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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] Estimating Watershed Biodiversity: An Empirical Study of the Chesapeake Bay in Maryland, USA

  There has been increasing demand for rigorous methods for evaluating biodiversity, one of the ecosystem services that sustains and fulfills human life. After carefully examining the literature, we found ...

  Citation × Citation Citation Abstract Copy Title: Estimating Watershed Biodiversity: An Empirical Study of the Chesapeake Bay in Maryland, USA Author: Morimoto, Junko, Voinov, Helena, Wilson, Matthew A., Costanza, Robert Year: 2003 There has been increasing demand for rigorous methods for evaluating biodiversity, one of the ecosystem services that sustains and fulfills human life. After carefully examining the literature, we found three key points that should be taken into account when we evaluate biodiversity. The first point is that any "indicator species" tends to be a leaky target of biodiversity. The second point is that "buffering" that is useful for representing the ecological concept of boundaries should have scientific meanings. The third point is that a "watershed" that integrates most natural processes is advantageous as the spatial range for evaluation. Based on these considerations, we developed the Biodiversity Probability Index (BPI) to account for biodiversity. We analyzed the relationship between BPI and total economic value of ecosystem services per unit area in order to test the reliability and utility of BPI. All BPI values were under a positive regression curve. The curve showed the highest economic value that could be achieved at a given biodiversity status. Based on our findings along the analysis, we conclude that the BPI has two advantages: (1) The BPI identifies the extent of the impact on biodiversity within a given landscape, and its composition of each category of species helps to identify what kind of wild life habitat could be seriously threatened by future land use development; (2) The BPI tells not only the biodiversity condition in ecological sense, but also provides the potential total economic value of ecosystem services, which will be achieved under ideal conditions. Title: Estimating Watershed Biodiversity: An Empirical Study of the Chesapeake Bay in Maryland, USA Author: Morimoto, Junko, Voinov, Helena, Wilson, Matthew A., Costanza, Robert Year: 2003 There has been increasing demand for rigorous methods for evaluating biodiversity, one of the ecosystem services that sustains and fulfills human life. After carefully examining the literature, we found three key points that should be taken into account when we evaluate biodiversity. The first point is that any "indicator species" tends to be a leaky target of biodiversity. The second point is that "buffering" that is useful for representing the ecological concept of boundaries should have scientific meanings. The third point is that a "watershed" that integrates most natural processes is advantageous as the spatial range for evaluation. Based on these considerations, we developed the Biodiversity Probability Index (BPI) to account for biodiversity. We analyzed the relationship between BPI and total economic value of ecosystem services per unit area in order to test the reliability and utility of BPI. All BPI values were under a positive regression curve. The curve showed the highest economic value that could be achieved at a given biodiversity status. Based on our findings along the analysis, we conclude that the BPI has two advantages: (1) The BPI identifies the extent of the impact on biodiversity within a given landscape, and its composition of each category of species helps to identify what kind of wild life habitat could be seriously threatened by future land use development; (2) The BPI tells not only the biodiversity condition in ecological sense, but also provides the potential total economic value of ecosystem services, which will be achieved under ideal conditions. Close

• 3. [Article] Mapping Conservation Opportunity Areas for the Intertwine's Regional Conservation Strategy

  As part of efforts to develop the Regional Conservation Strategy (RCS) for the greater Portland-Vancouver region, Oregon State University’s Institute for Natural Resources (INR) was asked to use spatial ...

  Citation × Citation Citation Abstract Copy Title: Mapping Conservation Opportunity Areas for the Intertwine's Regional Conservation Strategy Author: Burcsu, Theresa, Kagan, James S. Year: 2011 As part of efforts to develop the Regional Conservation Strategy (RCS) for the greater Portland-Vancouver region, Oregon State University’s Institute for Natural Resources (INR) was asked to use spatial modeling to identify conservation opportunity areas (COAs). To complete the project, INR analysts proposed a strategy that would map high value areas using a landscape approach that is focused on relatively high spatial resolution data sets available for the whole metropolitan region. The approach creates 2 main metrics: one focused on terrestrial organisms and the other focused on aquatic and riparian organisms. These are combined to create a map of highly ranked land areas that can be used to formulate a map of conservation opportunity areas. The purpose of the COA mapping project was to use geographic information system methods to identify landscape patches with conservation and restoration potential. The criteria used to identify these high value patches was based on a number of base- and derived-data sets that we call “data inputs.” The data ranged from recently mapped land use and land cover types, hydrological data to indicate species habitat requirements, and road influence on habitat patches. The project identified some areas in which data gaps exist (e.g., region-wide biodiversity data collected and mapped in consistent ways) and some opportunities for improving existent data sets (e.g., land use/land cover map). The project provided several layers that can be used to guide the final Regional Conservation Strategy in selecting conservation opportunity areas. The best layer will depend upon the needs of the RCS efforts, however, in our opinion the most appropriate layer to use is COA 3.11.1 which weights wetlands fairly high, but not as highly as the second data draft. COA 3.10.1 offers similar results as well. Overall it appears that the model results corroborate corridors analysis done previously (Hennings and Soll 2010). There are some issues remaining that we feel can most adequately be addressed by updating the base land use/land cover map. Title: Mapping Conservation Opportunity Areas for the Intertwine's Regional Conservation Strategy Author: Burcsu, Theresa, Kagan, James S. Year: 2011 As part of efforts to develop the Regional Conservation Strategy (RCS) for the greater Portland-Vancouver region, Oregon State University’s Institute for Natural Resources (INR) was asked to use spatial modeling to identify conservation opportunity areas (COAs). To complete the project, INR analysts proposed a strategy that would map high value areas using a landscape approach that is focused on relatively high spatial resolution data sets available for the whole metropolitan region. The approach creates 2 main metrics: one focused on terrestrial organisms and the other focused on aquatic and riparian organisms. These are combined to create a map of highly ranked land areas that can be used to formulate a map of conservation opportunity areas. The purpose of the COA mapping project was to use geographic information system methods to identify landscape patches with conservation and restoration potential. The criteria used to identify these high value patches was based on a number of base- and derived-data sets that we call “data inputs.” The data ranged from recently mapped land use and land cover types, hydrological data to indicate species habitat requirements, and road influence on habitat patches. The project identified some areas in which data gaps exist (e.g., region-wide biodiversity data collected and mapped in consistent ways) and some opportunities for improving existent data sets (e.g., land use/land cover map). The project provided several layers that can be used to guide the final Regional Conservation Strategy in selecting conservation opportunity areas. The best layer will depend upon the needs of the RCS efforts, however, in our opinion the most appropriate layer to use is COA 3.11.1 which weights wetlands fairly high, but not as highly as the second data draft. COA 3.10.1 offers similar results as well. Overall it appears that the model results corroborate corridors analysis done previously (Hennings and Soll 2010). There are some issues remaining that we feel can most adequately be addressed by updating the base land use/land cover map. Close

• 4. [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

• 5. [Article] Life history of Philophthalmus megalurus (Cort, 1914) in western Oregon

  The specific identification of a megalurous cercaria found in the snail Oxytrema plicifera was accomplished by completing the life cycle in the laboratory. This species is compared with the eastern Philophthalmus ...

  Citation × Citation Citation Abstract Copy Title: Life history of Philophthalmus megalurus (Cort, 1914) in western Oregon Author: McMillan, Toni Anne Year: 1971 The specific identification of a megalurous cercaria found in the snail Oxytrema plicifera was accomplished by completing the life cycle in the laboratory. This species is compared with the eastern Philophthalmus megalurus and P. gralli with which it was once confused. The eggs, miracidia, and rediae of the Oregon species were found to be similar to those of the above species. The body and organ sizes and sucker ratios for the cercariae and adult stages obviously indicate that the Oregon species is Philophthalmus megalurus. Title: Life history of Philophthalmus megalurus (Cort, 1914) in western Oregon Author: McMillan, Toni Anne Year: 1971 The specific identification of a megalurous cercaria found in the snail Oxytrema plicifera was accomplished by completing the life cycle in the laboratory. This species is compared with the eastern Philophthalmus megalurus and P. gralli with which it was once confused. The eggs, miracidia, and rediae of the Oregon species were found to be similar to those of the above species. The body and organ sizes and sucker ratios for the cercariae and adult stages obviously indicate that the Oregon species is Philophthalmus megalurus. 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] Population Structure of Island-Associated Pantropical Spotted Dolphins (Stenella attenuata) in Hawaiian Waters

  Understanding gene flow, diversity, and dispersal patterns is important for predicting effects of natural events and anthropogenic activities on dolphin populations. With the very recent exceptions of ...

  Citation × Citation Citation Abstract Copy Title: Population Structure of Island-Associated Pantropical Spotted Dolphins (Stenella attenuata) in Hawaiian Waters Author: Courbis, Sarah Shelby Year: 2011 Understanding gene flow, diversity, and dispersal patterns is important for predicting effects of natural events and anthropogenic activities on dolphin populations. With the very recent exceptions of false killer whales (Pseudorca crassidens), spinner dolphins (Stenella longirostris), and common bottlenose dolphins (Tursiops truncatus), Hawaiian odontocete species are managed as single stocks within the U.S. Hawaiian Exclusive Economic Zone. These exceptions are a result of recent studies that have indicated that some species have populations that show fidelity to individual islands or groups of islands, resulting in genetic differentiation, often with management implications. The first part of my study (following the introductory chapter) focused on population structure of pantropical spotted dolphins (Stenella attenuata) near the Hawaiian Islands. Because of the level of human interaction, pantropical spotted dolphin populations need to be defined accurately to be managed in a way that will avoid local population losses, especially given that the commercial and recreational troll fisheries near the islands "fish on dolphins" to catch tuna. I analyzed genetic samples for mtDNA and microsatellite loci from four island regions: Hawai'i, the 4-islands area, O'ahu, and Kaua'i/Ni'ihau. My results support genetic differentiation among the regions of Hawai'i, the 4-islands area, and O'ahu and suggest that pantropical spotted dolphins near Kaua'i/Ni'ihau are likely transient and in very low numbers. There was no strong evidence to support sex-biased dispersal or group fidelity. Possibly, differentiation is mediated by behavior adapted to differing habitat types. From a management perspective, spinner and bottlenose dolphin populations near the Hawaiian Islands have been split into separate stocks for management based on levels of genetic differentiation similar to those found for pantropical spotted dolphins. These precedents suggest that comparable action should be taken to split pantropical spotted dolphin stocks near the Hawaiian Islands. Most population studies rely heavily upon fixation indicies like FST to determine whether populations are genetically differentiated. When FST values are low but significantly different from zero, it can be difficult to interpret the biological significance of these values. As part of my study, I suggest that one way to evaluate whether small FST values indicate significant differentiation is to compare FST values with other populations considered to be separate based on factors such as extreme distance or morphological differences. I examined pantropical spotted dolphins from the coastal and offshore Eastern Tropical Pacificm (ETP), Hawaiian Islands, and China/Taiwan to examine the utility of comparing FST values across separate populations. Among Hawaiian Island regions, FST values are significantly different from zero but small. The comparison of these FST values with more distant populations in the ETP and China/Taiwan indicated that differences among Hawaiian Island regions were similar in magnitude to those found between the offshore and coastal ETP sub-species, but smaller than between the Hawaiian Island regions and the other regions examined. This suggests a level of reproductive isolation among the Hawaiian Islands regions that is comparable to that of offshore and coastal ETP populations, and supports the value of fixation index comparisons in evaluating differentiation among putative populations. My results suggest that assigning specific numerical baseline FST values may not always be biologically meaningful but that determining whether related populations with geographic or other separation show a preponderance of similar, lower, or higher fixation index values can help evaluate whether genetic differences among sympatric or parapatric groups warrants designating them as separate populations for management. Lastly, I explore whether the fast evolving mtDNA control region may be more suited to phylogenetic comparisons among the Stenella than slower evolving gene regions and whether the small number of haplotypes generally used in phylogenetic analyses is adequate for defining relationships among dolphins. Usually, slow evolving regions, such as gene regions, are used in phylogenetic analyses because species and genera have been isolated long enough for variation to have accumulated in such regions but not so long that many reversals (i.e. a mutational change in sequence that later changes back to the original sequence) have occured. The mtDNA control region is typically used for population genetic comparisons rather than phylogenetic comparisons because it is considered to be a fast evolving region. Historically, dolphin phylogeny has been examined using gene regions, which have resulted in ambiguous and unexpected relationships. However, the lack of variation in the mtDNA control region for pantropical spotted dolphin populations and the fact that recent studies have found that the mtDNA control region in cetaceans evolves at about one quarter the rate of other mammals, raises the question as to whether this region would be better suited to phylogenetic studies for the Stenella (and potentially other dolphin species). In comparing 346 haplotypes from five species of Stenella world-wide, I found that the mtDNA control region is probably not a good region to use for phylogenetic analyses, and that even faster evolving regions might perform better. The differences in the mtDNA control region were not sufficient to distinguish clear relationships among the Stenella. I also found that when subsets of haplotypes chosen at random were compared, the results differed among comparisons, suggesting that there is value in using more than the usual one or two haplotypes when making phylogentic comparisons. Given the recent increases in sequence availability (e.g. GenBank) and computing power, researchers should strongly consider using many haplotypes from a variety of populations in their phylogenetic comparisons. Title: Population Structure of Island-Associated Pantropical Spotted Dolphins (Stenella attenuata) in Hawaiian Waters Author: Courbis, Sarah Shelby Year: 2011 Understanding gene flow, diversity, and dispersal patterns is important for predicting effects of natural events and anthropogenic activities on dolphin populations. With the very recent exceptions of false killer whales (Pseudorca crassidens), spinner dolphins (Stenella longirostris), and common bottlenose dolphins (Tursiops truncatus), Hawaiian odontocete species are managed as single stocks within the U.S. Hawaiian Exclusive Economic Zone. These exceptions are a result of recent studies that have indicated that some species have populations that show fidelity to individual islands or groups of islands, resulting in genetic differentiation, often with management implications. The first part of my study (following the introductory chapter) focused on population structure of pantropical spotted dolphins (Stenella attenuata) near the Hawaiian Islands. Because of the level of human interaction, pantropical spotted dolphin populations need to be defined accurately to be managed in a way that will avoid local population losses, especially given that the commercial and recreational troll fisheries near the islands "fish on dolphins" to catch tuna. I analyzed genetic samples for mtDNA and microsatellite loci from four island regions: Hawai'i, the 4-islands area, O'ahu, and Kaua'i/Ni'ihau. My results support genetic differentiation among the regions of Hawai'i, the 4-islands area, and O'ahu and suggest that pantropical spotted dolphins near Kaua'i/Ni'ihau are likely transient and in very low numbers. There was no strong evidence to support sex-biased dispersal or group fidelity. Possibly, differentiation is mediated by behavior adapted to differing habitat types. From a management perspective, spinner and bottlenose dolphin populations near the Hawaiian Islands have been split into separate stocks for management based on levels of genetic differentiation similar to those found for pantropical spotted dolphins. These precedents suggest that comparable action should be taken to split pantropical spotted dolphin stocks near the Hawaiian Islands. Most population studies rely heavily upon fixation indicies like FST to determine whether populations are genetically differentiated. When FST values are low but significantly different from zero, it can be difficult to interpret the biological significance of these values. As part of my study, I suggest that one way to evaluate whether small FST values indicate significant differentiation is to compare FST values with other populations considered to be separate based on factors such as extreme distance or morphological differences. I examined pantropical spotted dolphins from the coastal and offshore Eastern Tropical Pacificm (ETP), Hawaiian Islands, and China/Taiwan to examine the utility of comparing FST values across separate populations. Among Hawaiian Island regions, FST values are significantly different from zero but small. The comparison of these FST values with more distant populations in the ETP and China/Taiwan indicated that differences among Hawaiian Island regions were similar in magnitude to those found between the offshore and coastal ETP sub-species, but smaller than between the Hawaiian Island regions and the other regions examined. This suggests a level of reproductive isolation among the Hawaiian Islands regions that is comparable to that of offshore and coastal ETP populations, and supports the value of fixation index comparisons in evaluating differentiation among putative populations. My results suggest that assigning specific numerical baseline FST values may not always be biologically meaningful but that determining whether related populations with geographic or other separation show a preponderance of similar, lower, or higher fixation index values can help evaluate whether genetic differences among sympatric or parapatric groups warrants designating them as separate populations for management. Lastly, I explore whether the fast evolving mtDNA control region may be more suited to phylogenetic comparisons among the Stenella than slower evolving gene regions and whether the small number of haplotypes generally used in phylogenetic analyses is adequate for defining relationships among dolphins. Usually, slow evolving regions, such as gene regions, are used in phylogenetic analyses because species and genera have been isolated long enough for variation to have accumulated in such regions but not so long that many reversals (i.e. a mutational change in sequence that later changes back to the original sequence) have occured. The mtDNA control region is typically used for population genetic comparisons rather than phylogenetic comparisons because it is considered to be a fast evolving region. Historically, dolphin phylogeny has been examined using gene regions, which have resulted in ambiguous and unexpected relationships. However, the lack of variation in the mtDNA control region for pantropical spotted dolphin populations and the fact that recent studies have found that the mtDNA control region in cetaceans evolves at about one quarter the rate of other mammals, raises the question as to whether this region would be better suited to phylogenetic studies for the Stenella (and potentially other dolphin species). In comparing 346 haplotypes from five species of Stenella world-wide, I found that the mtDNA control region is probably not a good region to use for phylogenetic analyses, and that even faster evolving regions might perform better. The differences in the mtDNA control region were not sufficient to distinguish clear relationships among the Stenella. I also found that when subsets of haplotypes chosen at random were compared, the results differed among comparisons, suggesting that there is value in using more than the usual one or two haplotypes when making phylogentic comparisons. Given the recent increases in sequence availability (e.g. GenBank) and computing power, researchers should strongly consider using many haplotypes from a variety of populations in their phylogenetic comparisons. Close

• 12. [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

• 13. [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

• 14. [Article] An analysis of Pteropus livingstonii roost habitat: Indicators for forest conservation on Anjouan and Moheli

  Livingstone's fruit bat (Pteropus livingstonii) is an endangered and endemic species found only on the islands of Anjouan and Mohéli, Comoros. A study was conducted into the habitats selected by P. livingstonii, ...

  Citation × Citation Citation Abstract Copy Title: An analysis of Pteropus livingstonii roost habitat: Indicators for forest conservation on Anjouan and Moheli Author: Granek, Elise F. Year: 2000 Livingstone's fruit bat (Pteropus livingstonii) is an endangered and endemic species found only on the islands of Anjouan and Mohéli, Comoros. A study was conducted into the habitats selected by P. livingstonii, as part of a project to assess areas for nature reserves which will be able to protect and conserve forest resources in the islands; the bat is postulated to be a useful indicator of undisturbed forest. Known roost sites (n=9) before the survey were between 500 and 1100 m altitude, on steeply sloping land, with some indigenous forest cover present. Thirteen new potential roost sites were identified, of which at least six were confirmed as roost sites for P. livingstonii. Bats showed positive associations with two tree species: Gambeya sp. and Nuxia pseudodentata. The study also investigated the participation by local village communities in monitoring bat populations, and the protection of roost sites. Title: An analysis of Pteropus livingstonii roost habitat: Indicators for forest conservation on Anjouan and Moheli Author: Granek, Elise F. Year: 2000 Livingstone's fruit bat (Pteropus livingstonii) is an endangered and endemic species found only on the islands of Anjouan and Mohéli, Comoros. A study was conducted into the habitats selected by P. livingstonii, as part of a project to assess areas for nature reserves which will be able to protect and conserve forest resources in the islands; the bat is postulated to be a useful indicator of undisturbed forest. Known roost sites (n=9) before the survey were between 500 and 1100 m altitude, on steeply sloping land, with some indigenous forest cover present. Thirteen new potential roost sites were identified, of which at least six were confirmed as roost sites for P. livingstonii. Bats showed positive associations with two tree species: Gambeya sp. and Nuxia pseudodentata. The study also investigated the participation by local village communities in monitoring bat populations, and the protection of roost sites. Close

• 15. [Article] Infection of smallmouth bass and goldfish by two species of Saprolegnia

  This study consisted of several experiments designed to compare the ability of two species of fungi, Saprolegnia ferax and S. parasitica to grow on two species of fish, smallmouth bass (Micropterus dolomieui) ...

  Citation × Citation Citation Abstract Copy Title: Infection of smallmouth bass and goldfish by two species of Saprolegnia Author: McGinley, Cheryl A. Year: 1974 This study consisted of several experiments designed to compare the ability of two species of fungi, Saprolegnia ferax and S. parasitica to grow on two species of fish, smallmouth bass (Micropterus dolomieui) and goldfish (Carassius auratus), and to determine the criteria necessary for the development of these infections. The results indicate that water in the fish tanks must be slightly acid (pH 6), warm (22°C), nonmoving, and that the fish must be wounded in order for fungal infection to occur. Cool water (18°C) and moving water, caused by aeration and filtration, are detrimental to fungal colony formation so that no infection occurs. Both S. ferax and S. parasitica infected both species of fish, on an average of three days after innoculation. The S. ferax infected a higher percentage of both fishes than did the S. parasitica. The difference in susceptibility of the two fish species to the fungi was negligible. Title: Infection of smallmouth bass and goldfish by two species of Saprolegnia Author: McGinley, Cheryl A. Year: 1974 This study consisted of several experiments designed to compare the ability of two species of fungi, Saprolegnia ferax and S. parasitica to grow on two species of fish, smallmouth bass (Micropterus dolomieui) and goldfish (Carassius auratus), and to determine the criteria necessary for the development of these infections. The results indicate that water in the fish tanks must be slightly acid (pH 6), warm (22°C), nonmoving, and that the fish must be wounded in order for fungal infection to occur. Cool water (18°C) and moving water, caused by aeration and filtration, are detrimental to fungal colony formation so that no infection occurs. Both S. ferax and S. parasitica infected both species of fish, on an average of three days after innoculation. The S. ferax infected a higher percentage of both fishes than did the S. parasitica. The difference in susceptibility of the two fish species to the fungi was negligible. Close

• 16. [Article] An Examination of Commercial Medicinal Plant Harvests, Mount Hood National Forest, Oregon

  During the past fifteen years, non-timber or special forest products have become an important economic resource in the Pacific Northwest. These products are primarily derived from understory species and ...

  Citation × Citation Citation Abstract Copy Title: An Examination of Commercial Medicinal Plant Harvests, Mount Hood National Forest, Oregon Author: Campbell, Shannon Michelle Year: 2000 During the past fifteen years, non-timber or special forest products have become an important economic resource in the Pacific Northwest. These products are primarily derived from understory species and contribute approximately $200 million to the regional economy. Medicinal plants are a little researched component of the non-timber forest product industry that relies on cultivated and wildcrafted (or wild-collected) medicinal plant species. This study examines the commercial extraction of wildcrafted medicinal plants from Mount Hood National Forest. Specifically, this study documents the medicinal plant species extracted from Mount Hood National Forest, their annual yield amounts, harvesting methods, and the changes in cover of target species after harvest. This research uses survey data obtained from employees of two herbal companies and representatives of the U.S. Forest Service to describe medicinal plant extraction and administration as it pertains to the commercial extraction of plant species from Mount Hood National Forest. Field data were also used to examine changes in plant cover for four medicinal plant species (kinnikinnick, yarrow, Oregon grape and valerian) following harvest. Field results indicate that medicinal plant cover decreased significantly in all but one harvested sampling unit. Permanent unit markers were established at all the study sites to provide opportunities for long-term monitoring of target species responses to harvest. Eleven medicinal plant species are commonly collected for commercial purposes from Mount Hood National Forest. The general lack of regulation and enforcement of commercial medicinal plant extraction coupled with an increasing demand for wildcrafted medicinal plants warrant a need for increased collaboration between regulatory agencies, herbal companies, and the general public. Additional management and research recommendations regarding the ecological impacts of medicinal plant removal are also presented. Title: An Examination of Commercial Medicinal Plant Harvests, Mount Hood National Forest, Oregon Author: Campbell, Shannon Michelle Year: 2000 During the past fifteen years, non-timber or special forest products have become an important economic resource in the Pacific Northwest. These products are primarily derived from understory species and contribute approximately $200 million to the regional economy. Medicinal plants are a little researched component of the non-timber forest product industry that relies on cultivated and wildcrafted (or wild-collected) medicinal plant species. This study examines the commercial extraction of wildcrafted medicinal plants from Mount Hood National Forest. Specifically, this study documents the medicinal plant species extracted from Mount Hood National Forest, their annual yield amounts, harvesting methods, and the changes in cover of target species after harvest. This research uses survey data obtained from employees of two herbal companies and representatives of the U.S. Forest Service to describe medicinal plant extraction and administration as it pertains to the commercial extraction of plant species from Mount Hood National Forest. Field data were also used to examine changes in plant cover for four medicinal plant species (kinnikinnick, yarrow, Oregon grape and valerian) following harvest. Field results indicate that medicinal plant cover decreased significantly in all but one harvested sampling unit. Permanent unit markers were established at all the study sites to provide opportunities for long-term monitoring of target species responses to harvest. Eleven medicinal plant species are commonly collected for commercial purposes from Mount Hood National Forest. The general lack of regulation and enforcement of commercial medicinal plant extraction coupled with an increasing demand for wildcrafted medicinal plants warrant a need for increased collaboration between regulatory agencies, herbal companies, and the general public. Additional management and research recommendations regarding the ecological impacts of medicinal plant removal are also presented. 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] Survey of Aquatic Plants in Corps of Engineers Reservoirs

  A survey of aquatic plants in a selected Corps of Engineers reservoirs in Oregon was conducted. Cottage Grove, Dorena, Fern Ridge, Dexter and Willow Creek Reservoirs contained abundant aquatic plants. ...

  Citation × Citation Citation Abstract Copy Title: Survey of Aquatic Plants in Corps of Engineers Reservoirs Author: Walker, Kimberly D., Sytsma, Mark D. Year: 2000 A survey of aquatic plants in a selected Corps of Engineers reservoirs in Oregon was conducted. Cottage Grove, Dorena, Fern Ridge, Dexter and Willow Creek Reservoirs contained abundant aquatic plants. Potamogeton pectinatus and Potamogeton epihydrous were the most common native plant species. Myriophyllum aquaticum and Potamogeton crispus were the most widespread nonnative plants. Species richness in the reservoirs was correlated with trophic status and basin morphology. Shallow reservoirs that included extensive areas of nutrient-rich sediments that were historic flood plain soils supported the greatest biomass and number of species. Mesotrophic reservoirs had lower species diversity. Oligotrophic reservoirs with steep basin morphology, nutrient-poor sediments, and large water level fluctuation did not support aquatic vascular plant populations. An aquatic plant management program should be developed for the reservoirs. The program should focus on preventing introduction and spread of invasive aquatic plants and on rapid response procedures for new infestations. Those reservoirs that currently support aquatic macrophyte communities may be most susceptible to invasion and rapid spread of new introductions, however, even reservoirs that are currently free of aquatic plants may be invaded. Early detection is critical to effective implementation of rapid response procedures for invasive aquatic plant control. Annual survey of the most productive reservoirs is recommended to document introduction of new species. Plant community composition changes during the growing season, and multiple surveys during the growing season are preferred over one-time visits. Management of established populations of invasive species in the reservoirs will be difficult. Where invasive plant abundance is limited in area and number management activities may be implemented to slow dispersal and perhaps eradicate the plants. Integrated pest management procedures should be followed to ensure effective and economical aquatic plant control. Title: Survey of Aquatic Plants in Corps of Engineers Reservoirs Author: Walker, Kimberly D., Sytsma, Mark D. Year: 2000 A survey of aquatic plants in a selected Corps of Engineers reservoirs in Oregon was conducted. Cottage Grove, Dorena, Fern Ridge, Dexter and Willow Creek Reservoirs contained abundant aquatic plants. Potamogeton pectinatus and Potamogeton epihydrous were the most common native plant species. Myriophyllum aquaticum and Potamogeton crispus were the most widespread nonnative plants. Species richness in the reservoirs was correlated with trophic status and basin morphology. Shallow reservoirs that included extensive areas of nutrient-rich sediments that were historic flood plain soils supported the greatest biomass and number of species. Mesotrophic reservoirs had lower species diversity. Oligotrophic reservoirs with steep basin morphology, nutrient-poor sediments, and large water level fluctuation did not support aquatic vascular plant populations. An aquatic plant management program should be developed for the reservoirs. The program should focus on preventing introduction and spread of invasive aquatic plants and on rapid response procedures for new infestations. Those reservoirs that currently support aquatic macrophyte communities may be most susceptible to invasion and rapid spread of new introductions, however, even reservoirs that are currently free of aquatic plants may be invaded. Early detection is critical to effective implementation of rapid response procedures for invasive aquatic plant control. Annual survey of the most productive reservoirs is recommended to document introduction of new species. Plant community composition changes during the growing season, and multiple surveys during the growing season are preferred over one-time visits. Management of established populations of invasive species in the reservoirs will be difficult. Where invasive plant abundance is limited in area and number management activities may be implemented to slow dispersal and perhaps eradicate the plants. Integrated pest management procedures should be followed to ensure effective and economical aquatic plant control. Close

• 19. [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

• 20. [Article] Effects of Increased Nitrogen Deposition on the Dominance of Hedera helix in the Pacific Northwest

  Increased nitrogen deposition has been shown to promote the dominance of invasive species, and nitrogen deposition rates have steadily increased in most of the Western United States in recent years due ...

  Citation × Citation Citation Abstract Copy Title: Effects of Increased Nitrogen Deposition on the Dominance of Hedera helix in the Pacific Northwest Author: Dolan, Bianca Christine Year: 2013 Increased nitrogen deposition has been shown to promote the dominance of invasive species, and nitrogen deposition rates have steadily increased in most of the Western United States in recent years due to population increases. The purpose of this study was to determine if increased rates of nitrogen deposition are contributing to the success of Hedera helix in the Pacific Northwest. Plots were established in Lesser Park in Portland, Oregon and received monthly treatments of ammonium nitrate for one year. Growth, measured as change in percent cover, was compared between treated and untreated plots for both H. helix and native species. Additionally, a greenhouse experiment was employed wherein H. helix was grown in shared pots with two native species, Fragaria vesca and Polystichum munitum, and three treatment levels were compared; none, low, and high nitrogen. Relative growth rate was compared between treatments for each species after twelve weeks of treatment. Results from the greenhouse experiment were highly variable and no general conclusions could be drawn about the effects of increased nitrogen deposition on competition between H. helix and native species. In the field, treatment did not have a significant effect on growth but species did have a significant effect, as H. helix had a greater increase in percent cover than native species regardless of treatment. However, a marginally significant interaction was found between species and treatment. Native species cover actually increased in plots that received nitrogen addition and decreased in control plots, while H. helix had a slightly higher increase in cover in control plots. Though the growth of H. helix was significantly higher than the growth of native species in control plots, nitrogen addition caused the growth rates to converge towards more similar means in treated plots. Results indicate that increased nitrogen deposition may actually have a positive effect on the growth of native species by reducing the invasive potential of H. helix. Title: Effects of Increased Nitrogen Deposition on the Dominance of Hedera helix in the Pacific Northwest Author: Dolan, Bianca Christine Year: 2013 Increased nitrogen deposition has been shown to promote the dominance of invasive species, and nitrogen deposition rates have steadily increased in most of the Western United States in recent years due to population increases. The purpose of this study was to determine if increased rates of nitrogen deposition are contributing to the success of Hedera helix in the Pacific Northwest. Plots were established in Lesser Park in Portland, Oregon and received monthly treatments of ammonium nitrate for one year. Growth, measured as change in percent cover, was compared between treated and untreated plots for both H. helix and native species. Additionally, a greenhouse experiment was employed wherein H. helix was grown in shared pots with two native species, Fragaria vesca and Polystichum munitum, and three treatment levels were compared; none, low, and high nitrogen. Relative growth rate was compared between treatments for each species after twelve weeks of treatment. Results from the greenhouse experiment were highly variable and no general conclusions could be drawn about the effects of increased nitrogen deposition on competition between H. helix and native species. In the field, treatment did not have a significant effect on growth but species did have a significant effect, as H. helix had a greater increase in percent cover than native species regardless of treatment. However, a marginally significant interaction was found between species and treatment. Native species cover actually increased in plots that received nitrogen addition and decreased in control plots, while H. helix had a slightly higher increase in cover in control plots. Though the growth of H. helix was significantly higher than the growth of native species in control plots, nitrogen addition caused the growth rates to converge towards more similar means in treated plots. Results indicate that increased nitrogen deposition may actually have a positive effect on the growth of native species by reducing the invasive potential of H. helix. Close

• 21. [Article] The Effectiveness of Vertebrate Passage and Prevention Structures: A Study of Boeckman Road in Wilsonville

  One of the most obvious impacts roads have on the natural world is direct mortality to individual animals that attempt to cross roads. A less obvious but likely more important impact of roads on many species ...

  Citation × Citation Citation Abstract Copy Title: The Effectiveness of Vertebrate Passage and Prevention Structures: A Study of Boeckman Road in Wilsonville Author: de Rivera, Catherine E., Bliss-Ketchum, Leslie L. Year: 2010 One of the most obvious impacts roads have on the natural world is direct mortality to individual animals that attempt to cross roads. A less obvious but likely more important impact of roads on many species is habitat fragmentation. The ability for individuals to travel between subpopulations is the key to genetic diversity as well as ultimately the survival of the species. Considering these impacts and management goals to increase habitat connectivity, increased attention has been given to creating road design that reduces wildlife collisions. Most studies, however, have been in other countries or regions and most focus on connectivity for just one or a few species and rarely in urban settings. This study examines the effectiveness of a variety of under-road passage structures for a community of animals in an urban wetland. Wildlife passage was taken into great consideration in the construction of the Boeckman Road Extension, the new road (2006) in Wilsonville, Oregon, examined in this study. As a result it includes a bridge, two box culverts and eleven round concrete culverts to facilitate wildlife passage as well as a mammal fence atop an amphibian/reptile wall. In order to monitor passage use we used a combination of sand-track monitoring and motion-detect cameras. We compared passage structure use to movement in the habitats surrounding the road by monitoring four habitat transects in addition to the passage structures (Road transect). We also conducted tag and release studies targeted to small mammals. Finally, camera data collected in passage structures were compared to camera monitoring at the end of the exclusionary fencing. A total of 26 species were detected in this study, 73% (19) of which were found to be using passage structures. 15% (4) of the identified species were detected on transects but not in passages and 11.5% (3) were detected in locations other than transects or passage structures. The bridge structure provided passage to the highest number of species (16), followed by the 24” and 18” culverts, which had a combined total of 11 species, and lastly the 9x4 culverts, which were flooded, with 2 species detected. Our results indicate that large and medium mammals overall did not use passages less than would be expected based on their local movement in habitats. In pit and Sherman traps sixteen of the 48 small mammals that were captured and tagged were re-caught, but only four of these moved from one transect to another, with two moving away from the road and the other two moving toward and under the road. Of the species detected with cameras at the passage structures and circumventing fencing, excluding small mammals, reptiles and amphibians (139), 19% (33) were found potentially crossing on the road surface. The proportion of deer detected using over-road crossings (23%) is of particular concern for driver safety. The bridge structure provided the greatest passage, in not only frequency of crossings but also species present. When maintenance factors, driver safety and species of greatest concern are included, the higher cost of the bridge structure would likely be even further balanced by the benefits. This study highlights the effectiveness and potential problems (and possible fixes) of some of the passage and prevention structures. Including passage and prevention structures such as these in road design is imperative for habitat connectivity and the need for this becomes even more apparent as Oregon’s native wildlife face an ever increasing urban landscape as well as the potential impacts of climate change. Title: The Effectiveness of Vertebrate Passage and Prevention Structures: A Study of Boeckman Road in Wilsonville Author: de Rivera, Catherine E., Bliss-Ketchum, Leslie L. Year: 2010 One of the most obvious impacts roads have on the natural world is direct mortality to individual animals that attempt to cross roads. A less obvious but likely more important impact of roads on many species is habitat fragmentation. The ability for individuals to travel between subpopulations is the key to genetic diversity as well as ultimately the survival of the species. Considering these impacts and management goals to increase habitat connectivity, increased attention has been given to creating road design that reduces wildlife collisions. Most studies, however, have been in other countries or regions and most focus on connectivity for just one or a few species and rarely in urban settings. This study examines the effectiveness of a variety of under-road passage structures for a community of animals in an urban wetland. Wildlife passage was taken into great consideration in the construction of the Boeckman Road Extension, the new road (2006) in Wilsonville, Oregon, examined in this study. As a result it includes a bridge, two box culverts and eleven round concrete culverts to facilitate wildlife passage as well as a mammal fence atop an amphibian/reptile wall. In order to monitor passage use we used a combination of sand-track monitoring and motion-detect cameras. We compared passage structure use to movement in the habitats surrounding the road by monitoring four habitat transects in addition to the passage structures (Road transect). We also conducted tag and release studies targeted to small mammals. Finally, camera data collected in passage structures were compared to camera monitoring at the end of the exclusionary fencing. A total of 26 species were detected in this study, 73% (19) of which were found to be using passage structures. 15% (4) of the identified species were detected on transects but not in passages and 11.5% (3) were detected in locations other than transects or passage structures. The bridge structure provided passage to the highest number of species (16), followed by the 24” and 18” culverts, which had a combined total of 11 species, and lastly the 9x4 culverts, which were flooded, with 2 species detected. Our results indicate that large and medium mammals overall did not use passages less than would be expected based on their local movement in habitats. In pit and Sherman traps sixteen of the 48 small mammals that were captured and tagged were re-caught, but only four of these moved from one transect to another, with two moving away from the road and the other two moving toward and under the road. Of the species detected with cameras at the passage structures and circumventing fencing, excluding small mammals, reptiles and amphibians (139), 19% (33) were found potentially crossing on the road surface. The proportion of deer detected using over-road crossings (23%) is of particular concern for driver safety. The bridge structure provided the greatest passage, in not only frequency of crossings but also species present. When maintenance factors, driver safety and species of greatest concern are included, the higher cost of the bridge structure would likely be even further balanced by the benefits. This study highlights the effectiveness and potential problems (and possible fixes) of some of the passage and prevention structures. Including passage and prevention structures such as these in road design is imperative for habitat connectivity and the need for this becomes even more apparent as Oregon’s native wildlife face an ever increasing urban landscape as well as the potential impacts of climate change. Close

• 22. [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

• 23. [Article] The Effects of Urbanization and Human Disturbance Upon Plant Community Structure and Bird Species Richness, Diversity, and Abundance in a Natural Forested Area (Forest Park) in Portland, Oregon

  The effects of urbanization and continual human disturbance on the plant and avian communities of Forest Park and forested lands surrounding Portland, Oregon, were studied. I examined characteristics of ...

  Citation × Citation Citation Abstract Copy Title: The Effects of Urbanization and Human Disturbance Upon Plant Community Structure and Bird Species Richness, Diversity, and Abundance in a Natural Forested Area (Forest Park) in Portland, Oregon Author: Broshot, Nancy Ellen Year: 1999 The effects of urbanization and continual human disturbance on the plant and avian communities of Forest Park and forested lands surrounding Portland, Oregon, were studied. I examined characteristics of plant and avian communities at 25 sites, 24 which were in Forest Park and surrounding areas and one which was in the Ancient Forest Preserve (old-growth stand) northwest of Forest Park. Data were analyzed using multiple regression, ANOV A, and Bonferonni/Dunn. Seven variables were selected representing different urbanization gradients. An additional covariable coded for the old-growth stand, allowing it to be used as a control. Many tree variables, especially those related to shade-tolerant species, were positively correlated with both the distance from downtown Portland and the number of houses in the surrounding area, and negatively correlated with the distance from the nearest forest edge; however, many shrub and herbaceous variables were negatively correlated with the distance from downtown Portland. Species diversity for herbaceous and shrub species was greater at more urban sites, but diversity of trees was lower at more urban sites. There were significantly more non-native species of plants in the city section. I found significantly fewer saplings and small trees, especially shade-tolerant species, in the section of Forest Park closest to downtown Portland, although tree mortality was positively correlated with distance from Portland. Summer bird data revealed significant increases in the abundances of urban and edge species at more urban sites, with concomitant reductions in forest species. There were significantly more ground gleaning birds and short distance migratory species. I also found a significantly greater abundance of birds in the old-growth stand during the winter. This increase was positively correlated with the depth of snow in the nearby Cascade Mountains. My results indicate that Forest Park is apparently progressing in a normal successional pattern with the exception of the city section. The reduction in shade tolerant saplings and small trees in the city section suggest that rate of succession has been slower at more urban sites. Avian data suggest that urbanization affects bird species abundance and guild composition in the more urban areas. Title: The Effects of Urbanization and Human Disturbance Upon Plant Community Structure and Bird Species Richness, Diversity, and Abundance in a Natural Forested Area (Forest Park) in Portland, Oregon Author: Broshot, Nancy Ellen Year: 1999 The effects of urbanization and continual human disturbance on the plant and avian communities of Forest Park and forested lands surrounding Portland, Oregon, were studied. I examined characteristics of plant and avian communities at 25 sites, 24 which were in Forest Park and surrounding areas and one which was in the Ancient Forest Preserve (old-growth stand) northwest of Forest Park. Data were analyzed using multiple regression, ANOV A, and Bonferonni/Dunn. Seven variables were selected representing different urbanization gradients. An additional covariable coded for the old-growth stand, allowing it to be used as a control. Many tree variables, especially those related to shade-tolerant species, were positively correlated with both the distance from downtown Portland and the number of houses in the surrounding area, and negatively correlated with the distance from the nearest forest edge; however, many shrub and herbaceous variables were negatively correlated with the distance from downtown Portland. Species diversity for herbaceous and shrub species was greater at more urban sites, but diversity of trees was lower at more urban sites. There were significantly more non-native species of plants in the city section. I found significantly fewer saplings and small trees, especially shade-tolerant species, in the section of Forest Park closest to downtown Portland, although tree mortality was positively correlated with distance from Portland. Summer bird data revealed significant increases in the abundances of urban and edge species at more urban sites, with concomitant reductions in forest species. There were significantly more ground gleaning birds and short distance migratory species. I also found a significantly greater abundance of birds in the old-growth stand during the winter. This increase was positively correlated with the depth of snow in the nearby Cascade Mountains. My results indicate that Forest Park is apparently progressing in a normal successional pattern with the exception of the city section. The reduction in shade tolerant saplings and small trees in the city section suggest that rate of succession has been slower at more urban sites. Avian data suggest that urbanization affects bird species abundance and guild composition in the more urban areas. Close

• 24. [Article] Biostratigraphy of the type Weberg Member, Snowshoe Formation, Grant County, Oregon

  Thirty three species of ammonites are recorded from the composite type section of the Weberg Member of the Snowshoe Formation in the Suplee area, Grant County, Oregon. Holcophylloceras burkei, Euhoploceras ...

  Citation × Citation Citation Abstract Copy Title: Biostratigraphy of the type Weberg Member, Snowshoe Formation, Grant County, Oregon Author: Taylor, David G. Year: 1977 Thirty three species of ammonites are recorded from the composite type section of the Weberg Member of the Snowshoe Formation in the Suplee area, Grant County, Oregon. Holcophylloceras burkei, Euhoploceras westi, E. tubereulosum and Strigoceras taylori are described as new, while four new species belonging to the genera Sonninia [?], Bradfordia, Pseudotoites and Witchellia are not formally named. Three ammonite zonules characterize the ammonite sequence of the type Weberg composite section. The sequence correlates with parts of the standard lower and middle Bajocian (Jurassic) of northwestern Europe. In addition, four associations (paleo-communities) of benthic mega invertebrates, the Gervillia, Protocardia, Isocyprina and Bositra buahii associations are delineated. The type Weberg composite section is a record of a local marine transgression westward onto an island system. The section also represents sedimentation over an irregular pre-Snowshoe topographic high, and indicates a progressive change from proximal to distal source of pre-Snowshoe sediments, from high to low energy conditions, and perhaps a slight deepening of the ocean bottom. Ammonites are rare in the lower division of the Weberg Member, locally present in fine sandy limestones of the lower part of the upper division, abundant and most diverse in silt-rich, clay-poor limestones of the upper part of the upper division, and locally abundant in mudstones of the Warm Springs Member. Recurrent associations of certain ammonite species, strong correlation of the associations with lithofacies and biofacies, and pervasive faunal differences of ammonites between facies indicate in general that the distributional patterns of the ammonites reflect spatial life-habitats. The spotty yet widespread geographic occurrence of several ammonite species suggest they had undergone extensive planktic dispersal, thus ocean currents probably played an important role in their distributional patterns. Title: Biostratigraphy of the type Weberg Member, Snowshoe Formation, Grant County, Oregon Author: Taylor, David G. Year: 1977 Thirty three species of ammonites are recorded from the composite type section of the Weberg Member of the Snowshoe Formation in the Suplee area, Grant County, Oregon. Holcophylloceras burkei, Euhoploceras westi, E. tubereulosum and Strigoceras taylori are described as new, while four new species belonging to the genera Sonninia [?], Bradfordia, Pseudotoites and Witchellia are not formally named. Three ammonite zonules characterize the ammonite sequence of the type Weberg composite section. The sequence correlates with parts of the standard lower and middle Bajocian (Jurassic) of northwestern Europe. In addition, four associations (paleo-communities) of benthic mega invertebrates, the Gervillia, Protocardia, Isocyprina and Bositra buahii associations are delineated. The type Weberg composite section is a record of a local marine transgression westward onto an island system. The section also represents sedimentation over an irregular pre-Snowshoe topographic high, and indicates a progressive change from proximal to distal source of pre-Snowshoe sediments, from high to low energy conditions, and perhaps a slight deepening of the ocean bottom. Ammonites are rare in the lower division of the Weberg Member, locally present in fine sandy limestones of the lower part of the upper division, abundant and most diverse in silt-rich, clay-poor limestones of the upper part of the upper division, and locally abundant in mudstones of the Warm Springs Member. Recurrent associations of certain ammonite species, strong correlation of the associations with lithofacies and biofacies, and pervasive faunal differences of ammonites between facies indicate in general that the distributional patterns of the ammonites reflect spatial life-habitats. The spotty yet widespread geographic occurrence of several ammonite species suggest they had undergone extensive planktic dispersal, thus ocean currents probably played an important role in their distributional patterns. Close

• 25. [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

• 26. [Article] Mammals of the Bull Run

  This study of mammals of the Bull Run Planning Unit has a dual character. First, mammals of special scientific or natural history interest such as threatened or endangered species were sought. This was ...

  Citation × Citation Citation Abstract Copy Title: Mammals of the Bull Run Author: Thatcher, Edward M. Year: 1976 This study of mammals of the Bull Run Planning Unit has a dual character. First, mammals of special scientific or natural history interest such as threatened or endangered species were sought. This was in conjunction with a Mt. Hood Bull Run Planning Unit. Second, a zoogeographical study of mammals of the Bull Run was performed. Abundance and distributional data was recorded for each species observed. This data was related to availability to moisture as indicated by plant associations trapped. Difference in habitat utilization along a moisture gradient was investigated as a possible coexistence mechanism for sympatric small mammals in the Bull Run Planning Unit. Title: Mammals of the Bull Run Author: Thatcher, Edward M. Year: 1976 This study of mammals of the Bull Run Planning Unit has a dual character. First, mammals of special scientific or natural history interest such as threatened or endangered species were sought. This was in conjunction with a Mt. Hood Bull Run Planning Unit. Second, a zoogeographical study of mammals of the Bull Run was performed. Abundance and distributional data was recorded for each species observed. This data was related to availability to moisture as indicated by plant associations trapped. Difference in habitat utilization along a moisture gradient was investigated as a possible coexistence mechanism for sympatric small mammals in the Bull Run Planning Unit. Close

• 27. [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

• 28. [Article] Pressure dependence of fluorescent and photolytic interferences in HO detection by laser-excited fluorescence

  In the measurement of HO concentrations by laser-excited fluorescence, expansion of the sampled air offers a way to reduce fluorescent and photolytic interference by other species. The decrease in [HO] ...

  Citation × Citation Citation Abstract Copy Title: Pressure dependence of fluorescent and photolytic interferences in HO detection by laser-excited fluorescence Author: Hard, Thomas M., O'Brien, Robert J., Cook, T. B. Year: 1980 In the measurement of HO concentrations by laser-excited fluorescence, expansion of the sampled air offers a way to reduce fluorescent and photolytic interference by other species. The decrease in [HO] upon expansion is balanced by an increase in HO fluorescence yield over a wide range of pressures. Background air fluorescence is reduced if the responsible species have fluorescence yields higher than those of HO. Preliminary experiments indicate that most of the fluorescence observed in laboratory air is due to such species. Upon expansion, the suppression of fluorescent interference can be no greater than the reduction in pressure, whereas the suppression of photolytic interference can be no less. Title: Pressure dependence of fluorescent and photolytic interferences in HO detection by laser-excited fluorescence Author: Hard, Thomas M., O'Brien, Robert J., Cook, T. B. Year: 1980 In the measurement of HO concentrations by laser-excited fluorescence, expansion of the sampled air offers a way to reduce fluorescent and photolytic interference by other species. The decrease in [HO] upon expansion is balanced by an increase in HO fluorescence yield over a wide range of pressures. Background air fluorescence is reduced if the responsible species have fluorescence yields higher than those of HO. Preliminary experiments indicate that most of the fluorescence observed in laboratory air is due to such species. Upon expansion, the suppression of fluorescent interference can be no greater than the reduction in pressure, whereas the suppression of photolytic interference can be no less. Close

• 29. [Article] The significance of hypovolemia in dehydrational death in anurans

  The importance of hypovolemia in dehydrational death was assessed in two anuran species. Xenopus laeyis, a species which experiences a significant reduction in circulating plasma volume with dehydration, ...

  Citation × Citation Citation Abstract Copy Title: The significance of hypovolemia in dehydrational death in anurans Author: Kimmel, Peter Blair Year: 1985 The importance of hypovolemia in dehydrational death was assessed in two anuran species. Xenopus laeyis, a species which experiences a significant reduction in circulating plasma volume with dehydration, was used to evaluate the role of sympathetic reflex compensation in hypovolemia. Adrenergic blockade with propranolol or phenoxybenzamine produced no significant reduction in dehydration tolerance in this species, although β-blockade with propranolol appeared to have a minor effect. The role of hypovolemic shock in the terminal circulatory collapse that precedes death in dehydrating anurans was investigated in the toad, Bufo marinus. The activity of lysosomal proteinases (cathepsins) was used as an indicator of the shock state. An assay was developed for the determination of cathepsin activity in toad plasma and was used to demonstrate the presence of proteinases similar in pH dependence to mammalian cathepsins Bl and D. Plasma cathepsin D-type activity increased with dehydration in toads but was not significantly different from the activity in controls or in toads subjected to splanchnic artery occlusion. Toads appear to maintain plasma volume to 20% water loss at the expense of other extracellular fluids. These results do not support the hypothesis that hypovolemia is a direct cause of dehydrational death in anurans. Title: The significance of hypovolemia in dehydrational death in anurans Author: Kimmel, Peter Blair Year: 1985 The importance of hypovolemia in dehydrational death was assessed in two anuran species. Xenopus laeyis, a species which experiences a significant reduction in circulating plasma volume with dehydration, was used to evaluate the role of sympathetic reflex compensation in hypovolemia. Adrenergic blockade with propranolol or phenoxybenzamine produced no significant reduction in dehydration tolerance in this species, although β-blockade with propranolol appeared to have a minor effect. The role of hypovolemic shock in the terminal circulatory collapse that precedes death in dehydrating anurans was investigated in the toad, Bufo marinus. The activity of lysosomal proteinases (cathepsins) was used as an indicator of the shock state. An assay was developed for the determination of cathepsin activity in toad plasma and was used to demonstrate the presence of proteinases similar in pH dependence to mammalian cathepsins Bl and D. Plasma cathepsin D-type activity increased with dehydration in toads but was not significantly different from the activity in controls or in toads subjected to splanchnic artery occlusion. Toads appear to maintain plasma volume to 20% water loss at the expense of other extracellular fluids. These results do not support the hypothesis that hypovolemia is a direct cause of dehydrational death in anurans. Close

• 30. [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

• 31. [Article] Avian population trends within the evolving agricultural landscape of the eastern and central United States

  State-level Breeding Bird Survey (1980-1998) and U.S. Department of Agriculture statistics were used to test the hypothesis that changes in agricultural land use within the eastern and central U.S. have ...

  Citation × Citation Citation Abstract Copy Title: Avian population trends within the evolving agricultural landscape of the eastern and central United States Author: Murphy, Michael T. Year: 2003 State-level Breeding Bird Survey (1980-1998) and U.S. Department of Agriculture statistics were used to test the hypothesis that changes in agricultural land use within the eastern and central U.S. have driven population trends of grassland and shrub habitat birds over the past two decades. The degree to which population trends differed between grassland and shrub habitats was evaluated with respect to migratory and nesting behavior. Grassland birds declined significantly between 1980 and 1999, but, on average, shrub habitat species did not. Grassland-breeding, long-distance migrants exhibited the strongest negative trends. Most species (78%; n = 63) exhibited at least one significant association between population trends and changes in agricultural land use, and in most, land use "explained" 25-30% of the variation in population trends among states. Changes in the farmland landscape accounted for more of the interstate variability of population trends of short-distance migrants than of both long-distance migrants and residents, and that variability was greater in grassland than shrub species. Declines in the area of rangeland and cover crops were followed by population declines and increases, respectively, by many species. Increases of land in the Conservation Reserve Program had negative associations with population trends of some shrub species. The results indicate that grassland birds have declined strongly over the past two decades, and that regardless of migratory behavior or nesting habits, avian population trends are linked strongly to changes in agricultural land use within North America. Title: Avian population trends within the evolving agricultural landscape of the eastern and central United States Author: Murphy, Michael T. Year: 2003 State-level Breeding Bird Survey (1980-1998) and U.S. Department of Agriculture statistics were used to test the hypothesis that changes in agricultural land use within the eastern and central U.S. have driven population trends of grassland and shrub habitat birds over the past two decades. The degree to which population trends differed between grassland and shrub habitats was evaluated with respect to migratory and nesting behavior. Grassland birds declined significantly between 1980 and 1999, but, on average, shrub habitat species did not. Grassland-breeding, long-distance migrants exhibited the strongest negative trends. Most species (78%; n = 63) exhibited at least one significant association between population trends and changes in agricultural land use, and in most, land use "explained" 25-30% of the variation in population trends among states. Changes in the farmland landscape accounted for more of the interstate variability of population trends of short-distance migrants than of both long-distance migrants and residents, and that variability was greater in grassland than shrub species. Declines in the area of rangeland and cover crops were followed by population declines and increases, respectively, by many species. Increases of land in the Conservation Reserve Program had negative associations with population trends of some shrub species. The results indicate that grassland birds have declined strongly over the past two decades, and that regardless of migratory behavior or nesting habits, avian population trends are linked strongly to changes in agricultural land use within North America. Close

• 32. [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

• 33. [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

• 34. [Article] The physiology and biochemistry of isolated skeletal muscle mitochondria : a comparative study

  The physiological limit to maximum aerobic capacity (VO2max) in vertebrates has been attributed to cardiovascular oxygen delivery, to the ability of the muscle cells to consume oxygen, or to a fine-tuned ...

  Citation × Citation Citation Abstract Copy Title: The physiology and biochemistry of isolated skeletal muscle mitochondria : a comparative study Author: Wagner, Mark Lowell Year: 1989 The physiological limit to maximum aerobic capacity (VO2max) in vertebrates has been attributed to cardiovascular oxygen delivery, to the ability of the muscle cells to consume oxygen, or to a fine-tuned development of all components of the respiratory system such that no single component can be shown to limit VO2max. The above hypotheses have each been developed using different experiments with different animals. The comparative studies uniting these animals and methods are limited. In order to further our knowledge of the cellular limit to VO2max, skeletal muscle mitochondria were isolated from species representing four vertebrate classes, and endothermic and ectothermic physiology. Mitochondrial VO2 was measured at 15, 25 and 35°C and the results were compared between species and endothermic and ectothermic groups. Mitochondrial enzyme activities were measured at the three treatment temperatures to ascertain which enzyme activity best represents VO2max for all vertebrates. Cytochrome difference spectra were measured to determine the concentrations of mitochondrial cytochromes c+c1 . The results show that mitochondria are unique in all species tested. Each species has its own response to changing temperature and its own mitochondrial enzyme activity profile. In addition, in vitro measurements of mitochondrial VO2 for all species show rates significantly higher than those estimated from whole organism measurements of VO2max, suggesting that mitochondrial oxygen uptake is not a factor limiting organismal V02max. The Q10 for mitochondrial VO2 differed significantly between groups, indicating that differences in VO2max between endotherms and ectotherms cannot be explained solely on the basis of temperature. The activation energy (Ea) of mitochondrial VO2 was significantly higher in endotherms compared to ectotherms. Mitochondrial enzyme activities did not show the same Q10 and Ea differences as the intact mitochondria. Since enzyme activities were measured on mitochondria disrupted with either detergent or sonication, physical properties of the mitochondrial inner membrane are suggested as being responsible for these differences. Title: The physiology and biochemistry of isolated skeletal muscle mitochondria : a comparative study Author: Wagner, Mark Lowell Year: 1989 The physiological limit to maximum aerobic capacity (VO2max) in vertebrates has been attributed to cardiovascular oxygen delivery, to the ability of the muscle cells to consume oxygen, or to a fine-tuned development of all components of the respiratory system such that no single component can be shown to limit VO2max. The above hypotheses have each been developed using different experiments with different animals. The comparative studies uniting these animals and methods are limited. In order to further our knowledge of the cellular limit to VO2max, skeletal muscle mitochondria were isolated from species representing four vertebrate classes, and endothermic and ectothermic physiology. Mitochondrial VO2 was measured at 15, 25 and 35°C and the results were compared between species and endothermic and ectothermic groups. Mitochondrial enzyme activities were measured at the three treatment temperatures to ascertain which enzyme activity best represents VO2max for all vertebrates. Cytochrome difference spectra were measured to determine the concentrations of mitochondrial cytochromes c+c1 . The results show that mitochondria are unique in all species tested. Each species has its own response to changing temperature and its own mitochondrial enzyme activity profile. In addition, in vitro measurements of mitochondrial VO2 for all species show rates significantly higher than those estimated from whole organism measurements of VO2max, suggesting that mitochondrial oxygen uptake is not a factor limiting organismal V02max. The Q10 for mitochondrial VO2 differed significantly between groups, indicating that differences in VO2max between endotherms and ectotherms cannot be explained solely on the basis of temperature. The activation energy (Ea) of mitochondrial VO2 was significantly higher in endotherms compared to ectotherms. Mitochondrial enzyme activities did not show the same Q10 and Ea differences as the intact mitochondria. Since enzyme activities were measured on mitochondria disrupted with either detergent or sonication, physical properties of the mitochondrial inner membrane are suggested as being responsible for these differences. Close

• 35. [Article] Biodiversity: Connecting with the Tapestry of Life

  Biodiversity is the extraordinary variety of life on Earth – from genes and species to ecosystems and the valuable functions they perform. E.O. Wilson, the noted biologist and author who coined the term ...

  Citation × Citation Citation Abstract Copy Title: Biodiversity: Connecting with the Tapestry of Life Author: Granek, Elise F., Dallmeier, Francisco, Alonso, Alfonso, Raven, Peter H. Year: 2001 Biodiversity is the extraordinary variety of life on Earth – from genes and species to ecosystems and the valuable functions they perform. E.O. Wilson, the noted biologist and author who coined the term “biodiversity,” explains it as “the very stuff of life.” Species and the ecosystems in which they live are indelibly linked. Conversion or loss of ecosystems inevitably impairs the species that depend on them. As well, changes in the life cycle of one species could impact the life cycles of many other species (including humans), alter ecosystems and ecosystem functions, and contribute to local, regional and, ultimately, global changes. Life as we know it will not be the same if our rich biodiversity heritage is dramatically altered. And the signs indicate that this is precisely what is happening. Biodiversity is threatened, and not because of catastrophic events such as the asteroid crash that scientists believe caused the extinction of the dinosaurs. The current threat to biodiversity, and thus to the tapestry of life, stems primarily from expanding human populations and increased human consumption of natural resources. Fortunately, together we can take steps to protect our rich biodiversity. The Smithsonian Institution’s Program on Monitoring and Assessment of Biodiversity, under the Conservation and Research Center of the National Zoological Park, and the President’s Committee of Advisors on Science and Technology worked together to prepare this booklet. It explains what biodiversity is, why it is so important, why it is threatened, and what can be done to conserve this valuable resource. Read on to learn more about what we can all do to help. Title: Biodiversity: Connecting with the Tapestry of Life Author: Granek, Elise F., Dallmeier, Francisco, Alonso, Alfonso, Raven, Peter H. Year: 2001 Biodiversity is the extraordinary variety of life on Earth – from genes and species to ecosystems and the valuable functions they perform. E.O. Wilson, the noted biologist and author who coined the term “biodiversity,” explains it as “the very stuff of life.” Species and the ecosystems in which they live are indelibly linked. Conversion or loss of ecosystems inevitably impairs the species that depend on them. As well, changes in the life cycle of one species could impact the life cycles of many other species (including humans), alter ecosystems and ecosystem functions, and contribute to local, regional and, ultimately, global changes. Life as we know it will not be the same if our rich biodiversity heritage is dramatically altered. And the signs indicate that this is precisely what is happening. Biodiversity is threatened, and not because of catastrophic events such as the asteroid crash that scientists believe caused the extinction of the dinosaurs. The current threat to biodiversity, and thus to the tapestry of life, stems primarily from expanding human populations and increased human consumption of natural resources. Fortunately, together we can take steps to protect our rich biodiversity. The Smithsonian Institution’s Program on Monitoring and Assessment of Biodiversity, under the Conservation and Research Center of the National Zoological Park, and the President’s Committee of Advisors on Science and Technology worked together to prepare this booklet. It explains what biodiversity is, why it is so important, why it is threatened, and what can be done to conserve this valuable resource. Read on to learn more about what we can all do to help. Close

• 36. [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

• 37. [Article] Stratigraphy and sedimentation of the Spencer Formation in Yamhill and Washington counties, Oregon

  The Spencer Formation in Yamhill and Washington Counties, Oregon, is exposed in a narrow belt 27 km long, from 1/4 to 3 km wide and with a maximum thickness of about 400 m. The formation is composed entirely ...

  Citation × Citation Citation Abstract Copy Title: Stratigraphy and sedimentation of the Spencer Formation in Yamhill and Washington counties, Oregon Author: Al-Azzaby, Fathi Ayoub Year: 1980 The Spencer Formation in Yamhill and Washington Counties, Oregon, is exposed in a narrow belt 27 km long, from 1/4 to 3 km wide and with a maximum thickness of about 400 m. The formation is composed entirely of sandstone with interbedded thin layers of mudstone in the uppermost member. The sedimentary structure and paleoecology indicate a shallow marine depositional environment. The upper member of the Spencer Formation contains more quartz, plagioclase, and hornblende than does the lower member, but K-feldspar is less than that of the lower member. Shallower water conditions for the deposition of the upper member are indicated by sedimentary structures and the abundance of pebbly lenses and coaly material. Eighteen species of megafossils collected from the formation indicate that the Spencer Formation is of the Tejon stage (late Eocene of the West Coast). Title: Stratigraphy and sedimentation of the Spencer Formation in Yamhill and Washington counties, Oregon Author: Al-Azzaby, Fathi Ayoub Year: 1980 The Spencer Formation in Yamhill and Washington Counties, Oregon, is exposed in a narrow belt 27 km long, from 1/4 to 3 km wide and with a maximum thickness of about 400 m. The formation is composed entirely of sandstone with interbedded thin layers of mudstone in the uppermost member. The sedimentary structure and paleoecology indicate a shallow marine depositional environment. The upper member of the Spencer Formation contains more quartz, plagioclase, and hornblende than does the lower member, but K-feldspar is less than that of the lower member. Shallower water conditions for the deposition of the upper member are indicated by sedimentary structures and the abundance of pebbly lenses and coaly material. Eighteen species of megafossils collected from the formation indicate that the Spencer Formation is of the Tejon stage (late Eocene of the West Coast). Close

• 38. [Article] Molecular Changes Associated with Anoxia Tolerance in Austrofundulus limnaeus embryos

  Embryos from the annual killifish Austrofundulus limnaeus have a unique and unequalled ability among vertebrates to withstand extended periods of anoxia (maximum lethal time to 50% mortality of 65 days ...

  Citation × Citation Citation Abstract Copy Title: Molecular Changes Associated with Anoxia Tolerance in Austrofundulus limnaeus embryos Author: Meller, Camie Lynn Year: 2010 Embryos from the annual killifish Austrofundulus limnaeus have a unique and unequalled ability among vertebrates to withstand extended periods of anoxia (maximum lethal time to 50% mortality of 65 days at 25°C). In addition, tolerance of anoxia is gained and subsequently lost during the normal development of this species. Thus, anoxia tolerant and anoxia sensitive individuals can be compared within the same species, making A. limnaeus an excellent model for studying the molecular changes associated with survival of oxygen deprivation in vertebrates. The aim of this project is to analyze the molecular changes associated with anoxia tolerance in the embryos of A. limnaeus. Understanding how the cells of these embryos become tolerant to anoxia will aid in identifying novel therapeutic targets to reduce cell death following periods of ischemia in heart, brain or other tissues. Three major analyses were used to investigate the molecular changes associated with anoxia tolerance in this species. The first was a cell cycle and cell cycle arrest analysis using flow cytometry along with an immunoblot analysis of both positive and negative regulators of cell cycle progression. The second was a cell death analysis utilizing caspase-3/7 activity as well as TUNEL staining. The third was an immunoblot analysis of three different post-translational modifers (ubiquitin, SUMO-1 and SUMO-2/3). The overall findings from this study indicate that the embryos of A. limnaeus do indeed experience some degree of cellular stress (i.e. increase in ubiquitinated proteins, increase in p53 expression, evidence of DNA damage from TUNEL staining and increases in caspase activity) in response to anoxic treatment, even in their most protective state of diapause II. However, despite these observations, the whole organisms are still able to recover from anoxia and do not succumb to death. The overall low levels of TUNEL-positive cells and caspase activity relative to the positive controls indicates that the damage accrued in response to anoxic treatment is minimal. It appears that embryos are able to either "sacrifice" a certain portion of cells or they are able to repair the damage required for resumed development following anoxia. Title: Molecular Changes Associated with Anoxia Tolerance in Austrofundulus limnaeus embryos Author: Meller, Camie Lynn Year: 2010 Embryos from the annual killifish Austrofundulus limnaeus have a unique and unequalled ability among vertebrates to withstand extended periods of anoxia (maximum lethal time to 50% mortality of 65 days at 25°C). In addition, tolerance of anoxia is gained and subsequently lost during the normal development of this species. Thus, anoxia tolerant and anoxia sensitive individuals can be compared within the same species, making A. limnaeus an excellent model for studying the molecular changes associated with survival of oxygen deprivation in vertebrates. The aim of this project is to analyze the molecular changes associated with anoxia tolerance in the embryos of A. limnaeus. Understanding how the cells of these embryos become tolerant to anoxia will aid in identifying novel therapeutic targets to reduce cell death following periods of ischemia in heart, brain or other tissues. Three major analyses were used to investigate the molecular changes associated with anoxia tolerance in this species. The first was a cell cycle and cell cycle arrest analysis using flow cytometry along with an immunoblot analysis of both positive and negative regulators of cell cycle progression. The second was a cell death analysis utilizing caspase-3/7 activity as well as TUNEL staining. The third was an immunoblot analysis of three different post-translational modifers (ubiquitin, SUMO-1 and SUMO-2/3). The overall findings from this study indicate that the embryos of A. limnaeus do indeed experience some degree of cellular stress (i.e. increase in ubiquitinated proteins, increase in p53 expression, evidence of DNA damage from TUNEL staining and increases in caspase activity) in response to anoxic treatment, even in their most protective state of diapause II. However, despite these observations, the whole organisms are still able to recover from anoxia and do not succumb to death. The overall low levels of TUNEL-positive cells and caspase activity relative to the positive controls indicates that the damage accrued in response to anoxic treatment is minimal. It appears that embryos are able to either "sacrifice" a certain portion of cells or they are able to repair the damage required for resumed development following anoxia. Close

• 39. [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

• 40. [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

• 41. [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

• 42. [Article] Genetic Substructure of Pacific Harbor Seal (Phoca vitulina richardsi) Populations Along the Coasts of Oregon and Washington

  It has been assumed that the considerable dispersal ability of many marine species would prevent genetic divergence in the absence of geographic isolation. However, recent work has shown that many marine ...

  Citation × Citation Citation Abstract Copy Title: Genetic Substructure of Pacific Harbor Seal (Phoca vitulina richardsi) Populations Along the Coasts of Oregon and Washington Author: Dishman, Diana Lynn Year: 2011 It has been assumed that the considerable dispersal ability of many marine species would prevent genetic divergence in the absence of geographic isolation. However, recent work has shown that many marine species often develop differentiation among areas within their known dispersal range. This 'paradox' of marine divergence is particularly important among marine mammal species where behavior can restrict gene flow. To investigate genetic substructure within such a species, I used tissue samples collected from 63 stranded Pacific harbor seals (Phoca vitulina richardsi) in Washington and Oregon between 2006 and 2010 for population stock analysis. DNA was extracted from frozen tissues, and a 551 bp fragment of mtDNA control region sequence and eight microsatellite loci were amplified to investigate localized genetic structure. Minimum spanning network and haplotype frequency analyses of mtDNA sequences indicated that while haplotype lineages are not isolated within a sampling region, there is some evidence of regional differentiation. On the other hand, microsatellite data suggest a lack of substructure among the animals sampled, with only a weak signal of limited gene flow between Puget Sound and coastal areas. Biased dispersal among age classes was also suggested, with juveniles showing less differentiation among areas than adults. Regardless of the historical scenario which has led to this complex pattern of genetic structure in Pacific harbor seals across the Pacific Northwest, my results suggest higher levels of exchange among areas than previously suspected, and will have important consequences for future management considerations for these stocks. Title: Genetic Substructure of Pacific Harbor Seal (Phoca vitulina richardsi) Populations Along the Coasts of Oregon and Washington Author: Dishman, Diana Lynn Year: 2011 It has been assumed that the considerable dispersal ability of many marine species would prevent genetic divergence in the absence of geographic isolation. However, recent work has shown that many marine species often develop differentiation among areas within their known dispersal range. This 'paradox' of marine divergence is particularly important among marine mammal species where behavior can restrict gene flow. To investigate genetic substructure within such a species, I used tissue samples collected from 63 stranded Pacific harbor seals (Phoca vitulina richardsi) in Washington and Oregon between 2006 and 2010 for population stock analysis. DNA was extracted from frozen tissues, and a 551 bp fragment of mtDNA control region sequence and eight microsatellite loci were amplified to investigate localized genetic structure. Minimum spanning network and haplotype frequency analyses of mtDNA sequences indicated that while haplotype lineages are not isolated within a sampling region, there is some evidence of regional differentiation. On the other hand, microsatellite data suggest a lack of substructure among the animals sampled, with only a weak signal of limited gene flow between Puget Sound and coastal areas. Biased dispersal among age classes was also suggested, with juveniles showing less differentiation among areas than adults. Regardless of the historical scenario which has led to this complex pattern of genetic structure in Pacific harbor seals across the Pacific Northwest, my results suggest higher levels of exchange among areas than previously suspected, and will have important consequences for future management considerations for these stocks. Close

• 43. [Article] Color Perception in Golden Mantled Ground Squirrels

  Squirrels appear to be unique among sub-primate mammals in being able to see at least some colors. A readily available Oregon squirrel species, golden mantled ground squirrels (Citellus lateralis), which ...

  Citation × Citation Citation Abstract Copy Title: Color Perception in Golden Mantled Ground Squirrels Author: Cooley, Robert F. Year: 1973 Squirrels appear to be unique among sub-primate mammals in being able to see at least some colors. A readily available Oregon squirrel species, golden mantled ground squirrels (Citellus lateralis), which has not previously been tested under laboratory conditions for color vision, was subjected to color discrimination testing in a Skinner box. On the basis of recent physiological tests of color reception capacity and behavioral tests of color discrimination response in closely related species, it was predicted that this species should be able to discriminate blue, green and possibly yellow, but not red. Three experiments were conducted. The first, a pilot study, checked for discrimination of blue from green and blue from gray; subjects were rewarded for pressing on one color, shocked for pressing on the other color. The second experiment, the main part of the study, used one subject tor each of three discriminations: green from gray, yellow from gray, and red from gray. Here, a choice approach was employed: two bars were used, with subjects having to choose the correct one tor each stimulus, receiving a food reward for correct choices and no reward for incorrect choices. Third, a series of tests was devised to check for use of cues other than color as a possible basis for discrimination in the main experiment. These squirrels succeeded in discriminating all four colors, and results of the series of cue tests indicate they were not making significant use of non-color cues. Despite past results, therefore, it was concluded that this species is capable of seeing all colors in the visible spectrum. This result should be of interest to evolutionary theorists and may have important implications for current theories of color vision processes. Title: Color Perception in Golden Mantled Ground Squirrels Author: Cooley, Robert F. Year: 1973 Squirrels appear to be unique among sub-primate mammals in being able to see at least some colors. A readily available Oregon squirrel species, golden mantled ground squirrels (Citellus lateralis), which has not previously been tested under laboratory conditions for color vision, was subjected to color discrimination testing in a Skinner box. On the basis of recent physiological tests of color reception capacity and behavioral tests of color discrimination response in closely related species, it was predicted that this species should be able to discriminate blue, green and possibly yellow, but not red. Three experiments were conducted. The first, a pilot study, checked for discrimination of blue from green and blue from gray; subjects were rewarded for pressing on one color, shocked for pressing on the other color. The second experiment, the main part of the study, used one subject tor each of three discriminations: green from gray, yellow from gray, and red from gray. Here, a choice approach was employed: two bars were used, with subjects having to choose the correct one tor each stimulus, receiving a food reward for correct choices and no reward for incorrect choices. Third, a series of tests was devised to check for use of cues other than color as a possible basis for discrimination in the main experiment. These squirrels succeeded in discriminating all four colors, and results of the series of cue tests indicate they were not making significant use of non-color cues. Despite past results, therefore, it was concluded that this species is capable of seeing all colors in the visible spectrum. This result should be of interest to evolutionary theorists and may have important implications for current theories of color vision processes. Close

• 44. [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

• 45. [Article] The McKee Preserve Management Options at Bandon Dunes Golf Resort

  The McKee Preserve is a new conservation area at Bandon Dunes Golf Resort, located on the southern Oregon coast. The Preserve is 250 acres in size and is made up of 13 different natural resource communities. ...

  Citation × Citation Citation Abstract Copy Title: The McKee Preserve Management Options at Bandon Dunes Golf Resort Author: Edwards, Ashley Marie Year: 2009 The McKee Preserve is a new conservation area at Bandon Dunes Golf Resort, located on the southern Oregon coast. The Preserve is 250 acres in size and is made up of 13 different natural resource communities. One important resource is silvery phacelia (Phacelia argentea), which is a state threatened plant species and is a species of concern federally. The goal of this project was to perform plant inventories for silvery phacelia and kinnikinnick that will be used to establish a functional management plan for the Preserve. Other resources of interest to the Preserve have been included in the literature review and management plan. A proposed par 3 golf course has also been included in the analysis and management plan of the report. Using Geographical Information Systems and Global Positioning Systems to conduct the silvery phacelia inventory showed that there are 6,803 individual plants at the Resort and 5,078 plants on the Preserve. A silvery phacelia community was found north of Cut Creek, which has not been listed as a historical site for this species. The species most likely established itself through fill materials that were seed rich, when building the second golf course on the property, Pacific Dunes. The kinnikinnick meadows have been reduced from building and opening Bandon Trails Golf Course. The remaining meadows are 1.4 acres in size. The par 3 golf course, if built, will be located in the northern portion of the Preserve and would share access with Bandon Trails Golf Course. Out of the 11 proposed holes, 9 have been approved so that impacts to the silvery phacelia will be minimized. Title: The McKee Preserve Management Options at Bandon Dunes Golf Resort Author: Edwards, Ashley Marie Year: 2009 The McKee Preserve is a new conservation area at Bandon Dunes Golf Resort, located on the southern Oregon coast. The Preserve is 250 acres in size and is made up of 13 different natural resource communities. One important resource is silvery phacelia (Phacelia argentea), which is a state threatened plant species and is a species of concern federally. The goal of this project was to perform plant inventories for silvery phacelia and kinnikinnick that will be used to establish a functional management plan for the Preserve. Other resources of interest to the Preserve have been included in the literature review and management plan. A proposed par 3 golf course has also been included in the analysis and management plan of the report. Using Geographical Information Systems and Global Positioning Systems to conduct the silvery phacelia inventory showed that there are 6,803 individual plants at the Resort and 5,078 plants on the Preserve. A silvery phacelia community was found north of Cut Creek, which has not been listed as a historical site for this species. The species most likely established itself through fill materials that were seed rich, when building the second golf course on the property, Pacific Dunes. The kinnikinnick meadows have been reduced from building and opening Bandon Trails Golf Course. The remaining meadows are 1.4 acres in size. The par 3 golf course, if built, will be located in the northern portion of the Preserve and would share access with Bandon Trails Golf Course. Out of the 11 proposed holes, 9 have been approved so that impacts to the silvery phacelia will be minimized. Close

• 46. [Article] Mechanisms of Methane Transport Through Trees

  Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global methane emission and the mechanisms of tree transport ...

  Citation × Citation Citation Abstract Copy Title: Mechanisms of Methane Transport Through Trees Author: Kutschera, Ellynne Marie Year: 2013 Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global methane emission and the mechanisms of tree transport are relatively unknown. Methane emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to methane enriched water and canopy emissions of methane were measured using a canopy enclosure. Methane accumulation in the canopy was generally linear and the average canopy methane flux was 3.0 ± 2.6 μg CH4 min-1. Flux magnitudes from stem experiments scaled to the area of the main tree stem are comparable to whole-canopy flux values, indicating that the majority of methane emitted from the tree leaves through the stem. Samples for stable carbon isotope composition were taken during the canopy experiments. Compared to the isotopic composition of root water methane, canopy methane was depleted in 13C on average by 8.6 ± 3.3 permil; this indicates that methane moving through the tree is not following a purely bulk flow pathway (where no depletion would occur), but is instead subject to at least one fractionating mechanism. When temperature was varied, the flux at the coolest temperature was significantly different from the higher flux at the warmest temperature (p-value less than 0.02). The calculated Q10 for methane flux was 2.4, which indicates a positive feedback with temperature increase. Analysis of δ13C values of emitted CH4 in the temperature experiments shows increasing depletion with cooler temperatures and lower flux. This indicates that not only does the magnitude of flux vary with temperature, but the actual dominant transport mechanism changes as well. Title: Mechanisms of Methane Transport Through Trees Author: Kutschera, Ellynne Marie Year: 2013 Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global methane emission and the mechanisms of tree transport are relatively unknown. Methane emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to methane enriched water and canopy emissions of methane were measured using a canopy enclosure. Methane accumulation in the canopy was generally linear and the average canopy methane flux was 3.0 ± 2.6 μg CH4 min-1. Flux magnitudes from stem experiments scaled to the area of the main tree stem are comparable to whole-canopy flux values, indicating that the majority of methane emitted from the tree leaves through the stem. Samples for stable carbon isotope composition were taken during the canopy experiments. Compared to the isotopic composition of root water methane, canopy methane was depleted in 13C on average by 8.6 ± 3.3 permil; this indicates that methane moving through the tree is not following a purely bulk flow pathway (where no depletion would occur), but is instead subject to at least one fractionating mechanism. When temperature was varied, the flux at the coolest temperature was significantly different from the higher flux at the warmest temperature (p-value less than 0.02). The calculated Q10 for methane flux was 2.4, which indicates a positive feedback with temperature increase. Analysis of δ13C values of emitted CH4 in the temperature experiments shows increasing depletion with cooler temperatures and lower flux. This indicates that not only does the magnitude of flux vary with temperature, but the actual dominant transport mechanism changes as well. Close

• 47. [Article] Antisense transcription is pervasive but rarely conserved in enteric bacteria

  Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent ...

  Citation × Citation Citation Abstract Copy Title: Antisense transcription is pervasive but rarely conserved in enteric bacteria Author: Raghavan, Rahul, Sloan, D. B., Ochman, H. Year: 2012 Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To investigate the biological relevance of antisense transcripts, we compared genome-wide patterns of asRNA expression in closely related enteric bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, by performing strand-specific transcriptome sequencing. Although antisense transcripts are abundant in both species, less than 3% of asRNAs are expressed at high levels in both species, and only about 14% appear to be conserved among species. And unlike the promoters of protein-coding genes, asRNA promoters show no evidence of sequence conservation between, or even within, species. Our findings suggest that many or even most bacterial asRNAs are nonadaptive by-products of the cell's transcription machinery. IMPORTANCE Application of high-throughput methods has revealed the expression throughout bacterial genomes of transcripts encoded on the strand complementary to protein-coding genes. Because transcription is costly, it is usually assumed that these transcripts, termed antisense RNAs (asRNAs), serve some function; however, the role of most asRNAs is unclear, raising questions about their relevance in cellular processes. Because natural selection conserves functional elements, comparisons between related species provide a method for assessing functionality genome-wide. Applying such an approach, we assayed all transcripts in two closely related bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, and demonstrate that, although the levels of genome-wide antisense transcription are similarly high in both bacteria, only a small fraction of asRNAs are shared across species. Moreover, the promoters associated with asRNAs show no evidence of sequence conservation between, or even within, species. These findings indicate that despite the genome-wide transcription of asRNAs, many of these transcripts are likely nonfunctional. Title: Antisense transcription is pervasive but rarely conserved in enteric bacteria Author: Raghavan, Rahul, Sloan, D. B., Ochman, H. Year: 2012 Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To investigate the biological relevance of antisense transcripts, we compared genome-wide patterns of asRNA expression in closely related enteric bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, by performing strand-specific transcriptome sequencing. Although antisense transcripts are abundant in both species, less than 3% of asRNAs are expressed at high levels in both species, and only about 14% appear to be conserved among species. And unlike the promoters of protein-coding genes, asRNA promoters show no evidence of sequence conservation between, or even within, species. Our findings suggest that many or even most bacterial asRNAs are nonadaptive by-products of the cell's transcription machinery. IMPORTANCE Application of high-throughput methods has revealed the expression throughout bacterial genomes of transcripts encoded on the strand complementary to protein-coding genes. Because transcription is costly, it is usually assumed that these transcripts, termed antisense RNAs (asRNAs), serve some function; however, the role of most asRNAs is unclear, raising questions about their relevance in cellular processes. Because natural selection conserves functional elements, comparisons between related species provide a method for assessing functionality genome-wide. Applying such an approach, we assayed all transcripts in two closely related bacteria, Escherichia coli and Salmonella enterica serovar Typhimurium, and demonstrate that, although the levels of genome-wide antisense transcription are similarly high in both bacteria, only a small fraction of asRNAs are shared across species. Moreover, the promoters associated with asRNAs show no evidence of sequence conservation between, or even within, species. These findings indicate that despite the genome-wide transcription of asRNAs, many of these transcripts are likely nonfunctional. Close

• 48. [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

• 49. [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

• 50. [Article] Mutual exclusion between Salmonberry and Douglas-fir in the Coast Range of Oregon

  One serious problem faced by the forest industry in the Pacific Northwest is poor regeneration of commercial trees on land which is harvested and subsequently dominated by brush species. In Coastal Oregon, ...

  Citation × Citation Citation Abstract Copy Title: Mutual exclusion between Salmonberry and Douglas-fir in the Coast Range of Oregon Author: Still, Kenneth Ray Year: 1972 One serious problem faced by the forest industry in the Pacific Northwest is poor regeneration of commercial trees on land which is harvested and subsequently dominated by brush species. In Coastal Oregon, salmonberry is one of these brush species. Detailed investigations of field sites indicate that light intensity in the brush stands was low but sufficient for germination and early growth of Douglas-fir seedlings and soil moisture percentages and nutrient levels were high enough to support early Douglas-fir growth. Laboratory tests demonstrated the presence of leachable phytotoxins in the leaves of salmonberry. The hypothesis resulting from this study is that salmonberry releases a phytotoxin that in synergism with environmental stresses (i.e., light), suppresses germination and growth of Douglas-fir seedlings in the field. Title: Mutual exclusion between Salmonberry and Douglas-fir in the Coast Range of Oregon Author: Still, Kenneth Ray Year: 1972 One serious problem faced by the forest industry in the Pacific Northwest is poor regeneration of commercial trees on land which is harvested and subsequently dominated by brush species. In Coastal Oregon, salmonberry is one of these brush species. Detailed investigations of field sites indicate that light intensity in the brush stands was low but sufficient for germination and early growth of Douglas-fir seedlings and soil moisture percentages and nutrient levels were high enough to support early Douglas-fir growth. Laboratory tests demonstrated the presence of leachable phytotoxins in the leaves of salmonberry. The hypothesis resulting from this study is that salmonberry releases a phytotoxin that in synergism with environmental stresses (i.e., light), suppresses germination and growth of Douglas-fir seedlings in the field. Close