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opencc-by-4.0Nov 2024View details →

Expansion of the early warning system for avian influenza in the EU to evaluate the risk of spillover from wild birds to poultry

GIF 1: Animated map of the spatiotemporal variations of the estimated number of infectious wild birds between February 2023 and March 2024 GIF 2: Animated map of the spatiotemporal variations of transmission rate from wild birds to indoor chicken between February 2023 and March 2024 GIF 3: Animated map of the spatiotemporal variations of transmission rate from wild birds to outdoor chicken between February 2023 and March 2024 GIF 4: Animated map of the spatiotemporal variations of transmission rate from wild birds to indoor duck between February 2023 and March 2024 GIF 5: Animated map of the spatiotemporal variations of transmission rate from wild birds to outdoor duck between February 2023 and March 2024 GIF 6: Animated map of the spatiotemporal variations of the probability of HPAI introduction into indoor chicken farms between February 2023 and March 2024 GIF 7: Animated map of the spatiotemporal variations of the probability of HPAI introduction into outdoor chicken farms between February 2023 and March 2024 GIF 8: Animated map of the spatiotemporal variations of the probability of HPAI introduction into indoor duck farms between February 2023 and March 2024 GIF 9: Animated map of the spatiotemporal variations of the probability of HPAI introduction into outdoor duck farms between February 2023 and March 2024 GIF 10: Animated map of the spatiotemporal variations of the probability of HPAI introduction into poultry farms between February 2023 and March 2024 (scenario A) GIF 11: Animated map of the spatiotemporal variations of the probability of HPAI introduction into poultry farms between February 2023 and March 2024 (scenario B)

opencc-by-4.0Jan 2022View details →

Correlation of urban avian species diversity present in heterogenous habitat types of the Silk city, Odisha, Eastern India

This is the complete metadata and the R code required to do the analysis of the paper regarding birds of Berhampur city.

opencc-zeroFeb 2022View details →

Avian botulism is a primary, year-round threat to adult survival in the endangered Hawaiian Duck (Anas wyvilliana) on Kaua'i, Hawai'i, USA

Adult survival is the most important demographic parameter influencing population dynamics for many bird taxa. Thus, understanding how survival probabilities and causes of mortality vary throughout the annual cycle is critical for developing informed and effective management strategies. In this study, we used radio-telemetry data to evaluate the effects of biotic (e.g., sex, peak [September–April] vs. off-peak [May–August] nesting seasons) and abiotic factors (e.g., rainfall, year, bi-monthly interval) on adult survival, estimate annual survival probabilities, and identify primary sources of mortality for Hawaiian Ducks (Anas wyvilliana), an endangered, non-migratory dabbling duck, on the island of Kaua'i, Hawai'i, USA over 2013 and 2014. Additionally, we used contemporaneous Hawaiian Duck carcass recovery and surveillance data to examine temporal and climatic associations with avian botulism outbreaks. Our results suggested bi-monthly survival decreased with total rainfall during the preceding two-month interval. Survival did not vary with sex, between peak and off-peak nesting seasons, or between the two years of this study. Annual survival probabilities (62–80%) were relatively low compared to the closely related Laysan Duck (Anas laysanensis) on Laysan Island. Primary causes of mortality included avian botulism and presumed predation by cats (Felis catus). The botulism surveillance dataset revealed support for the effect of rainfall on the number of sick and dead birds recovered (n = 216), with generally a greater number of recoveries during months with middle-range total rainfall during the concurrent and preceding months. Our study provides critical baseline demographic data for population monitoring and highlights the importance of managing botulism risk and non-native mammalian predators for the recovery of the endangered Hawaiian Duck.

opencc-zeroMar 2022View details →

Individual repeatability of avian migration phenology: a systematic review and meta-analysis

Changes in phenology and distribution are being widely reported for many migratory species in response to shifting environmental conditions. Understanding these changes and the situations in which they occur can be aided by understanding consistent individual differences in phenology and distribution and the situations in which consistency varies in strength or detectability. Studies tracking the same individuals over consecutive years are increasingly reporting migratory timings to be a repeatable trait, suggesting that flexible individual responses to environmental conditions may contribute little to population-level changes in phenology and distribution. However, how this varies across species and sexes, across the annual cycle and in relation to study (tracking method, study design) and/or ecosystem characteristics is not yet clear. Here, we take advantage of the growing number of publications in movement ecology to perform a phylogenetic multilevel meta-analysis of repeatability estimates for avian migratory timings to investigate these questions. Of 2,433 reviewed studies, 54 contained suitable information for meta-analysis, resulting in 177 effect sizes from 47 species. Individual repeatability of avian migratory timings averaged 0.414 (95% confidence interval: 0.3–0.5) across landbirds, waterbirds and seabirds, suggesting consistent individual differences in migratory timings is a common feature of migratory systems. Timing of departure from the non-breeding grounds was more repeatable than timings of arrival at or departure from breeding grounds, suggesting that conditions encountered on migratory journeys and outcome of breeding attempts can influence individual variation. Population-level shifts in phenology could arise through individual timings changing with environmental conditions and/or through shifts in the numbers of individuals with different timings. Our findings suggest that, in addition to identifying the conditions associated with individual variation in phenology, exploring the causes of between-individual variation will be key in predicting future rates and directions of changes in migratory timings. We, therefore, encourage researchers to report the within- and between- individual variance components underpinning the reported repeatability estimates to aid interpretation of migration behaviour. In addition, the lack of studies in the tropics means that levels of repeatability in less strongly seasonal environments are not yet clear.

opencc-by-4.0Sep 2020View details →

Fig. 3 in Ecology Of Avian Settlements In Lake Tonga (Northeast Algeria)

Fig. 3. Evolution of the specific richness of waterbirds at Lake Tonga. common coot is by far the most abundant. The purple swamphen Porphyrio porphyrio is also included in the IUCN Red List and therefore we can say that Lake Tonga is a very important site for waterbirds in our country (Boumezbeur, 1993; Benyacoub et al., 2011). It should be noted that Lake Tonga is the only nesting site of the Whiskered Tern Chlidonias hybrida in Algeria and North Africa (Bakaria et al., 2009).

opencc-by-4.0Jul 2014View details →

Fig. 1 in Avian Communities Of A Mixed Mopane-Acacia Savanna In The Cuvelai Drainage System, North-Central Namibia, During The Dry And Wet Season

Fig. 1. Seasonal changes in percentage contribution of main feeding guilds in avian assemblage in mixed Mopane-Acacia savanna (F — frugivores, G — granivores, I — insectivores, O — other guilds).

opencc-by-4.0May 2022View details →

Data for ZooMS analysis of avian fauna from Teotihuacan, Mexico, for Codlin et al. 2022

This data is associated with a manuscript on the analysis of avian fauna via Zooarchaeology by Mass Spectrometry (ZooMS) by Codlin et al. (2022) See publication for more details <a href="https://doi.org/10.1016/j.jas.2022.105692">https://doi.org/10.1016/j.jas.2022.105692</a>. Additional data will be made available on ProteomeXchange All samples were processed with HCl, gelatinized at 65ºC in AmBic and digested with trypsin. While some samples underwent purification using a C18 ZipTip, all digested peptide solutions were diluted to various concentrations prior to spotting and analysis on a Bruker Autoflex Speed LRF MALDI-TOF Mass Spectrometer. # Details of files uploaded ## "Sample_details.csv" Lists sample IDs and taxonomic information for modern reference specimens and archaeological specimens selected for LC-MS/MS analysis ## "MALDI_arch_samples.zip" Contains the unprocessed .MZML MALDI spectra for archaeological specimens.     File names are composed of:     - MCsample#_MALDIplate#_dilutionAND/ORziptip_platelocation ## "MALDI_modern_samples.zip" Contains the unprocessed .MZML MALDI spectra for modern reference specimens. All samples except MC2 are from AMNH collections. See "Sample_details.csv" for sample information     File names are composed of:     - MCsample#_dilution_speciesidentification_MALDIplatelocation ## "Curated_avian_collagen_fasta.zip" Contains two .fasta files with curated avian COL1a1 and COL1a2 sequences from publicly available data. ##"MS2_images.zip" Contains MS2 images from LC-MS/MS confirmation of biomarker peaks. See "Sample_details.csv" for sample information.     File names are composed of:     - COL1A2chain_markerlocation_masspeak_sample# ##"MALDI_spectra_images.zip" Contains images of representative spectra for modern and archaeological taxa identified in the study. These spectra were processed and averaged in mMass using the "MALDI-TOF Peptides" settings. Spectra were aligned to more closely fit confirmed biomarker peaks for each sample. See "Sample_details.csv" for sample information.     File names are composed of:     - Sample# ## "biomarkers_list.txt" Contains the list of peaks and deamidated peaks used in clustering MALDI spectra.

opencc-zeroJun 2022View details →

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds

Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, 9 of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum, which is increasing in distribution in Hawai`i as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawai`i `amakihi (Chlorodrepanis virens), persists in some areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 `amakihi and 172 malaria-resistant warbling white-eyes (Zosterops japonicus) from Hawai`i Island using 16S rRNA gene metabarcoding and qPCR. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp., which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.

opencc-zeroJun 2022View details →

Experimental test of selection against hybridization as a driver of avian signal divergence

Signal divergence may be pivotal in the generation and maintenance of new biodiversity by allowing closely related species to avoid some costs of co-occurrence. In birds, closely related, sympatric species are more divergent in their colour patterns than those that live apart, but the selective pressures driving this pattern remain unclear. Traditionally, signal divergence among sympatric species is thought to result from selection against hybridization, but broad evidence is lacking. Here, we conducted field experiments on naïve birds using spectrometer-matched, painted 3D-printed models to test whether selection against hybridization drives colour pattern divergence in the genus Poecile. To address selection for male colour pattern divergence without the influence of learning or the evolution of female discrimination in sympatry, we simulated secondary contact between Poecile species, and conducted mate choice experiments on naïve, allopatric females. We found that female black-capped chickadees (P. atricapillus) are equally likely to perform copulation solicitation displays to sympatric and allopatric heterospecific congeners when they are paired with conspecifics, but exhibit a strong preference for less divergent males when presented with paired heterospecific congeners. These results suggest that increased colour pattern divergence among sympatric species can reduce the likelihood of mixed mating in some contexts, and therefore should be favoured by selection against hybridization.

opencc-by-4.0Jun 2022View details →

Data complementing the Avian influenza overview March – June 2022

Annex A –     Characteristics of the HPAI A(H5Nx)-positive poultry establishments The Annex contains table with the characteristics of the HPAI A(H5Nx)-positive poultry establishments by affected EU Member State from 4 March to 1 June 2022. Annex B –     Applied prevention and control measures on avian influenza The Annex contains an overview of specific prevention and control measures applied in Albania, Belgium, Bulgaria, Czechia,  France, Hungary, Iceland, Italy, Moldova, Kosovo, The Netherlands, Poland, Romania, Slovakia, Spain from 1 December 2021 to 4 March 2022 in relation to HPAI outbreaks in poultry and in wild birds. Annex C –     Data on wild birds The Annex contains tables and plots on HPAI notifications in wild birds in Europe.

opencc-zeroAug 2022View details →

Population models used in: Method to assess potential magnitude of terrestrial European avian population reductions from ingestion of lead ammunition

Current estimates of terrestrial bird losses across Europe from ingestion of lead ammunition are based on uncertain or generic assumptions. A method is needed to develop defensible European-specific estimates compatible with available data that does not require long-term field studies. We propose a 2-step method using carcass data and population models. The method estimates percentage of deaths diagnosed as directly caused by lead poisoning as a lower bound and, as an upper bound, the percentage of possible deaths from sublethal lead poisoning that weakens birds, making them susceptible to death by other causes. We use these estimates to modify known population-level annual mortality. Our method also allows for potential reductions in reproduction from lead shot ingestion because reductions in survival and reproduction are entered into population models of species with life histories representative of the most groups of susceptible species. The models estimate the sustainability and potential population decreases from lead poisoning in Europe. Using the best available data, we demonstrate the method on two taxonomic groups of birds: gallinaceous birds and diurnal raptors. The direction of the population trends affects the estimate, and we incorporated such trends into the method. Our midpoint estimates of the reduction in population size of the European gallinaceous bird (< 2%) group and raptor group (2.9 – 7.7%) depend on the species life history, maximum growth rate, population trend, and if reproduction is assumed to be reduced. Our estimates can be refined as more information becomes available in countries with data gaps. We advocate use of this method to improve upon or supplement approaches currently being used. As we demonstrate, the method also can be applied to individual species of concern if enough data across countries are available.

opencc-by-4.0Sep 2022View details →

Data complementing the Avian influenza overview June – September 2022

Annex A –     Characteristics of the HPAI A(H5Nx)-positive poultry establishments The Annex contains table with the characteristics of the HPAI A(H5Nx)-positive poultry establishments by affected EU Member State from 2 June to  2 September 2022. Annex B –     Applied prevention and control measures on avian influenza The Annex contains an overview of specific prevention and control measures applied in Bulgaria, Croatia, France, Hungary, Germany, Moldova, the Netherlands, Poland, Portugal, Spain from 2 June to 2 September 2022 in relation to HPAI outbreaks in poultry and in wild birds. Annex C –     Data on wild birds The Annex contains tables and plots on HPAI virus notifications in wild birds in Europe.

opencc-zeroOct 2022View details →

Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change

Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a temporal (36–38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36–38 years, i.e., at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.

opencc-by-4.0Oct 2020View details →

Fig. 3 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease

Fig. 3 Brain histopathology of WNV-infected horses. Perivascular cuffs composed of lymphocytes and plasma cells in the brain of two horses, characteristic of viral encephalitis (marked by arrows). a Horse no. Eq111 (324085). b Horse no. Eq117 (325903). 100× magnification

opencc-by-4.0Oct 2020View details →

Fig. 2 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease

Fig. 2 Brain histopathology of WNV-infected long-eared owl (Asio otus) AV156. a A glial nodule in the brain stem (marked by an arrow). 100× magnification. b A glial nodule in the brain stem with few adjacent necrotic neurons, 400× magnification

opencc-zeroJun 2024View details →

Identification of age-related CpG sites from longitudinal avian methylomes

Sex chromosomes are thought to play an important role in sex-dependent ageing, yet they are neglected in epigenetic aging research. We identified genome-wide age-related CpG (AR-CpG) sites in two avian species (zebra finch and jackdaw) and found AR-CpG sites to be overrepresented on the haploid, female-specific W chromosome in both species, and on the Z chromosome in the zebra finch.

Figure 3. Haemoproteus multivacuolatus n in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species

Figure 3. Haemoproteus multivacuolatus n. sp. (lineage hBUBT1) from the blood of the Common buzzard Buteo buteo: a–d – young gametocytes, e–h – macrogametocytes, i–p – microgametocytes. Long simple arrows – nuclei of parasites. Short simple arrows – vacuoles. Simple arrowhead – pigment granules. Triangle arrowheads – volutin granules. Note that due to marked vacuolisation, the cytoplasm of macrogametocytes stains relatively pale and looks similar to microgametocytes based on the intensity of staining. Giemsa-stained thin blood films. Scale bar = 10 µm. All images were from the hapantotype preparation.

Figure 2 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species

Figure 2. Haemoproteus nisi (lineage hCIAE08) from the blood of Western marsh harrier Circus aeruginosus: a – young gametocytes, b–h – macrogametocytes, i–l – microgametocytes. Long simple arrows – nuclei of parasites. Short simple arrows – vacuoles. Simple arrowhead – pigment granules. Triangle arrowheads – clamps of volutin. Simple wide long arrows – spaces between gametocytes and erythrocyte nuclei. Giemsa-stained thin blood films. Scale bar = 10 µm.

Figure 1 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species

Figure 1. Haemoproteus nisi (lineage hACCNIS08) from the blood of Eurasian sparrowhawk Accipiter nisus: a–d – macrogametocytes, e–h – microgametocytes. Long simple arrows – nuclei of parasites. Short simple arrows – vacuoles. Simple arrowhead – pigment granules. Triangle arrowheads – volutin granules. Simple wide long arrows – spaces between gametocytes and erythrocyte nuclei. Giemsa-stained thin blood films. Scale bar = 10 µm.

Figure 5. Bayesian Inference tree calculated with complete cox1 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species

Figure 5. Bayesian Inference tree calculated with complete cox1 (1428 bp), cox3 (753 bp), and cytb (1127 bp) sequences of haemosporidian parasites and Klossiella equi (MH203050) and Klossia razorbacki (MT084562) as the outgroup. Bayesian posterior probabilities and Maximum Likelihood bootstrap values are indicated at most nodes. The scale bar indicates the expected number of substitutions per site according to the model of sequence evolution applied.