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• 1. [Article] Behavioral Observation and Paternal Investment of Eastern Kingbirds at Malheur National Wildlife Refuge

  We have been studying the population of Eastern Kingbirds breeding in riparian habitats in Malheur National Wildlife Refuge (eastern Oregon) since 2002. These efforts have created an ideal research environment ...

  Citation × Citation Citation Abstract Copy Title: Behavioral Observation and Paternal Investment of Eastern Kingbirds at Malheur National Wildlife Refuge Author: Chutter, Christopher Michael Year: 2014 We have been studying the population of Eastern Kingbirds breeding in riparian habitats in Malheur National Wildlife Refuge (eastern Oregon) since 2002. These efforts have created an ideal research environment wherein most adults in the population have been color banded and DNA sampled and, as part of other research projects, nearly all broods since 2003 have been paternity tested. I decided to use behavioral video recordings of parental nest behavior undertaken between 2003 and 2010 for two unrelated projects. First, I tested the effectiveness of video sampling nesting behavior (see below and chapter 2). Second, I tested whether male kingbirds were able to affect their level of paternal investment in accordance with their level or realized paternity (see below and chapter 3). Chapter 2 was split into three distinct questions: 1) are parental nesting behaviors repeatable, 2) is a one hour sample sufficient to capture variability in these behaviors, and 3) is the first hour of recording sufficient to capture variability in these behaviors. I found overwhelming evidence that the behaviors I measured were repeatable. This is truly important, for if repeatability was disproven, it would call into question the use of sampling throughout the field of animal behavior. I similarly found strong evidence that a one hour sample was sufficient to capture variability in parental behaviors. From this I was able to suggest that further sampling effort would be better spent increasing sample size rather than observation length. Testing whether the first hour of recording was sufficient to capture variability in parental behavior found more muddled results. While there generally was correlation between behavioral values in the first hour and those over a longer observation period, most behaviors were found to have significantly lower values in the first hour. I tested whether this was the result of a lingering observer effect or a natural effect of time of day and concluded that an observer effect was the more likely explanation. In chapter 3, I ran one of the more in depth and complicated tests for a relationship between paternal investment and realized paternity that I was able to find in the literature. I used the standard male feeding rate as a measure of male investment as well as a far more nuanced measure derived from the first Eigenvector of an analysis of six different paternal behaviors. These were both tested using Akaike's Information Criterion against a number of variables likely to affect parental behavior, including realized paternity. Ultimately, I found no evidence that kingbirds were able to affect paternal investment in response to lost paternity, and conclude that they likely had no means to assess realized paternity within the nest of their social mate. However, from the other parameters tested I was able to find that males increased their investment as brood size increased and as the female spent more time attending, but not feeding, the nestlings. Also, male investment decreased as territory density increased and flight feather length increased. Theory surrounding the variability of extrapair paternity in birds can be used to account for these results. In a denser population males are predicted to reduce paternal effort for one of two reasons: increased likelihood of paternity loss in his own nest and an increased investment in pursuing extrapair copulations of his own. Longer flight feathers are a sign of age and quality in kingbirds, so males with this trait are expected to spend more time pursuing extrapair copulations as they are more likely to be successful in this endeavor. Title: Behavioral Observation and Paternal Investment of Eastern Kingbirds at Malheur National Wildlife Refuge Author: Chutter, Christopher Michael Year: 2014 We have been studying the population of Eastern Kingbirds breeding in riparian habitats in Malheur National Wildlife Refuge (eastern Oregon) since 2002. These efforts have created an ideal research environment wherein most adults in the population have been color banded and DNA sampled and, as part of other research projects, nearly all broods since 2003 have been paternity tested. I decided to use behavioral video recordings of parental nest behavior undertaken between 2003 and 2010 for two unrelated projects. First, I tested the effectiveness of video sampling nesting behavior (see below and chapter 2). Second, I tested whether male kingbirds were able to affect their level of paternal investment in accordance with their level or realized paternity (see below and chapter 3). Chapter 2 was split into three distinct questions: 1) are parental nesting behaviors repeatable, 2) is a one hour sample sufficient to capture variability in these behaviors, and 3) is the first hour of recording sufficient to capture variability in these behaviors. I found overwhelming evidence that the behaviors I measured were repeatable. This is truly important, for if repeatability was disproven, it would call into question the use of sampling throughout the field of animal behavior. I similarly found strong evidence that a one hour sample was sufficient to capture variability in parental behaviors. From this I was able to suggest that further sampling effort would be better spent increasing sample size rather than observation length. Testing whether the first hour of recording was sufficient to capture variability in parental behavior found more muddled results. While there generally was correlation between behavioral values in the first hour and those over a longer observation period, most behaviors were found to have significantly lower values in the first hour. I tested whether this was the result of a lingering observer effect or a natural effect of time of day and concluded that an observer effect was the more likely explanation. In chapter 3, I ran one of the more in depth and complicated tests for a relationship between paternal investment and realized paternity that I was able to find in the literature. I used the standard male feeding rate as a measure of male investment as well as a far more nuanced measure derived from the first Eigenvector of an analysis of six different paternal behaviors. These were both tested using Akaike's Information Criterion against a number of variables likely to affect parental behavior, including realized paternity. Ultimately, I found no evidence that kingbirds were able to affect paternal investment in response to lost paternity, and conclude that they likely had no means to assess realized paternity within the nest of their social mate. However, from the other parameters tested I was able to find that males increased their investment as brood size increased and as the female spent more time attending, but not feeding, the nestlings. Also, male investment decreased as territory density increased and flight feather length increased. Theory surrounding the variability of extrapair paternity in birds can be used to account for these results. In a denser population males are predicted to reduce paternal effort for one of two reasons: increased likelihood of paternity loss in his own nest and an increased investment in pursuing extrapair copulations of his own. Longer flight feathers are a sign of age and quality in kingbirds, so males with this trait are expected to spend more time pursuing extrapair copulations as they are more likely to be successful in this endeavor. Close

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

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

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

• 3. [Article] The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations

  Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number ...

  Citation × Citation Citation Abstract Copy Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Close

• 4. [Article] Predator Exclosures, Predator Removal, and Habitat Improvement Increase Nest Success of Snowy Plovers in Oregon, USA

  Management to increase reproductive success is commonly used to aid recovery of threatened and endangered species. The Western Snowy Plover (Charadrius nivosus nivosus) breeds from coastal Washington, ...

  Citation × Citation Citation Abstract Copy Title: Predator Exclosures, Predator Removal, and Habitat Improvement Increase Nest Success of Snowy Plovers in Oregon, USA Author: Dinsmore, Stephen J., Lauten, David J., Castelein, Kathleen J., Gaines, Eleanor P., Stern, Mark A. Year: 2014 Management to increase reproductive success is commonly used to aid recovery of threatened and endangered species. The Western Snowy Plover (Charadrius nivosus nivosus) breeds from coastal Washington, USA, to Baja California, Mexico, and in disjunct interior sites. The Pacific coast population is federally listed as Threatened; habitat loss and nest loss to a suite of terrestrial and avian predators are thought to be primary factors limiting population growth in this species. In coastal Oregon, USA, a consortium of state and federal management agencies deployed nest exclosures on active Snowy Plover nests, initiated a lethal predator management program, and conducted local-scale habitat management in an effort to boost local productivity. During 1990–2009, we monitored 1,951 Snowy Plover nests at 9 sites with varying treatments. We examined the effectiveness of 3 types of nest exclosures (large, small, and outfitted with electric wire), predator removal, and habitat management on nest survival. Habitat management to remove invasive grasses and provide more suitable nesting substrate more than doubled nest survival. Predator management or use of any of the 3 types of exclosures also affected nest survival. There appeared to be no additional benefit to using both approaches, but the biological relevance of these findings is unclear because of site differences in treatments applied. Importantly, these management techniques only affected nesting success; their effect on other contributions to population viability (e.g., fledging success) was not correlated with nesting success. This long-term study illustrates the short-term benefits and tradeoffs of using nest exclosures, predator management, and habitat restoration to improve nesting success. Although we gained broader insight into the relative efficacy of common management techniques to improve avian nesting success, we cannot yet determine how improved nest success contributes to population growth. Title: Predator Exclosures, Predator Removal, and Habitat Improvement Increase Nest Success of Snowy Plovers in Oregon, USA Author: Dinsmore, Stephen J., Lauten, David J., Castelein, Kathleen J., Gaines, Eleanor P., Stern, Mark A. Year: 2014 Management to increase reproductive success is commonly used to aid recovery of threatened and endangered species. The Western Snowy Plover (Charadrius nivosus nivosus) breeds from coastal Washington, USA, to Baja California, Mexico, and in disjunct interior sites. The Pacific coast population is federally listed as Threatened; habitat loss and nest loss to a suite of terrestrial and avian predators are thought to be primary factors limiting population growth in this species. In coastal Oregon, USA, a consortium of state and federal management agencies deployed nest exclosures on active Snowy Plover nests, initiated a lethal predator management program, and conducted local-scale habitat management in an effort to boost local productivity. During 1990–2009, we monitored 1,951 Snowy Plover nests at 9 sites with varying treatments. We examined the effectiveness of 3 types of nest exclosures (large, small, and outfitted with electric wire), predator removal, and habitat management on nest survival. Habitat management to remove invasive grasses and provide more suitable nesting substrate more than doubled nest survival. Predator management or use of any of the 3 types of exclosures also affected nest survival. There appeared to be no additional benefit to using both approaches, but the biological relevance of these findings is unclear because of site differences in treatments applied. Importantly, these management techniques only affected nesting success; their effect on other contributions to population viability (e.g., fledging success) was not correlated with nesting success. This long-term study illustrates the short-term benefits and tradeoffs of using nest exclosures, predator management, and habitat restoration to improve nesting success. Although we gained broader insight into the relative efficacy of common management techniques to improve avian nesting success, we cannot yet determine how improved nest success contributes to population growth. Close

• 5. [Article] Hydrodynamic and Water Quality Modeling of the Chehalis River in Washington

  The Chehalis River Basin is located in the southwest region of Washington and is over 125 miles long flowing through agricultural, residential, industrial, and forest land. Four major rivers, many smaller ...

  Citation × Citation Citation Abstract Copy Title: Hydrodynamic and Water Quality Modeling of the Chehalis River in Washington Author: Van Glubt, Sarah, Wells, Scott A., Berger, Chris J. Year: 2017 The Chehalis River Basin is located in the southwest region of Washington and is over 125 miles long flowing through agricultural, residential, industrial, and forest land. Four major rivers, many smaller creeks, five wastewater treatment plants, and groundwater discharge to the Chehalis River. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure’s impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed for the years 2013 and 2014. Once calibration was complete, model scenarios for future climate conditions and dam operating regimes were conducted. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. Title: Hydrodynamic and Water Quality Modeling of the Chehalis River in Washington Author: Van Glubt, Sarah, Wells, Scott A., Berger, Chris J. Year: 2017 The Chehalis River Basin is located in the southwest region of Washington and is over 125 miles long flowing through agricultural, residential, industrial, and forest land. Four major rivers, many smaller creeks, five wastewater treatment plants, and groundwater discharge to the Chehalis River. Flooding is a major problem in the relatively flat areas surrounding the cities of Chehalis and Centralia. As a result, construction of a flood-control dam in the upper basin has been proposed. One major concern of constructing a dam is the potentially severe impacts to fish health and habitat. The Chehalis River has routinely violated water quality standards for primarily temperature and dissolved oxygen. CE-QUAL-W2, a two-dimensional (longitudinal and vertical) hydrodynamic and water quality model, was used to simulate the Chehalis River, including free flowing river stretches and stratified (in summer) lake-like stretches. The goals of this research were to assess the flood retention structure’s impacts to water quality, as well as river responses to potential climate change scenarios. In order to use the model to achieve these goals, calibration to field data for flow, temperature, and water quality constituents was performed for the years 2013 and 2014. Once calibration was complete, model scenarios for future climate conditions and dam operating regimes were conducted. Future conditions showed predictions of warmer water temperatures and slight changes to water quality conditions on the river. As fish in the area prefer cooler water temperatures, this could pose a threat to fish health and habitat. Flood retention structures with the purpose of flood retention only (only operating during times of flooding) gave model predictions for daily maximum temperature higher than structures that employed flood retention and flow augmentation (operating during all times of the year). This suggested the management of flow passage or retention by the dam is important for water quality on the river. Close

• 6. [Article] Forest Management Scenarios in a Changing Climate: Trade-Offs Between Carbon, Timber, and Old Forest

  Balancing economic, ecological, and social values has long been a challenge in the forests of the Pacific Northwest, where conflict over timber harvest and old-growth habitat on public lands has been contentious ...

  Citation × Citation Citation Abstract Copy Title: Forest Management Scenarios in a Changing Climate: Trade-Offs Between Carbon, Timber, and Old Forest Author: Scheller, Robert M., Creutzburg, Megan K., Lucash, Melissa S., LeDuc, Stephen D., Johnson, Mark G. Year: 2017 Balancing economic, ecological, and social values has long been a challenge in the forests of the Pacific Northwest, where conflict over timber harvest and old-growth habitat on public lands has been contentious for the past several decades. The Northwest Forest Plan, adopted two decades ago to guide management on federal lands, is currently being revised as the region searches for a balance between sustainable timber yields and habitat for sensitive species. In addition, climate change imposes a high degree of uncertainty on future forest productivity, sustainability of timber harvest, wildfire risk, and species habitat. We evaluated the long-term, landscape-scale trade-offs among carbon (C) storage, timber yield, and old forest habitat given projected climate change and shifts in forest management policy across 2.1 million hectares of forests in the Oregon Coast Range. Projections highlight the divergence between private and public lands under business-as-usual forest management, where private industrial forests are heavily harvested and many public (especially federal) lands increase C and old forest over time but provide little timber. Three alternative management scenarios altering the amount and type of timber harvest show widely varying levels of ecosystem C and old-forest habitat. On federal lands, ecological forestry practices also allowed a simultaneous increase in old forest and natural early-seral habitat. The ecosystem C implications of shifts away from current practices were large, with current practices retaining up to 105 Tg more C than the alternative scenarios by the end of the century. Our results suggest climate change is likely to increase forest productivity by 30–41% and total ecosystem C storage by 11–15% over the next century as warmer winter temperatures allow greater forest productivity in cooler months. These gains in C storage are unlikely to be offset by wildfire under climate change, due to the legacy of management and effective fire suppression. Our scenarios of future conditions can inform policy makers, land managers, and the public about the potential effects of land management alternatives, climate change, and the trade-offs that are inherent to management and policy in the region. Title: Forest Management Scenarios in a Changing Climate: Trade-Offs Between Carbon, Timber, and Old Forest Author: Scheller, Robert M., Creutzburg, Megan K., Lucash, Melissa S., LeDuc, Stephen D., Johnson, Mark G. Year: 2017 Balancing economic, ecological, and social values has long been a challenge in the forests of the Pacific Northwest, where conflict over timber harvest and old-growth habitat on public lands has been contentious for the past several decades. The Northwest Forest Plan, adopted two decades ago to guide management on federal lands, is currently being revised as the region searches for a balance between sustainable timber yields and habitat for sensitive species. In addition, climate change imposes a high degree of uncertainty on future forest productivity, sustainability of timber harvest, wildfire risk, and species habitat. We evaluated the long-term, landscape-scale trade-offs among carbon (C) storage, timber yield, and old forest habitat given projected climate change and shifts in forest management policy across 2.1 million hectares of forests in the Oregon Coast Range. Projections highlight the divergence between private and public lands under business-as-usual forest management, where private industrial forests are heavily harvested and many public (especially federal) lands increase C and old forest over time but provide little timber. Three alternative management scenarios altering the amount and type of timber harvest show widely varying levels of ecosystem C and old-forest habitat. On federal lands, ecological forestry practices also allowed a simultaneous increase in old forest and natural early-seral habitat. The ecosystem C implications of shifts away from current practices were large, with current practices retaining up to 105 Tg more C than the alternative scenarios by the end of the century. Our results suggest climate change is likely to increase forest productivity by 30–41% and total ecosystem C storage by 11–15% over the next century as warmer winter temperatures allow greater forest productivity in cooler months. These gains in C storage are unlikely to be offset by wildfire under climate change, due to the legacy of management and effective fire suppression. Our scenarios of future conditions can inform policy makers, land managers, and the public about the potential effects of land management alternatives, climate change, and the trade-offs that are inherent to management and policy in the region. Close

• 7. [Article] Environmental DNA (eDNA) Detects the Invasive Crayfishes Orconectes rusticus and Pacifastacus leniusculus in Large Lakes of North America

  We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, ...

  Citation × Citation Citation Abstract Copy Title: Environmental DNA (eDNA) Detects the Invasive Crayfishes Orconectes rusticus and Pacifastacus leniusculus in Large Lakes of North America Author: Larson, Eric R., Renshaw, Mark A., Gantz, Crysta A., Umek, John, Chandra, Sudeep, Lodge, David M., Egan, Scott P. Year: 2017 We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfish Orconectes rusticus (Girard, 1852), as well as for the invasion of O. rusticus into large lakes of California and Nevada, US known to be invaded by P. leniusculus. We compared eDNA detections to historic localities for O. rusticus within the Great Lakes, and to recent sampling for presence/absence and relative abundance of P. leniusculus in California and Nevada via overnight sets of baited traps. We successfully detected O. rusticus eDNA at six sites from the Great Lakes and P. leniusculus from six of seven lakes where it was known to occur in California and Nevada, but did not detect any range expansions by either species across the North American continent. eDNA appears suitable to detect benthic arthropods from exceptionally large lakes, and will likely be useful in applications for monitoring of new biological invasions into these and other freshwater and marine habitats. Title: Environmental DNA (eDNA) Detects the Invasive Crayfishes Orconectes rusticus and Pacifastacus leniusculus in Large Lakes of North America Author: Larson, Eric R., Renshaw, Mark A., Gantz, Crysta A., Umek, John, Chandra, Sudeep, Lodge, David M., Egan, Scott P. Year: 2017 We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfish Orconectes rusticus (Girard, 1852), as well as for the invasion of O. rusticus into large lakes of California and Nevada, US known to be invaded by P. leniusculus. We compared eDNA detections to historic localities for O. rusticus within the Great Lakes, and to recent sampling for presence/absence and relative abundance of P. leniusculus in California and Nevada via overnight sets of baited traps. We successfully detected O. rusticus eDNA at six sites from the Great Lakes and P. leniusculus from six of seven lakes where it was known to occur in California and Nevada, but did not detect any range expansions by either species across the North American continent. eDNA appears suitable to detect benthic arthropods from exceptionally large lakes, and will likely be useful in applications for monitoring of new biological invasions into these and other freshwater and marine habitats. Close

• 8. [Article] Ecological Investigations to Select Mitigation Options to Reduce Vehicle-Caused Mortality of a Threatened Butterfly

  Whereas roads that bisect habitat are known to decrease population size through animal-vehicle collisions or interruption of key life history events, it is not always obvious how to reduce such impacts, ...

  Citation × Citation Citation Abstract Copy Title: Ecological Investigations to Select Mitigation Options to Reduce Vehicle-Caused Mortality of a Threatened Butterfly Author: Zielin, Sara B., Littlejohn, Jalene, de Rivera, Catherine E., Smith, Winston P., Jacobson, Sandra L. Year: 2016 Whereas roads that bisect habitat are known to decrease population size through animal-vehicle collisions or interruption of key life history events, it is not always obvious how to reduce such impacts, especially for flying organisms. We needed a quick, cost-efficient and effective way to determine how best to decrease vehicle-caused mortality while maintaining habitat connectivity for the federally listed Oregon silverspot butterfly, Speyeria zerene hippolyta. Therefore, we gathered targeted ecological information that informed selection of a mitigation option prior to implementation. We sampled butterfly behavior and environmental conditions along a highway and conducted a small-scale experiment along a decommissioned road corridor used by these butterflies. Using our findings, we recommended vegetation management and helped managers eliminate options they were considering that would be ineffective such as increasing shade or wind in the road, and installing fencing or hedgerows aimed at directing flight above traffic. This quick and inexpensive approach of using ecological observations and small-scale experiments to evaluate the likely success of each available mitigation option can be used to determine effective, species-specific solutions for reducing traffic impacts on pollinators and other small, flying organisms of conservation concern. Title: Ecological Investigations to Select Mitigation Options to Reduce Vehicle-Caused Mortality of a Threatened Butterfly Author: Zielin, Sara B., Littlejohn, Jalene, de Rivera, Catherine E., Smith, Winston P., Jacobson, Sandra L. Year: 2016 Whereas roads that bisect habitat are known to decrease population size through animal-vehicle collisions or interruption of key life history events, it is not always obvious how to reduce such impacts, especially for flying organisms. We needed a quick, cost-efficient and effective way to determine how best to decrease vehicle-caused mortality while maintaining habitat connectivity for the federally listed Oregon silverspot butterfly, Speyeria zerene hippolyta. Therefore, we gathered targeted ecological information that informed selection of a mitigation option prior to implementation. We sampled butterfly behavior and environmental conditions along a highway and conducted a small-scale experiment along a decommissioned road corridor used by these butterflies. Using our findings, we recommended vegetation management and helped managers eliminate options they were considering that would be ineffective such as increasing shade or wind in the road, and installing fencing or hedgerows aimed at directing flight above traffic. This quick and inexpensive approach of using ecological observations and small-scale experiments to evaluate the likely success of each available mitigation option can be used to determine effective, species-specific solutions for reducing traffic impacts on pollinators and other small, flying organisms of conservation concern. Close

• 9. [Article] Nesting Microhabitat Use by a Ground-nesting Songbird: Strict Preferences or Random Choice?

  Nest site choice of birds has the potential to affect predation rates on nests and reproductive success for many bird species, and is thus tied closely to fitness. Vegetation at a particular site influences ...

  Citation × Citation Citation Abstract Copy Title: Nesting Microhabitat Use by a Ground-nesting Songbird: Strict Preferences or Random Choice? Author: Allen, Jazzmine Year: 2016 Nest site choice of birds has the potential to affect predation rates on nests and reproductive success for many bird species, and is thus tied closely to fitness. Vegetation at a particular site influences concealment (and predation rate as a result). Research has shown that birds of various species base nest site choice on variables like nest height, and especially vegetation cover within the microhabitat around a site. I studied nest site choice in ground-nesting birds, which tend to experience high predation rates near the nest site, and therefore might be expected to be particular choosy about vegetation near the nest. I used Spotted Towhees (Pipilo maculatus) nesting in Lesser Park in Portland, OR, as a model species for ground-nesting birds. I compared Spotted Towhees nest sites (n = 15) to both randomly-chosen sites within 10 m of the nests (n = 15; random territory sites) and other randomly-chosen locations throughout the park (n = 25; random park locations) to test whether vegetation structure and floristic composition differed. I measured (1) vegetation height and density near the nest, (2) size and spacing of trees around nests, and (3) floristic composition of vegetation near nests. I found that nest sites and both categories of random sites had dense and equal amounts of vegetation near ground level (0-20 cm above ground), but that nest sites had more vegetation between 21-40 cm and 61-100 cm above ground than random locations. However, there was no evidence that the structure of the tree community or species composition differed between nest sites and random locations. Towhees thus appear to prefer to place nests in locations with greater vertical cover directly over the nest. Title: Nesting Microhabitat Use by a Ground-nesting Songbird: Strict Preferences or Random Choice? Author: Allen, Jazzmine Year: 2016 Nest site choice of birds has the potential to affect predation rates on nests and reproductive success for many bird species, and is thus tied closely to fitness. Vegetation at a particular site influences concealment (and predation rate as a result). Research has shown that birds of various species base nest site choice on variables like nest height, and especially vegetation cover within the microhabitat around a site. I studied nest site choice in ground-nesting birds, which tend to experience high predation rates near the nest site, and therefore might be expected to be particular choosy about vegetation near the nest. I used Spotted Towhees (Pipilo maculatus) nesting in Lesser Park in Portland, OR, as a model species for ground-nesting birds. I compared Spotted Towhees nest sites (n = 15) to both randomly-chosen sites within 10 m of the nests (n = 15; random territory sites) and other randomly-chosen locations throughout the park (n = 25; random park locations) to test whether vegetation structure and floristic composition differed. I measured (1) vegetation height and density near the nest, (2) size and spacing of trees around nests, and (3) floristic composition of vegetation near nests. I found that nest sites and both categories of random sites had dense and equal amounts of vegetation near ground level (0-20 cm above ground), but that nest sites had more vegetation between 21-40 cm and 61-100 cm above ground than random locations. However, there was no evidence that the structure of the tree community or species composition differed between nest sites and random locations. Towhees thus appear to prefer to place nests in locations with greater vertical cover directly over the nest. Close

• 10. [Article] Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries

  The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, ...

  Citation × Citation Citation Abstract Copy Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Title: Intestinal Microbiota Diversity of Pre-Smolt Steelhead (Oncorhynchus mykiss) Across Six Oregon and Washington Hatcheries Author: Yildirimer, Christina Carrell Year: 2017 The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions. In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment. Close