Geology topics

Colleen M. Handel

Publications and source records attributed to Colleen M. Handel.

At least 19 recordsLinked to original sources

USGS2025

Land cover, elevation, and precipitation predict distribution and hotspots of three bird species of concern in boreal Alaska

The boreal forest biome is an important breeding area for migratory birds and is undergoing rapid changes, including drying of wetlands, changes to vegetation composition, and human development. Many boreal bird populations are declining, but information is often lacking on how these species associate with habitat characteristics and thus how they may respond to changing conditions. We used a large point-count dataset to describe habitat associations and hotspots for three boreal species of concern in Alaska, USA: Tringa flavipes (Lesser Yellowlegs), Contopus cooperi (Olive-sided Flycatcher), and Euphagus carolinus (Rusty Blackbird). We used an N-mixture model to evaluate covariates of abundance and two components of detection (availability and perceptibility). We then used the estimated relationships with covariates to predict density of each species across the Northwestern Interior Forest (Bird Conservation Region 4) in Alaska, including identifying hotspots where density was predicted to be in the top 10% of all locations. T. flavipes and E. carolinus were associated with wetlands and mean values of June precipitation; T. flavipes were also associated with low elevation and recent fire; and C. cooperi was associated with needleleaf forest and moderate elevation. Hotspots for T. flavipes and E. carolinus usually overlapped, while hotspots for C. cooperi almost never overlapped with those of the other two species. Following ground-truthing, these predicted distributions could be used to indicate areas of high importance for species of conservation concern and thus inform management decisions and mitigation measures. Our results could also help identify areas that are likely to be important for these species in the future, given the rapid changes now occurring across the boreal biome in response to climate warming and drying.

Alaska↗

USGS2025

Accounting for seasonal patterns in bird availability prevents biased population trend estimates with advancing spring phenology

Advancing spring phenology has been observed around the world, including changes in the timing of breeding of birds. When singing rates are tied to breeding stage, the rate at which birds are available for detection by surveyors can also show seasonal patterns that may shift with spring phenology. As the timing of peak bird availability changes over years, monitoring programs that do not account for changing availability could incorrectly conclude that there is a change in population size. We used a 20-yr point-count dataset to test for relationships between bird availability and spring vegetation phenology for 27 species in boreal Alaska. Nine of 22 migratory species showed a significant effect of day of spring (DOS) on availability, usually with availability declining over the survey window (late spring and early summer). In contrast, 3 of 5 resident species showed availability increasing over the survey window. We then conducted a simulation study to evaluate how changing spring phenology could affect estimates of population trend under a static survey window. We found that including DOS in the model as a covariate of availability prevented bias in the trend estimates and did not reduce precision. However, when the model ignored the effect of DOS on availability, population trend estimates were often significantly biased when spring phenology was advancing. Our study adds to previous evidence that bird availability is often related to spring phenology, and demonstrates that failing to account for seasonal changes in availability could result in the spurious estimation of a population trend when spring phenology changes over time. In some cases, the bias could be large enough to change species status assessments under IUCN Red List Criteria. Monitoring programs for birds and other taxa with seasonally varying availability could avoid bias by simply measuring and modeling the relationship between DOS and availability.

Alaska↗

USGS2025

Beak deformities in Buteo jamaicensis (Red-tailed Hawk) signal possible emergence of avian keratin disorder among raptors

Beginning in the late 1990s, an unusual cluster of beak deformities was observed among Buteo jamaicensis (Red-tailed Hawk) in the Pacific coastal region of North America. However, information was not available to determine the scope of this problem nor to assess a potential link between beak deformities in hawks and avian keratin disorder (AKD), an emerging disease primarily among passerines that causes overgrowth of the keratinized layer of the beak. To help address these knowledge gaps, we compiled capture records, citizen science reports, and other available data from across North America. As part of a long-term raptor monitoring program in Washington, we detected anomalously high rates of beak deformities in 29% and other keratin abnormalities in an additional 19% of B. jamaicensis between 2014 and 2021. We also identified more than 100 other AKD-like cases in B. jamaicensis , largely clustered in the Pacific coastal region, with most reports from 2000 to present. Pathologic examination of affected hawks revealed gross and microscopic features consistent with AKD in passerines, while shared epidemiological patterns, including timing of emergence, provided further evidence that this disease may impact an ecologically diverse suite of species. We detected poecivirus, a novel avian virus implicated as a likely cause of AKD in Poecile atricapillus (Black-capped Chickadee), in 1 out of 10 swabs collected from live B. jamaicensis , with gross beak deformities, suggesting the possibility of a shared viral etiology across species. However, additional work would be needed to determine the underlying cause of beak deformities in and their potential impacts on B. jamaicensis . By documenting this cluster of beak deformities, we hope to raise awareness among the ornithological community, including raptor researchers, to better track current and future outbreaks of beak deformities and related conditions.

Ornithology↗

USGS2023

Structure of breeding calls in three closely related bird species (Calidris Merrem, 1804; Scolopacidae)

We studied calls of three sandpiper species to document species’ similarities and differences. We hypothesized that functionally different calls would differ in degree of divergence. We studied two nuptial calls (complex “Song” and rhythmically repeated aerial call, RRC) of males, and a general-purpose call (“alarm” trill, AT) given by parents of both sexes in the presence of humans and other potential predators, in great knot, Calidris tenuirostris (Horsfeld, 1821); surfbird, Calidris virgata (Gmelin, 1789); and red knot, Calidris canutus (Linnaeus, 1758). Calls diverged unevenly across species—RRCs and Song diverged the most and ATs the least. Vocalizations of great knot and surfbird were most similar to one another, in agreement with a recently proposed phylogeny. Despite species differences in single acoustic traits, calls were evolutionarily conservative at higher structural levels, such as rhythmic temporal delivery of RRCs and harmonic structure (e.g., the fundamental frequency was suppressed in some call types). Some acoustic qualities that differed across species were similar across call types within species (e.g., tonality in red knot calls). Trait similarity across different calls suggests that a species’ calls cannot evolve independently of one another: common mechanisms of vocal production across different calls may impede differentiation within a species’ repertoire.

Canadian Journal of Zoology↗

USGS2022

The Pacific as the world’s greatest theater of bird migration: Extreme flights spark questions about physiological capabilities, behavior, and the evolution of migratory pathways

The Pacific Basin, by virtue of its vastness and its complex aeroscape, provides unique opportunities to address questions about the behavioral and physiological capabilities and mechanisms through which birds can complete spectacular flights. No longer is the Pacific seen just as a formidable barrier between terrestrial habitats in the north and the south, but rather as a gateway for specialized species, such as shorebirds, to make a living on hemispherically distributed seasonal resources. This recent change in perspective is dramatic, and the research that underpins it has presented new opportunities to learn about phenomena that often challenge a sense of normal. Ancient Polynesians were aware of the seasonal passage of shorebirds and other landbirds over the Pacific Ocean, incorporating these observations into their navigational “tool kit” as they explored and colonized the Pacific. Some ten centuries later, systematic visual observations and tracking technology have revealed much about movement of these shorebirds, especially the enormity of their individual nonstop flights. This invites a broad suite of questions, often requiring comparative studies with bird migration across other ocean basins, or across continents. For example, how do birds manage many days of nonstop exercise apparently without sleep? What mechanisms explain birds acting as if they possess a Global Positioning System? How do such extreme migrations evolve? Through advances in both theory and tracking technology, biologists are poised to greatly expand the horizons of movement ecology as we know it. In this integrative review, we present a series of intriguing questions about trans-Pacific migrant shorebirds and summarize recent advances in knowledge about migratory behavior operating at temporal scales ranging from immediate decisions during a single flight, to adaptive learning throughout a lifetime, to evolutionary development of migratory pathways. Recent advances in this realm should stimulate future research across the globe and across a broad array of disciplines.

Ornithology↗

USGS2022

Highly pathogenic avian influenza (HPAI): An emerging disease threat in North America

Highly pathogenic avian influenza (HPAI) is an ecologically and economically significant avian disease that is quickly spreading among wild and domestic birds throughout North America. In this blog post, we provide information and resources that can help you to be informed, be prepared, and be ready to take appropriate action should you observe wild birds that may be affected by HPAI.

Report↗

USGS2021

Willow drives changes in arthropod communities of northwestern Alaska: Ecological implications of shrub expansion

Arthropods serve as complex linkages between plants and higher-level predators in Arctic ecosystems and provide key ecosystem services such as pollination and nutrient cycling. Arctic plant communities are changing as tall woody shrubs expand onto tundra, but potential effects on arthropod abundance and food web structure remain unclear. Changes in vegetation structure can alter the physical habitat, thermal environment, and food available to arthropods, thereby having the potential to induce cascading effects throughout the ecosystem. We evaluated relationships between the abundance, biomass, and community composition of arthropods and the cover of several shrub taxa across tundra–shrub gradients in northwestern Alaska. While previous research had found a general positive association between arthropod biomass and shrub cover, we found heterogeneity in this relationship with finer-scale examination of (1) shrub taxa, (2) arthropod taxa, and (3) arthropod guilds. Abundance and biomass of arthropods showed strong, positive associations with the amount of cover of willow ( Salix spp.) but were not significantly influenced by shrub birch ( Betula spp.) or ericaceous (Ericaceae) vegetation. Significant shifts in arthropod community composition were also associated with willows. Among trophic groups of arthropods, herbivores and pollinators were most positively associated with willow cover. Due to geographical variation in both dominant shrub taxa and their rates of expansion, effects on arthropod communities are likely to be heterogeneous across the Arctic. Taken together, our results suggest that shrub expansion could increase food availability for higher-level insectivores and shift Arctic food web structure.

Alaska↗

USGS2021

Poecivirus is present in individuals with beak deformities in seven species of North American birds

Avian keratin disorder (AKD), a disease of unknown etiology characterized by debilitating beak overgrowth, has increasingly affected wild bird populations since the 1990s. A novel picornavirus, poecivirus, is closely correlated with disease status in Black-capped Chickadees ( Poecile atricapillus ) in Alaska. However, our knowledge of the relationship between poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of poecivirus: Mew Gull ( Larus canus ), Hairy Woodpecker ( Picoides villosus ), Black-billed Magpie ( Pica hudsonia ), American Crow ( Corvus brachyrhynchos ), Red-breasted Nuthatch ( Sitta canadensis ), and Blackpoll Warbler ( Setophaga striata ). The birds were sampled in Alaska and Maine (1999−2016). We used targeted PCR followed by Sanger sequencing to test for the presence of poecivirus in each specimen and to obtain viral genome sequence from virus-positive host individuals. We detected poecivirus in all individuals tested, but not in negative controls (water and tissue samples). Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two American Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequences from several specimens, including the complete coding region of poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.

Alaska, Maine↗

USGS2021

Alaska landbird montoring survey: Alaska regional protocol framework for monitoring landbirds using point counts

Alaska provides habitat for 143 species of landbirds that occur regularly in the state, about half of which breed predominantly north of the border between the contiguous United States and Canada. The road-based North American Breeding Bird Survey (BBS) provides some data on population trends in Alaska, but most northern populations are inadequately monitored by this program because of a paucity of roads. To remedy this deficiency, Boreal Partners in Flight developed the Alaska Landbird Monitoring Survey (ALMS) to monitor breeding populations of landbirds in off-road areas of Alaska in tandem with data collected from the roadside BBS. The primary objective of ALMS is to monitor long-term population trends of landbirds and other species that can be monitored by diurnal point counts during the breeding season, including many shorebirds and aquatic birds. A secondary objective is to estimate landbird densities by habitat, which can be used to model avian distribution and abundance across Alaska. ALMS is a collaborative program whereby agencies and other entities conduct standardized surveys of breeding birds and their habitats on the lands they manage and then contribute the data to the U.S. Geological Survey Alaska Science Center for storage and analysis. The short-term implementation goal of ALMS is to monitor birds systematically within each of 100 randomly selected survey blocks, thereby matching the number of BBS surveys conducted in each of Alaska's five Bird Conservation Regions (BCRs). Each block has a mini-grid of 15−25 points that are surveyed biennially, with half of the blocks surveyed in alternating years. Survey blocks are stratified by accessibility and cost-effectiveness. Refuges may opt to limit sites to those accessible by foot, vehicle, boat, or fixed-wing aircraft, as these can be surveyed more inexpensively and reliably over time. Observers survey each point within a survey block for birds using a 10-min point count once per summer on a biennial basis. They collect corresponding habitat data during the first visit and at subsequent 10-year intervals or whenever a disturbance (e.g., fire, wind) has caused a significant change. USGS analyzes ALMS data jointly with BBS data to test for differences between off-road and roadside areas and to increase power to detect statewide trends. Additional blocks can be surveyed in areas that are more difficult and expensive to access as resources become available in the future. Long-term monitoring enables detection of change in bird populations in relation to fire, disease and insect damage, resource development, climate-related change, and other landscape-level disturbances across Alaska. Results from ALMS can also help prioritize conservation and research towards species before they become endangered and require expensive recovery programs.

Alaska↗

USGS2021

Alaska Landbird Conservation Plan

Alaska is a land of extremes. The diversity of its avifauna reflects the heterogeneity of its landscape, with more than 500 species of birds recorded in the state. Species inhabiting primarily terrestrial habitats, known collectively as landbirds, constitute the largest and most ecologically diverse component of the Alaska avifauna. Habitats used by landbirds range from temperate rainforests in southeastern Alaska to Arctic tundra across much of northern Alaska. Most of these landbird species are migratory, and four major global migration flyways converge on rich breeding areas in Alaska. Alaska has one endemic landbird species, the McKay’s Bunting, and is home to an impressive number of landbird populations for which it hosts a large proportion of the regional, continental, or global population. Thus, Alaska has a significant stewardship responsibility for these particular landbird species and subspecies. Habitats in Alaska remain largely pristine due to the region’s remote nature, vast size, and small human population. Alaska’s growing population and attendant economic development, however, present many challenges that could affect all wildlife, including landbirds. Threats in Alaska are often considered to be less significant than those occurring elsewhere, where habitats are being altered by more rapidly increasing anthropogenic pressures, but they carry far-reaching consequences nonetheless. Habitats and ecosystem dynamics are changing rapidly due to the magnitude of climate warming at high latitudes. As such, effective landbird conservation in Alaska requires a broad, landscape-scale approach. Conservation of landbirds over such an extensive and diverse landscape also demands that we integrate efforts in habitat management, population monitoring, research, education, and outreach at local, regional, continental, and international scales. Information on distribution and habitat requirements of landbirds should be incorporated into land-use planning decisions. Synthesizing information on distribution and population trends of landbirds is a critical, time-sensitive task. Such information should be provided in a form that is readily available to land managers and policy decision-makers. The primary objectives of this plan are to (1) describe the region and Alaska’s landbird avifauna; (2) identify species of concern, important habitats, and key information needs; (3) highlight major conservation issues and threats to landbirds; and (4) identify potential conservation actions. We first examine landbird conservation at the statewide level within broad perspectives (regional, continental, and global), then take a detailed look at the specific issues, information needs, and potential conservation actions within each Bird Conservation Region in Alaska.

Alaska↗

USGS2020

Does habitat partitioning by sympatric plovers affect nest survival?

The vertical structure and composition of vegetation can influence the quantity and quality of potential nesting sites for birds. Interspecific competition for high-quality nesting habitat may force some individuals into suboptimal habitat and lead to reduced reproductive success, eventually leading to changes in distribution or abundance. Large climate-mediated shifts in vegetation, including the rapid expansion of shrubs onto tundra, are occurring in the Arctic across important breeding grounds of many shorebird species of conservation concern. We investigated effects of vegetation structure and composition on nest-site selection and nest success of sympatrically breeding American Golden-Plovers (Pluvialis dominica) and Pacific Golden-Plovers (P. fulva), which nest along an elevational gradient ranging from coastal tundra meadows to alpine tundra. Both species strongly selected nest sites with less cover of tall shrubs and other tall vegetation than available at random sites within their territories. American Golden-Plovers selected territories and nest sites that were higher in elevation and had more rocky substrates and less graminoid vegetation than those selected by Pacific Golden-Plovers. The daily nest survival rate was equivalent in the two species (0.966, 95% CI: 0.954, 0.974) and similar to that found in other Arctic-breeding shorebirds; however, contrary to predictions, nest survival was not associated with habitat features selected for nest sites for either species. Strong selection of open habitat for nest sites suggests that continued climate-related shrub expansion may reduce the amount of suitable breeding habitat for both species, but partitioning along the elevational gradient and differences in body size suggest that impacts may be more severe for Pacific Golden-Plovers. Additional research is needed to determine if differential selection of nesting habitat is related to survival of the adults or their young.

The Auk↗

USGS2020

Through thick and thin: Sexing Bristle-thighed Curlews Numenius tahitiensis using measures of bill depth

Birds often exhibit diagnostic traits that differ among individuals of the same species with regard to factors like sex, age, or breeding status. Shorebirds exhibit a wide diversity of colors, shapes, and sizes of their bills, and these traits are commonly used to determine the sex of individuals. In curlews (genus Numenius), length alone accurately separates the sexes in some species, but the shape of the bill has not typically been assessed for this purpose. We collected a suite of measurements on the bills of known-sex Bristle-thighed Curlews N. tahitiensis and determined that standardized measurements of bill depth separated the sexes with high accuracy. A model incorporating the length of a bird’s diagonal tarsus and multiple measurements of the bill was 93.1% accurate in predicting the sex of individual Bristle-thighed Curlews. Simpler models involving only the values of the bill depth near the tip and the base of the bill, however, produced similarly accurate results and are preferred for their parsimony. We advocate the use of one such model that is 93.4% accurate in determining the sex of Bristle-thighed Curlews. As a simple heuristic, a value for the ratio of the bill depth near the tip to that at the base of >0.5 indicated a female, providing an easy field calculation to help determine the sex of Bristle-thighed Curlews. In general, the bills of female Bristle-thighed Curlews are deeper and taper relatively less than those of males. Other observers have qualitatively noted apparent sex-specific differences in the shape of curlew bills, but the generality of our quantitative findings remains to be examined in other curlew species.

Wader Study↗

USGS2019

Prevalence and diversity of avian blood parasites in a resident northern passerine

Background: Climate-related changes are expected to influence the prevalence and distribution of vector-borne haemosporidian parasites at northern latitudes, although baseline information about resident birds is still lacking. In this study, we investigated prevalence and genetic diversity of Plasmodium, Haemoproteus, and Leucocytozoon parasites infecting the Northwestern Crow (Corvus caurinus), a non-migratory passerine with unique life-history characteristics. This species occupies both intertidal and forested habitats and is subject to high prevalence of avian keratin disorder (AKD), a disease that causes gross beak deformities. Investigation of avian blood parasites in Northwestern Crows at sites broadly distributed across coastal Alaska provided an opportunity to evaluate specific host factors related to parasite infection status and assess geographic patterns of prevalence. Results: We used molecular methods to screen for haemosporidian parasites in Northwestern Crows and estimated genus-specific parasite prevalence with occupancy modeling that accounts for imperfect detection of parasite infection. We observed considerable geographic and annual variation in prevalence of Plasmodium, Haemoproteus, and Leucocytozoon , but these patterns were not correlated with indices of local climatic conditions. Our models also did not provide support for relationships between the probability of parasite infection and body condition or the occurrence of co-infections with other parasite genera or clinical signs of AKD. In our phylogenetic analyses, we identified multiple lineages of each parasite genus, with Leucocytozoon showing greater diversity than Plasmodium or Haemoproteus. Conclusions: Results from this study expand our knowledge about the prevalence and diversity of avian blood parasites in northern resident birds as well as corvids worldwide. We detected all three genera of avian haemosporidians in Northwestern Crows in Alaska, although only Leucocytozoon occurred at all sites in both years. Given the strong geographic and interannual variation in parasite prevalence and apparent lack of correlation with climatic variables, it appears that there are other key factors responsible for driving transmission dynamics in this region. Thus, caution is warranted when using standard climatic or geographic attributes in a predictive framework. Our phylogenetic results demonstrate lower host specificity for some lineages of Leucocytozoon than is typically reported and provide insights about genetic diversity of local haemosporidian parasites in Alaska.

Parasites & Vectors↗

USGS2019

Evidence of Culiseta mosquitoes as vectors for Plasmodium parasites in Alaska

Mosquito vectors play a crucial role in the distribution of avian Plasmodium parasites worldwide. At northern latitudes, where climate warming is most pronounced, there are questions about possible changes in the abundance and distribution of Plasmodium parasites, their vectors, and their impacts to avian hosts. To better understand the transmission of Plasmodium among local birds and to gather baseline data on potential vectors, we sampled a total of 3,909 mosquitoes from three locations in south‐central Alaska during the summer of 2016. We screened mosquitoes for the presence of Plasmodium parasites using molecular techniques and estimated Plasmodium infection rates per 1,000 mosquitoes using maximum likelihood methods. We found low estimated infection rates across all mosquitoes (1.28 per 1,000), with significantly higher rates in Culiseta mosquitoes (7.91 per 1,000) than in Aedes mosquitoes (0.57 per 1,000). We detected Plasmodium in a single head/thorax sample of Culiseta , indicating potential for transmission of these parasites by mosquitoes of this genus. Plasmodium parasite DNA isolated from mosquitoes showed a 100% identity match to the BT7 Plasmodium lineage that has been detected in numerous avian species worldwide. Additionally, microscopic analysis of blood smears collected from black‐capped chickadees ( Poecile atricapillus ) at the same locations revealed infection by parasites preliminarily identified as Plasmodium circumflexum . Results from our study provide the first information on Plasmodium infection rates in Alaskan mosquitoes and evidence that Culiseta species may play a role in the transmission and maintenance of Plasmodium parasites in this region.

Alaska↗

USGS2019

Monitoring boreal avian populations: How can we estimate trends and trajectories from noisy data?

Substantial effort has been dedicated to developing reliable monitoring schemes for North American bird populations, but our ability to monitor bird populations in the boreal forest remains limited because of the sparsity of long-term data sets, particularly in northerly regions. Given the importance of the boreal forest for many migratory birds, we set out to (1) summarize the main challenges associated with monitoring avian populations, (2) describe the available statistical tools for population monitoring and their applications, and (3) identify future directions to overcome current challenges in monitoring bird populations in the boreal forest. Defining and delineating populations of interest and identifying the drivers that affect those populations present the greatest current challenges. This is because migratory birds may be affected by many population-limiting processes at different stages of their annual life cycles. These factors are often hierarchically structured and can influence populations at the local, regional, or continental scales. Some of the challenges associated with delineating populations and identifying population drivers can be addressed via the plethora of sampling and analytic methods available to examine population change over time. Choosing the proper analytic methods depends on the goals of the study and the nature of the data such as single or multiple populations, repeated occurrence or count-based surveys, or demographic rates. Recent advances in hierarchical and integrated population models make these analytic approaches some of the most promising avenues for the development of future methods. However, these tools require large data sets, and acquiring sufficient data on bird populations and potential explanatory variables is difficult in the boreal forest. If the current challenges to monitoring birds in the boreal forest are to be overcome, serious effort should be dedicated to integrating existing data and making them accessible. Enhancing survey effort through multispecies surveys will also play an important role. Implementing spatially balanced sampling plans with a rotating panel design could balance the trade-offs between spatial versus temporal replication at an affordable cost. Improving the accessibility of environmental covariates that are spatially and temporally explicit would also enable development of mechanistic population models that improve our understanding of migratory bird population dynamics. Finally, given that long-term monitoring programs can take many decades before delivering reliable population trends and that organizational priorities often change over time, we suggest that collaborative efforts will help ensure the long-term survival of new monitoring programs.

Avian Conservation and Ecology↗

USGS2018

Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection

Background Avian keratin disorder (AKD) is an epizootic of debilitating beak deformities, first documented in black-capped chickadees ( Poecile atricapillus ) in Alaska during the late 1990s. Similar deformities have now been recorded in dozens of species of birds across multiple continents. Despite this, the etiology of AKD has remained elusive, making it difficult to assess the impacts of this disease on wild populations. We previously identified an association between infection with a novel picornavirus, Poecivirus, and AKD in a small cohort of black-capped chickadees. Methods To test if the association between Poecivirus and AKD holds in a larger study population, we used targeted PCR followed by Sanger sequencing to screen 124 symptomatic and asymptomatic black-capped chickadees for Poecivirus infection. We further compared the efficacy of multiple non-terminal field sampling methods (buccal swabs, cloacal swabs, fecal samples, and blood samples) for Poecivirus screening. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to determine if virus is actively replicating in beak tissue. Results Poecivirus was detected in 28/28 (100%) individuals with AKD, but only 9/96 (9.4%) asymptomatic individuals with apparently normal beaks (p < 0.0001). We found that cloacal swabs are the most sensitive of these sample types for detecting Poecivirus in birds with AKD, but that buccal swabs should be combined with cloacal swabs in evaluating the infection status of asymptomatic birds. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to provide evidence of active viral replication. Conclusion The data presented here show a strong, statistically significant relationship between Poecivirus infection and AKD, and provide evidence that Poecivirus is indeed an avian virus, infecting and actively replicating in beak tissue of AKD-affected BCCH. Taken together, these data corroborate and extend the evidence for a potential causal association between Poecivirus and AKD in the black-capped chickadee. Poecivirus continues to warrant further investigation as a candidate agent of AKD.

Alaska↗

USGS2018

Montane-breeding bird distribution and abundance across national parks of southwestern Alaska

Between 2004 and 2008, biologists conducted an inventory of breeding birds during May–June primarily in montane areas (>100 m above sea level) in Aniakchak National Monument and Preserve (Aniakchak NMP), Katmai National Park and Preserve (Katmai NPP), and Lake Clark National Park and Preserve (Lake Clark NPP) in southwestern Alaska. Observers conducted 1,021 point counts along 169 transects within 63 10-km × 10-km plots that were randomly selected and stratified by ecological subsection. We created hierarchical N-mixture models to estimate detection probability and abundance for 15 species, including 12 passerines, 2 galliforms, and 1 shorebird. We first modeled detection probability relative to observer, date within season, and proportion of dense vegetation cover around the point, then modeled abundance as a function of land cover composition (proportion of seven coarse-scale land cover types) within 300 m of the survey point. Land cover relationships varied widely among species but most showed selection for low to tall shrubs (0.2–5 m tall) and an avoidance of alpine and 2 dwarf shrub–herbaceous cover types. After adjusting for species not observed, we estimated a minimum of 107 ± 9 species bred in the areas surveyed within the three parks combined. Species richness was negatively associated with elevation and associated land cover types. At comparable levels of survey effort (n = 721 birds detected), species richness was greatest in Lake Clark NPP (75 ± 12 species), lowest in Aniakchak NMP (45 ± 6 species), and intermediate at Katmai NPP (59 ± 10 species). Species richness was similar at equivalent survey effort (n = 973 birds detected) within the Lime Hills, Alaska Range, and Alaska Peninsula ecoregions (68 ± 8; 79 ± 11; 67 ± 11, respectively). Species composition was similar across all three parks and across the three major ecoregions (Alaska Range, Alaska Peninsula, Lime Hills) that encompass them. Our results provide baseline estimates of relative abundance and models of abundance and species richness relative to land cover that can be used to assess future changes in avian distribution. Additionally, these subarctic montane parks may serve as signals of landscape change and barometers for the assessment of population and distributional changes as a result of warming temperatures and changing precipitation patterns.

Alaska↗

USGS2017

Population trends of birds wintering in the Central Valley of California

Since the 1970s, the Central Valley of California has seen a large investment in preservation and restoration of wetlands and riparian areas. At the same time, grasslands have been lost to vineyards, orchards, and residential development at an accelerating rate. We analyzed data from 17 Christmas Bird Count circles that were surveyed regularly between winter 1978–79 and winter 2013–14 to document population trends for birds wintering in this region. We selected 112 taxa (species or species groups) that were relatively abundant and widespread in the Central Valley during winter and used a hierarchical model to estimate annual rates of population change from the count data while accounting for varying survey effort. A much larger proportion of taxa showed positive (46%) than negative (18%) trends; about a third (36%) showed no detectable change. Central Valley habitats that showed the highest proportion of taxa with increasing vs. decreasing trends were riparian (59% vs. 9%; n = 32), wetlands (49% vs. 11%; n = 47), and open water (44% vs. 0%; n = 9), likely reflecting the conservation efforts in these habitats in recent decades. In contrast, a greater proportion of the taxa associated with grasslands and other open habitats (n = 25) showed decreases (48%) than increases (28%). As expected, species that adapt well to areas of human habitation showed stable or increasing trends. Examples of such species with strong positive trends include Anna's Hummingbird ( Calypte anna ), Black Phoebe ( Sayornis nigricans ) and recent Central Valley arrivals, Eurasian Collared-Dove ( Streptopelia decaocto ) and Great-tailed Grackle ( Quiscalus mexicanus ). Scavenging, opportunistic species such as Turkey Vulture ( Cathartes aura ) and Common Raven ( Corvus corax ) also showed strong positive trends. Trends in wintering populations were largely concordant with estimated trends available from breeding areas in California and western North America. Overall, these abundance data suggest that recent efforts to preserve and restore wetland and riparian habitats may be benefiting birds. However, a similar focus on conservation of the Central Valley's remaining grasslands may be needed to maintain populations of grassland-associated birds.

Book chapter↗