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327 results for “wild birds”
Calling structural variants with confidence from short-read data in wild bird populations
<p>Comprehensive characterisation of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation (SV), reproducible and high-confidence SV callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (<em>Passer domesticus</em>) individuals. To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of SVs is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analysing short-read discovered SV datasets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality-filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence SV callsets.</p>
Data from: "Dead birds flying": Can North American rehabilitated raptors released into the wild mitigate anthropogenic mortality?
<p>As the human footprint expands to meet societal energy needs, so do the impacts on wildlife. Raptors in particular are highly susceptible to anthropogenic caused mortality. Industry sectors are encouraged to offset these causes of mortality. Several options to mitigate these losses have been proposed, including raptor rehabilitation. However, its role as a conservation tool is untested. Currently, no peer-reviewed demographic analyses exist using post-release data from rehabilitated raptors to evaluate its effectiveness at continental scales. Our objectives were to estimate annual survival of rehabilitated and wild raptors, and then use those estimates in demographic models to assess potential effects at individual and population levels. We hypothesized that rehabilitated raptors would survive similarly to their wild counterparts after an acclimation period, and that longer-lived species (<em>K-</em>selected) would benefit most from these releases. We used U.S. Geological Survey Bird Banding Lab band-recovery data (1974 – 2018) from 20 raptor species for modeling survival of rehabilitated individuals (<em>n </em>= 125,740) in comparison to wild birds (<em>n </em>= 1,913,352). Results from 17 species with adequate recovery data indicated that 5 species rehabilitated ≠ wild survival, 2 species had uncertain estimates, and 10 species rehabilitated ≈ wild survival by years 2 and 3 post-release. We acquired admission (<em>n </em>= 69,707) and release (<em>n = </em>25,740) data from 24 rehabilitation centers across the U.S. (2012-2021). We integrated survival, fecundity, and numbers of releases into demographic models. These models quantified the extent to which rehabilitated raptors may contribute to broader conservation efforts, especially in the context of individual take. All but two species had measurable numbers of individuals added to the population regardless of the number of releases. The general pattern was for <em>K</em>-selected species to yield larger benefits from rehabilitated supplementation to the population. These results provide evidence that rehabilitation may serve as a mitigation tool to offset incidental take.</p>
Empirical tests of habitat selection theory reveal that conspecific density and patch quality, but not habitat amount, drive long-distance immigration in a wild bird
<p>Individuals that disperse long distances from their natal site must select breeding patches with no prior knowledge of patch suitability. Despite decades of theoretical studies examining which cues dispersing individuals should use to select breeding patches, few empirical studies have tested the predictions of these theories at spatial scales relevant to long-distance dispersal in wild animal populations. Here, we use a novel assignment model based on multiple intrinsic markers to quantify natal dispersal distances of Wood Thrush (<i>Hylocichla mustelina</i>) breeding in forest fragments. We show that long-distance natal dispersal in this species is more frequent than commonly assumed for songbirds and that habitat selection by these individuals is driven by density-dependence and patch quality but not the amount of habitat surrounding breeding patches. These results represent an important contribution to understanding habitat selection by dispersing individuals, especially with regards to long-distance dispersal.</p>
Male song stability shows cross-year repeatability but does not affect reproductive success in a wild passerine bird
<p>Predictable behaviour (or "behavioural stability") might be favoured in certain ecological contexts, e.g. when representing a quality signal. Costs associated with producing stable phenotypes imply selection should favour plasticity in stability when beneficial. Repeatable among-individual differences in degree of stability are simultaneously expected if individuals differ in ability to pay these costs, or in how they resolve cost-benefit trade-offs. Bird song represents a prime example, where stability may be costly yet beneficial when stable singing is a quality signal favoured by sexual selection. Assuming energetic costs, ecological variation (e.g. in food availability) should result in both within- and among-individual variation in stability. If song stability represents a quality signal, we expect directional selection favouring stable singers. For a three-year period, we monitored 12 nest box plots of great tits Parus major during breeding. We recorded male songs during simulated territory intrusions, twice during their mate's laying stage, and twice during incubation. Each preceding winter, we manipulated food availability. Assuming that stability is costly, we expected food-supplemented males to sing more stable songs. We also expected males to sing more stable songs early in the breeding season (when paternity is not decided), and stable singers to have increased reproductive success. We found strong support for plasticity in stability for two key song characteristics: minimum frequency and phrase length. Males were plastic because they became more stable over the season, contrary to expectations. Food-supplementation did not affect body condition but increased stability in minimum frequency. This treatment effect occurred only in one year, implying that food supplementation affected stability only in interaction with (unknown) year-specific ecological factors. We found no support for directional, correlational, or fluctuating selection on the stability in minimum frequency (i.e., the song trait whose stability exhibited cross-year repeatability): stable singers did not have higher reproductive success. Our findings imply that stability in minimum frequency is not a fitness quality indicator unless males enjoy fitness benefits via pathways not studied here. Future studies should thus address the mechanisms shaping and maintaining individual repeatability of song stability in the wild.</p>
Microclimate and host body condition influence mite population growth in a wild bird-ectoparasite system
<p>Parasite populations are never evenly distributed among the hosts they infect. Avian nest ectoparasites, such as mites, are no exception, as their distribution across the landscape is highly aggregated. It remains unclear if this pattern is driven by differences in transmission events alone, or if the environment that parasites inhabit after transmission also plays a role. Here, we experimentally examined the influence of the post-transmission microclimate, nest characteristics, and host condition on ectoparasite population growth in a bird-ectoparasite system. We infested barn swallow (Hirundo rustica erythrogaster) nests with a standardized number of Northern Fowl Mites (Ornithonyssus sylvarium) and analyzed both biotic (nestling mass, wing length, number of other arthropods present in the nest, and brood size) and abiotic (temperature, humidity, nest lining, nest dimensions, and substrate upon which the nest was built) predictors of mite population growth. Our results suggest that mite populations were most successful, in terms of growth, in nests with higher temperatures, lower humidity, few other arthropods, and hosts in good condition. We also found that nests built on wooden substrates support larger populations of mites than those constructed on metal or concrete. These findings lend insight into the factors that drive large-scale patterns of ectoparasite distributions.</p>
Global dissemination of Influenza A virus is driven by wild bird migration through arctic and subarctic zones
<p><span>Influenza A viruses (IAV) circulate endemically among many wild aquatic bird populations that seasonally migrate between wintering grounds in southern latitudes to breeding ranges along the perimeter of the circumpolar arctic. </span>Arctic and subarctic zones are hypothesized to serve as ecologic drivers of the intercontinental movement and reassortment of IAVs <span>due to high densities of disparate populations of long distance migratory and native bird species present during breeding season</span>s. <span>Iceland</span> is a staging ground that connects <span>the East Atlantic and </span><span>North Atlantic</span><span> American flyways, providing a unique study system for characterizing viral flow between eastern and western hemispheres. Using Bayesian phylodynamic analyses, we sought to evaluate the </span><span>viral connectivity of Iceland to proximal regions and how inter-species transmission and reassortment dynamics in this region influence the geographic spread of low and highly pathogenic IAVs. </span><span>Findings demonstrate that IAV movement in the arctic and subarctic follows seabird migration around the perimeter of the circumpolar north, favoring short-distance flights between proximal regions rather than long distance flights over the polar interior. Iceland connects virus movement between mainland Europe and North America, particularly due to the westward migration of wild birds from mainland Europe to Northeastern Canada and Greenland. Though virus diffusion rates were similar among avian taxonomic groups in Iceland, g</span>ulls act as recipients and not sources of IAVs to other avian hosts prior to onward migration. <span>These data identify patterns of virus movement in northern latitudes and inform future surveillance strategies related to seasonal and emergent IAVs with pandemic potential</span>.</p>
Fig. 1 in Chewing lice (Phthiraptera) species of wild birds in northwestern Turkey with a new host record
Fig. 1. Degeerialla nisus from the common buzzard (Bute buteo). (A), Male, (B) male genitalia.
Data and R code used in the preprint "Parasite intensity is driven by temperature in a wild bird" (doi 10.1101/323311)
<p>Data (as text files) and R code used in the preprint entitled "Parasite intensity is driven by temperature in a wild bird", recommended by <em>Peer Community In Ecology </em>(doi 10.1101/323311). See preprint and supplementary material; some explanations are also included in the R code. </p>
Data from: Genome-wide variation in DNA methylation is associated with stress resilience and plumage brightness in a wild bird
Individuals often differ in their ability to cope with challenging environmental and social conditions. Evidence from model systems suggests that patterns of DNA methylation are associated with variation in coping ability. These associations could arise directly if methylation plays a role in controlling the physiological response to stressors by, among other things, regulating the release of glucocorticoids in response to challenges. Alternatively, the association could arise indirectly if methylation and resilience have a common cause, such as early life conditions. In either case, methylation might act as a biomarker for coping ability. At present, however, relatively little is known about whether variation in methylation is associated with organismal performance and resilience under natural conditions. We studied genome-wide patterns of DNA methylation in free-living female tree swallows (Tachycineta bicolor) using methylated DNA immunoprecipitation (MeDIP) and a tree swallow genome that was assembled for this study. We identified areas of the genome that were differentially methylated with respect to social signal expression (breast brightness) and physiological traits (ability to terminate the glucocorticoid stress response through negative feedback). We also asked whether methylation predicted resilience to a subsequent experimentally imposed challenge. Individuals with brighter breast plumage and higher stress resilience had lower methylation at differentially methylated regions across the genome. Thus, widespread differences in methylation predicted both social signal expression and the response to future challenges under natural conditions. These results have implications for predicting individual differences in resilience, and for understanding the mechanistic basis of resilience and its environmental and social mediators.
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Cyprus
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Iceland
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Estonia
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Croatia
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union – Belgium
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Romania
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Denmark
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Sweden
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Spain
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Poland
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Norway
<p>This dataset contains the results of the surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.