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• 1. [Article] Distribution of bats in Southeast Alaska and selection of day-roosts in trees by Keen’s myotis on Prince of Wales Island, Southeast Alaska

  We conducted capture and acoustic surveys for bats in six areas along a latitudinal gradient in Southeast Alaska from mid-May to September in 2005 and we continued surveys on Prince of Wales Island from ...

  Citation × Citation Citation Abstract Copy Title: Distribution of bats in Southeast Alaska and selection of day-roosts in trees by Keen’s myotis on Prince of Wales Island, Southeast Alaska Author: Boland, Julia L. We conducted capture and acoustic surveys for bats in six areas along a latitudinal gradient in Southeast Alaska from mid-May to September in 2005 and we continued surveys on Prince of Wales Island from mid-May to September in 2006. We determined the level of effort required to catch each species and documented ranges in morphology and periods of reproduction. We captured little brown myotis, Myotis lucifugus; California myotis, M. californicus; long-legged myotis, M. volans; and Keen’s myotis, M. keenii, and we acoustically detected and sighted the silver-haired bat, Lasionycteris noctivagans. Capture success varied by species, year, and type of capture site. Our surveys support prior research suggesting that the little brown myotis is the most abundant species in the region, although densities appear to be low relative to other parts of its range. California myotis and Keen’s myotis were captured as far north as Juneau. The long-legged myotis was captured on Wrangell and Prince of Wales Islands and the silver-haired bat was detected on Prince of Wales Island. Prince of Wales Island is the southernmost area we sampled and was the only area where all species were detected. Given low rates of detection, all species appear to occur in low densities in Southeast Alaska. Better understanding of population status and trends and examination of habitat ecology and response to forest management in the region is needed to prioritize conservation strategies. The Keen’s myotis is rare and has one of the most limited distributions of any bat species in North America. Understanding gender-specific roosting ecologies of bats at relevant spatial scales is necessary to effectively evaluate the impact of habitat alteration and prioritize conservation efforts for bats in temperate forests. We examined selection of day-roosts in trees by Keen’s myotis from mid-May to September, 2006 on Prince of Wales Island, Southeast Alaska. Our objectives were to 1) examine relationships between and determine relative importance of habitat characteristics on selection of day-roosts at three spatial scales and 2) determine if habitat associations for males and females differed at each scale. We tracked 13 females to 62 roosts in trees and 6 males to 24 roosts in trees. Features at each spatial scale appeared to influence selection of day-roosts by female Keen’s myotis, but associations were strongest at the tree scale and trees used as roosts were primarily large in diameter with structural defects and located in old-growth forests. Trees in plots around roosts of females had large mean diameters and these plots had a high abundance of roost-like trees. Roosts were generally located near to roads and streams and surrounded by landscapes with a high abundance of old-growth and riparian habitat. Associations were evident for male Keen’s myotis at each spatial scale, but associations at the landscape scale were strongest. Male Keen’s myotis exhibited flexibility with the types of roosts they chose, but tree roosts were primarily snags in early to intermediate decay surrounded by a high relative abundance of roost-like trees that were closer to roads and further from riparian habitat. Habitat associations differed between males and females at each spatial scale and differences are likely a reflection of higher energetic constraints associated with reproduction for females. Energetic benefits gained from optimal roosting habitat may be critical for successful reproduction by females. Females primarily roosted in old-growth habitat and we suggest that maintaining structural components characteristic of old growth will promote conservation of Keen’s myotis in Southeast Alaska. Title: Distribution of bats in Southeast Alaska and selection of day-roosts in trees by Keen’s myotis on Prince of Wales Island, Southeast Alaska Author: Boland, Julia L. We conducted capture and acoustic surveys for bats in six areas along a latitudinal gradient in Southeast Alaska from mid-May to September in 2005 and we continued surveys on Prince of Wales Island from mid-May to September in 2006. We determined the level of effort required to catch each species and documented ranges in morphology and periods of reproduction. We captured little brown myotis, Myotis lucifugus; California myotis, M. californicus; long-legged myotis, M. volans; and Keen’s myotis, M. keenii, and we acoustically detected and sighted the silver-haired bat, Lasionycteris noctivagans. Capture success varied by species, year, and type of capture site. Our surveys support prior research suggesting that the little brown myotis is the most abundant species in the region, although densities appear to be low relative to other parts of its range. California myotis and Keen’s myotis were captured as far north as Juneau. The long-legged myotis was captured on Wrangell and Prince of Wales Islands and the silver-haired bat was detected on Prince of Wales Island. Prince of Wales Island is the southernmost area we sampled and was the only area where all species were detected. Given low rates of detection, all species appear to occur in low densities in Southeast Alaska. Better understanding of population status and trends and examination of habitat ecology and response to forest management in the region is needed to prioritize conservation strategies. The Keen’s myotis is rare and has one of the most limited distributions of any bat species in North America. Understanding gender-specific roosting ecologies of bats at relevant spatial scales is necessary to effectively evaluate the impact of habitat alteration and prioritize conservation efforts for bats in temperate forests. We examined selection of day-roosts in trees by Keen’s myotis from mid-May to September, 2006 on Prince of Wales Island, Southeast Alaska. Our objectives were to 1) examine relationships between and determine relative importance of habitat characteristics on selection of day-roosts at three spatial scales and 2) determine if habitat associations for males and females differed at each scale. We tracked 13 females to 62 roosts in trees and 6 males to 24 roosts in trees. Features at each spatial scale appeared to influence selection of day-roosts by female Keen’s myotis, but associations were strongest at the tree scale and trees used as roosts were primarily large in diameter with structural defects and located in old-growth forests. Trees in plots around roosts of females had large mean diameters and these plots had a high abundance of roost-like trees. Roosts were generally located near to roads and streams and surrounded by landscapes with a high abundance of old-growth and riparian habitat. Associations were evident for male Keen’s myotis at each spatial scale, but associations at the landscape scale were strongest. Male Keen’s myotis exhibited flexibility with the types of roosts they chose, but tree roosts were primarily snags in early to intermediate decay surrounded by a high relative abundance of roost-like trees that were closer to roads and further from riparian habitat. Habitat associations differed between males and females at each spatial scale and differences are likely a reflection of higher energetic constraints associated with reproduction for females. Energetic benefits gained from optimal roosting habitat may be critical for successful reproduction by females. Females primarily roosted in old-growth habitat and we suggest that maintaining structural components characteristic of old growth will promote conservation of Keen’s myotis in Southeast Alaska. Close

• 2. [Article] Nesting ecology of Marbled Murrelets at a remote mainland fjord in southeast Alaska

  This is the publisher’s final pdf. The published article is copyrighted by the Cooper Ornithological Society and can be found at: http://www.bioone.org/loi/cond.

  Citation × Citation Citation Abstract Copy Title: Nesting ecology of Marbled Murrelets at a remote mainland fjord in southeast Alaska Author: Carter, Harry R., Roby, Daniel D., Dugger, Bruce D., Barbaree, Blake A., Whitworth, Darrell L., Nelson, S. Kim, Newman, Scott H. This is the publisher’s final pdf. The published article is copyrighted by the Cooper Ornithological Society and can be found at: http://www.bioone.org/loi/cond. Title: Nesting ecology of Marbled Murrelets at a remote mainland fjord in southeast Alaska Author: Carter, Harry R., Roby, Daniel D., Dugger, Bruce D., Barbaree, Blake A., Whitworth, Darrell L., Nelson, S. Kim, Newman, Scott H. This is the publisher’s final pdf. The published article is copyrighted by the Cooper Ornithological Society and can be found at: http://www.bioone.org/loi/cond. Close

• 3. [Article] Migration, movement, and habitat use of humpback whitefish (Coregonus pidschian) in the Copper River Delta, Alaska

  Research conducted on humpback whitefish Coregonus pidschian in the Copper River Delta, Alaska has revealed a complex life history involving seasonal migrations and the occupation of a variety of freshwater ...

  Citation × Citation Citation Abstract Copy Title: Migration, movement, and habitat use of humpback whitefish (Coregonus pidschian) in the Copper River Delta, Alaska Author: Neilson, Brian J. Research conducted on humpback whitefish Coregonus pidschian in the Copper River Delta, Alaska has revealed a complex life history involving seasonal migrations and the occupation of a variety of freshwater and marine habitats including lacustrine, riverine, estuarine, and marine. Forty-five whitefish were tagged with radio transmitters in 2006 and 2007, and another 29 whitefish were tagged with acoustic tags in 2008. In addition, otolith chemistry was used to evaluate marine habitat use of humpback whitefish sampled from McKinley Lake in the Copper River Delta, Alaska. Movements and migration of tagged fish were tracked using biotelemetry techniques from boats, airplanes, and fixed receiver stations throughout the spring, summer, and fall. Sagittal otoliths were extracted from 20 humpback whitefish and a chemical analysis was performed to evaluate levels of Sr:Ca. Biotelemetry and sampling results revealed seasonal migrations where humpback whitefish migrated into McKinley Lake in mid to late spring and left the lake by late summer and early fall. Fish migrated to the Copper River in the fall by traveling down Alaganik Slough and then to the Copper River by traveling through Pete Dahl Cutoff Slough or the Gulf of Alaska. Fish travel up the Copper River presumably to their spawning grounds. Nine tagged fish returned to McKinley Lake in 2007 and four tagged fish in 2008, indicating some fidelity to the summer feeding site. Otolith chemistry detected marine migrations in 45% of the samples. Three migratory behaviors were observed, while some individuals inhabited only freshwater environments, some individuals made single migrations to marine habitats, and other individuals made multiple migrations to marine habitats. Age of whitefish ranged from 2 to 9 years. Analysis of small-scale movement of humpback whitefish in McKinley Lake found movement rates to be significantly higher at dusk compared to night in one sampling period. However, diel movement activity in all other diel periods did not significantly differ, suggesting arrhythmic diel movement. A large portion of the lake was occupied at any given time, but not all areas were used equally. Activity levels, measured by change in zones, were variable between dates and indicated that fish often moved between detection zones. An increase in activity was observed in individuals 48 h prior to migration from the lake. This study provides the first documentation of migration, movement, and habitat use of humpback whitefish in the Copper River Delta, Alaska. Results of this study will help inform management of humpback whitefish in order to sustain populations into the future. This information should be considered in land use and species management planning in the Copper River basin including fish passage and harvest regulations. Title: Migration, movement, and habitat use of humpback whitefish (Coregonus pidschian) in the Copper River Delta, Alaska Author: Neilson, Brian J. Research conducted on humpback whitefish Coregonus pidschian in the Copper River Delta, Alaska has revealed a complex life history involving seasonal migrations and the occupation of a variety of freshwater and marine habitats including lacustrine, riverine, estuarine, and marine. Forty-five whitefish were tagged with radio transmitters in 2006 and 2007, and another 29 whitefish were tagged with acoustic tags in 2008. In addition, otolith chemistry was used to evaluate marine habitat use of humpback whitefish sampled from McKinley Lake in the Copper River Delta, Alaska. Movements and migration of tagged fish were tracked using biotelemetry techniques from boats, airplanes, and fixed receiver stations throughout the spring, summer, and fall. Sagittal otoliths were extracted from 20 humpback whitefish and a chemical analysis was performed to evaluate levels of Sr:Ca. Biotelemetry and sampling results revealed seasonal migrations where humpback whitefish migrated into McKinley Lake in mid to late spring and left the lake by late summer and early fall. Fish migrated to the Copper River in the fall by traveling down Alaganik Slough and then to the Copper River by traveling through Pete Dahl Cutoff Slough or the Gulf of Alaska. Fish travel up the Copper River presumably to their spawning grounds. Nine tagged fish returned to McKinley Lake in 2007 and four tagged fish in 2008, indicating some fidelity to the summer feeding site. Otolith chemistry detected marine migrations in 45% of the samples. Three migratory behaviors were observed, while some individuals inhabited only freshwater environments, some individuals made single migrations to marine habitats, and other individuals made multiple migrations to marine habitats. Age of whitefish ranged from 2 to 9 years. Analysis of small-scale movement of humpback whitefish in McKinley Lake found movement rates to be significantly higher at dusk compared to night in one sampling period. However, diel movement activity in all other diel periods did not significantly differ, suggesting arrhythmic diel movement. A large portion of the lake was occupied at any given time, but not all areas were used equally. Activity levels, measured by change in zones, were variable between dates and indicated that fish often moved between detection zones. An increase in activity was observed in individuals 48 h prior to migration from the lake. This study provides the first documentation of migration, movement, and habitat use of humpback whitefish in the Copper River Delta, Alaska. Results of this study will help inform management of humpback whitefish in order to sustain populations into the future. This information should be considered in land use and species management planning in the Copper River basin including fish passage and harvest regulations. Close

• 4. [Article] Emerging infectious disease in lentic environments : the ecology and biogeography of the amphibian chytrid fungus Batrachochytrium dendrobatidis, with perspectives on water quality, limnology, and chemical contaminants

  Biodiversity losses in terrestrial, freshwater, and marine systems are accelerating at a global scale and the most threatened vertebrate taxa are those associated with freshwater habitats. The causes of ...

  Citation × Citation Citation Abstract Copy Title: Emerging infectious disease in lentic environments : the ecology and biogeography of the amphibian chytrid fungus Batrachochytrium dendrobatidis, with perspectives on water quality, limnology, and chemical contaminants Author: Chestnut, Tara Biodiversity losses in terrestrial, freshwater, and marine systems are accelerating at a global scale and the most threatened vertebrate taxa are those associated with freshwater habitats. The causes of biodiversity losses are often complex and include synergistic effects of natural and human-induced stressors, such as habitat loss and fragmentation, urbanization, invasive species, contaminants, global climate change, and emerging infectious diseases. In the last 35 years, the amphibian extinction rate has been estimated to exceed 105 times the baseline expected rate for all species and in the USA, the number of occupied amphibian sites has been reported to be declining by 3.7% per year. Among the many threats to amphibians, the role of disease in population declines has been recognized increasingly over the last two decades. Numerous amphibian diseases have been identified and attributed to mass mortality events. Chytridiomycosis, the emerging infectious disease caused by the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), is implicated as a causal agent in many recent global amphibian population declines and extinctions. To understand the pathology and conservation implications of Bd, a greater understanding of its ecology, life history, and distribution in the wild is of paramount importance. Although it has an impact on the persistence of selected amphibian populations around the world, the full scope of the effects of chytridiomycosis on global amphibian population declines are not well understood. Most Bd research efforts have focused on Bd in amphibian hosts per se, with little attention to understand the environmental associations and dynamics of free-living Bd outside of the amphibian host. In particular, information on Bd responses to climatic variation outside of hosts is a research gap. Furthermore, as a microorganism within an aquatic environment, studies are lacking of potential water quality associations, how Bd may interact with other members of their biological communities, and how Bd responses to chemical contaminants found in aquatic environments. My research begins to fill these gaps by studying the basic ecology of free-living Bd in field settings, and investigating factors that may influence its distribution at a landscape scale, occurrence at a regional scale, and detection at a site scale. Herein, I describe spatial and temporal patterns in the detection and density of free-living Bd in aquatic habitats in two different geographic regions of the United States, Alaska (Chapter 2) and Oregon (Chapter 3). The Alaska work examines Bd ecology at the northernmost extent of amphibian occurrence in North America, where climate associations may be particularly relevant and where Bd occurrence may be representative of one of the most novel pathogen-host systems in the world. I also describe (Chapter 2) experimental results of Bd and amphibian response to extreme cold temperatures they may experience in continental settings, at high elevations, and at high latitudes. My Oregon studies (Chapter 3) focus on multivariate associations of free-living Bd occurrences with a suite of aquatic environmental factors, both abiotic and biotic in nature. In Chapter 4, I describe how amphibians and Bd respond to agricultural chemicals (fungicides) that they may be exposed to in field settings. These results are specific to Bd, but might also warrant consideration as fungicidal treatments for a newly described chytrid affecting salamanders; both of these amphibian chytrids have been detected in captive animals and solutions to treat trade animals for the pathogen are gaining relevancy. Finally, in Chapter 5, I reflect upon the journey of conservation biologists and herpetologists for 25 years of amphibian decline research, with global losses becoming widely recognized in 1989. In this context, my research significantly advances understanding of the geographic distribution and ecology of one potential threat factor to amphibian populations on Earth, Batrachochytrium dendrobatidis. The factors that I report to both promote or limit free-living Bd distribution and abundance will further inform pathogen dynamics research. Title: Emerging infectious disease in lentic environments : the ecology and biogeography of the amphibian chytrid fungus Batrachochytrium dendrobatidis, with perspectives on water quality, limnology, and chemical contaminants Author: Chestnut, Tara Biodiversity losses in terrestrial, freshwater, and marine systems are accelerating at a global scale and the most threatened vertebrate taxa are those associated with freshwater habitats. The causes of biodiversity losses are often complex and include synergistic effects of natural and human-induced stressors, such as habitat loss and fragmentation, urbanization, invasive species, contaminants, global climate change, and emerging infectious diseases. In the last 35 years, the amphibian extinction rate has been estimated to exceed 105 times the baseline expected rate for all species and in the USA, the number of occupied amphibian sites has been reported to be declining by 3.7% per year. Among the many threats to amphibians, the role of disease in population declines has been recognized increasingly over the last two decades. Numerous amphibian diseases have been identified and attributed to mass mortality events. Chytridiomycosis, the emerging infectious disease caused by the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), is implicated as a causal agent in many recent global amphibian population declines and extinctions. To understand the pathology and conservation implications of Bd, a greater understanding of its ecology, life history, and distribution in the wild is of paramount importance. Although it has an impact on the persistence of selected amphibian populations around the world, the full scope of the effects of chytridiomycosis on global amphibian population declines are not well understood. Most Bd research efforts have focused on Bd in amphibian hosts per se, with little attention to understand the environmental associations and dynamics of free-living Bd outside of the amphibian host. In particular, information on Bd responses to climatic variation outside of hosts is a research gap. Furthermore, as a microorganism within an aquatic environment, studies are lacking of potential water quality associations, how Bd may interact with other members of their biological communities, and how Bd responses to chemical contaminants found in aquatic environments. My research begins to fill these gaps by studying the basic ecology of free-living Bd in field settings, and investigating factors that may influence its distribution at a landscape scale, occurrence at a regional scale, and detection at a site scale. Herein, I describe spatial and temporal patterns in the detection and density of free-living Bd in aquatic habitats in two different geographic regions of the United States, Alaska (Chapter 2) and Oregon (Chapter 3). The Alaska work examines Bd ecology at the northernmost extent of amphibian occurrence in North America, where climate associations may be particularly relevant and where Bd occurrence may be representative of one of the most novel pathogen-host systems in the world. I also describe (Chapter 2) experimental results of Bd and amphibian response to extreme cold temperatures they may experience in continental settings, at high elevations, and at high latitudes. My Oregon studies (Chapter 3) focus on multivariate associations of free-living Bd occurrences with a suite of aquatic environmental factors, both abiotic and biotic in nature. In Chapter 4, I describe how amphibians and Bd respond to agricultural chemicals (fungicides) that they may be exposed to in field settings. These results are specific to Bd, but might also warrant consideration as fungicidal treatments for a newly described chytrid affecting salamanders; both of these amphibian chytrids have been detected in captive animals and solutions to treat trade animals for the pathogen are gaining relevancy. Finally, in Chapter 5, I reflect upon the journey of conservation biologists and herpetologists for 25 years of amphibian decline research, with global losses becoming widely recognized in 1989. In this context, my research significantly advances understanding of the geographic distribution and ecology of one potential threat factor to amphibian populations on Earth, Batrachochytrium dendrobatidis. The factors that I report to both promote or limit free-living Bd distribution and abundance will further inform pathogen dynamics research. Close

• 5. [Article] Factors associated with dusky Canada goose nesting and nest success on artificial nest islands of the western Copper River Delta

  The population of dusky Canada geese (Branta canadensis occidentalis; hereafter, dusky geese) nesting on the western Copper River Delta (CRD) in south- central Alaska has been in decline since the late ...

  Citation × Citation Citation Abstract Copy Title: Factors associated with dusky Canada goose nesting and nest success on artificial nest islands of the western Copper River Delta Author: Maggiulli, Nicole Marie The population of dusky Canada geese (Branta canadensis occidentalis; hereafter, dusky geese) nesting on the western Copper River Delta (CRD) in south- central Alaska has been in decline since the late 1970s. In an effort to alleviate mammalian predation, increase nest success, and avoid a listing under the U.S. Endangered Species Act, an artificial nest island (island) program was implemented on the western CRD in 1983. The installation of new islands on the CRD is the sole management action of the Pacific Flyway Council on the breeding grounds, but no comprehensive evaluation of the program has been published. I examined general trends in island use and nest success over time for three island types (donut islands, fiberglass floater islands, and sandbag islands) from 1984-2005. I used data from the island program to identify factors associated with dusky Canada goose nesting (hereafter, use) and nest success on islands from 1996-2005. I generated a series of candidate models and used logistic regression with model selection techniques to determine how variables representing pond characteristics, vegetative characteristics, interactions with conspecifics and larid species, the previous year’s island status, and the distance to predator corridors were associated with island use and nest success for each year. Use of islands by dusky geese nesting on the western CRD increased between 1987 and 2005 from a low of 10% in 1987 to 44% in 2005. There was annual variability in factors associated with island use; however, use of islands was most consistently and strongly associated with the previous year’s island status. The odds of a nest being placed on an island that contained a successful nest the previous year were 2.91 to 6.62 times greater than for islands not used the previous year. There was also evidence for an increased likelihood of island use further from shore and for islands with up to 55% aerial shrub cover and shrubs up to 1 m tall. Nest success was consistently high, indicating islands have long term potential for increasing dusky goose nest success on the Copper River Delta. Compared to island use, my analysis of nest success and habitat features resulted in many more competitive models (average 10 v. 2 per year) with fewer strong (95% confidence intervals for parameter estimates excluded zero) associations between explanatory variables and nest success. Explanatory variables representing vegetative characteristics, interactions with conspecifics and larid species, and the distance to predator corridors had a relatively low capacity to explain nest success on artificial islands. However, there was some evidence for an increased likelihood of nest success on islands further from shore with shorter shrubs. Lower variability in factors associated with island use is likely because factors associated with nest site selection are controlled by decisions of the nesting goose. The importance of previous year’s island status on island use likely reflects high site fidelity by breeding adult geese, with fidelity being higher for birds that have successful nests. Alternately, dusky geese use cues from the previous year’s nesting activity when prospecting for island nest sites. In contrast, nest success is dependent on a more complex combination of factors that vary within and among years outside the control of a nesting goose. Inter-annual variation in the timing and magnitude of eulachon (Thaleichthys pacificus) spawning runs on large sloughs of the CRD and prey-switching by important dusky goose nest predators may have considerable influence on dusky goose nest success on islands, similar to mainland- nesting dusky geese. The inability to control for eulachon presence and abundance may have confounded my analysis of habitat features important to nest success. Therefore, factors such as presence of alternate prey (and predator abundance) may be more important to dusky goose nest success on islands than habitat features. Current use of available nest islands is at a program high of 44% and nest success also remains high (63%); suggesting the artificial nest island program is valuable for dusky geese. However, the contribution of island-nesting dusky geese to the dusky goose population on the Copper River Delta is unclear. There is a need for a population model that incorporates all recent information on dusky goose reproductive ecology to determine if artificial nest islands can increase dusky goose population size, and if so, how many islands are needed. Title: Factors associated with dusky Canada goose nesting and nest success on artificial nest islands of the western Copper River Delta Author: Maggiulli, Nicole Marie The population of dusky Canada geese (Branta canadensis occidentalis; hereafter, dusky geese) nesting on the western Copper River Delta (CRD) in south- central Alaska has been in decline since the late 1970s. In an effort to alleviate mammalian predation, increase nest success, and avoid a listing under the U.S. Endangered Species Act, an artificial nest island (island) program was implemented on the western CRD in 1983. The installation of new islands on the CRD is the sole management action of the Pacific Flyway Council on the breeding grounds, but no comprehensive evaluation of the program has been published. I examined general trends in island use and nest success over time for three island types (donut islands, fiberglass floater islands, and sandbag islands) from 1984-2005. I used data from the island program to identify factors associated with dusky Canada goose nesting (hereafter, use) and nest success on islands from 1996-2005. I generated a series of candidate models and used logistic regression with model selection techniques to determine how variables representing pond characteristics, vegetative characteristics, interactions with conspecifics and larid species, the previous year’s island status, and the distance to predator corridors were associated with island use and nest success for each year. Use of islands by dusky geese nesting on the western CRD increased between 1987 and 2005 from a low of 10% in 1987 to 44% in 2005. There was annual variability in factors associated with island use; however, use of islands was most consistently and strongly associated with the previous year’s island status. The odds of a nest being placed on an island that contained a successful nest the previous year were 2.91 to 6.62 times greater than for islands not used the previous year. There was also evidence for an increased likelihood of island use further from shore and for islands with up to 55% aerial shrub cover and shrubs up to 1 m tall. Nest success was consistently high, indicating islands have long term potential for increasing dusky goose nest success on the Copper River Delta. Compared to island use, my analysis of nest success and habitat features resulted in many more competitive models (average 10 v. 2 per year) with fewer strong (95% confidence intervals for parameter estimates excluded zero) associations between explanatory variables and nest success. Explanatory variables representing vegetative characteristics, interactions with conspecifics and larid species, and the distance to predator corridors had a relatively low capacity to explain nest success on artificial islands. However, there was some evidence for an increased likelihood of nest success on islands further from shore with shorter shrubs. Lower variability in factors associated with island use is likely because factors associated with nest site selection are controlled by decisions of the nesting goose. The importance of previous year’s island status on island use likely reflects high site fidelity by breeding adult geese, with fidelity being higher for birds that have successful nests. Alternately, dusky geese use cues from the previous year’s nesting activity when prospecting for island nest sites. In contrast, nest success is dependent on a more complex combination of factors that vary within and among years outside the control of a nesting goose. Inter-annual variation in the timing and magnitude of eulachon (Thaleichthys pacificus) spawning runs on large sloughs of the CRD and prey-switching by important dusky goose nest predators may have considerable influence on dusky goose nest success on islands, similar to mainland- nesting dusky geese. The inability to control for eulachon presence and abundance may have confounded my analysis of habitat features important to nest success. Therefore, factors such as presence of alternate prey (and predator abundance) may be more important to dusky goose nest success on islands than habitat features. Current use of available nest islands is at a program high of 44% and nest success also remains high (63%); suggesting the artificial nest island program is valuable for dusky geese. However, the contribution of island-nesting dusky geese to the dusky goose population on the Copper River Delta is unclear. There is a need for a population model that incorporates all recent information on dusky goose reproductive ecology to determine if artificial nest islands can increase dusky goose population size, and if so, how many islands are needed. Close

• 6. [Article] Non-parametric methods reveal non-linear functional trait variation of lichens along environmental and fire age gradients

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by International Association ...

  Citation × Citation Citation Abstract Copy Title: Non-parametric methods reveal non-linear functional trait variation of lichens along environmental and fire age gradients Author: Roland, Carl, Nelson, Peter R., Stehn, Sarah, McCune, Bruce To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by International Association for Vegetation Science and published by John Wiley & Sons Ltd. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291654-1103 Title: Non-parametric methods reveal non-linear functional trait variation of lichens along environmental and fire age gradients Author: Roland, Carl, Nelson, Peter R., Stehn, Sarah, McCune, Bruce To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article is copyrighted by International Association for Vegetation Science and published by John Wiley & Sons Ltd. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291654-1103 Close

• 7. [Article] Patterns of distribution, abundance, and change over time in the marine bird community of Prince William Sound, Alaska, 1989-2012

  Over recent decades, the marine ecosystems of Prince William Sound (PWS), Alaska have experienced the concurrent effects of a major anthropogenic disturbance, the 1989 Exxon Valdez oil spill (EVOS), and ...

  Citation × Citation Citation Abstract Copy Title: Patterns of distribution, abundance, and change over time in the marine bird community of Prince William Sound, Alaska, 1989-2012 Author: Cushing, Daniel A. (Daniel Arel) Over recent decades, the marine ecosystems of Prince William Sound (PWS), Alaska have experienced the concurrent effects of a major anthropogenic disturbance, the 1989 Exxon Valdez oil spill (EVOS), and a dynamic atmospheric-oceanic environment. Studies of top marine consumers can provide insights into processes of ecosystem change. Using data collected during boat-based marine bird surveys in PWS over the period 1989-2012, I used complimentary taxon- and community-centric approaches to investigate patterns of distribution and abundance of marine birds across space and time. In doing so, I sought to provide insight into processes that may have affected both the birds themselves and the ecosystems of which they are a part. I found that the marine bird community as a whole was spatially structured along a primary onshore-offshore environmental gradient, and secondarily structured along an estuarine-marine environmental gradient. I found two patterns of community variability across time. The first temporal community-level pattern was likely related to sustained rates of change in the abundance of some genera, likely caused by demographic processes. This pattern was correlated with climate variability at time-scales of several years to a decade. The second temporal community-level pattern was characterized by fluctuations that correlated with climate variability at an annual time-scale, likely caused by movements of birds between PWS and the adjacent Gulf of Alaska. I also evaluated changes in the abundance of 18 genera of marine birds, and found that seven had declined in abundance and three had increased over the study period; all genera that declined were piscivorous or planktivorous. Furthermore, the rates of population change of genera were related to their position in the onshore-offshore gradient, with the highest rates of decline occurring in offshore-associated genera. I also investigated spatial habitat associations and temporal changes in abundance of a focal taxon, the seabird genus Brachyramphus. Two species within this piscivorous, pursuit-diving genus occur in PWS, the marbled murrelet (B. marmoratus) and the Kittlitz’s murrelet (B. brevirostris). Both are species of conservation concern, and both experienced acute mortality in PWS caused by the EVOS. Using a statistical model that accounted for variables affecting observed abundance across space and time, I found that abundance decreased by more than two-thirds over the study period. I found no evidence that rates of change differed along environmental or geographic gradients. There was also no evidence that changes in seasonal patterns of abundance occurred. These results are indicative of a widespread decline in the abundance of Brachyramphus murrelets within PWS. Taken as a whole, the results of my thesis are consistent with the hypothesis that climate change has differentially affected nearshore and offshore components of PWS food webs. This in turn has likely contributed to the failure of some taxa, including Brachyramphus murrelets, to recover from population injury caused by the EVOS. Title: Patterns of distribution, abundance, and change over time in the marine bird community of Prince William Sound, Alaska, 1989-2012 Author: Cushing, Daniel A. (Daniel Arel) Over recent decades, the marine ecosystems of Prince William Sound (PWS), Alaska have experienced the concurrent effects of a major anthropogenic disturbance, the 1989 Exxon Valdez oil spill (EVOS), and a dynamic atmospheric-oceanic environment. Studies of top marine consumers can provide insights into processes of ecosystem change. Using data collected during boat-based marine bird surveys in PWS over the period 1989-2012, I used complimentary taxon- and community-centric approaches to investigate patterns of distribution and abundance of marine birds across space and time. In doing so, I sought to provide insight into processes that may have affected both the birds themselves and the ecosystems of which they are a part. I found that the marine bird community as a whole was spatially structured along a primary onshore-offshore environmental gradient, and secondarily structured along an estuarine-marine environmental gradient. I found two patterns of community variability across time. The first temporal community-level pattern was likely related to sustained rates of change in the abundance of some genera, likely caused by demographic processes. This pattern was correlated with climate variability at time-scales of several years to a decade. The second temporal community-level pattern was characterized by fluctuations that correlated with climate variability at an annual time-scale, likely caused by movements of birds between PWS and the adjacent Gulf of Alaska. I also evaluated changes in the abundance of 18 genera of marine birds, and found that seven had declined in abundance and three had increased over the study period; all genera that declined were piscivorous or planktivorous. Furthermore, the rates of population change of genera were related to their position in the onshore-offshore gradient, with the highest rates of decline occurring in offshore-associated genera. I also investigated spatial habitat associations and temporal changes in abundance of a focal taxon, the seabird genus Brachyramphus. Two species within this piscivorous, pursuit-diving genus occur in PWS, the marbled murrelet (B. marmoratus) and the Kittlitz’s murrelet (B. brevirostris). Both are species of conservation concern, and both experienced acute mortality in PWS caused by the EVOS. Using a statistical model that accounted for variables affecting observed abundance across space and time, I found that abundance decreased by more than two-thirds over the study period. I found no evidence that rates of change differed along environmental or geographic gradients. There was also no evidence that changes in seasonal patterns of abundance occurred. These results are indicative of a widespread decline in the abundance of Brachyramphus murrelets within PWS. Taken as a whole, the results of my thesis are consistent with the hypothesis that climate change has differentially affected nearshore and offshore components of PWS food webs. This in turn has likely contributed to the failure of some taxa, including Brachyramphus murrelets, to recover from population injury caused by the EVOS. Close

• 8. [Article] The influence of local fidelity and recruitment on population dynamics and specialized foraging of humpback whales in Glacier Bay and Icy Strait, Alaska

  Humpback whales (Megaptera novaeangliae, Borowski 1781) in the North Pacific migrate from mid- to high- latitude summer feeding grounds along the Pacific Rim, including areas off the coasts of the U.S., ...

  Citation × Citation Citation Abstract Copy Title: The influence of local fidelity and recruitment on population dynamics and specialized foraging of humpback whales in Glacier Bay and Icy Strait, Alaska Author: Pierszalowski, Sophie Penny Humpback whales (Megaptera novaeangliae, Borowski 1781) in the North Pacific migrate from mid- to high- latitude summer feeding grounds along the Pacific Rim, including areas off the coasts of the U.S., Canada, Russia and eastern Asia, to tropical breeding grounds each winter along Pacific coasts of Mexico and Central America as well as the offshore islands of Mexico, Hawaii, and Japan. Humpback whales in the North Pacific and elsewhere were reduced to very low numbers during a period of intense commercial exploitation that ended in 1965. As the population recovers in abundance, the range of cultural and genetic diversity that survived the exploitation-driven bottleneck is able to adapt, endure and evolve. My work uses genetic tools and photo identification data to investigate the population dynamics, mitochondrial (mt) DNA control region evolution and potential drivers of a specialized feeding behavior in a recovering subpopulation of humpback whales in the Glacier Bay and Icy Strait (GBIS) sub-region of the southeastern Alaska (SEAK) feeding ground. I first collated and reconciled available DNA profiles (mtDNA control region, 10 microsatellite loci and sex) from 556 individuals using tissue samples collected from 1987 to 2012. Photo identification records associated with 692 of 1,026 total genetic samples collected in SEAK (now archived within the SEAK DNA Register and Tissue Database) corresponded to extensive life-history information, extending back to the early 1970s, as archived within the SEAK Regional Database, curated by the National Park Service (NPS) and University of Alaska, Southeast (UAS). Changes in population structure in GBIS over 32 years (1973-2005) were investigated in order to determine whether the increase in local abundance was attributable to local fidelity and recruitment or immigration from outside of SEAK. Two temporal strata were defined: 'Founder' individuals identified between 1973-1985 (n = 74, n = 46 with DNA profiles) and 'Contemporary' individuals identified between 2004-2005 (n = 171, n = 114 with DNA profiles). There was no significant genetic differentiation between the strata, indicating that it is unlikely that the population increase within GBIS was due largely to immigration of whales from elsewhere in the North Pacific. However, two additional haplotypes were documented in the Contemporary stratum at low frequency, one of which was previously unreported in the North Pacific (haplotype A8, see below). This relative stability in haplotype frequencies over time argues for strong regional fidelity of the maternal lineages represented in GBIS between 1973 and 1985. After excluding the 42 Contemporary whales with no photo ID record of a mother or genotype available for maternity inference, at least 73.6% (n = 95) of the Contemporary stratum was either a returning Founder or a recruited descendant of a Founder female. Of all genetically confirmed females with genotypes in the Founder stratum, 96% (n = 24) were either represented in the Contemporary stratum, had at least one confirmed descendant in the Contemporary stratum, or both. This high proportion, in addition to the large proportion of the verifiable Contemporary stratum that were either returning Founders or a descendant of a Founder female, provides clear evidence for local fidelity and recruitment to GBIS. The discovery of the A8 haplotype, which differs by one base pair from a common haplotype referred to as A-, represents an increase in mtDNA diversity for the North Pacific humpback whale from 28 to 29 haplotypes. To investigate the origin of this new haplotype, we re-evaluated n = 1089 electropherograms of n = 710 individuals with A- haplotypes from both the SEAK DNA Register and Tissue Database and the ocean-wide program, SPLASH (Baker et al. 2013). From this review, we identified two individuals with the A8 haplotype (a cow and calf, both sampled in GBIS) and n = 20 individuals with clear heteroplasmy for haplotypes A-/A8. The majority of A-/A8 individuals (n = 15) were sampled in SEAK. Genotype exclusion and likelihood were used to identify one of the heteroplasmic females, #196 (first sighted in SEAK in 1982), as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. Based on life history records and estimates of pairwise relatedness from microsatellite genotypes, it appears likely that the A-/A8 and the A8 individuals are descendants from a common maternal ancestor one or more generations prior to the three generations documented here. Humpback whale sociality takes a distinct form in Icy Strait, where whales form large, coordinated groups with repeated membership across several decades. Twenty-one years of group association records (1985-2005, n = 2,204 groups) were used to investigate the hypothesis that kin selection influences membership in large, stable groups. Of the 2204 groups recorded, 113 consisted of 6 or more individuals; a size considered unexpectedly large assuming a Poisson distribution of group size with a mean of 1.7. A total of n = 71 individuals (n = 48 with DNA profiles) were encountered in a large group in at least one year, n = 38 individuals (n = 34 with DNA profiles) were encountered in a large group in at least two years, n = 29 individuals (n = 27 with DNA profiles) were encountered in a large group in at least three years, decreasing to n = 2 individuals (n = 2 with DNA profiles) that were encountered in a large group in at least 20 years. There were no significant differences in mtDNA frequencies between large group feeders and the Founder and Contemporary strata or when compared to whales never encountered in large groups in Icy Strait, indicating that group membership is not predominately passed through one maternal lineage. Sex ratios did not deviate significantly from 1:1 for those feeding in large groups over an increasing number of years, as would be expected if females were actively recruiting offspring into large groups. The average pairwise relatedness for large group feeders was not significantly greater than expected by chance and did not increase for those feeding in large groups over an increasing number of years. Of the 179 known offspring of females encountered in a large group, only 6% were also encountered in a large group in Icy Strait as an adult and only 2.2% in the same large group as their mother. These results indicate that kin selection is not the primary driver of membership in large, stable groups and pose an interesting dynamic in local habitat use: individuals are recruited to GBIS through local maternal fidelity but do not usually associate closely with direct maternal kin. The extensive collection of DNA profiles now archived with the individual-based data within the SEAK Regional Database allowed us to integrate genetics and photo ID to answer ecologically relevant questions regarding the whales in GBIS. Together, these results demonstrate that GBIS provide habitat for a distinct collection of individuals that exhibit strong fidelity and local recruitment, some of which engage in a highly specialized feeding behavior. Further, GBIS is a local feeding habitat for two individuals with a newly arising North Pacific mtDNA haplotype. These findings reveal local genotypic and cultural variation and highlight the importance of habitat protection for species with fine-scale habitat use and strong fidelity to local migratory destinations. Title: The influence of local fidelity and recruitment on population dynamics and specialized foraging of humpback whales in Glacier Bay and Icy Strait, Alaska Author: Pierszalowski, Sophie Penny Humpback whales (Megaptera novaeangliae, Borowski 1781) in the North Pacific migrate from mid- to high- latitude summer feeding grounds along the Pacific Rim, including areas off the coasts of the U.S., Canada, Russia and eastern Asia, to tropical breeding grounds each winter along Pacific coasts of Mexico and Central America as well as the offshore islands of Mexico, Hawaii, and Japan. Humpback whales in the North Pacific and elsewhere were reduced to very low numbers during a period of intense commercial exploitation that ended in 1965. As the population recovers in abundance, the range of cultural and genetic diversity that survived the exploitation-driven bottleneck is able to adapt, endure and evolve. My work uses genetic tools and photo identification data to investigate the population dynamics, mitochondrial (mt) DNA control region evolution and potential drivers of a specialized feeding behavior in a recovering subpopulation of humpback whales in the Glacier Bay and Icy Strait (GBIS) sub-region of the southeastern Alaska (SEAK) feeding ground. I first collated and reconciled available DNA profiles (mtDNA control region, 10 microsatellite loci and sex) from 556 individuals using tissue samples collected from 1987 to 2012. Photo identification records associated with 692 of 1,026 total genetic samples collected in SEAK (now archived within the SEAK DNA Register and Tissue Database) corresponded to extensive life-history information, extending back to the early 1970s, as archived within the SEAK Regional Database, curated by the National Park Service (NPS) and University of Alaska, Southeast (UAS). Changes in population structure in GBIS over 32 years (1973-2005) were investigated in order to determine whether the increase in local abundance was attributable to local fidelity and recruitment or immigration from outside of SEAK. Two temporal strata were defined: 'Founder' individuals identified between 1973-1985 (n = 74, n = 46 with DNA profiles) and 'Contemporary' individuals identified between 2004-2005 (n = 171, n = 114 with DNA profiles). There was no significant genetic differentiation between the strata, indicating that it is unlikely that the population increase within GBIS was due largely to immigration of whales from elsewhere in the North Pacific. However, two additional haplotypes were documented in the Contemporary stratum at low frequency, one of which was previously unreported in the North Pacific (haplotype A8, see below). This relative stability in haplotype frequencies over time argues for strong regional fidelity of the maternal lineages represented in GBIS between 1973 and 1985. After excluding the 42 Contemporary whales with no photo ID record of a mother or genotype available for maternity inference, at least 73.6% (n = 95) of the Contemporary stratum was either a returning Founder or a recruited descendant of a Founder female. Of all genetically confirmed females with genotypes in the Founder stratum, 96% (n = 24) were either represented in the Contemporary stratum, had at least one confirmed descendant in the Contemporary stratum, or both. This high proportion, in addition to the large proportion of the verifiable Contemporary stratum that were either returning Founders or a descendant of a Founder female, provides clear evidence for local fidelity and recruitment to GBIS. The discovery of the A8 haplotype, which differs by one base pair from a common haplotype referred to as A-, represents an increase in mtDNA diversity for the North Pacific humpback whale from 28 to 29 haplotypes. To investigate the origin of this new haplotype, we re-evaluated n = 1089 electropherograms of n = 710 individuals with A- haplotypes from both the SEAK DNA Register and Tissue Database and the ocean-wide program, SPLASH (Baker et al. 2013). From this review, we identified two individuals with the A8 haplotype (a cow and calf, both sampled in GBIS) and n = 20 individuals with clear heteroplasmy for haplotypes A-/A8. The majority of A-/A8 individuals (n = 15) were sampled in SEAK. Genotype exclusion and likelihood were used to identify one of the heteroplasmic females, #196 (first sighted in SEAK in 1982), as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. Based on life history records and estimates of pairwise relatedness from microsatellite genotypes, it appears likely that the A-/A8 and the A8 individuals are descendants from a common maternal ancestor one or more generations prior to the three generations documented here. Humpback whale sociality takes a distinct form in Icy Strait, where whales form large, coordinated groups with repeated membership across several decades. Twenty-one years of group association records (1985-2005, n = 2,204 groups) were used to investigate the hypothesis that kin selection influences membership in large, stable groups. Of the 2204 groups recorded, 113 consisted of 6 or more individuals; a size considered unexpectedly large assuming a Poisson distribution of group size with a mean of 1.7. A total of n = 71 individuals (n = 48 with DNA profiles) were encountered in a large group in at least one year, n = 38 individuals (n = 34 with DNA profiles) were encountered in a large group in at least two years, n = 29 individuals (n = 27 with DNA profiles) were encountered in a large group in at least three years, decreasing to n = 2 individuals (n = 2 with DNA profiles) that were encountered in a large group in at least 20 years. There were no significant differences in mtDNA frequencies between large group feeders and the Founder and Contemporary strata or when compared to whales never encountered in large groups in Icy Strait, indicating that group membership is not predominately passed through one maternal lineage. Sex ratios did not deviate significantly from 1:1 for those feeding in large groups over an increasing number of years, as would be expected if females were actively recruiting offspring into large groups. The average pairwise relatedness for large group feeders was not significantly greater than expected by chance and did not increase for those feeding in large groups over an increasing number of years. Of the 179 known offspring of females encountered in a large group, only 6% were also encountered in a large group in Icy Strait as an adult and only 2.2% in the same large group as their mother. These results indicate that kin selection is not the primary driver of membership in large, stable groups and pose an interesting dynamic in local habitat use: individuals are recruited to GBIS through local maternal fidelity but do not usually associate closely with direct maternal kin. The extensive collection of DNA profiles now archived with the individual-based data within the SEAK Regional Database allowed us to integrate genetics and photo ID to answer ecologically relevant questions regarding the whales in GBIS. Together, these results demonstrate that GBIS provide habitat for a distinct collection of individuals that exhibit strong fidelity and local recruitment, some of which engage in a highly specialized feeding behavior. Further, GBIS is a local feeding habitat for two individuals with a newly arising North Pacific mtDNA haplotype. These findings reveal local genotypic and cultural variation and highlight the importance of habitat protection for species with fine-scale habitat use and strong fidelity to local migratory destinations. Close

• 9. [Article] Lichen traits and species as indicators of vegetation and environment

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by American ...

  Citation × Citation Citation Abstract Copy Title: Lichen traits and species as indicators of vegetation and environment Author: Swanson, David K., McCune, Bruce, Nelson, Peter R. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by American Bryological and Lichenological Society and can be found at: http://www.bioone.org/loi/bryo Title: Lichen traits and species as indicators of vegetation and environment Author: Swanson, David K., McCune, Bruce, Nelson, Peter R. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by American Bryological and Lichenological Society and can be found at: http://www.bioone.org/loi/bryo Close

• 10. [Article] Geomorphic and Climatic Controls on Water Temperature and Streambed Scour, Copper River Delta, Alaska : Implications for Understanding Climate Change Impacts to the Pacific Salmon Egg Incubation Environment

  Pacific salmon (Oncorhynchus spp.) face numerous challenges associated with climate change. Most research has emphasized the potential effects of elevated summer water temperatures; however, climatic changes ...

  Citation × Citation Citation Abstract Copy Title: Geomorphic and Climatic Controls on Water Temperature and Streambed Scour, Copper River Delta, Alaska : Implications for Understanding Climate Change Impacts to the Pacific Salmon Egg Incubation Environment Author: Adelfio, Luca A. Pacific salmon (Oncorhynchus spp.) face numerous challenges associated with climate change. Most research has emphasized the potential effects of elevated summer water temperatures; however, climatic changes are also projected to significantly alter incubation and rearing habitats during the late autumn, winter, and spring months ("the incubation period"). Along the southern coast of Alaska, projected climatic changes include increases in the frequency of above freezing winter temperatures and reductions in low elevation snowpack. These changes are expected to impact the hydrology of salmon streams by increasing both water temperatures and the magnitude and frequency of winter floods. Projected increases in water temperature may accelerate embryo development, impacting juvenile viability. More powerful and more frequent winter floods could reduce the survival of salmon eggs by increasing streambed scour. Here, I investigate climatic and geomorphic controls of water temperature and potential scour depth at salmon spawning and rearing sites on the Copper River Delta, a large coastal foreland in Southcentral Alaska. In chapter 2, I utilized surface water temperature data collected at 18 sites to test the abilities of regression models to project year-round water temperature metrics based on catchment characteristics (elevation, slope, area, percent lake area) and air-water temperature correlations. Considerable variability in water temperature was observed on spatial and temporal scales. Both temperature maxima and the frequency of freezing conditions were positively correlated with percent lake area and negatively correlated with catchment elevation and slope. Sites with upwelling groundwater and sites with high-relief, high elevation catchments exhibited lower thermal sensitivity and water temperatures are anticipated to be less impacted by projected climatic changes. In chapter 3, I utilized surface and streambed water temperature data collected at 8 spawning sites to compare water temperatures during incubation periods under climatological mean ("severe winter") and anomalously warm ("mild winter") conditions. I also collected stream stage and channel geometry data at a subset of 3 sites and calculated streambed scour at bankfull discharge. The magnitude and seasonality of accumulated thermal units (°C/day) (ATU) within spawning gravels varied significantly between severe and mild winters at shallow flowpath sites, but not at upwelling groundwater sites. When seasonal snow and ice was absent, increases in spring ATU at shallow flowpath sites were particularly significant. Modelled mean scour depths varied from 3 to 72 cm, suggesting the impacts of scour on egg mortality will be variable across the landscape. I conclude that the impacts of projected climatic changes are likely to vary in magnitude across the Copper River Delta, even at small spatial scales, due to heterogeneity in climatic and geomorphic controls. Title: Geomorphic and Climatic Controls on Water Temperature and Streambed Scour, Copper River Delta, Alaska : Implications for Understanding Climate Change Impacts to the Pacific Salmon Egg Incubation Environment Author: Adelfio, Luca A. Pacific salmon (Oncorhynchus spp.) face numerous challenges associated with climate change. Most research has emphasized the potential effects of elevated summer water temperatures; however, climatic changes are also projected to significantly alter incubation and rearing habitats during the late autumn, winter, and spring months ("the incubation period"). Along the southern coast of Alaska, projected climatic changes include increases in the frequency of above freezing winter temperatures and reductions in low elevation snowpack. These changes are expected to impact the hydrology of salmon streams by increasing both water temperatures and the magnitude and frequency of winter floods. Projected increases in water temperature may accelerate embryo development, impacting juvenile viability. More powerful and more frequent winter floods could reduce the survival of salmon eggs by increasing streambed scour. Here, I investigate climatic and geomorphic controls of water temperature and potential scour depth at salmon spawning and rearing sites on the Copper River Delta, a large coastal foreland in Southcentral Alaska. In chapter 2, I utilized surface water temperature data collected at 18 sites to test the abilities of regression models to project year-round water temperature metrics based on catchment characteristics (elevation, slope, area, percent lake area) and air-water temperature correlations. Considerable variability in water temperature was observed on spatial and temporal scales. Both temperature maxima and the frequency of freezing conditions were positively correlated with percent lake area and negatively correlated with catchment elevation and slope. Sites with upwelling groundwater and sites with high-relief, high elevation catchments exhibited lower thermal sensitivity and water temperatures are anticipated to be less impacted by projected climatic changes. In chapter 3, I utilized surface and streambed water temperature data collected at 8 spawning sites to compare water temperatures during incubation periods under climatological mean ("severe winter") and anomalously warm ("mild winter") conditions. I also collected stream stage and channel geometry data at a subset of 3 sites and calculated streambed scour at bankfull discharge. The magnitude and seasonality of accumulated thermal units (°C/day) (ATU) within spawning gravels varied significantly between severe and mild winters at shallow flowpath sites, but not at upwelling groundwater sites. When seasonal snow and ice was absent, increases in spring ATU at shallow flowpath sites were particularly significant. Modelled mean scour depths varied from 3 to 72 cm, suggesting the impacts of scour on egg mortality will be variable across the landscape. I conclude that the impacts of projected climatic changes are likely to vary in magnitude across the Copper River Delta, even at small spatial scales, due to heterogeneity in climatic and geomorphic controls. Close