount of wildfire on the landscape resulted in significant changes in the C pool, and that strategically placed fuel treatments substantially reduced wildfire risk, increased fire resiliency of the forest, and is beneficial for long-term C management. Implications for landscape management included consideration for prioritization of treatment areas and creating ideal re-entry schedules that meet logistic, safety, and conservation goals. In forests with a concentrated wildland urban interface, fuel treatments may be vital for ensuring human welfare and enhancing forest integrity in a fire-prone future. Close

• 66. [Article] Walking Behavior of Zoo Elephants: Associations between GPS-Measured Daily Walking Distances and Environmental Factors, Social Factors, and Welfare Indicators

  Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important ...

  Citation × Citation Citation Abstract Copy Title: Walking Behavior of Zoo Elephants: Associations between GPS-Measured Daily Walking Distances and Environmental Factors, Social Factors, and Welfare Indicators Author: Holdgate, Matthew Robert, Meehan, Cheryl L., Hogan, Jennifer N., Miller, Lance J., Soltis, Josesph, Andrews, Jeff, Shepherdson, David J. Year: 2016 Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important to elephant welfare, and that zoo elephant exhibits should be designed to allow for more walking. Our study is the first to address this suggestion empirically by measuring the mean daily walking distance of elephants in North American zoos, determining the factors that are associated with variations in walking distance, and testing for associations between walking and welfare indicators. We used anklets equipped with GPS data loggers to measure outdoor daily walking distance in 56 adult female African (n = 33) and Asian (n = 23) elephants housed in 30 North American zoos. We collected 259 days of data and determined associations between distance walked and social, housing, management, and demographic factors. Elephants walked an average of 5.3 km/day with no significant difference between species. In our multivariable model, more diverse feeding regimens were correlated with increased walking, and elephants who were fed on a temporally unpredictable feeding schedule walked 1.29 km/day more than elephants fed on a predictable schedule. Distance walked was also positively correlated with an increase in the number of social groupings and negatively correlated with age. We found a small but significant negative correlation between distance walked and nighttime Space Experience, but no other associations between walking distances and exhibit size were found. Finally, distance walked was not related to health or behavioral outcomes including foot health, joint health, body condition, and the performance of stereotypic behavior, suggesting that more research is necessary to determine explicitly how differences in walking may impact elephant welfare. Title: Walking Behavior of Zoo Elephants: Associations between GPS-Measured Daily Walking Distances and Environmental Factors, Social Factors, and Welfare Indicators Author: Holdgate, Matthew Robert, Meehan, Cheryl L., Hogan, Jennifer N., Miller, Lance J., Soltis, Josesph, Andrews, Jeff, Shepherdson, David J. Year: 2016 Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important to elephant welfare, and that zoo elephant exhibits should be designed to allow for more walking. Our study is the first to address this suggestion empirically by measuring the mean daily walking distance of elephants in North American zoos, determining the factors that are associated with variations in walking distance, and testing for associations between walking and welfare indicators. We used anklets equipped with GPS data loggers to measure outdoor daily walking distance in 56 adult female African (n = 33) and Asian (n = 23) elephants housed in 30 North American zoos. We collected 259 days of data and determined associations between distance walked and social, housing, management, and demographic factors. Elephants walked an average of 5.3 km/day with no significant difference between species. In our multivariable model, more diverse feeding regimens were correlated with increased walking, and elephants who were fed on a temporally unpredictable feeding schedule walked 1.29 km/day more than elephants fed on a predictable schedule. Distance walked was also positively correlated with an increase in the number of social groupings and negatively correlated with age. We found a small but significant negative correlation between distance walked and nighttime Space Experience, but no other associations between walking distances and exhibit size were found. Finally, distance walked was not related to health or behavioral outcomes including foot health, joint health, body condition, and the performance of stereotypic behavior, suggesting that more research is necessary to determine explicitly how differences in walking may impact elephant welfare. Close

• 67. [Article] Increased Taxonomic and Functional Similarity Does Not Increase the Trophic Similarity of Communities

  Aim: Despite a long-standing research interest in the association between the biodiversity (i.e. taxonomic and functional composition) and trophic structure of communities, our understanding of the relationship ...

  Citation × Citation Citation Abstract Copy Title: Increased Taxonomic and Functional Similarity Does Not Increase the Trophic Similarity of Communities Author: Pool, Thomas K., Cucherousset, Julien, Boulêtreau, Stéphanie, Villéger, Sébastien, Strecker, Angela L., Grenouillet, Gaël Year: 2015 Aim: Despite a long-standing research interest in the association between the biodiversity (i.e. taxonomic and functional composition) and trophic structure of communities, our understanding of the relationship remains limited. Community assembly theory predicts that niche partitioning will result in communities with a diverse array of functional traits, which in turn may facilitate a correspondingly diverse array of trophic interactions that define the trophic niche of those communities. The aim of our study is to test this prediction. Methods: We built a database composed of functional traits and stable isotope values (δ13C and δ15N) for 63 freshwater fish communities containing 109 species in 34 lentic and 29 lotic ecosystems. First, using linear mixed models (i.e. an alpha-diversity approach), we tested whether the taxonomic diversity of communities was positively associated with their functional diversity and if their functional diversity was positively associated with their trophic diversity. Second, we assessed the taxonomic, functional and trophic similarity of communities using multiple regression on distance matrices (MRM) and their respective ‘turnover’ and ‘nestedness-resultant’ components to test if the taxonomic similarity of communities was positively correlated with their functional similarity and if their functional similarity was positively associated with their trophic similarity (i.e. a beta-diversity approach). Results: We found that the functional diversity of communities increased as their taxonomic diversity increased. Similarly, the trophic diversity of communities increased as their functional diversity increased. The pairwise taxonomic and functional similarity of communities were also positively associated, but there was a weak relationship between the functional and trophic similarities of communities. Main conclusions: Our study demonstrates that communities with similar functional characteristics can have disparate food web structures, suggesting that additional site-specific factors influence community variation in trophic niche geometry. Determining the relative importance of functional characteristics and site-specific factors in shaping trophic interactions is crucial for a better understanding of how future species loss and species introductions will affect food web structure and ecosystem functioning. Title: Increased Taxonomic and Functional Similarity Does Not Increase the Trophic Similarity of Communities Author: Pool, Thomas K., Cucherousset, Julien, Boulêtreau, Stéphanie, Villéger, Sébastien, Strecker, Angela L., Grenouillet, Gaël Year: 2015 Aim: Despite a long-standing research interest in the association between the biodiversity (i.e. taxonomic and functional composition) and trophic structure of communities, our understanding of the relationship remains limited. Community assembly theory predicts that niche partitioning will result in communities with a diverse array of functional traits, which in turn may facilitate a correspondingly diverse array of trophic interactions that define the trophic niche of those communities. The aim of our study is to test this prediction. Methods: We built a database composed of functional traits and stable isotope values (δ13C and δ15N) for 63 freshwater fish communities containing 109 species in 34 lentic and 29 lotic ecosystems. First, using linear mixed models (i.e. an alpha-diversity approach), we tested whether the taxonomic diversity of communities was positively associated with their functional diversity and if their functional diversity was positively associated with their trophic diversity. Second, we assessed the taxonomic, functional and trophic similarity of communities using multiple regression on distance matrices (MRM) and their respective ‘turnover’ and ‘nestedness-resultant’ components to test if the taxonomic similarity of communities was positively correlated with their functional similarity and if their functional similarity was positively associated with their trophic similarity (i.e. a beta-diversity approach). Results: We found that the functional diversity of communities increased as their taxonomic diversity increased. Similarly, the trophic diversity of communities increased as their functional diversity increased. The pairwise taxonomic and functional similarity of communities were also positively associated, but there was a weak relationship between the functional and trophic similarities of communities. Main conclusions: Our study demonstrates that communities with similar functional characteristics can have disparate food web structures, suggesting that additional site-specific factors influence community variation in trophic niche geometry. Determining the relative importance of functional characteristics and site-specific factors in shaping trophic interactions is crucial for a better understanding of how future species loss and species introductions will affect food web structure and ecosystem functioning. Close

• 68. [Article] Investigation of Ambient Reactive Nitrogen Emissions Sources and Deposition in the Columbia River Gorge National Scenic Area

  Anthropogenic reactive nitrogen is emitted into the atmosphere from fossil fuel combustion (nitrogen oxides) and agricultural activities (nitrogen oxides and ammonia). Nitrogen oxide emissions have long ...

  Citation × Citation Citation Abstract Copy Title: Investigation of Ambient Reactive Nitrogen Emissions Sources and Deposition in the Columbia River Gorge National Scenic Area Author: Mainord, Jacinda L. Year: 2017 Anthropogenic reactive nitrogen is emitted into the atmosphere from fossil fuel combustion (nitrogen oxides) and agricultural activities (nitrogen oxides and ammonia). Nitrogen oxide emissions have long been controlled for their role in ambient air pollution and human health effects. However, reactive nitrogen deposition is less understood even though it can play a significant role in altering biodiversity, impairing ecosystem and biogeochemical function and degrading cultural artifacts. Although nitrogen deposition is a natural part of biogeochemical cycling, many ecosystems across the United States are at risk of exceeding the critical nitrogen deposition load. While nitrogen oxides are routinely measured in urban areas, far less is known in non-urban landscapes where ecosystems may be especially sensitive. Regional chemical transport models have been used to predict the impacts of ambient reactive nitrogen deposition in non-urban areas, but models have difficulty simulating reactive nitrogen due to poorly quantified emissions, especially from the agricultural sector. My research explores the speciated deposition of reactive nitrogen through monitoring and modeling in the unique field setting of the 150 mile Columbia River Gorge (CRG) located along the border of Oregon and Washington. This site is ideally suited for this investigation due to the large sources of reactive nitrogen at either end of the CRG and unique seasonally driven channel wind flow. Seasonally driven wind allowed us to look at the reactive nitrogen emissions flowing through the CRG to assess ambient the reactive nitrogen partitioning and deposition gradient. Using data collected by the United States Forest Service to control ambient haze in the CRG and our co-located nitrogen oxides (NOx) gas analyzer, we first characterized the influence of seasonal, bimodal wind distributions on the spatial distribution of reactive nitrogen. We found that during winter months with predominantly easterly winds, particulate nitrate and ammonium and gas-phase nitrogen dioxide levels create a gradient from the eastern end to the western end. Particulate nitrate and sulfate mass concentrations influence the CRG gradient during summer months with predominantly western winds. We also found that the magnitude of the impact from east is greater than the magnitude of impact from the west. When we compared our observations to regional chemistry transport models, we found that models are significantly under-predicting levels of reactive nitrogen in the CRG. This bias is not isolated to a single station within the Gorge, but throughout the whole Columbia Basin. Our results indicate that there are under-represented emissions in the region leading to this bias. Partly due to the bias in reactive N gas-phase species in the CRG, regional models have been underestimating the impact of gas-phase reactive N on dry N deposition. We conducted field studies at two sites within the CRG monitoring reactive nitrogen species (nitric oxide, nitrogen dioxide, ammonia, nitric acid, particulate nitrate, particulate ammonium, and particulate sulfate) as well as ozone and meteorological parameters. These measurements allowed us to conduct the first comprehensive analysis of reactive nitrogen partitioning and deposition in the CRG. Through our measurements, we found reactive nitrogen was higher in the spring than the summer. We found concentrations ranging from 0-15 ppbv ammonia, 0-7 ppbv nitric acid, 0-2 μg/m3 ammonium nitrate and 0-1 μg/m3 ammonium sulfate at the sites. Through the measurements of all these species, we evaluated the limiting gas-phase precursor to inorganic nitrogen particle formation. In the springtime, ammonia limits the formation of particulate reactive nitrogen; while in the summer, nitric acid and oxidized sulfur limit the formation of inorganic nitrogen particles. This suggests that there may be more sources of ammonia in the spring with fertilizer application or perhaps reactive nitrogen reservoirs are renoxified through thermal dissociation during warmer summer months. Our estimated deposition from gas and particle phase reactive nitrogen ranged from 0 – 0.14 kg N/ha per day. We also found that gas-phase reactive nitrogen plays the largest role in dry N deposition in the CRG with particle-phase contributing less than 15% of total dry N deposition. These results are important for land managers to understand the total impact of reactive nitrogen to non-urban areas. This research can inform mitigation strategies for haze formation, identify the major species and sources involved in dry N deposition and assess the potential impacts to ecosystems and cultural artifacts. Title: Investigation of Ambient Reactive Nitrogen Emissions Sources and Deposition in the Columbia River Gorge National Scenic Area Author: Mainord, Jacinda L. Year: 2017 Anthropogenic reactive nitrogen is emitted into the atmosphere from fossil fuel combustion (nitrogen oxides) and agricultural activities (nitrogen oxides and ammonia). Nitrogen oxide emissions have long been controlled for their role in ambient air pollution and human health effects. However, reactive nitrogen deposition is less understood even though it can play a significant role in altering biodiversity, impairing ecosystem and biogeochemical function and degrading cultural artifacts. Although nitrogen deposition is a natural part of biogeochemical cycling, many ecosystems across the United States are at risk of exceeding the critical nitrogen deposition load. While nitrogen oxides are routinely measured in urban areas, far less is known in non-urban landscapes where ecosystems may be especially sensitive. Regional chemical transport models have been used to predict the impacts of ambient reactive nitrogen deposition in non-urban areas, but models have difficulty simulating reactive nitrogen due to poorly quantified emissions, especially from the agricultural sector. My research explores the speciated deposition of reactive nitrogen through monitoring and modeling in the unique field setting of the 150 mile Columbia River Gorge (CRG) located along the border of Oregon and Washington. This site is ideally suited for this investigation due to the large sources of reactive nitrogen at either end of the CRG and unique seasonally driven channel wind flow. Seasonally driven wind allowed us to look at the reactive nitrogen emissions flowing through the CRG to assess ambient the reactive nitrogen partitioning and deposition gradient. Using data collected by the United States Forest Service to control ambient haze in the CRG and our co-located nitrogen oxides (NOx) gas analyzer, we first characterized the influence of seasonal, bimodal wind distributions on the spatial distribution of reactive nitrogen. We found that during winter months with predominantly easterly winds, particulate nitrate and ammonium and gas-phase nitrogen dioxide levels create a gradient from the eastern end to the western end. Particulate nitrate and sulfate mass concentrations influence the CRG gradient during summer months with predominantly western winds. We also found that the magnitude of the impact from east is greater than the magnitude of impact from the west. When we compared our observations to regional chemistry transport models, we found that models are significantly under-predicting levels of reactive nitrogen in the CRG. This bias is not isolated to a single station within the Gorge, but throughout the whole Columbia Basin. Our results indicate that there are under-represented emissions in the region leading to this bias. Partly due to the bias in reactive N gas-phase species in the CRG, regional models have been underestimating the impact of gas-phase reactive N on dry N deposition. We conducted field studies at two sites within the CRG monitoring reactive nitrogen species (nitric oxide, nitrogen dioxide, ammonia, nitric acid, particulate nitrate, particulate ammonium, and particulate sulfate) as well as ozone and meteorological parameters. These measurements allowed us to conduct the first comprehensive analysis of reactive nitrogen partitioning and deposition in the CRG. Through our measurements, we found reactive nitrogen was higher in the spring than the summer. We found concentrations ranging from 0-15 ppbv ammonia, 0-7 ppbv nitric acid, 0-2 μg/m3 ammonium nitrate and 0-1 μg/m3 ammonium sulfate at the sites. Through the measurements of all these species, we evaluated the limiting gas-phase precursor to inorganic nitrogen particle formation. In the springtime, ammonia limits the formation of particulate reactive nitrogen; while in the summer, nitric acid and oxidized sulfur limit the formation of inorganic nitrogen particles. This suggests that there may be more sources of ammonia in the spring with fertilizer application or perhaps reactive nitrogen reservoirs are renoxified through thermal dissociation during warmer summer months. Our estimated deposition from gas and particle phase reactive nitrogen ranged from 0 – 0.14 kg N/ha per day. We also found that gas-phase reactive nitrogen plays the largest role in dry N deposition in the CRG with particle-phase contributing less than 15% of total dry N deposition. These results are important for land managers to understand the total impact of reactive nitrogen to non-urban areas. This research can inform mitigation strategies for haze formation, identify the major species and sources involved in dry N deposition and assess the potential impacts to ecosystems and cultural artifacts. Close

• 69. [Article] Predicting Parturition in a Long-Gestating Species: Behavioral and Hormonal Indicators in the Asian Elephant (Elephas maximus)

  Captive populations of Asian elephants (Elephas maximus) in North America are not self-sustaining, and increasing reproductive success within captive populations is a high priority. The ability to accurately ...

  Citation × Citation Citation Abstract Copy Title: Predicting Parturition in a Long-Gestating Species: Behavioral and Hormonal Indicators in the Asian Elephant (Elephas maximus) Author: Velonis, Heather Kelly Year: 2017 Captive populations of Asian elephants (Elephas maximus) in North America are not self-sustaining, and increasing reproductive success within captive populations is a high priority. The ability to accurately predict parturition can have a direct impact on elephant welfare. Elephants in captivity often require significant preparation and management throughout the birthing process, and complications during labor and delivery can necessitate immediate intervention, including stillbirth, protracted labor, maternal aggression towards a newborn calf, and dystocia. Being able to predict when parturition will commence can ensure appropriate staff is available and adequate monitoring is performed. Routine endocrine sampling can be used to predict parturition in Asian elephants, with a drop in progesterone (P4) to baseline levels signaling parturition in 2-5 days. However, we determined this method is not without limitations, and it is not used in all institutions that house elephants. As changes in hormones regulate and alter behaviors, we investigated behavioral indicators as an additional management tool for predicting parturition, a time of drastic hormone changes. We conducted a study of five pregnancies in Asian elephants at the Oregon Zoo, U.S.A, and Taronga Zoo, Australia, between 2008 and 2012. In Chapter 2, I evaluated progesterone (P4) and cortisol levels across three time periods: Baseline; Pre, (the week preceding the drop in P4); and Post, (the period after the P4 drop). Levels of P4 were significantly lower, and levels of cortisol were significantly higher in the days just prior to parturition. I found considerable intra- and inter-individual variation in both endocrine profiles, which can make endocrine assessments difficult to interpret in real time. In Chapter 3, I investigated whether behaviors in the preparturition period could be predictive of impending parturition in the Asian elephant. ANOVA results indicated a significant difference in the amount of time that elephants spent walking backwards across three time periods (F(2) = 3.723, p = 0.033), with the behavior increasing as parturition approached. These results were supported by a non-parametric Kruskal- Wallis. Using a generalized linear mixed model (GLMM), I found that as P4 levels decrease, walking backwards behavior significantly increases. In Chapter 4, I evaluated investigative trunk behaviors, or “trunk checks”, directed towards the temporal gland near the ear, mammary glands, vulva and anus of the pregnant dam. Investigative behaviors included both self-directed behaviors and those sent from herd mates towards the pregnant dam. Self-directed behaviors are most likely associated with physical changes in the pregnant dam, such as using the trunk to pull on swollen teats. Other-directed behaviors may stem from chemo-sensory signaling or other types of communication between herd mates, such as detecting changes in progesterone or cortisol. I ran GLMM and found that four trunk-check behaviors varied significantly with P4 and/or cortisol profiles. These were: self-checks of mammary glands increased with decreasing P4 levels; herd-mate-checks of mammary glands increased with decreasing P4 levels; self-checks of vulva increased with decreasing P4 levels and increasing cortisol levels; herd-mate-checks of anus increased with increasing cortisol levels. In Chapter 5, I evaluated activity budget behaviors in the pregnant elephants. Generalized comparisons were made to published activity budgets of typical captive Asian elephants. I report that activity budgets are within the range of normal activity, though I note a high level of inter-individual variation. In addition, I compared two sampling techniques, including one-zero and instantaneous sampling, that were used for activity budget data collection. I discuss the different results obtained by each sampling technique. These results are a very promising indication that behaviors, including walking backwards and multiple trunk-check behaviors, are changing over time or with parturition-related hormone profiles. We recommend that keepers, veterinary staff, and other observers that are familiar with the regular behavioral repertoire of a pregnant female should pay close attention to these highlighted behaviors. Keeping track of these behaviors, especially in conjunction with P4 and cortisol tracking, can help staff refine existing windows of expected parturition. Title: Predicting Parturition in a Long-Gestating Species: Behavioral and Hormonal Indicators in the Asian Elephant (Elephas maximus) Author: Velonis, Heather Kelly Year: 2017 Captive populations of Asian elephants (Elephas maximus) in North America are not self-sustaining, and increasing reproductive success within captive populations is a high priority. The ability to accurately predict parturition can have a direct impact on elephant welfare. Elephants in captivity often require significant preparation and management throughout the birthing process, and complications during labor and delivery can necessitate immediate intervention, including stillbirth, protracted labor, maternal aggression towards a newborn calf, and dystocia. Being able to predict when parturition will commence can ensure appropriate staff is available and adequate monitoring is performed. Routine endocrine sampling can be used to predict parturition in Asian elephants, with a drop in progesterone (P4) to baseline levels signaling parturition in 2-5 days. However, we determined this method is not without limitations, and it is not used in all institutions that house elephants. As changes in hormones regulate and alter behaviors, we investigated behavioral indicators as an additional management tool for predicting parturition, a time of drastic hormone changes. We conducted a study of five pregnancies in Asian elephants at the Oregon Zoo, U.S.A, and Taronga Zoo, Australia, between 2008 and 2012. In Chapter 2, I evaluated progesterone (P4) and cortisol levels across three time periods: Baseline; Pre, (the week preceding the drop in P4); and Post, (the period after the P4 drop). Levels of P4 were significantly lower, and levels of cortisol were significantly higher in the days just prior to parturition. I found considerable intra- and inter-individual variation in both endocrine profiles, which can make endocrine assessments difficult to interpret in real time. In Chapter 3, I investigated whether behaviors in the preparturition period could be predictive of impending parturition in the Asian elephant. ANOVA results indicated a significant difference in the amount of time that elephants spent walking backwards across three time periods (F(2) = 3.723, p = 0.033), with the behavior increasing as parturition approached. These results were supported by a non-parametric Kruskal- Wallis. Using a generalized linear mixed model (GLMM), I found that as P4 levels decrease, walking backwards behavior significantly increases. In Chapter 4, I evaluated investigative trunk behaviors, or “trunk checks”, directed towards the temporal gland near the ear, mammary glands, vulva and anus of the pregnant dam. Investigative behaviors included both self-directed behaviors and those sent from herd mates towards the pregnant dam. Self-directed behaviors are most likely associated with physical changes in the pregnant dam, such as using the trunk to pull on swollen teats. Other-directed behaviors may stem from chemo-sensory signaling or other types of communication between herd mates, such as detecting changes in progesterone or cortisol. I ran GLMM and found that four trunk-check behaviors varied significantly with P4 and/or cortisol profiles. These were: self-checks of mammary glands increased with decreasing P4 levels; herd-mate-checks of mammary glands increased with decreasing P4 levels; self-checks of vulva increased with decreasing P4 levels and increasing cortisol levels; herd-mate-checks of anus increased with increasing cortisol levels. In Chapter 5, I evaluated activity budget behaviors in the pregnant elephants. Generalized comparisons were made to published activity budgets of typical captive Asian elephants. I report that activity budgets are within the range of normal activity, though I note a high level of inter-individual variation. In addition, I compared two sampling techniques, including one-zero and instantaneous sampling, that were used for activity budget data collection. I discuss the different results obtained by each sampling technique. These results are a very promising indication that behaviors, including walking backwards and multiple trunk-check behaviors, are changing over time or with parturition-related hormone profiles. We recommend that keepers, veterinary staff, and other observers that are familiar with the regular behavioral repertoire of a pregnant female should pay close attention to these highlighted behaviors. Keeping track of these behaviors, especially in conjunction with P4 and cortisol tracking, can help staff refine existing windows of expected parturition. Close

• 70. [Article] Applying GPS and Accelerometers to the Study of African Savanna (Loxodonta africana) and Asian Elephant (Elephas maximus) Welfare in Zoos

  African savanna elephants (Loxodonta africana) and Asian elephants (Elephas maximus) are a focus of welfare research in zoos due to their high intelligence, complex social structure, and sheer size. Due ...

  Citation × Citation Citation Abstract Copy Title: Applying GPS and Accelerometers to the Study of African Savanna (Loxodonta africana) and Asian Elephant (Elephas maximus) Welfare in Zoos Author: Holdgate, Matthew Robert Year: 2015 African savanna elephants (Loxodonta africana) and Asian elephants (Elephas maximus) are a focus of welfare research in zoos due to their high intelligence, complex social structure, and sheer size. Due to these challenges, some argue that zoos are inherently incapable of providing appropriate care for elephants, while others believe that zoos can fulfill the needs of these species with improved husbandry. There is a general consensus from both within and outside of zoos, however, that zoos must improve their elephant programs or cease exhibiting these animals altogether. Now more than ever, applied research on zoo elephant welfare is needed to provide context for this debate. Researchers are interested in how far zoo elephants walk due to the potential health and welfare benefits of walking in these highly mobile species. Zoo researchers recently adopted GPS technology to study elephant walking, and preliminary evidence suggests that African elephants in large zoo exhibits walk distances that correspond with wild elephants under non-extreme conditions. However, data are limited from Asian elephants and from elephants in more typically-sized exhibits. In Chapter Two, I discuss important methodological considerations of utilizing GPS in a zoo environment, including an introduction to the technology, sources of error and mitigation, methods to improve GPS performance, and possible effects of GPS device attachment on animal behavior. This review shows GPS performance is adequate for tracking zoo elephant walking when proper methodological techniques are applied, and should serve as a useful reference for zoo researchers considering using GPS. In Chapter Three, I used GPS anklets to measure outdoor daily walking distance in 56 adult female African (n = 33) and Asian (n = 23) elephants housed in 30 zoos. I collected 259 days of data and found that elephants walked an average of 5.34 km/day with no significant difference between species. Multivariate regression models predicted that elephants with more dynamic feeding regimens (more diverse feeding types and frequencies; unscheduled feeding times) will walk more. Distance walked was also predicted to be higher in elephants that spend time in a greater number of different social groups. Distance walked was predicted to decline with age. Finally, I found a significant negative correlation between distance walked and nighttime space experience. The results of the analysis suggest that zoos that want to increase walking in their elephants need not rely solely on larger exhibits, but can increase walking by adding quality and complexity to exhibits. However, my results failed to establish a definitive link between walking distance and other validated measures of elephant welfare. Thus, the direct health and welfare benefits of walking in zoo elephants remain unresolved. Resting behaviors are an essential component of animal welfare, but have received little attention in zoological research. In Chapter Four, I used accelerometers in anklets to complete the first large-scale multi-species investigation of zoo elephant recumbence. I collected 344 days of data from 72 adult female African (n = 44) and Asian (n = 28) elephants at 40 zoos. I found that African elephants are recumbent an average of 2.14 hours/day, which is significantly less than Asian elephants at 3.22 hours/day. Multivariate regression models predicted that African elephant recumbence increases when they experience more space at night, and Asian elephant recumbence increases when they spend time housed alone. Both species showed a similar response to substrate, such that African elephants spending time on all-hard substrates are predicted to be recumbent less, while Asian elephants spending time on all-soft substrates are predicted to be recumbent more. The discovery that occasional non-recumbence is a common behavior in zoo elephants also introduces a new area of research that may have important animal welfare consequences. Finally, this study established that zoos should continue their efforts to replace hard substrate with soft substrate in order to provide zoo elephants with environments that facilitate recumbence. Overall, this work assessed walking and recumbence in zoo elephants, which will allow zoos to gauge the prevalence of these behaviors in their elephants as compared to the sub-population studied here. A variety of factors that are associated with these behaviors were also identified. With this information, zoos can prioritize modifications to their facilities and animal management programs to create an environment that encourages zoo elephants to express walking and recumbence behavior, should they choose to do so. This work is one component of the Elephant Welfare Project, the largest zoo animal welfare project ever undertaken, and is unprecedented in both scope and scale. The project was funded by the Institute of Museum and Library Services (IMLS), an independent, U.S., federal, grant-making agency that supports libraries, museums, and zoos. At the time of this writing, the first manuscripts from this project are being submitted to academic journals. These papers will describe the prevalence and distribution of a variety of elephant behaviors and welfare indicators, serve as a benchmark for future elephant welfare studies, and aid in decision making with regard to best practices in elephant management. Title: Applying GPS and Accelerometers to the Study of African Savanna (Loxodonta africana) and Asian Elephant (Elephas maximus) Welfare in Zoos Author: Holdgate, Matthew Robert Year: 2015 African savanna elephants (Loxodonta africana) and Asian elephants (Elephas maximus) are a focus of welfare research in zoos due to their high intelligence, complex social structure, and sheer size. Due to these challenges, some argue that zoos are inherently incapable of providing appropriate care for elephants, while others believe that zoos can fulfill the needs of these species with improved husbandry. There is a general consensus from both within and outside of zoos, however, that zoos must improve their elephant programs or cease exhibiting these animals altogether. Now more than ever, applied research on zoo elephant welfare is needed to provide context for this debate. Researchers are interested in how far zoo elephants walk due to the potential health and welfare benefits of walking in these highly mobile species. Zoo researchers recently adopted GPS technology to study elephant walking, and preliminary evidence suggests that African elephants in large zoo exhibits walk distances that correspond with wild elephants under non-extreme conditions. However, data are limited from Asian elephants and from elephants in more typically-sized exhibits. In Chapter Two, I discuss important methodological considerations of utilizing GPS in a zoo environment, including an introduction to the technology, sources of error and mitigation, methods to improve GPS performance, and possible effects of GPS device attachment on animal behavior. This review shows GPS performance is adequate for tracking zoo elephant walking when proper methodological techniques are applied, and should serve as a useful reference for zoo researchers considering using GPS. In Chapter Three, I used GPS anklets to measure outdoor daily walking distance in 56 adult female African (n = 33) and Asian (n = 23) elephants housed in 30 zoos. I collected 259 days of data and found that elephants walked an average of 5.34 km/day with no significant difference between species. Multivariate regression models predicted that elephants with more dynamic feeding regimens (more diverse feeding types and frequencies; unscheduled feeding times) will walk more. Distance walked was also predicted to be higher in elephants that spend time in a greater number of different social groups. Distance walked was predicted to decline with age. Finally, I found a significant negative correlation between distance walked and nighttime space experience. The results of the analysis suggest that zoos that want to increase walking in their elephants need not rely solely on larger exhibits, but can increase walking by adding quality and complexity to exhibits. However, my results failed to establish a definitive link between walking distance and other validated measures of elephant welfare. Thus, the direct health and welfare benefits of walking in zoo elephants remain unresolved. Resting behaviors are an essential component of animal welfare, but have received little attention in zoological research. In Chapter Four, I used accelerometers in anklets to complete the first large-scale multi-species investigation of zoo elephant recumbence. I collected 344 days of data from 72 adult female African (n = 44) and Asian (n = 28) elephants at 40 zoos. I found that African elephants are recumbent an average of 2.14 hours/day, which is significantly less than Asian elephants at 3.22 hours/day. Multivariate regression models predicted that African elephant recumbence increases when they experience more space at night, and Asian elephant recumbence increases when they spend time housed alone. Both species showed a similar response to substrate, such that African elephants spending time on all-hard substrates are predicted to be recumbent less, while Asian elephants spending time on all-soft substrates are predicted to be recumbent more. The discovery that occasional non-recumbence is a common behavior in zoo elephants also introduces a new area of research that may have important animal welfare consequences. Finally, this study established that zoos should continue their efforts to replace hard substrate with soft substrate in order to provide zoo elephants with environments that facilitate recumbence. Overall, this work assessed walking and recumbence in zoo elephants, which will allow zoos to gauge the prevalence of these behaviors in their elephants as compared to the sub-population studied here. A variety of factors that are associated with these behaviors were also identified. With this information, zoos can prioritize modifications to their facilities and animal management programs to create an environment that encourages zoo elephants to express walking and recumbence behavior, should they choose to do so. This work is one component of the Elephant Welfare Project, the largest zoo animal welfare project ever undertaken, and is unprecedented in both scope and scale. The project was funded by the Institute of Museum and Library Services (IMLS), an independent, U.S., federal, grant-making agency that supports libraries, museums, and zoos. At the time of this writing, the first manuscripts from this project are being submitted to academic journals. These papers will describe the prevalence and distribution of a variety of elephant behaviors and welfare indicators, serve as a benchmark for future elephant welfare studies, and aid in decision making with regard to best practices in elephant management. Close

• 71. [Article] Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs

  Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering ...

  Citation × Citation Citation Abstract Copy Title: Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs Author: Smith, Samson W., Latta, Leigh C., IV, Denver, Dee R., Estes, Suzanne Year: 2014 Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments–consistent with the oxidative stress theory of aging. Conclusions: Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory. Title: Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs Author: Smith, Samson W., Latta, Leigh C., IV, Denver, Dee R., Estes, Suzanne Year: 2014 Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments–consistent with the oxidative stress theory of aging. Conclusions: Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory. Close

• 72. [Article] Factors Affecting Snowy Plover Chick Survival in a Managed Population

  Understanding survival of precocial chicks in the period immediately following hatching has important conservation implications because population growth is often sensitive to post-hatching survival. We ...

  Citation × Citation Citation Abstract Copy Title: Factors Affecting Snowy Plover Chick Survival in a Managed Population Author: Dinsmore, Stephen J., Gaines, Eleanor P., Pearson, Scott F., Lauten, David J., Castelein, Kathleen J. Year: 2017 Understanding survival of precocial chicks in the period immediately following hatching has important conservation implications because population growth is often sensitive to post-hatching survival. We studied federally threatened Western Snowy Plover (Charadrius nivosus nivosus) broods at the northern limit of their range in coastal Oregon (n ¼ 1,157) and Washington (n ¼ 84) from 1991 to 2011 in an attempt to understand seasonal, annual, and spatial patterns of chick survival. In Oregon, plover chick survival increased with age, varied between sites, and was greater at sites with predator management. The mean probability of surviving from hatch to fledging at 28 days of age in Oregon was 0.57 (95% CI: 0.50, 0.63). In Washington, where predator management was not employed, we conducted separate analyses using individually banded and unbanded chicks and results indicated that survival generally increased with chick age. The mean estimated probability of surviving from hatch to fledging at 28 days of age in Washington was 0.27 (95% CI: 0.20, 0.35) for individually banded chicks when perfect detection was assumed. This probability increased to 0.67 (95% CI: 0.41, 0.83) when we analyzed unbanded chicks and included detection probability. Our findings confirm the importance of considering age effects in the survival of Snowy Plover chicks and raise questions about the validity of assuming perfect detection of plover chicks during brood checks. This work also highlights the benefit of predator management on chick survival. Title: Factors Affecting Snowy Plover Chick Survival in a Managed Population Author: Dinsmore, Stephen J., Gaines, Eleanor P., Pearson, Scott F., Lauten, David J., Castelein, Kathleen J. Year: 2017 Understanding survival of precocial chicks in the period immediately following hatching has important conservation implications because population growth is often sensitive to post-hatching survival. We studied federally threatened Western Snowy Plover (Charadrius nivosus nivosus) broods at the northern limit of their range in coastal Oregon (n ¼ 1,157) and Washington (n ¼ 84) from 1991 to 2011 in an attempt to understand seasonal, annual, and spatial patterns of chick survival. In Oregon, plover chick survival increased with age, varied between sites, and was greater at sites with predator management. The mean probability of surviving from hatch to fledging at 28 days of age in Oregon was 0.57 (95% CI: 0.50, 0.63). In Washington, where predator management was not employed, we conducted separate analyses using individually banded and unbanded chicks and results indicated that survival generally increased with chick age. The mean estimated probability of surviving from hatch to fledging at 28 days of age in Washington was 0.27 (95% CI: 0.20, 0.35) for individually banded chicks when perfect detection was assumed. This probability increased to 0.67 (95% CI: 0.41, 0.83) when we analyzed unbanded chicks and included detection probability. Our findings confirm the importance of considering age effects in the survival of Snowy Plover chicks and raise questions about the validity of assuming perfect detection of plover chicks during brood checks. This work also highlights the benefit of predator management on chick survival. Close

• 73. [Article] Comparison of Fish Assemblages in Restored and Natural Mangrove Habitats Along an Urban Shoreline

  The installation of living shorelines is one strategy used to ameliorate habitat degradation along developed coastlines. In this process, existing hard structures, such as sea walls and riprap revetments, ...

  Citation × Citation Citation Abstract Copy Title: Comparison of Fish Assemblages in Restored and Natural Mangrove Habitats Along an Urban Shoreline Author: Peters, Joseph R., Yeager, Laura A., Layman, Craig A. Year: 2015 The installation of living shorelines is one strategy used to ameliorate habitat degradation along developed coastlines. In this process, existing hard structures, such as sea walls and riprap revetments, are supplemented with habitat forming species, e.g., oysters and mangrove trees, to improve habitat quality and function. Shoreline restorations in Biscayne Bay, Florida, USA, often utilize red mangroves, Rhizophora mangle (Linneaus, 1753), in addition to riprap revetments, to help stabilize the shoreline. This riprap-mangrove habitat provides structure for marine organisms to utilize and is believed to improve shoreline habitats in areas previously cleared of mangroves. We examined whether habitat provisioning was similar between restored mangrove habitat with the inclusion of riprap boulders and natural mangrove shorelines. We compared fish assemblages between natural mangrove and riprapmangrove habitats within two areas of northern Biscayne Bay. Fish community structure and certain benthic cover types varied between mangroves and riprap-mangrove habitats. Total fish abundance was greater in mangrove habitat, while taxonomic richness was highest in riprap-mangrove sites in the northern part of the bay. Our findings suggest that fish assemblages and community structure are different between these habitat types, although the geographic context may mediate the effect of habitat type. Therefore, it is likely that these restored mangroves provide different ecological services than unaltered mangrove shorelines. Title: Comparison of Fish Assemblages in Restored and Natural Mangrove Habitats Along an Urban Shoreline Author: Peters, Joseph R., Yeager, Laura A., Layman, Craig A. Year: 2015 The installation of living shorelines is one strategy used to ameliorate habitat degradation along developed coastlines. In this process, existing hard structures, such as sea walls and riprap revetments, are supplemented with habitat forming species, e.g., oysters and mangrove trees, to improve habitat quality and function. Shoreline restorations in Biscayne Bay, Florida, USA, often utilize red mangroves, Rhizophora mangle (Linneaus, 1753), in addition to riprap revetments, to help stabilize the shoreline. This riprap-mangrove habitat provides structure for marine organisms to utilize and is believed to improve shoreline habitats in areas previously cleared of mangroves. We examined whether habitat provisioning was similar between restored mangrove habitat with the inclusion of riprap boulders and natural mangrove shorelines. We compared fish assemblages between natural mangrove and riprapmangrove habitats within two areas of northern Biscayne Bay. Fish community structure and certain benthic cover types varied between mangroves and riprap-mangrove habitats. Total fish abundance was greater in mangrove habitat, while taxonomic richness was highest in riprap-mangrove sites in the northern part of the bay. Our findings suggest that fish assemblages and community structure are different between these habitat types, although the geographic context may mediate the effect of habitat type. Therefore, it is likely that these restored mangroves provide different ecological services than unaltered mangrove shorelines. Close

• 74. [Article] Investigations into the Effects of Water Exchange and the Structure of Lanthanide Chelates

  Lanthanide chelates are effective agents for improving contrast in MR images. Optimizing the relaxation of inner sphere water molecules is a common focus of research in this field. However, the efforts ...

  Citation × Citation Citation Abstract Copy Title: Investigations into the Effects of Water Exchange and the Structure of Lanthanide Chelates Author: Payne, Katherine Marie Year: 2016 Lanthanide chelates are effective agents for improving contrast in MR images. Optimizing the relaxation of inner sphere water molecules is a common focus of research in this field. However, the efforts to design an optimal contrast agent have commonly over-looked the relationship of water position and water exchange kinetics. This work explores structural conformation, the impact of very fast water exchange kinetics on hydration, and differing tumbling rates for regioisomers of a number of lanthanide chelates. We have grown crystals of LnDOTMA and obtained structural data by X-ray diffraction that provide a picture of the chelate during water exchange and demonstrate that chelate conformation is associated with water position. We observe increased population of the major isomer with increased water exchange rates in variable temperature 1H NMR studies of HoDOTMA. This suggests that water position and water exchange rates are linked. We therefore recommend that accurate water exchange data be included in the application of the SBM equations when interpreting experimental data. As further support of this recommendation, we measured water exchange kinetics with 17O NMR for the rigid GdNB-DOTMA chelates. These results were used in the fitting of 1H NMRD profiles to establish tumbling parameters. Similar results were also observed in the less rigid GdNB-DOTA, establishing the first identification of regioisomers in these chelates and their biphenyl derivatives. Binding studies of GdBP-DOTA indicate that the side isomer is a more effective agent, but it is the minor species in solution. Our work herein shows that predicting efficacy of contrast agents with SBM equations requires a more complete consideration of chelate hydration (q/r6). Title: Investigations into the Effects of Water Exchange and the Structure of Lanthanide Chelates Author: Payne, Katherine Marie Year: 2016 Lanthanide chelates are effective agents for improving contrast in MR images. Optimizing the relaxation of inner sphere water molecules is a common focus of research in this field. However, the efforts to design an optimal contrast agent have commonly over-looked the relationship of water position and water exchange kinetics. This work explores structural conformation, the impact of very fast water exchange kinetics on hydration, and differing tumbling rates for regioisomers of a number of lanthanide chelates. We have grown crystals of LnDOTMA and obtained structural data by X-ray diffraction that provide a picture of the chelate during water exchange and demonstrate that chelate conformation is associated with water position. We observe increased population of the major isomer with increased water exchange rates in variable temperature 1H NMR studies of HoDOTMA. This suggests that water position and water exchange rates are linked. We therefore recommend that accurate water exchange data be included in the application of the SBM equations when interpreting experimental data. As further support of this recommendation, we measured water exchange kinetics with 17O NMR for the rigid GdNB-DOTMA chelates. These results were used in the fitting of 1H NMRD profiles to establish tumbling parameters. Similar results were also observed in the less rigid GdNB-DOTA, establishing the first identification of regioisomers in these chelates and their biphenyl derivatives. Binding studies of GdBP-DOTA indicate that the side isomer is a more effective agent, but it is the minor species in solution. Our work herein shows that predicting efficacy of contrast agents with SBM equations requires a more complete consideration of chelate hydration (q/r6). Close

• 75. [Article] Assessing the Utility of Transcriptome Data for Inferring Phylogenetic Relationships Among Coleoid Cephalopods

  Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity ...

  Citation × Citation Citation Abstract Copy Title: Assessing the Utility of Transcriptome Data for Inferring Phylogenetic Relationships Among Coleoid Cephalopods Author: Lindgren, Annie R., Anderson, Frank E. Year: 2018 Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives). To do so, we took new and previously published transcriptome data and used a unique cephalopod core ortholog set to generate a dataset that was subjected to an array of filtering and analytical methods to assess the impacts of: taxon sampling, ortholog number, compositional and rate heterogeneity and incongruence across loci. Analyses indicated that datasets that maximized taxonomic coverage but included fewer orthologs were less stable than datasets that sacrificed taxon sampling to increase the number of orthologs. Clades recovered irrespective of dataset, filtering or analytical method included Octopodiformes (Vampyroteuthis infernalis + octopods), Decapodiformes (squids, cuttlefishes and their relatives), and orders Oegopsida (open-eyed squids) and Myopsida (e.g., loliginid squids). Ordinal-level relationships within Decapodiformes were the most susceptible to dataset perturbation, further emphasizing the challenges associated with uncovering relationships at deep nodes in the cephalopod tree of life. Title: Assessing the Utility of Transcriptome Data for Inferring Phylogenetic Relationships Among Coleoid Cephalopods Author: Lindgren, Annie R., Anderson, Frank E. Year: 2018 Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives). To do so, we took new and previously published transcriptome data and used a unique cephalopod core ortholog set to generate a dataset that was subjected to an array of filtering and analytical methods to assess the impacts of: taxon sampling, ortholog number, compositional and rate heterogeneity and incongruence across loci. Analyses indicated that datasets that maximized taxonomic coverage but included fewer orthologs were less stable than datasets that sacrificed taxon sampling to increase the number of orthologs. Clades recovered irrespective of dataset, filtering or analytical method included Octopodiformes (Vampyroteuthis infernalis + octopods), Decapodiformes (squids, cuttlefishes and their relatives), and orders Oegopsida (open-eyed squids) and Myopsida (e.g., loliginid squids). Ordinal-level relationships within Decapodiformes were the most susceptible to dataset perturbation, further emphasizing the challenges associated with uncovering relationships at deep nodes in the cephalopod tree of life. Close

• 76. [Article] Advancing Collaborative Solutions: Lessons from the Oregon Sage-Grouse Conservation Partnership (SageCon)

  The Sage-Grouse Conservation Partnership, also known as “SageCon,” was an unprecedented collaborative effort among federal, state, and private stakeholders to address landscape-scale threats to greater ...

  Citation × Citation Citation Abstract Copy Title: Advancing Collaborative Solutions: Lessons from the Oregon Sage-Grouse Conservation Partnership (SageCon) Author: Allen, Jennifer H., Odell, Turner, Babcock, Julia, Henrie, Charis Year: 2017 The Sage-Grouse Conservation Partnership, also known as “SageCon,” was an unprecedented collaborative effort among federal, state, and private stakeholders to address landscape-scale threats to greater sage-grouse while also acknowledging rural economic and community interests across eastern Oregon’s sagebrush range. A U.S. Fish and Wildlife Service (USFWS) preliminary finding that the sage-grouse warranted listing under the endangered species act, and a subsequent court settlement setting a deadline for a final listing decision were key drivers for SageCon participants to seek proactive solutions to protect the bird. A cadre of diverse Eastern Oregon stakeholders with experience working collaboratively on related public lands issues helped set the stage for the collaborative effort. As part of what the Department of the Interior described as a historic outcome, SageCon produced the 2015 Oregon Sage-Grouse Action Plan, which details voluntary and state-regulated conservation measures to preserve habitat and protect Oregon’s sage-grouse population from threats on public and private land. SageCon—as one part of a broader multi-state collaborative effort—led to a subsequent USFWS finding that the sage-grouse no longer warranted listing as endangered. In our study of this collaborative effort, we interviewed seventeen SageCon participants to identify collaborative approaches that may offer promise for other conservation and public policy efforts. We explored participant motivation for engaging in the process, collaborative process design, integration of science into the SageCon deliberations, and other experiences that interviewees found relevant. Title: Advancing Collaborative Solutions: Lessons from the Oregon Sage-Grouse Conservation Partnership (SageCon) Author: Allen, Jennifer H., Odell, Turner, Babcock, Julia, Henrie, Charis Year: 2017 The Sage-Grouse Conservation Partnership, also known as “SageCon,” was an unprecedented collaborative effort among federal, state, and private stakeholders to address landscape-scale threats to greater sage-grouse while also acknowledging rural economic and community interests across eastern Oregon’s sagebrush range. A U.S. Fish and Wildlife Service (USFWS) preliminary finding that the sage-grouse warranted listing under the endangered species act, and a subsequent court settlement setting a deadline for a final listing decision were key drivers for SageCon participants to seek proactive solutions to protect the bird. A cadre of diverse Eastern Oregon stakeholders with experience working collaboratively on related public lands issues helped set the stage for the collaborative effort. As part of what the Department of the Interior described as a historic outcome, SageCon produced the 2015 Oregon Sage-Grouse Action Plan, which details voluntary and state-regulated conservation measures to preserve habitat and protect Oregon’s sage-grouse population from threats on public and private land. SageCon—as one part of a broader multi-state collaborative effort—led to a subsequent USFWS finding that the sage-grouse no longer warranted listing as endangered. In our study of this collaborative effort, we interviewed seventeen SageCon participants to identify collaborative approaches that may offer promise for other conservation and public policy efforts. We explored participant motivation for engaging in the process, collaborative process design, integration of science into the SageCon deliberations, and other experiences that interviewees found relevant. Close

• 77. [Article] Role of Metabolic Shifts in Protection from Mutation Damage: Characterizing Mitochondrial Membrane Potential in C. Elegans Gas-1 Mutants

  Many terminal human diseases are caused by mutations affecting mitochondrial functioning. Mitochondria are essential organelles responsible for producing cellular energy, adenosine triphosphate (ATP) via ...

  Citation × Citation Citation Abstract Copy Title: Role of Metabolic Shifts in Protection from Mutation Damage: Characterizing Mitochondrial Membrane Potential in C. Elegans Gas-1 Mutants Author: Muñoz-Tremblay, Lauren S. Year: 2015 Many terminal human diseases are caused by mutations affecting mitochondrial functioning. Mitochondria are essential organelles responsible for producing cellular energy, adenosine triphosphate (ATP) via oxidative phosphorylation (OXPHOS) at mitochondrial electron transport chains (ETC). Proper ETC functioning relies on maintenance of the electrochemical gradient essential for energy production, known as mitochondrial membrane potential (ΔψM). The inner mitochondrial membrane is the site of the ETC and is most closely in contact with the enzymatic processes occurring within the mitochondrial matrix. Mutations affecting protein components of the ETC are especially troublesome for organelle health. ETC mutants commonly express altered ΔψM, as well as increased production of damaging reactive oxygen species (ROS), which are hypothesized to cause genomic damage and lasting mutation. The nematode C. elegans is a practical model organism for investigating the phenotypic and genomic consequences of ETC mutations. Despite expressing higher levels of damaging ROS, the ETC protein complex 1 mutant, gas-1, expresses heritable mtDNA and nDNA mutation rates identical to those of wild type animals. I am using a mitochondria-targeted dye and fluorescence microscopy to quantify and compare ΔψM levels of the gas-1 mutant and wild type animals. This work will provide a novel phenotypic characterization of this mutant and indicate whether decreased metabolic activity (e.g., reduced reliance on OXPHOS) is occurring in gas-1, and perhaps conferring protection from genomic degradation. Based on gas-1’s characteristically low ATP production and high ROS production, I expect that ΔψM will be higher in gas-1 as compared to wild type levels. Title: Role of Metabolic Shifts in Protection from Mutation Damage: Characterizing Mitochondrial Membrane Potential in C. Elegans Gas-1 Mutants Author: Muñoz-Tremblay, Lauren S. Year: 2015 Many terminal human diseases are caused by mutations affecting mitochondrial functioning. Mitochondria are essential organelles responsible for producing cellular energy, adenosine triphosphate (ATP) via oxidative phosphorylation (OXPHOS) at mitochondrial electron transport chains (ETC). Proper ETC functioning relies on maintenance of the electrochemical gradient essential for energy production, known as mitochondrial membrane potential (ΔψM). The inner mitochondrial membrane is the site of the ETC and is most closely in contact with the enzymatic processes occurring within the mitochondrial matrix. Mutations affecting protein components of the ETC are especially troublesome for organelle health. ETC mutants commonly express altered ΔψM, as well as increased production of damaging reactive oxygen species (ROS), which are hypothesized to cause genomic damage and lasting mutation. The nematode C. elegans is a practical model organism for investigating the phenotypic and genomic consequences of ETC mutations. Despite expressing higher levels of damaging ROS, the ETC protein complex 1 mutant, gas-1, expresses heritable mtDNA and nDNA mutation rates identical to those of wild type animals. I am using a mitochondria-targeted dye and fluorescence microscopy to quantify and compare ΔψM levels of the gas-1 mutant and wild type animals. This work will provide a novel phenotypic characterization of this mutant and indicate whether decreased metabolic activity (e.g., reduced reliance on OXPHOS) is occurring in gas-1, and perhaps conferring protection from genomic degradation. Based on gas-1’s characteristically low ATP production and high ROS production, I expect that ΔψM will be higher in gas-1 as compared to wild type levels. Close

• 78. [Article] Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content

  Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish ...

  Citation × Citation Citation Abstract Copy Title: Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content Author: Faber-Hammond, Joshua J., Brown, Kim H. Year: 2015 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences given the reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence dataset indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads we identified 1,514,491 novel contigs covering ~224 Mb of genomic sequence. Among these, 1,083 contigs were found to contain potential gene coding sequence. RNA-seq data comparison confirmed 362 contigs contained transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in zebrafish. By utilizing the bioinformatics pipeline developed in this study the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Title: Data From: <i>Pseudo-De Novo</i> Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveals Novel Gene Content Author: Faber-Hammond, Joshua J., Brown, Kim H. Year: 2015 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences given the reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence dataset indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads we identified 1,514,491 novel contigs covering ~224 Mb of genomic sequence. Among these, 1,083 contigs were found to contain potential gene coding sequence. RNA-seq data comparison confirmed 362 contigs contained transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in zebrafish. By utilizing the bioinformatics pipeline developed in this study the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Close

• 79. [Article] Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveal Novel Gene Content

  Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish ...

  Citation × Citation Citation Abstract Copy Title: Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveal Novel Gene Content Author: Faber-Hammond, Joshua, Brown, Kim Year: 2016 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences, given that the genome reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish, which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence data set indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads, we identified 1,514,491 novel contigs covering ∼224 Mb of genomic sequence. Among these, 1083 contigs were found to contain a potential gene coding sequence. RNA-seq data comparison confirmed that 362 contigs contained a transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in the zebrafish reference genome. By utilizing the bioinformatics pipeline developed in this study, the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Title: Pseudo-De Novo Assembly and Analysis of Unmapped Genome Sequence Reads in Wild Zebrafish Reveal Novel Gene Content Author: Faber-Hammond, Joshua, Brown, Kim Year: 2016 Zebrafish represents the third vertebrate with an officially completed genome, yet it remains incomplete with additions and corrections continuing with the current release, GRCz10, having 13% of zebrafish cDNA sequences unmapped. This disparity may result from population differences, given that the genome reference was generated from clonal individuals with limited genetic diversity. This is supported by the recent analysis of a single wild zebrafish, which identified over 5.2 million SNPs and 1.6 million in/dels in the previous genome build, zv9. Re-examination of this sequence data set indicated that 13.8% of quality sequence reads failed to align to GRCz10. Using a novel bioinformatics de novo assembly pipeline on these unmappable reads, we identified 1,514,491 novel contigs covering ∼224 Mb of genomic sequence. Among these, 1083 contigs were found to contain a potential gene coding sequence. RNA-seq data comparison confirmed that 362 contigs contained a transcribed DNA sequence, suggesting that a large amount of functional genomic sequence remains unannotated in the zebrafish reference genome. By utilizing the bioinformatics pipeline developed in this study, the zebrafish genome will be bolstered as a model for human disease research. Adaptation of the pipeline described here also offers a cost-efficient and effective method to identify and map novel genetic content across any genome and will ultimately aid in the completion of additional genomes for a broad range of species. Close

• 80. [Article] Modeling Vegetation Mosaics in Sub-Alpine Tasmania Under Various Fire Regimes

  Western Tasmania, Australia contains some of the highest levels of biological endemism of any temperate region in the world, including vegetation types that are conservation priorities: fire-sensitive ...

  Citation × Citation Citation Abstract Copy Title: Modeling Vegetation Mosaics in Sub-Alpine Tasmania Under Various Fire Regimes Author: Yospin, Gabriel I., Wood, Samuel W., Holz, Andrés, Bowman, David M.J.S., Keane, Robert E., Whitlock, Cathy Year: 2015 Western Tasmania, Australia contains some of the highest levels of biological endemism of any temperate region in the world, including vegetation types that are conservation priorities: fire-sensitive rainforest dominated by endemic conifer species in the genus Athrotaxis; and fire-tolerant buttongrass moorlands. Current management focuses on fire suppression, but increasingly there are calls for the use of prescribed fire in flammable vegetation types to manage these ecosystems. The long-term effects of climate and alternative management strategies on the vegetated landscape are unknown. To help identify controls over successional trajectories, we parameterized a spatially explicit landscape-scale model of vegetation and fire (FireBGCv2) for a study area in Cradle Mountain-Lake St Clair National Park in western Tasmania using new data on fine-scale topography, plant communities, and fuels loads. Our parameterized model displays a high level of agreement with previous empirical and modeling studies for the region. The model was experimentally tested for three different levels of ignition suppression (0, 50, and 90 %); simulations ran for 1000 years and were replicated 10 times. The different scenarios yielded distinct fire return intervals, with cascading effects on successional dynamics and vegetation composition. Model results indicate that fire-sensitive endemic conifer rainforest will be restricted to upland refugia that total far less area than its present distribution, even under maximal ignition suppression. Because the distribution of vegetation types was unstable temporally and across stochastic replicates, present distributions may be a legacy of previous climate, Aboriginal fire management, or both. Title: Modeling Vegetation Mosaics in Sub-Alpine Tasmania Under Various Fire Regimes Author: Yospin, Gabriel I., Wood, Samuel W., Holz, Andrés, Bowman, David M.J.S., Keane, Robert E., Whitlock, Cathy Year: 2015 Western Tasmania, Australia contains some of the highest levels of biological endemism of any temperate region in the world, including vegetation types that are conservation priorities: fire-sensitive rainforest dominated by endemic conifer species in the genus Athrotaxis; and fire-tolerant buttongrass moorlands. Current management focuses on fire suppression, but increasingly there are calls for the use of prescribed fire in flammable vegetation types to manage these ecosystems. The long-term effects of climate and alternative management strategies on the vegetated landscape are unknown. To help identify controls over successional trajectories, we parameterized a spatially explicit landscape-scale model of vegetation and fire (FireBGCv2) for a study area in Cradle Mountain-Lake St Clair National Park in western Tasmania using new data on fine-scale topography, plant communities, and fuels loads. Our parameterized model displays a high level of agreement with previous empirical and modeling studies for the region. The model was experimentally tested for three different levels of ignition suppression (0, 50, and 90 %); simulations ran for 1000 years and were replicated 10 times. The different scenarios yielded distinct fire return intervals, with cascading effects on successional dynamics and vegetation composition. Model results indicate that fire-sensitive endemic conifer rainforest will be restricted to upland refugia that total far less area than its present distribution, even under maximal ignition suppression. Because the distribution of vegetation types was unstable temporally and across stochastic replicates, present distributions may be a legacy of previous climate, Aboriginal fire management, or both. Close

• 81. [Article] The Relationship Between Concentrations of Polycyclic Aromatic Hydrocarbons in Moss and Tree Cover in Portland OR

  This study is a spatial analysis of Polycyclic Aromatic Hydrocarbons (PAH) across the Portland Metro area using data collected from samples of moss tissue (Orthotrichum spp.), and an exploration of the ...

  Citation × Citation Citation Abstract Copy Title: The Relationship Between Concentrations of Polycyclic Aromatic Hydrocarbons in Moss and Tree Cover in Portland OR Author: Mautz, Andrew S. Year: 2017 This study is a spatial analysis of Polycyclic Aromatic Hydrocarbons (PAH) across the Portland Metro area using data collected from samples of moss tissue (Orthotrichum spp.), and an exploration of the relationship between PAH deposition and urban tree canopy in Portland Oregon. PAH are a class of common environmental pollutants created by the incomplete combustion of organic materials; largely via anthropocentric activity. Species of lichens and mosses have been shown to be suitable bioindicators of air pollutants (including PAH contamination) in other studies. Urban tree canopy is known to mitigate other environmental pollutants, as well as provide numerous environmental services to urban populations. In this study ArcGIS was used to create a raster of PAH across Portland. A raster of tree canopy volume across Portland was used with the PAH raster in a zonal analysis to calculate mean levels of PAH concentrations and tree canopy volume in each census block laying within the extent of the PAH raster. Two maps were created of the Portland census blocks within the extent of the PAH/moss study, and Excel was used to create scatter plots and a regression analysis of the correlation between tree canopy volume and PAH concentration. A statistically relevant correlation was found between greater urban tree canopy and lower PAH, but the data is variable and the relationship is demonstrated to be complex. More research is needed to determine if the correlation has to do with land use and industry or a physiological function of the tree canopy. Title: The Relationship Between Concentrations of Polycyclic Aromatic Hydrocarbons in Moss and Tree Cover in Portland OR Author: Mautz, Andrew S. Year: 2017 This study is a spatial analysis of Polycyclic Aromatic Hydrocarbons (PAH) across the Portland Metro area using data collected from samples of moss tissue (Orthotrichum spp.), and an exploration of the relationship between PAH deposition and urban tree canopy in Portland Oregon. PAH are a class of common environmental pollutants created by the incomplete combustion of organic materials; largely via anthropocentric activity. Species of lichens and mosses have been shown to be suitable bioindicators of air pollutants (including PAH contamination) in other studies. Urban tree canopy is known to mitigate other environmental pollutants, as well as provide numerous environmental services to urban populations. In this study ArcGIS was used to create a raster of PAH across Portland. A raster of tree canopy volume across Portland was used with the PAH raster in a zonal analysis to calculate mean levels of PAH concentrations and tree canopy volume in each census block laying within the extent of the PAH raster. Two maps were created of the Portland census blocks within the extent of the PAH/moss study, and Excel was used to create scatter plots and a regression analysis of the correlation between tree canopy volume and PAH concentration. A statistically relevant correlation was found between greater urban tree canopy and lower PAH, but the data is variable and the relationship is demonstrated to be complex. More research is needed to determine if the correlation has to do with land use and industry or a physiological function of the tree canopy. Close

• 82. [Article] Toward Optimal Use of Bangladesh Hilsa Resource: Bio-Economic Modelling

  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: Toward Optimal Use of Bangladesh Hilsa Resource: Bio-Economic Modelling Author: Hossain, Mohammod, Arnason, Ragnar 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: Toward Optimal Use of Bangladesh Hilsa Resource: Bio-Economic Modelling Author: Hossain, Mohammod, Arnason, Ragnar 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

• 83. [Article] THE SCIURIDAE (RODENTIA: MAMMALIA) OF CAVE BASIN (OREGON), A NEW MIDDLE MIOCENE MICROFOSSIL LOCALITY

  69 pages. A thesis presented to the Department of Geological Sciences and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, ...

  Citation × Citation Citation Abstract Copy Title: THE SCIURIDAE (RODENTIA: MAMMALIA) OF CAVE BASIN (OREGON), A NEW MIDDLE MIOCENE MICROFOSSIL LOCALITY Author: Biedron, Eva Marie Year: 2016 69 pages. A thesis presented to the Department of Geological Sciences 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 SCIURIDAE (RODENTIA: MAMMALIA) OF CAVE BASIN (OREGON), A NEW MIDDLE MIOCENE MICROFOSSIL LOCALITY Author: Biedron, Eva Marie Year: 2016 69 pages. A thesis presented to the Department of Geological Sciences 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

• 84. [Article] PSYCHOSOCIAL AND ENDOCRINE ANTECEDENTS OF RESPONSES TO SOCIAL-EVALUATIVE STRESS

  Stress often precedes the onset of physical and mental health disorders, leading to costly and extended disability and even increased risk for death. I investigate psychosocial and endocrine precursors ...

  Citation × Citation Citation Abstract Copy Title: PSYCHOSOCIAL AND ENDOCRINE ANTECEDENTS OF RESPONSES TO SOCIAL-EVALUATIVE STRESS Author: Knight, Erik Year: 2017 Stress often precedes the onset of physical and mental health disorders, leading to costly and extended disability and even increased risk for death. I investigate psychosocial and endocrine precursors to stress responses, specifically examining the causal effects of status-relevant factors that modulate endocrine, affective, and behavioral responses to social-evaluative stressors. For example, while high social status reduces stress responses in numerous species, this stress-buffering effect of status may dissipate or even reverse during times of hierarchical instability. Similarly, some research links testosterone to reduced stress system activity, but correlational research indicates that higher testosterone is related to increased stress responses in threatening social situations. In each case, the causal influence of these psychosocial (status and hierarchy stability) and endocrine (testosterone) antecedents to stress responses was unclear. Results from this work (Chapter 2) reveal that high status in a stable hierarchy buffered stress responses and improved behavioral responses to the stressor, but high status in an unstable hierarchy boosted stress responses and did not lead to better performance. This general pattern of effects was observed across endocrine (cortisol and testosterone), psychological (feeling in control), and behavioral (competence, dominance, and warmth) responses to the stressor. Further (Chapters 4 & 6), exogenous testosterone treatment caused increased motivated persistence – which can help persevere through stressful encounters – but, once exposed to a stressor, testosterone caused increased cortisol reactivity, increased negative affect, and decreased motivation in response to social-evaluative stress, especially for individuals high in trait dominance. This work provides evidence of the causal effects of psychosocial and endocrine factors on stress responses and demonstrates the importance of considering these status-relevant precursors when investigating stress within social contexts. Title: PSYCHOSOCIAL AND ENDOCRINE ANTECEDENTS OF RESPONSES TO SOCIAL-EVALUATIVE STRESS Author: Knight, Erik Year: 2017 Stress often precedes the onset of physical and mental health disorders, leading to costly and extended disability and even increased risk for death. I investigate psychosocial and endocrine precursors to stress responses, specifically examining the causal effects of status-relevant factors that modulate endocrine, affective, and behavioral responses to social-evaluative stressors. For example, while high social status reduces stress responses in numerous species, this stress-buffering effect of status may dissipate or even reverse during times of hierarchical instability. Similarly, some research links testosterone to reduced stress system activity, but correlational research indicates that higher testosterone is related to increased stress responses in threatening social situations. In each case, the causal influence of these psychosocial (status and hierarchy stability) and endocrine (testosterone) antecedents to stress responses was unclear. Results from this work (Chapter 2) reveal that high status in a stable hierarchy buffered stress responses and improved behavioral responses to the stressor, but high status in an unstable hierarchy boosted stress responses and did not lead to better performance. This general pattern of effects was observed across endocrine (cortisol and testosterone), psychological (feeling in control), and behavioral (competence, dominance, and warmth) responses to the stressor. Further (Chapters 4 & 6), exogenous testosterone treatment caused increased motivated persistence – which can help persevere through stressful encounters – but, once exposed to a stressor, testosterone caused increased cortisol reactivity, increased negative affect, and decreased motivation in response to social-evaluative stress, especially for individuals high in trait dominance. This work provides evidence of the causal effects of psychosocial and endocrine factors on stress responses and demonstrates the importance of considering these status-relevant precursors when investigating stress within social contexts. Close

• 85. [Article] Production Risk, Inefficiency, and Sustainability of Pangas Fish Farming: Lessons from the Bangladesh Aquaculture Sector

  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: Production Risk, Inefficiency, and Sustainability of Pangas Fish Farming: Lessons from the Bangladesh Aquaculture Sector Author: Begum, Ratna, Nielsen, Rasmus, Akhtaruzzaman, Khan Md. 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: Production Risk, Inefficiency, and Sustainability of Pangas Fish Farming: Lessons from the Bangladesh Aquaculture Sector Author: Begum, Ratna, Nielsen, Rasmus, Akhtaruzzaman, Khan Md. 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

• 86. [Article] Landing Obligation Economic Impact Analysis

  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: Landing Obligation Economic Impact Analysis Author: Mardle, Simon, Metz, Sebastien, Russell, Jennifer, Cappell, Rod, Curtis, Hazel 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: Landing Obligation Economic Impact Analysis Author: Mardle, Simon, Metz, Sebastien, Russell, Jennifer, Cappell, Rod, Curtis, Hazel 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

• 87. [Article] Estimation of Commercial Fishing Trip Costs Using Sea Sampling Data

  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: Estimation of Commercial Fishing Trip Costs Using Sea Sampling Data Author: DePiper, Geret, Kitts, Andrew, Jin, Di 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: Estimation of Commercial Fishing Trip Costs Using Sea Sampling Data Author: DePiper, Geret, Kitts, Andrew, Jin, Di 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

• 88. [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

• 89. [Article] Urban Impacts to Forest Productivity, Soil Quality, and Canopy Structure in Forest Park, Portland, Oregon

  Land use practices and exposure to low impact disturbances associated with an urban environment can alter forest structure and function. Past and ongoing research in Forest Park, a large urban forest in ...

  Citation × Citation Citation Abstract Copy Title: Urban Impacts to Forest Productivity, Soil Quality, and Canopy Structure in Forest Park, Portland, Oregon Author: Addessi, Andrew David Year: 2017 Land use practices and exposure to low impact disturbances associated with an urban environment can alter forest structure and function. Past and ongoing research in Forest Park, a large urban forest in Portland, Oregon, suggests that mature mixed Douglas-fir (Psuedotsuga meziesii)-hardwood stands in the more urban end of the park lack a shade-tolerant conifer understory composed of the late successional conifer tree species, such western hemlock (Tsuga heterophylla) and western red-cedar (Thuja plicata). 5-year plot remeasurement data that characterizes productivity and mortality patterns did not show a strong relationship to urban proximity. Plot productivity was generally consistent with values taken from studies of other similarly aged (~100 years old) Douglas-fir /Western Hemlock stands. Mortality was highest in rural plots, and was driven by large windthrow events to canopy trees. Soil organic matter, soil pH, and depth of organic horizon indicated a legacy of soil impact in urban areas most impacted by past intensive logging. The urban mature plot had higher mean soil pH at site (5.87, se: ±0.06) compared to a rural mature, and old growth reference sites located within the park. Although surface organic and A layer soil horizon depth was thinnest at the urban mature site, soil organic matter was not found to be significantly different across sites. Light detection and ranging ( LiDAR) data showed that old-growth plots and plots in the middle section of the park had the highest degree of canopy structure as measured by Rumple and standard deviation of point elevation. Measures of stand height showed OG plots and urban plots to have the tallest trees. Rural plots showed a high degree of variability in all LiDAR metrics, showing a wider range of stand height and complexity than urban and middle plots. These results suggest that past land-use and urban proximity affect plot level productivity, soil quality, and above-ground canopy structure in Forest Park. These results clarify how the lack of late-successional tree species might be most linked to differing histories of intensive logging activity within the park. Reduced old-growth legacy features (remnant seed trees, coarse woody debris) in plots with a clear history of aggressive clear-cuts has led to a reduction in regeneration of western hemlock and western red-cedar in the understory. Title: Urban Impacts to Forest Productivity, Soil Quality, and Canopy Structure in Forest Park, Portland, Oregon Author: Addessi, Andrew David Year: 2017 Land use practices and exposure to low impact disturbances associated with an urban environment can alter forest structure and function. Past and ongoing research in Forest Park, a large urban forest in Portland, Oregon, suggests that mature mixed Douglas-fir (Psuedotsuga meziesii)-hardwood stands in the more urban end of the park lack a shade-tolerant conifer understory composed of the late successional conifer tree species, such western hemlock (Tsuga heterophylla) and western red-cedar (Thuja plicata). 5-year plot remeasurement data that characterizes productivity and mortality patterns did not show a strong relationship to urban proximity. Plot productivity was generally consistent with values taken from studies of other similarly aged (~100 years old) Douglas-fir /Western Hemlock stands. Mortality was highest in rural plots, and was driven by large windthrow events to canopy trees. Soil organic matter, soil pH, and depth of organic horizon indicated a legacy of soil impact in urban areas most impacted by past intensive logging. The urban mature plot had higher mean soil pH at site (5.87, se: ±0.06) compared to a rural mature, and old growth reference sites located within the park. Although surface organic and A layer soil horizon depth was thinnest at the urban mature site, soil organic matter was not found to be significantly different across sites. Light detection and ranging ( LiDAR) data showed that old-growth plots and plots in the middle section of the park had the highest degree of canopy structure as measured by Rumple and standard deviation of point elevation. Measures of stand height showed OG plots and urban plots to have the tallest trees. Rural plots showed a high degree of variability in all LiDAR metrics, showing a wider range of stand height and complexity than urban and middle plots. These results suggest that past land-use and urban proximity affect plot level productivity, soil quality, and above-ground canopy structure in Forest Park. These results clarify how the lack of late-successional tree species might be most linked to differing histories of intensive logging activity within the park. Reduced old-growth legacy features (remnant seed trees, coarse woody debris) in plots with a clear history of aggressive clear-cuts has led to a reduction in regeneration of western hemlock and western red-cedar in the understory. Close

• 90. [Article] Climate Change and Land Management Impact Rangeland Condition and Sage-Grouse Habitat in Southeastern Oregon

  Contemporary pressures on sagebrush steppe from climate change, exotic species, wildfire, and land use change threaten rangeland species such as the greater sage-grouse (Centrocercus urophasianus). To ...

  Citation × Citation Citation Abstract Copy Title: Climate Change and Land Management Impact Rangeland Condition and Sage-Grouse Habitat in Southeastern Oregon Author: Creutzburg, Megan K., Henderson, Emilie B., Conklin, David R. Year: 2015 Contemporary pressures on sagebrush steppe from climate change, exotic species, wildfire, and land use change threaten rangeland species such as the greater sage-grouse (Centrocercus urophasianus). To effectively manage sagebrush steppe landscapes for long-term goals, managers need information about the potential impacts of climate change, disturbances, and management activities. We integrated information from a dynamic global vegetation model, a sage-grouse habitat climate envelope model, and a state-and-transition simulation model to project broad-scale vegetation dynamics and potential sage-grouse habitat across 23.5 million acres in southeastern Oregon. We evaluated four climate scenarios, including continuing current climate and three scenarios of global climate change, and three management scenarios, including no management, current management and a sage-grouse habitat restoration scenario. All climate change scenarios projected expansion of moist shrub steppe and contraction of dry shrub steppe, but climate scenarios varied widely in the projected extent of xeric shrub steppe, where hot, dry summer conditions are unfavorable for sage-grouse. Wildfire increased by 26% over the century under current climate due to exotic grass encroachment, and by two- to four-fold across all climate change scenarios as extreme fire years became more frequent. Exotic grasses rapidly expanded in all scenarios as large areas of the landscape initially in semi-degraded condition converted to exotic-dominated systems. Due to the combination of exotic grass invasion, juniper encroachment, and climatic unsuitability for sage-grouse, projected sage-grouse habitat declined in the first several decades, but increased in area under the three climate change scenarios later in the century, as moist shrub steppe increased and rangeland condition improved. Management activities in the model were generally unsuccessful in controlling exotic grass invasion but were effective in slowing woodland expansion. Current levels of restoration treatments were insufficient to prevent some juniper expansion, but increased treatment rates under the restoration scenario maintained juniper near initial levels in priority treatment areas. Our simulations indicate that climate change may have both positive and negative implications for maintaining sage-grouse habitat. Title: Climate Change and Land Management Impact Rangeland Condition and Sage-Grouse Habitat in Southeastern Oregon Author: Creutzburg, Megan K., Henderson, Emilie B., Conklin, David R. Year: 2015 Contemporary pressures on sagebrush steppe from climate change, exotic species, wildfire, and land use change threaten rangeland species such as the greater sage-grouse (Centrocercus urophasianus). To effectively manage sagebrush steppe landscapes for long-term goals, managers need information about the potential impacts of climate change, disturbances, and management activities. We integrated information from a dynamic global vegetation model, a sage-grouse habitat climate envelope model, and a state-and-transition simulation model to project broad-scale vegetation dynamics and potential sage-grouse habitat across 23.5 million acres in southeastern Oregon. We evaluated four climate scenarios, including continuing current climate and three scenarios of global climate change, and three management scenarios, including no management, current management and a sage-grouse habitat restoration scenario. All climate change scenarios projected expansion of moist shrub steppe and contraction of dry shrub steppe, but climate scenarios varied widely in the projected extent of xeric shrub steppe, where hot, dry summer conditions are unfavorable for sage-grouse. Wildfire increased by 26% over the century under current climate due to exotic grass encroachment, and by two- to four-fold across all climate change scenarios as extreme fire years became more frequent. Exotic grasses rapidly expanded in all scenarios as large areas of the landscape initially in semi-degraded condition converted to exotic-dominated systems. Due to the combination of exotic grass invasion, juniper encroachment, and climatic unsuitability for sage-grouse, projected sage-grouse habitat declined in the first several decades, but increased in area under the three climate change scenarios later in the century, as moist shrub steppe increased and rangeland condition improved. Management activities in the model were generally unsuccessful in controlling exotic grass invasion but were effective in slowing woodland expansion. Current levels of restoration treatments were insufficient to prevent some juniper expansion, but increased treatment rates under the restoration scenario maintained juniper near initial levels in priority treatment areas. Our simulations indicate that climate change may have both positive and negative implications for maintaining sage-grouse habitat. Close

• 91. [Article] Bending the Carbon Curve: Fire Management for Carbon Resilience under Climate Change

  Context: Forest landscapes are increasingly managed for fire resilience, particularly in the western US which has recently experienced drought and widespread, high-severity wildfires. Fuel reduction treatments ...

  Citation × Citation Citation Abstract Copy Title: Bending the Carbon Curve: Fire Management for Carbon Resilience under Climate Change Author: Loudermilk, E. Louise, Scheller, Robert M., Weisberg, Peter J., Kretchun, Alec M. Year: 2017 Context: Forest landscapes are increasingly managed for fire resilience, particularly in the western US which has recently experienced drought and widespread, high-severity wildfires. Fuel reduction treatments have been effective where fires coincide with treated areas. Fuel treatments also have the potential to reduce drought-mortality if tree density is uncharacteristically high, and to increase long-term carbon storage by reducing high-severity fire probability. Objective: Assess whether fuel treatments reduce fire intensity and spread and increase carbon storage under climate change. Methods: We used a simulation modeling approach that couples a landscape model of forest disturbance and succession with an ecosystem model of carbon dynamics (Century), to quantify the interacting effects of climate change, fuel treatments and wildfire for carbon storage potential in a mixed-conifer forest in the western USA. Results: Our results suggest that fuel treatments have the potential to ‘bend the C curve’, maintaining carbon resilience despite climate change and climate-related changes to the fire regime. Simulated fuel treatments resulted in reduced fire spread and severity. There was partial compensation of C lost during fuel treatments with increased growth of residual stock due to greater available soil water, as well as a shift in species composition to more drought- and fire-tolerant Pinus jeffreyi at the expense of shade-tolerant, fire-susceptible Abies concolor. Conclusions: Forest resilience to global change can be achieved through management that reduces drought stress and supports the establishment and dominance of tree species that are more fire- and drought-resistant, however, achieving a net C gain from fuel treatments may take decades. Title: Bending the Carbon Curve: Fire Management for Carbon Resilience under Climate Change Author: Loudermilk, E. Louise, Scheller, Robert M., Weisberg, Peter J., Kretchun, Alec M. Year: 2017 Context: Forest landscapes are increasingly managed for fire resilience, particularly in the western US which has recently experienced drought and widespread, high-severity wildfires. Fuel reduction treatments have been effective where fires coincide with treated areas. Fuel treatments also have the potential to reduce drought-mortality if tree density is uncharacteristically high, and to increase long-term carbon storage by reducing high-severity fire probability. Objective: Assess whether fuel treatments reduce fire intensity and spread and increase carbon storage under climate change. Methods: We used a simulation modeling approach that couples a landscape model of forest disturbance and succession with an ecosystem model of carbon dynamics (Century), to quantify the interacting effects of climate change, fuel treatments and wildfire for carbon storage potential in a mixed-conifer forest in the western USA. Results: Our results suggest that fuel treatments have the potential to ‘bend the C curve’, maintaining carbon resilience despite climate change and climate-related changes to the fire regime. Simulated fuel treatments resulted in reduced fire spread and severity. There was partial compensation of C lost during fuel treatments with increased growth of residual stock due to greater available soil water, as well as a shift in species composition to more drought- and fire-tolerant Pinus jeffreyi at the expense of shade-tolerant, fire-susceptible Abies concolor. Conclusions: Forest resilience to global change can be achieved through management that reduces drought stress and supports the establishment and dominance of tree species that are more fire- and drought-resistant, however, achieving a net C gain from fuel treatments may take decades. Close

• 92. [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

• 93. [Article] Open Space as an Armature for Urban Expansion: A Future Scenarios Study to Assess the Effects of Spatial Concepts on Wildlife Populations

  Urbanization is one of the biggest threats to biodiversity. To address this problem, landscape planners have increasingly adopted landscape ecology as a theoretical basis for planning. They use spatial ...

  Citation × Citation Citation Abstract Copy Title: Open Space as an Armature for Urban Expansion: A Future Scenarios Study to Assess the Effects of Spatial Concepts on Wildlife Populations Author: Penteado, Homero Year: 2014 Urbanization is one of the biggest threats to biodiversity. To address this problem, landscape planners have increasingly adopted landscape ecology as a theoretical basis for planning. They use spatial concepts that express principles of landscape ecology in diagrammatic form to create frameworks for planning. This dissertation presents a quantitative approach to evaluate the application of spatial concepts developed to create an armature of open space in areas subject to urbanization. It focuses on the predicted urban expansion of Damascus, Oregon, as a case study. An alternative futures study was used to test three open space spatial concepts for patches, corridors and networks in combination with compact and dispersed urban development patterns. The resulting eight scenarios of land use and land cover were then modeled for the year 2060 to evaluate their effects on habitat quantity, quality and configuration and to identify tradeoffs between urban development and conservation for three focal wildlife species: Red-legged frog, Western meadowlark, and Douglas squirrel. Open space spatial concepts strongly influenced habitat quantity and quality differences among future scenarios. Development patterns showed less influence on those variables. Scenarios with no landscape ecological spatial concept provided the most land for urban development but reduced habitat quantity and quality. Greenway scenarios showed habitat increases but failed to provide sufficient habitat for Western meadowlark. Park system scenarios showed habitat increases, but high-quality habitats for Western meadowlark and Red-legged frog decreased. Network scenarios presented the best overall amount of habitats and high-quality habitats for the three species but constrained urban development options. Next, I used an individual-based wildlife model, HexSim, to simulate the effects of habitat configuration and to compare and contrast resulting wildlife population sizes among the eight future scenarios with the ca. 2010 baseline landscape. Network scenarios supported the largest number of Red-legged frog breeders. Park scenarios performed best for meadowlarks, while greenway scenarios showed the largest populations of squirrels. Four of the eight scenarios sustained viable populations of Western meadowlarks. Compact development scenarios performed best for most indicators, but dispersed development scenarios performed better for Western meadowlarks. This dissertation includes both previously published and unpublished material. Title: Open Space as an Armature for Urban Expansion: A Future Scenarios Study to Assess the Effects of Spatial Concepts on Wildlife Populations Author: Penteado, Homero Year: 2014 Urbanization is one of the biggest threats to biodiversity. To address this problem, landscape planners have increasingly adopted landscape ecology as a theoretical basis for planning. They use spatial concepts that express principles of landscape ecology in diagrammatic form to create frameworks for planning. This dissertation presents a quantitative approach to evaluate the application of spatial concepts developed to create an armature of open space in areas subject to urbanization. It focuses on the predicted urban expansion of Damascus, Oregon, as a case study. An alternative futures study was used to test three open space spatial concepts for patches, corridors and networks in combination with compact and dispersed urban development patterns. The resulting eight scenarios of land use and land cover were then modeled for the year 2060 to evaluate their effects on habitat quantity, quality and configuration and to identify tradeoffs between urban development and conservation for three focal wildlife species: Red-legged frog, Western meadowlark, and Douglas squirrel. Open space spatial concepts strongly influenced habitat quantity and quality differences among future scenarios. Development patterns showed less influence on those variables. Scenarios with no landscape ecological spatial concept provided the most land for urban development but reduced habitat quantity and quality. Greenway scenarios showed habitat increases but failed to provide sufficient habitat for Western meadowlark. Park system scenarios showed habitat increases, but high-quality habitats for Western meadowlark and Red-legged frog decreased. Network scenarios presented the best overall amount of habitats and high-quality habitats for the three species but constrained urban development options. Next, I used an individual-based wildlife model, HexSim, to simulate the effects of habitat configuration and to compare and contrast resulting wildlife population sizes among the eight future scenarios with the ca. 2010 baseline landscape. Network scenarios supported the largest number of Red-legged frog breeders. Park scenarios performed best for meadowlarks, while greenway scenarios showed the largest populations of squirrels. Four of the eight scenarios sustained viable populations of Western meadowlarks. Compact development scenarios performed best for most indicators, but dispersed development scenarios performed better for Western meadowlarks. This dissertation includes both previously published and unpublished material. Close

• 94. [Article] QueF and QueF-like: Diverse Chemistries in a Common Fold

  The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional ...

  Citation × Citation Citation Abstract Copy Title: QueF and QueF-like: Diverse Chemistries in a Common Fold Author: Bon Ramos, Adriana Year: 2016 The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional structure these enzymes perform very diverse chemistries. QueF is a bacterial NADPH-dependent oxidoreductase that catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to a primary amine (preQ1) in the queuosine biosynthetic pathway. Previous work on this enzyme has revealed the mechanism of reaction but the cofactor binding residues remain unknown. The experiments discussed herein aim to elucidate the role of residues lysine 80, lysine 83, and arginine 125 (B. subtilis numbering) in NADPH binding. The biological role of the disulfide bond between the conserved residues cysteine 55 and cysteine 99 observed in several crystal structures is also examined. Characterization of QueF mutants K80A, K83, R125A and R125K revealed lysine 80, lysine 83 and arginine 125 are required for turnover. Further analysis of turnover rates for R125K are consistent with this residue and both lysines being involved in cofactor binding presumably by interacting with the negatively charged phosphate tail of NADPH and are therefore involved in cofactor binding. Based on bond angles and energies, the disulfide bond between Cys55 and Cys99 was characterized as non-structural. Enzyme oxidation assays were consistent with the bond serving to protect QueF against irreversible oxidation of Cys55, which would render the enzyme inactive. This is the only known example of a stress protective mechanism in the Tunneling-fold superfamily. QueF-like is an amidinotransferase found in some species of Crenarchaeota and involved in the biosynthesis of archaeosine-tRNA. The work presented here is focused on the preliminary characterization of this enzyme, including the elucidation of the natural substrate as well as the source of ammonia. The structure of the enzyme was solved and is also discussed. Substrate analysis for QueF-like indicated this enzyme is capable of binding both preQ0 and preQ0-tRNA and reacting to form a thioimide intermediate analogous to QueF but only the latter serves as a substrate for the reaction. This makes QueF-like the first example of a nucleic acid binding enzyme in the Tunneling-fold superfamily. Ammonia, glutamine and asparagine were tested as nitrogen sources and unlike most known amidotransferases, QueF-like can only use free ammonia to produce the archaeosine-tRNA product. The crystal structure of P. calidifontis QueF-like indicates the functional enzyme is a dimer of pentamers pinned together by a large number of salt bridges. The structure presents a high degree of similarity to that of QueF albeit the higher twist of the QueF-like pentamers with respect to QueF results in a more compact structure. Title: QueF and QueF-like: Diverse Chemistries in a Common Fold Author: Bon Ramos, Adriana Year: 2016 The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional structure these enzymes perform very diverse chemistries. QueF is a bacterial NADPH-dependent oxidoreductase that catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to a primary amine (preQ1) in the queuosine biosynthetic pathway. Previous work on this enzyme has revealed the mechanism of reaction but the cofactor binding residues remain unknown. The experiments discussed herein aim to elucidate the role of residues lysine 80, lysine 83, and arginine 125 (B. subtilis numbering) in NADPH binding. The biological role of the disulfide bond between the conserved residues cysteine 55 and cysteine 99 observed in several crystal structures is also examined. Characterization of QueF mutants K80A, K83, R125A and R125K revealed lysine 80, lysine 83 and arginine 125 are required for turnover. Further analysis of turnover rates for R125K are consistent with this residue and both lysines being involved in cofactor binding presumably by interacting with the negatively charged phosphate tail of NADPH and are therefore involved in cofactor binding. Based on bond angles and energies, the disulfide bond between Cys55 and Cys99 was characterized as non-structural. Enzyme oxidation assays were consistent with the bond serving to protect QueF against irreversible oxidation of Cys55, which would render the enzyme inactive. This is the only known example of a stress protective mechanism in the Tunneling-fold superfamily. QueF-like is an amidinotransferase found in some species of Crenarchaeota and involved in the biosynthesis of archaeosine-tRNA. The work presented here is focused on the preliminary characterization of this enzyme, including the elucidation of the natural substrate as well as the source of ammonia. The structure of the enzyme was solved and is also discussed. Substrate analysis for QueF-like indicated this enzyme is capable of binding both preQ0 and preQ0-tRNA and reacting to form a thioimide intermediate analogous to QueF but only the latter serves as a substrate for the reaction. This makes QueF-like the first example of a nucleic acid binding enzyme in the Tunneling-fold superfamily. Ammonia, glutamine and asparagine were tested as nitrogen sources and unlike most known amidotransferases, QueF-like can only use free ammonia to produce the archaeosine-tRNA product. The crystal structure of P. calidifontis QueF-like indicates the functional enzyme is a dimer of pentamers pinned together by a large number of salt bridges. The structure presents a high degree of similarity to that of QueF albeit the higher twist of the QueF-like pentamers with respect to QueF results in a more compact structure. Close

• 95. [Article] Localized Ecological and Educational Effects of Environmental Service-Learning in Portland, Oregon

  Environmental service-learning is an intentional educational experience(s) wherein learners engage in meaningful activities designed to serve the environment. Environmental service-learning activities ...

  Citation × Citation Citation Abstract Copy Title: Localized Ecological and Educational Effects of Environmental Service-Learning in Portland, Oregon Author: Braun, Steven Matthew Year: 2015 Environmental service-learning is an intentional educational experience(s) wherein learners engage in meaningful activities designed to serve the environment. Environmental service-learning activities vary according to their learning and service goals and include ecomanagement, persuasion, legal action, economic action and political action. The purpose of this mixed methods research was to explore the ecological and educational impacts of grades 6-12 environmental education, with special attention to environmental service-learning throughout Portland, Oregon. Ecological impacts considered restoration and conservation outcomes of several environmental service-learning programs including plant communities, soils, litter removal and trail maintenance. Educational outcomes considered aspects of environmental literacy including locus of control, environmental sensitivity, indicated environmentally responsible behaviors, investigating environmental issues and knowledge of physical systems. The relative influence of some significant life experiences on youths' response to environmental education, including environmental service-learning, was also considered. Telephone surveys were used to gather data from 22 Portland metropolitan area environmental education programs. Data included 2014 annual biophysical impacts (e.g., area of invasive species removed, pounds of litter removed) and information on programming (e.g., length of program, % time outside). Eleven programs administered a 33-question environmental literacy assessment to participants of their programs (n=393). The assessment included the New Environmental Paradigm, the Inclusion of Nature in Self, questions from Environmental Identity Scale and self-constructed questions. One 8th grade program was identified for a detailed case study. In this 8th grade programs, slight variations in educational activities occurred among three treatment groups which varied the amount of time youth spent engaged in ecomanagement. Youth from the three treatment groups and a control group were administered the environmental literacy assessment at the beginning and end of the program. Qualitative data for the youth in the treatment groups were gathered to further consider how environmental literacy was impacted by participation in the program. Stronger associational correlations to environmental literacy occurred for the percentage of time an environmental education program spent outdoors rather than the percentage of time an environmental education program engaged in environmental service-learning (e.g., "With other people, I can work to make a positive impact on the environment." rho: .276 vs. "I have the skills necessary to make a positive impact on the environment" rho: .176). Random forests indicated that environmental education program features and some significant life experiences could predict collapsed environmental literacy variables (locus of control, environmental sensitivity and environmentally responsible behaviors). 22.4% of the variance in a collapsed environmental sensitivity variable was explained by nine predictor variables; those variables with the strongest influence were youth response to "Before this program, how frequently did you spend time in the outdoors," age and the presence of a positive adult role model who cares for the environment. Youth participating in environmental education programs showed higher environmental literacy than control groups (e.g., "I feel an important part of my life would be missing if I couldn't get out and enjoy nature from time to time" U: 3642.500, p: 0.025). Youth with significant formative life experiences (e.g., those indicating previous environmental education or a positive adult role model that cares for the environment) responded better (higher environmental literacy) to environmental education than those youth without ("I pay special attention to things outdoors" chi 10.633, p: 0.031). This research provides insight on the efficacy of environmental service-learning. Environmental service-learning positively affected environmental literacy, but outdoor environmental education was more effective in terms of environmental literacy. Results corroborate the body of literature regarding significant life experiences. Further, results suggest that significant life experiences are a critical development milestone necessary for youth to respond to environmental education on a developmental trajectory to empowered environmentally literate citizens. Title: Localized Ecological and Educational Effects of Environmental Service-Learning in Portland, Oregon Author: Braun, Steven Matthew Year: 2015 Environmental service-learning is an intentional educational experience(s) wherein learners engage in meaningful activities designed to serve the environment. Environmental service-learning activities vary according to their learning and service goals and include ecomanagement, persuasion, legal action, economic action and political action. The purpose of this mixed methods research was to explore the ecological and educational impacts of grades 6-12 environmental education, with special attention to environmental service-learning throughout Portland, Oregon. Ecological impacts considered restoration and conservation outcomes of several environmental service-learning programs including plant communities, soils, litter removal and trail maintenance. Educational outcomes considered aspects of environmental literacy including locus of control, environmental sensitivity, indicated environmentally responsible behaviors, investigating environmental issues and knowledge of physical systems. The relative influence of some significant life experiences on youths' response to environmental education, including environmental service-learning, was also considered. Telephone surveys were used to gather data from 22 Portland metropolitan area environmental education programs. Data included 2014 annual biophysical impacts (e.g., area of invasive species removed, pounds of litter removed) and information on programming (e.g., length of program, % time outside). Eleven programs administered a 33-question environmental literacy assessment to participants of their programs (n=393). The assessment included the New Environmental Paradigm, the Inclusion of Nature in Self, questions from Environmental Identity Scale and self-constructed questions. One 8th grade program was identified for a detailed case study. In this 8th grade programs, slight variations in educational activities occurred among three treatment groups which varied the amount of time youth spent engaged in ecomanagement. Youth from the three treatment groups and a control group were administered the environmental literacy assessment at the beginning and end of the program. Qualitative data for the youth in the treatment groups were gathered to further consider how environmental literacy was impacted by participation in the program. Stronger associational correlations to environmental literacy occurred for the percentage of time an environmental education program spent outdoors rather than the percentage of time an environmental education program engaged in environmental service-learning (e.g., "With other people, I can work to make a positive impact on the environment." rho: .276 vs. "I have the skills necessary to make a positive impact on the environment" rho: .176). Random forests indicated that environmental education program features and some significant life experiences could predict collapsed environmental literacy variables (locus of control, environmental sensitivity and environmentally responsible behaviors). 22.4% of the variance in a collapsed environmental sensitivity variable was explained by nine predictor variables; those variables with the strongest influence were youth response to "Before this program, how frequently did you spend time in the outdoors," age and the presence of a positive adult role model who cares for the environment. Youth participating in environmental education programs showed higher environmental literacy than control groups (e.g., "I feel an important part of my life would be missing if I couldn't get out and enjoy nature from time to time" U: 3642.500, p: 0.025). Youth with significant formative life experiences (e.g., those indicating previous environmental education or a positive adult role model that cares for the environment) responded better (higher environmental literacy) to environmental education than those youth without ("I pay special attention to things outdoors" chi 10.633, p: 0.031). This research provides insight on the efficacy of environmental service-learning. Environmental service-learning positively affected environmental literacy, but outdoor environmental education was more effective in terms of environmental literacy. Results corroborate the body of literature regarding significant life experiences. Further, results suggest that significant life experiences are a critical development milestone necessary for youth to respond to environmental education on a developmental trajectory to empowered environmentally literate citizens. Close

• 96. [Article] Understanding the Importance of Intermittently Fragmented Stream Habitat for Isolated Westslope Cutthroat Trout (<i>Oncorhynchus clarki lewisi</i>) in the Colville National Forest, Washington

  Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern ...

  Citation × Citation Citation Abstract Copy Title: Understanding the Importance of Intermittently Fragmented Stream Habitat for Isolated Westslope Cutthroat Trout (<i>Oncorhynchus clarki lewisi</i>) in the Colville National Forest, Washington Author: Carpenter, Forrest Michael Year: 2016 Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern Washington where this study was conducted. Many native salmonid populations have declined in abundance since the early 1900s due to a variety of climate- and human-driven forces. Westslope Cutthroat Trout are especially sensitive to habitat loss or degradation and to climate change. Together, climate change, habitat degradation, and non-native salmonid invasions are contributing to increasingly fragmented WCT populations. Ongoing and predicted future warming trends are expected to further fragment these populations and isolate them in headwater stream reaches, with populations in the spatial margins of their distributions facing greater risk. Native salmonid populations are often separated or isolated by natural or artificial upstream migration barriers (i.e., waterfalls, culverts, etc.). Prior to continuing conservation and management actions targeting WCT, it is imperative to understand habitat requirements of this keystone species in fragmented areas. Field survey data were collected in the summer of 2015 on channel geomorphic characteristics and WCT presence/absence in 26 streams located in the Colville National Forest. A clear spatial separation was observed between Eastern Brook Trout (Salvenius fontinalis, EBT) and WCT above four culvert road crossings and the habitat in both of these areas was compared statistically to identify explicit differences. This dataset was also analyzed using logistic regression modeling to determine the best habitat predictors of the presence of isolated WCT populations existing upstream of these crossing. In general, stream habitat in the Middle and South Forks of Mill Creek had low large substrate, high fine sediments, and exhibited pool-riffle channel morphology. Pool habitat supporting isolated WCT was significantly smaller, in terms of volume and surface area, than pool habitat supporting sympatric populations of WCT and EBT, largely due to the headwater nature of channel units supporting isolated WCT populations. Additionally, due to the extreme drought conditions during 2015, stream flow was substantially diminished in the study area causing these reaches to be highly fragmented and largely disconnected from the rest of the stream channel. Fine sediments were generally higher in headwater reaches supporting isolated WCT, including in pools and riffles, which was unexpected, mainly because they exist above sediment delivery points in the longitudinal extent of the system. Logistic regression analysis indicated that the presence of isolated WCT populations was primarily positively associated with an increase in large wood and boulders, and negatively associated with increasing gravel, bedrock, habitat unit length, depth, and width (Significant x2, R2=0.174, misclassification rate = 14.9%, α=0.05). The final model correctly predicted 37.5% of isolated WCT presence observations and 96.5% of the WCT/EBT presence observations significantly better than by chance alone (k=0.81). This model, in fact, may be useful in identifying limited habitat due to the fragmented nature of the channel units supporting IWCT. Large wood and boulders were positively correlated to WCT presence, likely because both are important in the formation of pools and cascades. Channel unit length, width, depth, active channel width as well as gravel and bedrock substrates, were all negatively associated with WCT presence. This suggests that isolated WCT are primarily associated with small headwater cascades with complex shelter, which may provide greater thermal and predation refuge compared to shallow glide or large pool habitats. Future model analysis should include additional habitat variables such as water temperature, stream gradient, and species interactions to strengthen the prediction of Westslope Cutthroat Trout presence. Overall, I concluded that differences in stream habitat above and below blocking culverts are not driving Westslope Cutthroat Trout distributions in the study area due to confounding factors such as the presence of problematic barriers and small sample size. I also conclude that future conservation and management decisions specific to WCT should prioritize complex cascade habitat in headwater stream reaches because of the type and quantity of habitat they may provide, especially during severe drought or low flow conditions. Title: Understanding the Importance of Intermittently Fragmented Stream Habitat for Isolated Westslope Cutthroat Trout (<i>Oncorhynchus clarki lewisi</i>) in the Colville National Forest, Washington Author: Carpenter, Forrest Michael Year: 2016 Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern Washington where this study was conducted. Many native salmonid populations have declined in abundance since the early 1900s due to a variety of climate- and human-driven forces. Westslope Cutthroat Trout are especially sensitive to habitat loss or degradation and to climate change. Together, climate change, habitat degradation, and non-native salmonid invasions are contributing to increasingly fragmented WCT populations. Ongoing and predicted future warming trends are expected to further fragment these populations and isolate them in headwater stream reaches, with populations in the spatial margins of their distributions facing greater risk. Native salmonid populations are often separated or isolated by natural or artificial upstream migration barriers (i.e., waterfalls, culverts, etc.). Prior to continuing conservation and management actions targeting WCT, it is imperative to understand habitat requirements of this keystone species in fragmented areas. Field survey data were collected in the summer of 2015 on channel geomorphic characteristics and WCT presence/absence in 26 streams located in the Colville National Forest. A clear spatial separation was observed between Eastern Brook Trout (Salvenius fontinalis, EBT) and WCT above four culvert road crossings and the habitat in both of these areas was compared statistically to identify explicit differences. This dataset was also analyzed using logistic regression modeling to determine the best habitat predictors of the presence of isolated WCT populations existing upstream of these crossing. In general, stream habitat in the Middle and South Forks of Mill Creek had low large substrate, high fine sediments, and exhibited pool-riffle channel morphology. Pool habitat supporting isolated WCT was significantly smaller, in terms of volume and surface area, than pool habitat supporting sympatric populations of WCT and EBT, largely due to the headwater nature of channel units supporting isolated WCT populations. Additionally, due to the extreme drought conditions during 2015, stream flow was substantially diminished in the study area causing these reaches to be highly fragmented and largely disconnected from the rest of the stream channel. Fine sediments were generally higher in headwater reaches supporting isolated WCT, including in pools and riffles, which was unexpected, mainly because they exist above sediment delivery points in the longitudinal extent of the system. Logistic regression analysis indicated that the presence of isolated WCT populations was primarily positively associated with an increase in large wood and boulders, and negatively associated with increasing gravel, bedrock, habitat unit length, depth, and width (Significant x2, R2=0.174, misclassification rate = 14.9%, α=0.05). The final model correctly predicted 37.5% of isolated WCT presence observations and 96.5% of the WCT/EBT presence observations significantly better than by chance alone (k=0.81). This model, in fact, may be useful in identifying limited habitat due to the fragmented nature of the channel units supporting IWCT. Large wood and boulders were positively correlated to WCT presence, likely because both are important in the formation of pools and cascades. Channel unit length, width, depth, active channel width as well as gravel and bedrock substrates, were all negatively associated with WCT presence. This suggests that isolated WCT are primarily associated with small headwater cascades with complex shelter, which may provide greater thermal and predation refuge compared to shallow glide or large pool habitats. Future model analysis should include additional habitat variables such as water temperature, stream gradient, and species interactions to strengthen the prediction of Westslope Cutthroat Trout presence. Overall, I concluded that differences in stream habitat above and below blocking culverts are not driving Westslope Cutthroat Trout distributions in the study area due to confounding factors such as the presence of problematic barriers and small sample size. I also conclude that future conservation and management decisions specific to WCT should prioritize complex cascade habitat in headwater stream reaches because of the type and quantity of habitat they may provide, especially during severe drought or low flow conditions. Close

• 97. [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

• 98. [Article] New 4-Aminoquinoline Compounds to Reverse Drug Resistance in <i>P. falciparum</i> Malaria, and a Survey of Early European Antimalarial Treatments

  Intermittent fevers caused by Plasmodium parasites have been known for millennia, and have caused untold human suffering. Today, millions of people are afflicted by malaria each year, and hundreds of thousands ...

  Citation × Citation Citation Abstract Copy Title: New 4-Aminoquinoline Compounds to Reverse Drug Resistance in <i>P. falciparum</i> Malaria, and a Survey of Early European Antimalarial Treatments Author: Liebman, Katherine May Year: 2014 Intermittent fevers caused by Plasmodium parasites have been known for millennia, and have caused untold human suffering. Today, millions of people are afflicted by malaria each year, and hundreds of thousands die. Historically, the most successful synthetic antimalarial drug was chloroquine, as it was safe, inexpensive, and highly efficacious. However, plasmodial resistance to chloroquine now greatly limits its utility. Previously in our laboratories it has been shown that attachment of a "reversal agent moiety" to the side chain of chloroquine can result in the restoration of activity against chloroquine-resistant strains of P. falciparum malaria. In the first part of the work presented here, a study has been made of the importance of the quinoline ring substitution pattern to the activity of such reversed chloroquines. The compounds presented here include those bearing a substituent in the 2-, 5, 6-, 7-, and/or 8- position, and include those with chloro, bromo, iodo, fluoro, nitro, trifluoromethyl, methyl, and methoxy substituents. For reversed chloroquines, 2-, 5-, and 8- substituents have been found to decrease in vitro antiplasmodial activity against P. falciparum relative to 7-chloro substitution, whereas 6- and 7- substituted compounds with various substituents have in many cases similar activity to that of 7-chloro substituted compounds. Little difference has been observed between 6- and 7- substitution, or between chlorine and a methyl group in position 6. In most cases these effects on activity are directionally similar to those observed for chloroquine analogs without an attached reversal agent, but the magnitude of the effect is generally smaller, suggesting that the activities of reversed chloroquines are less affected by modifications to the quinoline ring system than is true for chloroquine analogs without an attached reversal agent. The second portion of this work presents an asymmetrical bis-quinoline (PL241) that is highly active against P. falciparum malaria, with an IC50 of less than 0.1 nM for all strains tested. Mechanistic studies have been performed in which the substitution patterns of the two quinoline rings of PL241 are modified in ways that indicate that either ring system is equally capable of participating in the antimalarial activity of these compounds. The excellent in vitro antiplasmodial activity of PL241 makes this a compound of great interest for further development as a potential antimalarial drug. In the third part of this work, a survey has been made of antimalarial treatments recommended in the European medical literature from the time of Pliny the Elder (active in the first century A.D.) through the advent of modern malaria chemotherapy in the early twentieth century. In the fifteen primary sources utilized in this study, 251 distinct substances - primarily plants - were identified as having likely been used in the treatment of malaria. Of the 38 substances that were described in three or more sources, at least fifteen have been examined by other workers for antiplasmodial activity; in many cases, they were found to have antiplasmodial activity in vitro or in vivo. However, the majority of the phytotherapies for malaria identified in this project have not yet been tested against Plasmodium species, and may provide valuable leads in the search for new compounds active against drug-resistant malaria. Title: New 4-Aminoquinoline Compounds to Reverse Drug Resistance in <i>P. falciparum</i> Malaria, and a Survey of Early European Antimalarial Treatments Author: Liebman, Katherine May Year: 2014 Intermittent fevers caused by Plasmodium parasites have been known for millennia, and have caused untold human suffering. Today, millions of people are afflicted by malaria each year, and hundreds of thousands die. Historically, the most successful synthetic antimalarial drug was chloroquine, as it was safe, inexpensive, and highly efficacious. However, plasmodial resistance to chloroquine now greatly limits its utility. Previously in our laboratories it has been shown that attachment of a "reversal agent moiety" to the side chain of chloroquine can result in the restoration of activity against chloroquine-resistant strains of P. falciparum malaria. In the first part of the work presented here, a study has been made of the importance of the quinoline ring substitution pattern to the activity of such reversed chloroquines. The compounds presented here include those bearing a substituent in the 2-, 5, 6-, 7-, and/or 8- position, and include those with chloro, bromo, iodo, fluoro, nitro, trifluoromethyl, methyl, and methoxy substituents. For reversed chloroquines, 2-, 5-, and 8- substituents have been found to decrease in vitro antiplasmodial activity against P. falciparum relative to 7-chloro substitution, whereas 6- and 7- substituted compounds with various substituents have in many cases similar activity to that of 7-chloro substituted compounds. Little difference has been observed between 6- and 7- substitution, or between chlorine and a methyl group in position 6. In most cases these effects on activity are directionally similar to those observed for chloroquine analogs without an attached reversal agent, but the magnitude of the effect is generally smaller, suggesting that the activities of reversed chloroquines are less affected by modifications to the quinoline ring system than is true for chloroquine analogs without an attached reversal agent. The second portion of this work presents an asymmetrical bis-quinoline (PL241) that is highly active against P. falciparum malaria, with an IC50 of less than 0.1 nM for all strains tested. Mechanistic studies have been performed in which the substitution patterns of the two quinoline rings of PL241 are modified in ways that indicate that either ring system is equally capable of participating in the antimalarial activity of these compounds. The excellent in vitro antiplasmodial activity of PL241 makes this a compound of great interest for further development as a potential antimalarial drug. In the third part of this work, a survey has been made of antimalarial treatments recommended in the European medical literature from the time of Pliny the Elder (active in the first century A.D.) through the advent of modern malaria chemotherapy in the early twentieth century. In the fifteen primary sources utilized in this study, 251 distinct substances - primarily plants - were identified as having likely been used in the treatment of malaria. Of the 38 substances that were described in three or more sources, at least fifteen have been examined by other workers for antiplasmodial activity; in many cases, they were found to have antiplasmodial activity in vitro or in vivo. However, the majority of the phytotherapies for malaria identified in this project have not yet been tested against Plasmodium species, and may provide valuable leads in the search for new compounds active against drug-resistant malaria. Close

• 99. [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

• 100. [Article] Investigating the Link Between Surface Water and Groundwater in the Tule Lake Subbasin, Oregon and California

  Water allocation in the upper Klamath Basin of Oregon and California has been challenging. Irrigators have increasingly turned to groundwater to make up for surface water shortages because of shifts in ...

  Citation × Citation Citation Abstract Copy Title: Investigating the Link Between Surface Water and Groundwater in the Tule Lake Subbasin, Oregon and California Author: Pischel, Esther Maria Year: 2014 Water allocation in the upper Klamath Basin of Oregon and California has been challenging. Irrigators have increasingly turned to groundwater to make up for surface water shortages because of shifts in allocation toward in-stream flows for Endangered Species Act listed fishes. The largest increase in groundwater pumping has been in and around the Bureau of Reclamation's Klamath Irrigation Project, which includes the Tule Lake subbasin in the southern part of the upper Klamath Basin. Previous groundwater flow model simulations indicate that water level declines from pumping may result in decreased flow to agricultural drains in the Tule Lake subbasin. Agricultural drains on the Klamath Project are an important source of water for downstream irrigators and for the Tule Lake and Lower Klamath Lake National Wildlife Refuges. To better assess the impact of increased pumping on drain flow and on the water balance of the groundwater system, flow data from agricultural drains were evaluated to investigate the changes that have taken place in groundwater discharge to drains since pumping volumes increased. Additionally, a fine-grid groundwater model of the Tule Lake subbasin was developed based on the existing regional flow model. The fine-grid model has sufficient vertical and horizontal resolution to simulate vertical head gradients, takes advantage of time-series data from 38 observation wells for model calibration, and allows agricultural drains to be more explicitly represented. Results of the drain flow analysis show that the groundwater discharge to agricultural drains has decreased by approximately 4000 hectare-meters from the 1997-2000 average discharge. Most of this decrease takes place in the northern and southeastern portions of the subbasin. Results of the groundwater model show that the initial source of water to wells is groundwater storage. By 2006, approximately 56% of the water from wells is sourced from agricultural drains. Title: Investigating the Link Between Surface Water and Groundwater in the Tule Lake Subbasin, Oregon and California Author: Pischel, Esther Maria Year: 2014 Water allocation in the upper Klamath Basin of Oregon and California has been challenging. Irrigators have increasingly turned to groundwater to make up for surface water shortages because of shifts in allocation toward in-stream flows for Endangered Species Act listed fishes. The largest increase in groundwater pumping has been in and around the Bureau of Reclamation's Klamath Irrigation Project, which includes the Tule Lake subbasin in the southern part of the upper Klamath Basin. Previous groundwater flow model simulations indicate that water level declines from pumping may result in decreased flow to agricultural drains in the Tule Lake subbasin. Agricultural drains on the Klamath Project are an important source of water for downstream irrigators and for the Tule Lake and Lower Klamath Lake National Wildlife Refuges. To better assess the impact of increased pumping on drain flow and on the water balance of the groundwater system, flow data from agricultural drains were evaluated to investigate the changes that have taken place in groundwater discharge to drains since pumping volumes increased. Additionally, a fine-grid groundwater model of the Tule Lake subbasin was developed based on the existing regional flow model. The fine-grid model has sufficient vertical and horizontal resolution to simulate vertical head gradients, takes advantage of time-series data from 38 observation wells for model calibration, and allows agricultural drains to be more explicitly represented. Results of the drain flow analysis show that the groundwater discharge to agricultural drains has decreased by approximately 4000 hectare-meters from the 1997-2000 average discharge. Most of this decrease takes place in the northern and southeastern portions of the subbasin. Results of the groundwater model show that the initial source of water to wells is groundwater storage. By 2006, approximately 56% of the water from wells is sourced from agricultural drains. Close