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Imperfect detection during animal surveys biases estimates of abundance and can lead to improper conclusions regarding distribution and population trends. Farnsworth et al. (2005) developed a combined distance-sampling and time-removal model for point-transect surveys that addresses both availability (the probability that an animal is available for detection; e.g., that a bird sings) and perceptibility (the probability that an observer detects an animal, given that it is available for detection). We developed a hierarchical extension of the combined model that provides an integrated analysis framework for a collection of survey points at which both distance from the observer and time of initial detection are recorded. Implemented in a Bayesian framework, this extension facilitates evaluating covariates on abundance and detection probability, incorporating excess zero counts (i.e. zero-inflation), accounting for spatial autocorrelation, and estimating population density. Species-specific characteristics, such as behavioral displays and territorial dispersion, may lead to different patterns of availability and perceptibility, which may, in turn, influence the performance of such hierarchical models. Therefore, we first test our proposed model using simulated data under different scenarios of availability and perceptibility. We then illustrate its performance with empirical point-transect data for a songbird that consistently produces loud, frequent, primarily auditory signals, the Golden-crowned Sparrow (Zonotrichia atricapilla); and for 2 ptarmigan species (Lagopus spp.) that produce more intermittent, subtle, and primarily visual cues. Data were collected by multiple observers along point transects across a broad landscape in southwest Alaska, so we evaluated point-level covariates on perceptibility (observer and habitat), availability (date within season and time of day), and abundance (habitat, elevation, and slope), and included a nested point-within-transect and park-level effect. Our results suggest that this model can provide insight into the detection process during avian surveys and reduce bias in estimates of relative abundance but is best applied to surveys of species with greater availability (e.g., breeding songbirds).

Mountain ranges, deserts, ice fields and oceans generally act as barriers to the movement of land-dependent animals, often profoundly shaping migration routes. We used satellite telemetry to track the southward flights of bar-tailed godwits (Limosa lapponica baueri), shorebirds whose breeding and non-breeding areas are separated by the vast central Pacific Ocean. Seven females with surgically implanted transmitters flew non-stop 8117-11 680 km (10 153±1043 s.d.) directly across the Pacific Ocean; two males with external transmitters flew non-stop along the same corridor for 7008-7390 km. Flight duration ranged from 6.0 to 9.4 days (7.8±1.3 s.d.) for birds with implants and 5.0 to 6.6 days for birds with externally attached transmitters. These extraordinary non-stop flights establish new extremes for avian flight performance, have profound implications for understanding the physiological capabilities of vertebrates and how birds navigate, and challenge current physiological paradigms on topics such as sleep, dehydration and phenotypic flexibility. Predicted changes in climatic systems may affect survival rates if weather conditions at their departure hub or along the migration corridor should change. We propose that this transoceanic route may function as an ecological corridor rather than a barrier, providing a wind-assisted passage relatively free of pathogens and predators.

Climate-related environmental changes have increasingly been linked to emerging infectious diseases in wildlife. The Arctic is facing a major ecological transition that is expected to substantially affect animal and human health. Changes in phenology or environmental conditions that result from climate warming may promote novel species assemblages as host and pathogen ranges expand to previously unoccupied areas. Recent evidence from the Arctic and subarctic suggests an increase in the spread and prevalence of some wildlife diseases, but baseline data necessary to detect and verify such changes are still lacking. Wild birds are undergoing rapid shifts in distribution and have been implicated in the spread of wildlife and zoonotic diseases. Here, we review evidence of current and projected changes in the abundance and distribution of avian diseases and outline strategies for future research. We discuss relevant climatic and environmental factors, emerging host-pathogen contact zones, the relationship between host condition and immune function, and potential wildlife and human health outcomes in northern regions.

Climate change is facilitating rapid changes in the composition and distribution of vegetation at northern latitudes, raising questions about the responses of wildlife that rely on arctic ecosystems. One widely observed change occurring in arctic tundra ecosystems is an increasing dominance of deciduous shrub vegetation. Our goals were to examine the tolerance of arctic-nesting bird species to existing gradients of vegetation along the boreal forest-tundra ecotone, to predict the abundance of species across different heights and densities of shrubs, and to identify species that will be most or least responsive to ongoing expansion of shrubs in tundra ecosystems. We conducted 1,208 point counts on 12 study blocks from 2012-2014 in northwestern Alaska, using repeated surveys to account for imperfect detection of birds. We considered the importance of shrub height, density of low and tall shrubs (i.e. shrubs >0.5 m tall), percent of ground cover attributed to shrubs (including dwarf shrubs <0.5 m tall), and percent of herbaceous plant cover in predicting bird abundance. Among 17 species considered, only gray-cheeked thrush (Catharus minimus) abundance was associated with the highest values of all shrub metrics in its top predictive model. All other species either declined in abundance in response to one or more shrub metrics or reached a threshold where further increases in shrubs did not contribute to greater abundance. In many instances the relationship between avian abundance and shrubs was nonlinear, with predicted abundance peaking at moderate values of the covariate, then declining at high values. In particular, a large number of species were responsive to increasing values of average shrub height with six species having highest abundance at near-zero values of shrub height and abundance of four other species decreasing once heights reached moderate values (≤ 33 cm). Our findings suggest that increases in shrub cover and density will negatively affect abundance of only a few bird species and may potentially be beneficial for many others. As shrub height increases further, however, a considerable number of tundra bird species will likely find habitat increasingly unsuitable.

Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multispecies occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real data set of bird observations in northwestern Alaska, USA, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results indicate that neglecting the effects of site covariates on species detection probabilities may lead to significant bias in estimation of species richness, as well as the inferred relationships between community size and environmental covariates.

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 geographical 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 geographical 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 geographical and annual 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 geographical 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.

We revisit the common standards recommended by Ralph et al. (1993, 1995a) for conducting point-count surveys to assess the relative abundance of landbirds breeding in North America. The standards originated from discussions among ornithologists in 1991 and were developed so that point-count survey data could be broadly compared and jointly analyzed by national data centers with the goals of monitoring populations and managing habitat. Twenty years later, we revisit these standards because (1) they have not been universally followed and (2) new methods allow estimation of absolute abundance from point counts, but these methods generally require data beyond the original standards to account for imperfect detection. Lack of standardization and the complications it introduces for analysis become apparent from aggregated data. For example, only 3% of 196,000 point counts conducted during the period 1992–2011 across Alaska and Canada followed the standards recommended for the count period and count radius. Ten-minute, unlimited-count-radius surveys increased the number of birds detected by >300% over 3-minute, 50-m-radius surveys. This effect size, which could be eliminated by standardized sampling, was ≥10 times the published effect sizes of observers, time of day, and date of the surveys. We suggest that the recommendations by Ralph et al. (1995a) continue to form the common standards when conducting point counts. This protocol is inexpensive and easy to follow but still allows the surveys to be adjusted for detection probabilities. Investigators might optionally collect additional information so that they can analyze their data with more flexible forms of removal and time-of-detection models, distance sampling, multiple-observer methods, repeated counts, or combinations of these methods. Maintaining the common standards as a base protocol, even as these study-specific modifications are added, will maximize the value of point-count data, allowing compilation and analysis by regional and national data centers.

Avian keratin disorder (AKD), characterized by debilitating overgrowth of the avian beak, was first documented in black-capped chickadees ( Poecile atricapillus ) in Alaska. Subsequently, similar deformities have appeared in numerous species across continents. Despite the widespread distribution of this emerging pathology, the cause of AKD remains elusive. As a result, it is unknown whether suspected cases of AKD in the afflicted species are causally linked, and the impacts of this pathology at the population and community levels are difficult to evaluate. We applied unbiased, metagenomic next-generation sequencing to search for candidate pathogens in birds affected with AKD. We identified and sequenced the complete coding region of a novel picornavirus, which we are calling poecivirus. Subsequent screening of 19 AKD-affected black-capped chickadees and 9 control individuals for the presence of poecivirus revealed that 19/19 (100%) AKD-affected individuals were positive, while only 2/9 (22%) control individuals were infected with poecivirus. Two northwestern crows ( Corvus caurinus ) and two red-breasted nuthatches ( Sitta canadensis ) with AKD-consistent pathology also tested positive for poecivirus. We suggest that poecivirus is a candidate etiological agent of AKD. IMPORTANCE Avian keratin disorder (AKD) is an increasingly common disease of wild birds. This disease, characterized by beak overgrowth, was first described in the late 1990s and has been spreading rapidly both geographically and in terms of host species affected. AKD decreases host fitness and can be fatal. However, the cause of the disease has remained elusive, and its impact on host populations is poorly understood. We found a novel and divergent picornavirus in 19/19 AKD-affected black-capped chickadees that we examined but in only 2/9 control cases. We also found this virus in 4 individuals of 2 other passerine species that exhibited symptoms consistent with AKD. Our data suggest that this novel picornavirus warrants further investigation as the causative agent of AKD. Avian keratin disorder (AKD) is an increasingly common disease of wild birds. This disease, characterized by beak overgrowth, was first described in the late 1990s and has been spreading rapidly both geographically and in terms of host species affected. AKD decreases host fitness and can be fatal. However, the cause of the disease has remained elusive, and its impact on host populations is poorly understood. We found a novel and divergent picornavirus in 19/19 AKD-affected black-capped chickadees that we examined but in only 2/9 control cases. We also found this virus in 4 individuals of 2 other passerine species that exhibited symptoms consistent with AKD. Our data suggest that this novel picornavirus warrants further investigation as the causative agent of AKD.

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.

Many of the Neotropical migrant bird species that breed throughout the Canadian boreal region are not found in the Alaskan boreal region, separated by the northwestern cordilleran mountains, despite the presence of climatically suitable habitat. We asked whether biological or climatic factors constrain certain species from crossing this geographic barrier. Analyzing a comprehensive dataset for 80 boreal passerine species, we used phylogenetic logistic regression to evaluate the relative importance of physical, migratory and competition metrics versus current and paleoclimatic suitability factors. Controlling for current climatic suitability within boreal Alaska, we found that species with the greatest climatic suitability across the northwestern cordillera, presently and also during the mid-Holocene period, were most likely to be regular breeders in the Alaskan boreal region. Migratory strategy also played a role, but could not be disentangled from its strong phylogenetic basis. Our analysis suggests that the perceived barrier of the northwestern cordillera may be easily weakened as climate change improves conditions there for many forest species. The weakening of this barrier may lead to relatively rapid range expansions and the reshuffling of species communities. Species’ realized distributional shifts will be a function of the interplay between a changing climate and static topographic features.