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• 1. [Article] Vocalizations of the Townsend chipmunk (Eutamias townsendii)

  This study describes and analyzes the vocalizations of the Townsend chipmunk (Eutamias townsendii) in Oregon. Tape recordings of calls were collected primarily from Forest Park in Portland (Oregon) during ...

  Citation × Citation Citation Abstract Copy Title: Vocalizations of the Townsend chipmunk (Eutamias townsendii) Author: Warner, Greig Michael Year: 1971 This study describes and analyzes the vocalizations of the Townsend chipmunk (Eutamias townsendii) in Oregon. Tape recordings of calls were collected primarily from Forest Park in Portland (Oregon) during 1970 and 1971, and sonograms of these recordings were produced. Findings were compared with those of Brand (1970) who investigated E. townsendii vocalizations in California. The prominent calls in the vocal repertoire of townsendii are the quist, the quirt, and the chipper. These calls all appear to be warning calls. The quist note is a a chevron-shaped (A) figure representing a sound which begins at a low frequency (1-2 KC), sharply rises to a peak at about 11 KC, and then drops sharply to the lower frequencies again. Quists are arranged into bursts, and bursts into sequences. The number of quists per burst and the frequency of the top of the note decreased significantly over time. The interval between burst increased significantly, while the interval between quists seems to increase over time. The variation in the quist rate and related character6istics between Oregon and California townsendii populations is probably a result of subspecific differences. There seems to be a trend in the sciurids from the specific vocal system (one definite meaning per call) of the forest dwellers towards the unspecific vocal systems of animal groups which live in the more open habitats. E. townsendii displays a specific vocal system in which each call seems to have a specific function. Title: Vocalizations of the Townsend chipmunk (Eutamias townsendii) Author: Warner, Greig Michael Year: 1971 This study describes and analyzes the vocalizations of the Townsend chipmunk (Eutamias townsendii) in Oregon. Tape recordings of calls were collected primarily from Forest Park in Portland (Oregon) during 1970 and 1971, and sonograms of these recordings were produced. Findings were compared with those of Brand (1970) who investigated E. townsendii vocalizations in California. The prominent calls in the vocal repertoire of townsendii are the quist, the quirt, and the chipper. These calls all appear to be warning calls. The quist note is a a chevron-shaped (A) figure representing a sound which begins at a low frequency (1-2 KC), sharply rises to a peak at about 11 KC, and then drops sharply to the lower frequencies again. Quists are arranged into bursts, and bursts into sequences. The number of quists per burst and the frequency of the top of the note decreased significantly over time. The interval between burst increased significantly, while the interval between quists seems to increase over time. The variation in the quist rate and related character6istics between Oregon and California townsendii populations is probably a result of subspecific differences. There seems to be a trend in the sciurids from the specific vocal system (one definite meaning per call) of the forest dwellers towards the unspecific vocal systems of animal groups which live in the more open habitats. E. townsendii displays a specific vocal system in which each call seems to have a specific function. Close

• 2. [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

• 3. [Article] Winter Diet of Bobolink, a Long-Distance Migratory Grassland Bird, Inferred from Feather Isotopes

  Effective conservation of migratory bird populations depends on advancements in our understanding of processes throughout the life cycle. Fundamental information about wintering ecology (e.g., habitat ...

  Citation × Citation Citation Abstract Copy Title: Winter Diet of Bobolink, a Long-Distance Migratory Grassland Bird, Inferred from Feather Isotopes Author: Renfrew, Rosalind B., Hill, Jason M., Kim, Daniel H., Romanek, Christopher, Perlut, Noah G. Year: 2017 Effective conservation of migratory bird populations depends on advancements in our understanding of processes throughout the life cycle. Fundamental information about wintering ecology (e.g., habitat use and diet composition) remains limited, which limits assessment of threats to populations during winter. Bobolink (Dolichonyx oryzivorus) is a year-round grassland obligate and Nearctic-Neotropical migrant that undergoes 2 complete molts each year, including a complete prealternate molt on the South American wintering grounds. This unusual winter molt provides a rare opportunity to examine, using stable isotope analysis, the timing and contribution of foraging resources in the Bobolink diet prior to northbound migration from disparate breeding populations. We compared winter diet composition among 3 breeding populations of Bobolinks and during 3 stages of winter molt using stable carbon isotope ratios. We used mixing models to compare the ratio of carbon-12 to carbon-13 isotope (d13C value) in feathers—grown on the wintering grounds but collected from individuals (n ¼ 105) breeding in Vermont, Nebraska, and North Dakota, USA—to estimate diet during early, middle, and late winter molt. Across the 3 breeding populations, Bobolinks relied on C3 sources for nearly one-third of their diet during the winter molt. Isotope data from feathers collected while growing on the wintering grounds from birds in rice vs. non-rice regions supported our assumption that C3 signatures are primarily due to a rice diet. The proportion of rice consumed was highest during late molt, corresponding with a period of greater rice availability to Bobolinks. Our results demonstrate that rice was a substantial component of the diet throughout the winter molt and was most exploited prior to northbound migration. Research is needed on the potential trade-offs of feeding on abundant cultivated rice, including its nutritional value and associated risks and conflicts from foraging in an agricultural setting. Title: Winter Diet of Bobolink, a Long-Distance Migratory Grassland Bird, Inferred from Feather Isotopes Author: Renfrew, Rosalind B., Hill, Jason M., Kim, Daniel H., Romanek, Christopher, Perlut, Noah G. Year: 2017 Effective conservation of migratory bird populations depends on advancements in our understanding of processes throughout the life cycle. Fundamental information about wintering ecology (e.g., habitat use and diet composition) remains limited, which limits assessment of threats to populations during winter. Bobolink (Dolichonyx oryzivorus) is a year-round grassland obligate and Nearctic-Neotropical migrant that undergoes 2 complete molts each year, including a complete prealternate molt on the South American wintering grounds. This unusual winter molt provides a rare opportunity to examine, using stable isotope analysis, the timing and contribution of foraging resources in the Bobolink diet prior to northbound migration from disparate breeding populations. We compared winter diet composition among 3 breeding populations of Bobolinks and during 3 stages of winter molt using stable carbon isotope ratios. We used mixing models to compare the ratio of carbon-12 to carbon-13 isotope (d13C value) in feathers—grown on the wintering grounds but collected from individuals (n ¼ 105) breeding in Vermont, Nebraska, and North Dakota, USA—to estimate diet during early, middle, and late winter molt. Across the 3 breeding populations, Bobolinks relied on C3 sources for nearly one-third of their diet during the winter molt. Isotope data from feathers collected while growing on the wintering grounds from birds in rice vs. non-rice regions supported our assumption that C3 signatures are primarily due to a rice diet. The proportion of rice consumed was highest during late molt, corresponding with a period of greater rice availability to Bobolinks. Our results demonstrate that rice was a substantial component of the diet throughout the winter molt and was most exploited prior to northbound migration. Research is needed on the potential trade-offs of feeding on abundant cultivated rice, including its nutritional value and associated risks and conflicts from foraging in an agricultural setting. Close

• 4. [Article] A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment

  The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of ...

  Citation × Citation Citation Abstract Copy Title: A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment Author: Lindgren, Annie R., Pankey, Molly S., Hochberg, Frederick G., Oakley, Todd H. Year: 2012 The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses of correlated evolution. To test for convergence and correlation, we generate the most taxonomically comprehensive multi-gene phylogeny of cephalopods to date. We then create a character matrix of habitat type and morphological characters, which we use to infer ancestral character states and test for correlation between habitat and morphology. Our study utilizes a taxonomically well-sampled phylogeny to show convergent evolution in all six morphological characters we analyzed. Three of these characters also correlate with habitat. The presence of an autogenic photophore (those relying upon autonomous enzymatic light reactions) is correlated with a pelagic habitat, while the cornea and accessory nidamental gland correlate with a benthic lifestyle. Here, we present the first statistical tests for correlation between convergent traits and habitat in cephalopods to better understand the evolutionary history of characters that are adaptive in benthic or pelagic environments, respectively. Our study supports the hypothesis that habitat has influenced convergent evolution in the marine environment: benthic organisms tend to exhibit similar characteristics that confer protection from invasion by other benthic taxa, while pelagic organisms possess features that facilitate crypsis and communication in an environment lacking physical refuges. Features that have originated multiple times in distantly related lineages are likely adaptive for the organisms inhabiting a particular environment: studying the frequency and evolutionary history of such convergent characters can increase understanding of the underlying forces driving ecological and evolutionary transitions in the marine environment. Title: A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment Author: Lindgren, Annie R., Pankey, Molly S., Hochberg, Frederick G., Oakley, Todd H. Year: 2012 The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses of correlated evolution. To test for convergence and correlation, we generate the most taxonomically comprehensive multi-gene phylogeny of cephalopods to date. We then create a character matrix of habitat type and morphological characters, which we use to infer ancestral character states and test for correlation between habitat and morphology. Our study utilizes a taxonomically well-sampled phylogeny to show convergent evolution in all six morphological characters we analyzed. Three of these characters also correlate with habitat. The presence of an autogenic photophore (those relying upon autonomous enzymatic light reactions) is correlated with a pelagic habitat, while the cornea and accessory nidamental gland correlate with a benthic lifestyle. Here, we present the first statistical tests for correlation between convergent traits and habitat in cephalopods to better understand the evolutionary history of characters that are adaptive in benthic or pelagic environments, respectively. Our study supports the hypothesis that habitat has influenced convergent evolution in the marine environment: benthic organisms tend to exhibit similar characteristics that confer protection from invasion by other benthic taxa, while pelagic organisms possess features that facilitate crypsis and communication in an environment lacking physical refuges. Features that have originated multiple times in distantly related lineages are likely adaptive for the organisms inhabiting a particular environment: studying the frequency and evolutionary history of such convergent characters can increase understanding of the underlying forces driving ecological and evolutionary transitions in the marine environment. Close

• 5. [Article] The Hyperthermophilic Archaeon Sulfolobus : from Exploration to Exploitation

  In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea ...

  Citation × Citation Citation Abstract Copy Title: The Hyperthermophilic Archaeon Sulfolobus : from Exploration to Exploitation Author: Brouns, Stan J.J., Ettema, Thijs J.G., Stedman, Kenneth M., Walther, Jasper, Smith, Hauke, Snijders, Ambrosius P.L., Young, Mark, Bernander, Rolf, Wright, Phillip C., Siebers, Betina, Van der Oost, John Year: 2003 In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea in general, and of Crenarchaea in particular. Many of its unusual physiological characteristics have been investigated, and several of its thermostable enzymes have been studied in considerable detail. For fundamental reasons, and because of its potential for industrial applications, Sulfolobus has been selected for a genome sequence project. The recent completion of the Sulfolobus solfataricus genome has set the stage for a series of postgenome research lines that will be reviewed here. Comparative genomics aims to unravel the cell’s metabolic potential (enzymes, pathways, and regulation) and compare it to other organisms. This in silico analysis of Sulfolobus has revealed several unique metabolic features and confirmed that the major control processes (transcription, translation, and replication) resemble eukaryal much more than bacterial equivalents. Currently, several research groups use a functional genomics approach—a genomebased, high-throughput analysis of the complete Sulfolobus cell—at the level of RNA (transcriptomics), protein (proteomics), and metabolic intermediates and products (metabolomics). Apart from analyzing the cell’s response to different cultivation conditions, the comparison of different genotypes (wild type and mutants) would be very interesting for both basic science and applied reasons. Much effort has recently been put into the establishment of tools that allow genetic engineering of Sulfolobus. The future challenge is to integrate available knowledge in order to understand the relevant mechanisms that enable Sulfolobus to thrive in its extreme habitats. Moreover, such a Systems Biology approach is essential as a basis for the directed engineering and industrial exploitation of this unique microorganism. Title: The Hyperthermophilic Archaeon Sulfolobus : from Exploration to Exploitation Author: Brouns, Stan J.J., Ettema, Thijs J.G., Stedman, Kenneth M., Walther, Jasper, Smith, Hauke, Snijders, Ambrosius P.L., Young, Mark, Bernander, Rolf, Wright, Phillip C., Siebers, Betina, Van der Oost, John Year: 2003 In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea in general, and of Crenarchaea in particular. Many of its unusual physiological characteristics have been investigated, and several of its thermostable enzymes have been studied in considerable detail. For fundamental reasons, and because of its potential for industrial applications, Sulfolobus has been selected for a genome sequence project. The recent completion of the Sulfolobus solfataricus genome has set the stage for a series of postgenome research lines that will be reviewed here. Comparative genomics aims to unravel the cell’s metabolic potential (enzymes, pathways, and regulation) and compare it to other organisms. This in silico analysis of Sulfolobus has revealed several unique metabolic features and confirmed that the major control processes (transcription, translation, and replication) resemble eukaryal much more than bacterial equivalents. Currently, several research groups use a functional genomics approach—a genomebased, high-throughput analysis of the complete Sulfolobus cell—at the level of RNA (transcriptomics), protein (proteomics), and metabolic intermediates and products (metabolomics). Apart from analyzing the cell’s response to different cultivation conditions, the comparison of different genotypes (wild type and mutants) would be very interesting for both basic science and applied reasons. Much effort has recently been put into the establishment of tools that allow genetic engineering of Sulfolobus. The future challenge is to integrate available knowledge in order to understand the relevant mechanisms that enable Sulfolobus to thrive in its extreme habitats. Moreover, such a Systems Biology approach is essential as a basis for the directed engineering and industrial exploitation of this unique microorganism. Close

• 6. [Article] Residential Edges as Ecological Traps: Postfledgling Survival of a Ground-Nesting Passerine in a Forested Urban Park

  Substantial offspring mortality can occur during the postfledging period of birds, but few postfledging survival studies have been conducted within the context of habitat suitability. We conducted a 2-year ...

  Citation × Citation Citation Abstract Copy Title: Residential Edges as Ecological Traps: Postfledgling Survival of a Ground-Nesting Passerine in a Forested Urban Park Author: Shipley, Amy A., Murphy, Michael T., Elzinga, Adam H. Year: 2013 Substantial offspring mortality can occur during the postfledging period of birds, but few postfledging survival studies have been conducted within the context of habitat suitability. We conducted a 2-year radiotelemetry study of Spotted Towhee (Pipilo maculatus) reproductive success and fledgling survival in a 24-ha forested park in a residential area of Lake Oswego, Oregon. In corroboration of previous research on this species, we found (1) that Spotted Towhees nested closer to the edge between the park and residential neighborhoods than expected by chance, and (2) that pairs nesting near edges produced the largest and most offspring. However, fates were reversed during the postfledging period. Thirty-six of 52 fledglings survived the 27-day tracking period, and although fledglings were more likely to be found near edges than in the interior, fledglings near edges had a far higher probability of dying. All deaths were from predation, and at least 11 of 16 predation events were attributable to Domestic Cats (Felis catus) and Western Screech-Owls (Megascops kennicottii). A stochastic model that incorporated probability of nest success, nestling production from successful nests, and fledgling survival showed that the number of independent offspring produced per nest was greatest in the park interior. Heavy use of, and apparent preference for, edge by nesting Spotted Towhees, coupled with high fledgling mortality near edges, created a severe ecological trap that was not apparent until the final stage of parental care. Hence, failure to document offspring survival in the late stages of reproduction may lead to incorrect assessment of habitat suitability and poor management decisions. Title: Residential Edges as Ecological Traps: Postfledgling Survival of a Ground-Nesting Passerine in a Forested Urban Park Author: Shipley, Amy A., Murphy, Michael T., Elzinga, Adam H. Year: 2013 Substantial offspring mortality can occur during the postfledging period of birds, but few postfledging survival studies have been conducted within the context of habitat suitability. We conducted a 2-year radiotelemetry study of Spotted Towhee (Pipilo maculatus) reproductive success and fledgling survival in a 24-ha forested park in a residential area of Lake Oswego, Oregon. In corroboration of previous research on this species, we found (1) that Spotted Towhees nested closer to the edge between the park and residential neighborhoods than expected by chance, and (2) that pairs nesting near edges produced the largest and most offspring. However, fates were reversed during the postfledging period. Thirty-six of 52 fledglings survived the 27-day tracking period, and although fledglings were more likely to be found near edges than in the interior, fledglings near edges had a far higher probability of dying. All deaths were from predation, and at least 11 of 16 predation events were attributable to Domestic Cats (Felis catus) and Western Screech-Owls (Megascops kennicottii). A stochastic model that incorporated probability of nest success, nestling production from successful nests, and fledgling survival showed that the number of independent offspring produced per nest was greatest in the park interior. Heavy use of, and apparent preference for, edge by nesting Spotted Towhees, coupled with high fledgling mortality near edges, created a severe ecological trap that was not apparent until the final stage of parental care. Hence, failure to document offspring survival in the late stages of reproduction may lead to incorrect assessment of habitat suitability and poor management decisions. Close

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

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

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

• 8. [Article] The Impact of Weather on Kingbird Foraging Behavior

  Foraging data on Eastern Kingbirds (Tyrannus tyrannus) were collected during the early breeding season in eastern Kansas to test the hypothesis that foraging rate and other aspects of foraging behavior ...

  Citation × Citation Citation Abstract Copy Title: The Impact of Weather on Kingbird Foraging Behavior Author: Murphy, Michael T. Year: 1987 Foraging data on Eastern Kingbirds (Tyrannus tyrannus) were collected during the early breeding season in eastern Kansas to test the hypothesis that foraging rate and other aspects of foraging behavior vary with weather. Foraging characteristics of five additional kingbird species were also examined to assess Fitzpatrick's (1980) generalization that kingbirds (Tyrannus spp.) are aerial hawking specialists. In Eastern Kingbirds, total foraging rate was independent of air temperature, cloud cover, wind speed, and time of day, but the rate of aerial hawking varied directly with air temperature and inversely with cloud cover (both P < 0.05). Effects of the two variables were additive. The percentage of foraging movements that were aerial hawks also increased with temperature and declined with cloud cover, and, hover-gleaning and perch-to-ground sallying were observed mainly during cloudy weather. Sally (i.e., foraging flight) distance correlated directly with perch height and air temperature, and large insects were captured almost exclusively in long upward or horizontal flights. I interpret these data to indicate that foraging behavior and the capture of large, flying insects depends on weather because of how it affects the activity of insect prey. Foraging data on kingbirds support Fitzpatrick's generalization, but the relative use of aerial hawking varies considerably among species. Resident Tropical Kingbirds( T. melancholicus) are the most specialized foragers, whereas the migrant and widely distributed Eastern Kingbird appears to be the most generalized. Certain habitats also appear to favor the use of particular foraging methods (e.g., outward striking in grasslands and perch-to-ground sallying in drier, open habitats). Title: The Impact of Weather on Kingbird Foraging Behavior Author: Murphy, Michael T. Year: 1987 Foraging data on Eastern Kingbirds (Tyrannus tyrannus) were collected during the early breeding season in eastern Kansas to test the hypothesis that foraging rate and other aspects of foraging behavior vary with weather. Foraging characteristics of five additional kingbird species were also examined to assess Fitzpatrick's (1980) generalization that kingbirds (Tyrannus spp.) are aerial hawking specialists. In Eastern Kingbirds, total foraging rate was independent of air temperature, cloud cover, wind speed, and time of day, but the rate of aerial hawking varied directly with air temperature and inversely with cloud cover (both P < 0.05). Effects of the two variables were additive. The percentage of foraging movements that were aerial hawks also increased with temperature and declined with cloud cover, and, hover-gleaning and perch-to-ground sallying were observed mainly during cloudy weather. Sally (i.e., foraging flight) distance correlated directly with perch height and air temperature, and large insects were captured almost exclusively in long upward or horizontal flights. I interpret these data to indicate that foraging behavior and the capture of large, flying insects depends on weather because of how it affects the activity of insect prey. Foraging data on kingbirds support Fitzpatrick's generalization, but the relative use of aerial hawking varies considerably among species. Resident Tropical Kingbirds( T. melancholicus) are the most specialized foragers, whereas the migrant and widely distributed Eastern Kingbird appears to be the most generalized. Certain habitats also appear to favor the use of particular foraging methods (e.g., outward striking in grasslands and perch-to-ground sallying in drier, open habitats). Close

• 9. [Article] The Impeccable Timing of the Apple Maggot Fly, <i>Rhagoletis pomonella</i> (Dipetera: Tephritidae), and its Implications for Ecological Speciation

  Speciation is the process by which life diversifies into discrete forms, and understanding its underlying mechanisms remains a primary focus for biologists. Increasingly, empirical studies are helping ...

  Citation × Citation Citation Abstract Copy Title: The Impeccable Timing of the Apple Maggot Fly, <i>Rhagoletis pomonella</i> (Dipetera: Tephritidae), and its Implications for Ecological Speciation Author: Mattsson, Monte Arthur Year: 2015 Speciation is the process by which life diversifies into discrete forms, and understanding its underlying mechanisms remains a primary focus for biologists. Increasingly, empirical studies are helping explain the role of ecology in generating biodiversity. Adaptive radiations are often propelled by selective fitness tradeoffs experienced by individuals that invade new habitats, resulting in reproductive isolation from ancestral conspecifics and potentially cladogenesis. Host specialist insects are among the most speciose organisms known and serve as highly useful models for studying adaptive radiations. We are just beginning to understand the pace and degree with which these insects diversify. The apple maggot, Rhagoletis pomonella, is a well-studied insect whose eastern and southern populations are models for ecological speciation. Recently (40–65 ya), the fly has invaded the Pacific Northwestern United States through human-transported apples infested with larvae. There, populations of R. pomonella have rapidly colonized two novel hawthorn hosts whose fruiting times bracket apple’s (early-season native Crataegus douglasii and introduced C. monogyna, which fruits late in the season). The recent introduction might initiate host shifts, providing opportunities to examine the pace and mechanistic means with which host races (an evolutionary stage preceding speciation) become established. Here, I demonstrate that host-associated populations at a site in southwest Washington are partially allochronically isolated from one another, and life cycles temporally match with natal host fruit ripening times in sympatry. If spatially widespread, these temporal barriers could result in reproductive isolation and possibly cladogenesis. Implications of these findings reach beyond academic import, as R. pomonella is expanding not only its host range, but its geographic range is encroaching upon central Washington, the site of a multi-billion dollar per year apple-growing industry. Title: The Impeccable Timing of the Apple Maggot Fly, <i>Rhagoletis pomonella</i> (Dipetera: Tephritidae), and its Implications for Ecological Speciation Author: Mattsson, Monte Arthur Year: 2015 Speciation is the process by which life diversifies into discrete forms, and understanding its underlying mechanisms remains a primary focus for biologists. Increasingly, empirical studies are helping explain the role of ecology in generating biodiversity. Adaptive radiations are often propelled by selective fitness tradeoffs experienced by individuals that invade new habitats, resulting in reproductive isolation from ancestral conspecifics and potentially cladogenesis. Host specialist insects are among the most speciose organisms known and serve as highly useful models for studying adaptive radiations. We are just beginning to understand the pace and degree with which these insects diversify. The apple maggot, Rhagoletis pomonella, is a well-studied insect whose eastern and southern populations are models for ecological speciation. Recently (40–65 ya), the fly has invaded the Pacific Northwestern United States through human-transported apples infested with larvae. There, populations of R. pomonella have rapidly colonized two novel hawthorn hosts whose fruiting times bracket apple’s (early-season native Crataegus douglasii and introduced C. monogyna, which fruits late in the season). The recent introduction might initiate host shifts, providing opportunities to examine the pace and mechanistic means with which host races (an evolutionary stage preceding speciation) become established. Here, I demonstrate that host-associated populations at a site in southwest Washington are partially allochronically isolated from one another, and life cycles temporally match with natal host fruit ripening times in sympatry. If spatially widespread, these temporal barriers could result in reproductive isolation and possibly cladogenesis. Implications of these findings reach beyond academic import, as R. pomonella is expanding not only its host range, but its geographic range is encroaching upon central Washington, the site of a multi-billion dollar per year apple-growing industry. Close

• 10. [Article] Developmental Mechanisms that Support Genome Stability and Embryonic Survival in Stress-tolerant Embryos of the Annual Killifish <i>Austrofundulus limnaeus</i>

  In order to complete their life cycles, vertebrates require oxygen and water. However, environments are not always forgiving when it comes to constantly providing these basic needs for vertebrate life. ...

  Citation × Citation Citation Abstract Copy Title: Developmental Mechanisms that Support Genome Stability and Embryonic Survival in Stress-tolerant Embryos of the Annual Killifish <i>Austrofundulus limnaeus</i> Author: Wagner, Josiah Tad Year: 2015 In order to complete their life cycles, vertebrates require oxygen and water. However, environments are not always forgiving when it comes to constantly providing these basic needs for vertebrate life. The annual killifish Austrofundulus limnaeus is possibly the most well described extremophile vertebrate and its embryos have been shown to tolerate extremes in oxygen, salinity, and water availability. This phenotype is likely a result of the annual killifish life history, which includes periods of temporary habitat desiccation and oxygen deprivation, and requires the production of stress-tolerant embryos that depress metabolism in a state of suspended animation, known as diapause. Over the past several decades, the basic morphology and physiology of annual killifish development has become better characterized. However, there are still basic cellular processes that remain to be described in annual killifish such as A. limnaeus. Specifically, changes in DNA structure, expression, and copy number are known to have profound impacts on the phenotype and survival of an organism. Little is known as to how A. limnaeus maintains genome integrity during cell stress, nor how the A. limnaeus nuclear and mitochondrial genomes may have evolved under the unpredictable conditions in which A. limnaeus thrive. Early annual killifish embryonic development is also characterized by a complete dispersion and subsequent reaggregation of embryonic blastomeres prior to formation of the embryonic axis. This unusual period of early development may provide a functional adaptation that allows annual killifish embryos to survive these extreme conditions. The overall goals of this project were to (1) characterize the ability of A. limnaeus to tolerate and repair DNA damage through enzymatic and developmental mechanisms, (2) to determine possible consequences of mitochondrial DNA sequence and copy number on the metabolism of A. limnaeus, and (3) to establish a draft genome of A. limnaeus for future comparative genome studies. The results of this project show that embryos of A. limnaeus have an impressive ability to survive and reverse high doses of DNA damage induced by ultraviolet-C (UV-C) radiation, especially when allowed to recover under photoreactivating light. Surprisingly, embryos that survived irradiation during blastomere dispersion phases were able to develop normally. Characterization of gene expression during embryonic development for genes important for axis formation and cellular differentiation suggests that A. limnaeus embryos may delay axis formation until several days after epiboly is complete, thus allowing time for cells that become damaged to be replaced by surrounding pluripotent cells. This outcome would represent first case of a developmental buffering stage in a vertebrate. A. limnaeus embryos are also unique in their mitochondrial response to anoxia. Whereas in other species the amount of mitochondrial DNA (mtDNA) copy number fluctuates following extremes in oxygen availability, A. limnaeus embryonic mtDNA remains stable. Additionally, characterization of the fully sequenced A. limnaeus mitochondrial genome reveals possible evolutionary adaptations that may have facilitated dormancy and anoxia tolerance when compared to other species within the Order Cyprinodontiformes. The final chapter of this project characterizes the draft genome of A. limnaeus and I provide evidence suggesting that epigenetic DNA methylation that may be involved in regulating diapause. Title: Developmental Mechanisms that Support Genome Stability and Embryonic Survival in Stress-tolerant Embryos of the Annual Killifish <i>Austrofundulus limnaeus</i> Author: Wagner, Josiah Tad Year: 2015 In order to complete their life cycles, vertebrates require oxygen and water. However, environments are not always forgiving when it comes to constantly providing these basic needs for vertebrate life. The annual killifish Austrofundulus limnaeus is possibly the most well described extremophile vertebrate and its embryos have been shown to tolerate extremes in oxygen, salinity, and water availability. This phenotype is likely a result of the annual killifish life history, which includes periods of temporary habitat desiccation and oxygen deprivation, and requires the production of stress-tolerant embryos that depress metabolism in a state of suspended animation, known as diapause. Over the past several decades, the basic morphology and physiology of annual killifish development has become better characterized. However, there are still basic cellular processes that remain to be described in annual killifish such as A. limnaeus. Specifically, changes in DNA structure, expression, and copy number are known to have profound impacts on the phenotype and survival of an organism. Little is known as to how A. limnaeus maintains genome integrity during cell stress, nor how the A. limnaeus nuclear and mitochondrial genomes may have evolved under the unpredictable conditions in which A. limnaeus thrive. Early annual killifish embryonic development is also characterized by a complete dispersion and subsequent reaggregation of embryonic blastomeres prior to formation of the embryonic axis. This unusual period of early development may provide a functional adaptation that allows annual killifish embryos to survive these extreme conditions. The overall goals of this project were to (1) characterize the ability of A. limnaeus to tolerate and repair DNA damage through enzymatic and developmental mechanisms, (2) to determine possible consequences of mitochondrial DNA sequence and copy number on the metabolism of A. limnaeus, and (3) to establish a draft genome of A. limnaeus for future comparative genome studies. The results of this project show that embryos of A. limnaeus have an impressive ability to survive and reverse high doses of DNA damage induced by ultraviolet-C (UV-C) radiation, especially when allowed to recover under photoreactivating light. Surprisingly, embryos that survived irradiation during blastomere dispersion phases were able to develop normally. Characterization of gene expression during embryonic development for genes important for axis formation and cellular differentiation suggests that A. limnaeus embryos may delay axis formation until several days after epiboly is complete, thus allowing time for cells that become damaged to be replaced by surrounding pluripotent cells. This outcome would represent first case of a developmental buffering stage in a vertebrate. A. limnaeus embryos are also unique in their mitochondrial response to anoxia. Whereas in other species the amount of mitochondrial DNA (mtDNA) copy number fluctuates following extremes in oxygen availability, A. limnaeus embryonic mtDNA remains stable. Additionally, characterization of the fully sequenced A. limnaeus mitochondrial genome reveals possible evolutionary adaptations that may have facilitated dormancy and anoxia tolerance when compared to other species within the Order Cyprinodontiformes. The final chapter of this project characterizes the draft genome of A. limnaeus and I provide evidence suggesting that epigenetic DNA methylation that may be involved in regulating diapause. Close