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

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

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

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

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

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

• 3. [Article] 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

• 4. [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

• 5. [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

• 6. [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

• 7. [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

• 8. [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

• 9. [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

• 10. [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