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• 1. [Article] Potential Economic Impacts of Zebra Mussels on the Hydropower Facilities in the Columbia River Basin

  The purpose of this study was to estimate costs to the Federal Columbia River Power System hydroelectric projects in the event of a zebra mussel infestation.

  Citation × Citation Citation Abstract Copy Title: Potential Economic Impacts of Zebra Mussels on the Hydropower Facilities in the Columbia River Basin Author: Phillips, Stephen, Darland, Tim, Sytsma, Mark Year: 2005 The purpose of this study was to estimate costs to the Federal Columbia River Power System hydroelectric projects in the event of a zebra mussel infestation. Title: Potential Economic Impacts of Zebra Mussels on the Hydropower Facilities in the Columbia River Basin Author: Phillips, Stephen, Darland, Tim, Sytsma, Mark Year: 2005 The purpose of this study was to estimate costs to the Federal Columbia River Power System hydroelectric projects in the event of a zebra mussel infestation. Close

• 2. [Article] Prioritizing Zebra and Quagga Mussel Monitoring in the Columbia River Basin

  The purpose of this report is to provide a framework for the prioritization of water bodies in the Columbia River Basin and the Greater Northwest region (surrounding areas in Oregon, Washington, California, ...

  Citation × Citation Citation Abstract Copy Title: Prioritizing Zebra and Quagga Mussel Monitoring in the Columbia River Basin Author: Wells, Steve W., Counihan, Timothy D., Puls, Amy, Sytsma, Mark, Adair, Brian Year: 2011 The purpose of this report is to provide a framework for the prioritization of water bodies in the Columbia River Basin and the Greater Northwest region (surrounding areas in Oregon, Washington, California, Nevada, Idaho, Utah, and Wyoming) for early detection monitoring for dreissenid mussels. Our ability to assess the relative risk of establishment and introduction of dreissenid mussels was confounded by significant gaps in the data necessary to rigorously predict where dreissenid mussels will become introduced and subsequently established. Consequently, local jurisdictions should evaluate the prioritized lists provided critically and make adjustments where local knowledge and additional information dictates. Further, since invasive species can be introduced and become established in areas identified with low to very low risk of establishment and introduction, monitoring these areas will increase the probability of detecting mussels before they become locally established. Title: Prioritizing Zebra and Quagga Mussel Monitoring in the Columbia River Basin Author: Wells, Steve W., Counihan, Timothy D., Puls, Amy, Sytsma, Mark, Adair, Brian Year: 2011 The purpose of this report is to provide a framework for the prioritization of water bodies in the Columbia River Basin and the Greater Northwest region (surrounding areas in Oregon, Washington, California, Nevada, Idaho, Utah, and Wyoming) for early detection monitoring for dreissenid mussels. Our ability to assess the relative risk of establishment and introduction of dreissenid mussels was confounded by significant gaps in the data necessary to rigorously predict where dreissenid mussels will become introduced and subsequently established. Consequently, local jurisdictions should evaluate the prioritized lists provided critically and make adjustments where local knowledge and additional information dictates. Further, since invasive species can be introduced and become established in areas identified with low to very low risk of establishment and introduction, monitoring these areas will increase the probability of detecting mussels before they become locally established. Close

• 3. [Article] Theoretical Basis for the CE-QUAL-W2 River Basin Model

  The primary objective of this research is to integrate a riverine model into the existing W2 code that would provide the capability for modeling entire watersheds. This task was accomplished by the following ...

  Citation × Citation Citation Abstract Copy Title: Theoretical Basis for the CE-QUAL-W2 River Basin Model Author: Wells, Scott A., Cole, Thomas M. Year: 2000 The primary objective of this research is to integrate a riverine model into the existing W2 code that would provide the capability for modeling entire watersheds. This task was accomplished by the following steps: • Formal derivation of governing equations and solution algorithm with general channel slope • Detailed analysis of algorithm for linking branches and smooth implementation of boundary conditions between branches • Algorithm development and changes to basic model code (including branch definitions with slope, slope correction to solution algorithm, transfer of momentum between internal branches) These tasks were performed with the following constraints and initiatives: • Utilize the same solution algorithms as the existing code for hydrodynamics and water quality for the riverine system • Allow momentum transfer between adjacent branches for internal head boundary conditions • Refine the turbulence closure hypothesis for riverine sections Title: Theoretical Basis for the CE-QUAL-W2 River Basin Model Author: Wells, Scott A., Cole, Thomas M. Year: 2000 The primary objective of this research is to integrate a riverine model into the existing W2 code that would provide the capability for modeling entire watersheds. This task was accomplished by the following steps: • Formal derivation of governing equations and solution algorithm with general channel slope • Detailed analysis of algorithm for linking branches and smooth implementation of boundary conditions between branches • Algorithm development and changes to basic model code (including branch definitions with slope, slope correction to solution algorithm, transfer of momentum between internal branches) These tasks were performed with the following constraints and initiatives: • Utilize the same solution algorithms as the existing code for hydrodynamics and water quality for the riverine system • Allow momentum transfer between adjacent branches for internal head boundary conditions • Refine the turbulence closure hypothesis for riverine sections Close

• 4. [Article] Scenario Development and Analysis of Freshwater Ecosystem Services under Land Cover and Climate Change in the Tualatin and Yamhill River Basins, Oregon

  Humans make decisions within ecosystems to enhance their well-being, but choices can lead to unintended consequences. The ecosystem services (ES) approach supports decision-making that considers all environmental ...

  Citation × Citation Citation Abstract Copy Title: Scenario Development and Analysis of Freshwater Ecosystem Services under Land Cover and Climate Change in the Tualatin and Yamhill River Basins, Oregon Author: Hoyer, Robert Wesley Year: 2013 Humans make decisions within ecosystems to enhance their well-being, but choices can lead to unintended consequences. The ecosystem services (ES) approach supports decision-making that considers all environmental goods and services. Many challenges remain in the implementation of the ES approach like how specific ES vary through space and time. We address this research problem using the Tualatin and Yamhill river basins in northwestern Oregon as a study area. Freshwater ES are quantified and mapped with the spatially-explicit ES modeling tool, Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST). In chapter II, we develop a simple urban land cover change modeling approach with selected stakeholder input. The products of this analysis are used in part to answer the question of how the freshwater ES of water yield, nutrient retention, and sediment retention will change in the future, and how their distribution potentially will change? In chapter III, these ES are modeled in InVEST using the land cover scenarios and three downscaled global climate models. The base period is 1981 to 2010 and the future period is 2036 to 2065. The models are calibrated to empirical estimates, and display different sensitivities to inputs. Water yield increases with higher rainfall but decreases with the highest temperature scenario. Nutrient export and retention estimates are positively correlated. In the Tualatin basin, more urban lands generally lead to increases in nutrient exports and retention. The effect is reversed in the Yamhill basin from much larger agricultural exports. Sediment exports and retention increase with higher winter rainfall but are negatively spatially correlated due to topographic effects. Simulation of a landscape scale installation of riparian buffers leads to decreases in exports and increases in retention. The distribution of the provision of freshwater ES remains unchanged throughout the scenarios. With few parameters in each InVEST model, all display a high degree of sensitivity. Parameterization is subject to high uncertainty even with calibrated values. We discuss the assumptions and limitations of InVEST's freshwater models. The spatially explicit nature of InVEST is its main advantage. This work coupled with other analyses in the study area can facilitate the identification of tradeoffs amongst ES leading to better ecosystem management. Title: Scenario Development and Analysis of Freshwater Ecosystem Services under Land Cover and Climate Change in the Tualatin and Yamhill River Basins, Oregon Author: Hoyer, Robert Wesley Year: 2013 Humans make decisions within ecosystems to enhance their well-being, but choices can lead to unintended consequences. The ecosystem services (ES) approach supports decision-making that considers all environmental goods and services. Many challenges remain in the implementation of the ES approach like how specific ES vary through space and time. We address this research problem using the Tualatin and Yamhill river basins in northwestern Oregon as a study area. Freshwater ES are quantified and mapped with the spatially-explicit ES modeling tool, Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST). In chapter II, we develop a simple urban land cover change modeling approach with selected stakeholder input. The products of this analysis are used in part to answer the question of how the freshwater ES of water yield, nutrient retention, and sediment retention will change in the future, and how their distribution potentially will change? In chapter III, these ES are modeled in InVEST using the land cover scenarios and three downscaled global climate models. The base period is 1981 to 2010 and the future period is 2036 to 2065. The models are calibrated to empirical estimates, and display different sensitivities to inputs. Water yield increases with higher rainfall but decreases with the highest temperature scenario. Nutrient export and retention estimates are positively correlated. In the Tualatin basin, more urban lands generally lead to increases in nutrient exports and retention. The effect is reversed in the Yamhill basin from much larger agricultural exports. Sediment exports and retention increase with higher winter rainfall but are negatively spatially correlated due to topographic effects. Simulation of a landscape scale installation of riparian buffers leads to decreases in exports and increases in retention. The distribution of the provision of freshwater ES remains unchanged throughout the scenarios. With few parameters in each InVEST model, all display a high degree of sensitivity. Parameterization is subject to high uncertainty even with calibrated values. We discuss the assumptions and limitations of InVEST's freshwater models. The spatially explicit nature of InVEST is its main advantage. This work coupled with other analyses in the study area can facilitate the identification of tradeoffs amongst ES leading to better ecosystem management. Close

• 5. [Article] Waldo Lake Research in 2003

  This report summarizes the first year of an effort to develop a more complete understanding of the physical, chemical, and biological characteristics that drive the ecological processes of Waldo Lake. ...

  Citation × Citation Citation Abstract Copy Title: Waldo Lake Research in 2003 Author: Sytsma, Mark D., Rueter, John, Petersen, Richard, Koch, Roy, Wells, Scott A., Miller, Rich, Johnson, Laura, Annear, Robert Leslie Year: 2004 This report summarizes the first year of an effort to develop a more complete understanding of the physical, chemical, and biological characteristics that drive the ecological processes of Waldo Lake. Modern limnology recognizes the importance of watershed processes as well as in- lake processes in lake ecosystem functioning. Therefore, the approach included consideration of watershed hydrology and forcing functions that determine hydrodynamics of the system as well physical and chemical factors that may be important in regulating primary production in the lake. Data collected since 1998 was summarized and bathymetry of the basin was mapped using state-of-the-art digital depth sounding and GPS technology. A hypothesis that UV light may play an important role in regulating phytoplankton efficiency was examined in an effort to move toward more hypothesis-driven investigations to elucidate the factors controlling productivity. A Quality Assurance/Quality Control Plan was developed to guide data collection for long-term monitoring of the lake. Lastly, initial steps were made in the development of a model of lake hydrodynamics and primary production to aid in integration of the physical, chemical, and biological data that has been collected on the lake. Title: Waldo Lake Research in 2003 Author: Sytsma, Mark D., Rueter, John, Petersen, Richard, Koch, Roy, Wells, Scott A., Miller, Rich, Johnson, Laura, Annear, Robert Leslie Year: 2004 This report summarizes the first year of an effort to develop a more complete understanding of the physical, chemical, and biological characteristics that drive the ecological processes of Waldo Lake. Modern limnology recognizes the importance of watershed processes as well as in- lake processes in lake ecosystem functioning. Therefore, the approach included consideration of watershed hydrology and forcing functions that determine hydrodynamics of the system as well physical and chemical factors that may be important in regulating primary production in the lake. Data collected since 1998 was summarized and bathymetry of the basin was mapped using state-of-the-art digital depth sounding and GPS technology. A hypothesis that UV light may play an important role in regulating phytoplankton efficiency was examined in an effort to move toward more hypothesis-driven investigations to elucidate the factors controlling productivity. A Quality Assurance/Quality Control Plan was developed to guide data collection for long-term monitoring of the lake. Lastly, initial steps were made in the development of a model of lake hydrodynamics and primary production to aid in integration of the physical, chemical, and biological data that has been collected on the lake. Close

• 6. [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

• 7. [Article] Modeling the Bull Run River-Reservoir System

  The City of Portland, Water Bureau currently operates 2 Bull Run reservoirs, Reservoir #2 and Reservoir #1 as a water supply source in the Bull Run watershed shown in Figure 1 and Figure 2. The Water Bureau ...

  Citation × Citation Citation Abstract Copy Title: Modeling the Bull Run River-Reservoir System Author: Wells, Scott A. Year: 2000 The City of Portland, Water Bureau currently operates 2 Bull Run reservoirs, Reservoir #2 and Reservoir #1 as a water supply source in the Bull Run watershed shown in Figure 1 and Figure 2. The Water Bureau wants to operate their water supply system in order to meet both water supply objectives and fish habitat objectives downstream of the Bull Run reservoirs in Bull Run River. In addition, a third Bull Run reservoir has been proposed as an additional water supply source. This reservoir also may be used to meet water supply and fish habitat objectives in Bull Run River. This proposal addresses performing the following tasks to evaluate these objectives: Gather data to construct a computer simulation model of the Bull Run system including Bull Run River, Bull Run Reservoirs #1 through #3 and the river basin without reservoirs. Ensure that the model accurately represents the system physics, chemistry and biology. Use the model to evaluate how to meet water supply and fish habitat objectives by implementation of management scenarios. Title: Modeling the Bull Run River-Reservoir System Author: Wells, Scott A. Year: 2000 The City of Portland, Water Bureau currently operates 2 Bull Run reservoirs, Reservoir #2 and Reservoir #1 as a water supply source in the Bull Run watershed shown in Figure 1 and Figure 2. The Water Bureau wants to operate their water supply system in order to meet both water supply objectives and fish habitat objectives downstream of the Bull Run reservoirs in Bull Run River. In addition, a third Bull Run reservoir has been proposed as an additional water supply source. This reservoir also may be used to meet water supply and fish habitat objectives in Bull Run River. This proposal addresses performing the following tasks to evaluate these objectives: Gather data to construct a computer simulation model of the Bull Run system including Bull Run River, Bull Run Reservoirs #1 through #3 and the river basin without reservoirs. Ensure that the model accurately represents the system physics, chemistry and biology. Use the model to evaluate how to meet water supply and fish habitat objectives by implementation of management scenarios. Close

• 8. [Article] Spokane River in Idaho and Washington TMDL Water Quality and Hydrodynamic Modeling Quality Assurance Project Plan -- DRAFT

  The focus of this present study is to perform the following tasks: • Converting the Upper Spokane River CE‐QUAL‐W2 models (Washington and Idaho) to version 3.6 • Combining the Washington and Idaho models • ...

  Citation × Citation Citation Abstract Copy Title: Spokane River in Idaho and Washington TMDL Water Quality and Hydrodynamic Modeling Quality Assurance Project Plan -- DRAFT Author: Wells, Scott A., Berger, Chris Year: 2009 The focus of this present study is to perform the following tasks: • Converting the Upper Spokane River CE‐QUAL‐W2 models (Washington and Idaho) to version 3.6 • Combining the Washington and Idaho models • Reviewing and updating model boundary conditions • Check model calibration • Meet with stakeholders • Develop and Run Modeling Scenarios • Create reports on calibration and scenario runs Title: Spokane River in Idaho and Washington TMDL Water Quality and Hydrodynamic Modeling Quality Assurance Project Plan -- DRAFT Author: Wells, Scott A., Berger, Chris Year: 2009 The focus of this present study is to perform the following tasks: • Converting the Upper Spokane River CE‐QUAL‐W2 models (Washington and Idaho) to version 3.6 • Combining the Washington and Idaho models • Reviewing and updating model boundary conditions • Check model calibration • Meet with stakeholders • Develop and Run Modeling Scenarios • Create reports on calibration and scenario runs Close

• 9. [Article] Lower Columbia River Aquatic Nonindigenous Species Survey 2001-2004

  Rates of aquatic nonindigenous species (ANS) introductions and their social, economic, and ecological impacts are increasing. Introductions of nonnative marine organisms have increased exponentially over ...

  Citation × Citation Citation Abstract Copy Title: Lower Columbia River Aquatic Nonindigenous Species Survey 2001-2004 Author: Sytsma, Mark, Cordell, Jeffery, Chapman, John, Draheim, Robyn Year: 2004 Rates of aquatic nonindigenous species (ANS) introductions and their social, economic, and ecological impacts are increasing. Introductions of nonnative marine organisms have increased exponentially over the last two centuries and expenditures on outreach, control, and research exceed millions of dollars per species for several invaders of particular concern to the United States. These trends suggest that major changes are occurring in the freshwater, estuarine, and marine ecosystems of North America, but their magnitude is probably underestimated. Title: Lower Columbia River Aquatic Nonindigenous Species Survey 2001-2004 Author: Sytsma, Mark, Cordell, Jeffery, Chapman, John, Draheim, Robyn Year: 2004 Rates of aquatic nonindigenous species (ANS) introductions and their social, economic, and ecological impacts are increasing. Introductions of nonnative marine organisms have increased exponentially over the last two centuries and expenditures on outreach, control, and research exceed millions of dollars per species for several invaders of particular concern to the United States. These trends suggest that major changes are occurring in the freshwater, estuarine, and marine ecosystems of North America, but their magnitude is probably underestimated. Close

• 10. [Article] Stream-Associated Amphibian Habitat Assessment in the Portland-Vancouver Metropolitan Region

  This study assessed the influence of landscape development on stream-associated amphibians in forested riparian areas within the Portland-Vancouver metropolitan region. Human alteration of landscapes may ...

  Citation × Citation Citation Abstract Copy Title: Stream-Associated Amphibian Habitat Assessment in the Portland-Vancouver Metropolitan Region Author: Dietrich, Andrew Evans Year: 2012 This study assessed the influence of landscape development on stream-associated amphibians in forested riparian areas within the Portland-Vancouver metropolitan region. Human alteration of landscapes may dramatically affect the ecology of neighboring aquatic systems. It was hypothesized that lotic amphibians would be negatively associated with greater amounts of landscape development and positively associated with forested area within the surrounding watershed. Thirty-seven 1st-3rd order streams were sampled between June 21st and September 21st in 2011. Streams potentially providing adequate habitat for stream-obligate amphibians were randomly selected. Amphibians were surveyed along 30-meter stream transects using an active-cover search (ACS). Environmental variables associated with development in surrounding landscapes were measured in situ. GIS delineation was conducted to define landscape-scale variables at stratified distances from riparian networks up-stream of each site via the utilization of the 2006 NLCD dataset and a finer-scale, regional dataset compiled by the Institute for Natural Resources (INR). Amphibians were detected at seventeen of the thirty-seven sampled streams. The most commonly detected species were Dicamptadon tenebrosus, Plethadon vehiculum and Plethadon dunni. Streams where amphibians were observed had lower average water temperature and conductivity, coarser stream substrate and were located on public property more often than streams where no amphibians were detected. Landscape variables were most significant to amphibians within 100 and 200 meters of the upstream stream network. Occupancy of a site by facultative species was best explained by the proportion of mixed forest in the surrounding watershed (R2=0.343, p<0.001). Occupancy of a stream by obligate species was best predicted by measurements of water quality and in-stream cover (Water Temperature: R2=0.275, p<0.001; Water Conductivity: R2=0.248, p<0.001; Cover: R2=0.323, p<0.001). Occupancy of stream refugia by all observed amphibians was positively influenced by higher percentages of forest cover and lower percentages of urban development and herbaceous vegetation in the surrounding watershed. Results of this study indicate that urban refugia must contain adequate riparian forest area, coarse stream substrate and clean, cool water to sustain stream-amphibian communities. Protection of remnant forested headwater stream networks is essential to the conservation of lotic amphibians in this urbanized region. Title: Stream-Associated Amphibian Habitat Assessment in the Portland-Vancouver Metropolitan Region Author: Dietrich, Andrew Evans Year: 2012 This study assessed the influence of landscape development on stream-associated amphibians in forested riparian areas within the Portland-Vancouver metropolitan region. Human alteration of landscapes may dramatically affect the ecology of neighboring aquatic systems. It was hypothesized that lotic amphibians would be negatively associated with greater amounts of landscape development and positively associated with forested area within the surrounding watershed. Thirty-seven 1st-3rd order streams were sampled between June 21st and September 21st in 2011. Streams potentially providing adequate habitat for stream-obligate amphibians were randomly selected. Amphibians were surveyed along 30-meter stream transects using an active-cover search (ACS). Environmental variables associated with development in surrounding landscapes were measured in situ. GIS delineation was conducted to define landscape-scale variables at stratified distances from riparian networks up-stream of each site via the utilization of the 2006 NLCD dataset and a finer-scale, regional dataset compiled by the Institute for Natural Resources (INR). Amphibians were detected at seventeen of the thirty-seven sampled streams. The most commonly detected species were Dicamptadon tenebrosus, Plethadon vehiculum and Plethadon dunni. Streams where amphibians were observed had lower average water temperature and conductivity, coarser stream substrate and were located on public property more often than streams where no amphibians were detected. Landscape variables were most significant to amphibians within 100 and 200 meters of the upstream stream network. Occupancy of a site by facultative species was best explained by the proportion of mixed forest in the surrounding watershed (R2=0.343, p<0.001). Occupancy of a stream by obligate species was best predicted by measurements of water quality and in-stream cover (Water Temperature: R2=0.275, p<0.001; Water Conductivity: R2=0.248, p<0.001; Cover: R2=0.323, p<0.001). Occupancy of stream refugia by all observed amphibians was positively influenced by higher percentages of forest cover and lower percentages of urban development and herbaceous vegetation in the surrounding watershed. Results of this study indicate that urban refugia must contain adequate riparian forest area, coarse stream substrate and clean, cool water to sustain stream-amphibian communities. Protection of remnant forested headwater stream networks is essential to the conservation of lotic amphibians in this urbanized region. Close