Find research datasets worth reusing

opencc-by-4.0Feb 2024View details →

Figure 4 in Novel phylogenetic clade of avian Haemoproteus parasites (Haemosporida, Haemoproteidae) from Accipitridae raptors, with description of a new Haemoproteus species

Figure 4. Median-Joining DNA haplotype network showing the host and geographic distribution of six Haemoproteus nisi group lineages (478 bp cytb sequences) found in accipitriform raptors from Austria and France.

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Eye morphology contributes to the ecology and evolution of the avian tree of life

The avian eye is the single most important external anatomical trait for interpreting light environments by birds and varies widely in size and shape across the avian tree of life. The attached dataset provides measurements on eye size taken from preserved museum specimens for roughly one third of the avian tree of life (N = 3,475 species). The original dataset was collected by Stanley Ritland and Alice Hutchinson and archived as appendices in Stanley Ritland's Dissertation from the University of Chicago (1982): "The Allometry of the Vertebrate Eye".

opencc-zeroJun 2024View details →

opencc-by-4.0Jul 2024View details →

Data complementing the Avian influenza overview March - June 2024

Data complementing the Avian influenza overview March - June 2024   Annex A – Data on birds and mammals The annex contains tables and figures on birds and mammals, including HPAI virus detections in these species.   Annex B – Characteristics of the HPAI A(H5Nx)-affected poultry establishments The annex contains a table with the characteristics of the HPAI A(H5Nx)-affected poultry establishments by affected European country submitted to ADIS between 16 March and 14 June 2024.   Annex C – Data on virus sequences The annex contains information on authors, originating and submitting laboratories of the sequences from GISAID's EpiFlu™ Database on which this research is based. All data submitters may be contacted directly via <a title="https://eur03.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.gisaid.org%2f&data=05%7c02%7c%7cbccd5bb40f5e4a4ccee508dbfbeb3823%7c406a174be31548bdaa0acdaddc44250b%7c1%7c0%7c638380763212264062%7cunknown%7ctwfpbgzsb3d8eyjwijoimc4wljawmdailcjqijoiv2lumziilcjbtii6ik1hawwilcjxvci6mn0%3d%7c3000%7c%7c%7c&sdata=yxkh9bn0bh3m4pak8dja4mkdj1ptc6%2fyqioei05qg1m%3d&reserved=0" href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gisaid.org%2F&data=05%7C02%7C%7Cbccd5bb40f5e4a4ccee508dbfbeb3823%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C638380763212264062%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Yxkh9bN0bH3m4Pak8DJa4Mkdj1PTc6%2FYqIoei05qg1M%3D&reserved=0" target="_blank" rel="noreferrer noopener">www.gisaid.org</a>.

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Genetic variability and telomeres: Insights from a tropical avian hybrid zone

Telomere lengths and telomere dynamics can correlate with lifespan, behavior, and individual quality. Such relationships have spurred interest in understanding variation in telomere lengths and their dynamics within and between populations. Many studies have identified how environmental processes can influence telomere dynamics, but the role of genetic variation is much less well characterized. To provide a novel perspective on how telomeric variation relates to genetic variability, we longitudinally sampled individuals across a narrow hybrid zone (n = 127 samples), wherein two Manacus species characterized by contrasting genome-wide heterozygosity interbreed. We measured individual (n = 66) and population (n = 3) differences in genome-wide heterozygosity and, among hybrids, amount of genetic admixture using RADseq-generated SNPs. We tested for population differences in telomere lengths and telomere dynamics. We then examined how telomere lengths and telomere dynamics covaried with genome-wide heterozygosity within populations. Hybrid individuals exhibited longer telomeres, on average, than individuals sampled in the adjacent parental populations. No population differences in telomere dynamics were observed. Within the parental population characterized by relatively low heterozygosity, higher genome-wide heterozygosity was associated with shorter telomeres and higher rates of telomere shortening – a pattern that was less apparent in the other populations. All of these relationships were independent of sex, despite the contrasting life histories of male and female manakins. Our study highlights how population comparisons can reveal interrelationships between genetic variation and telomeres, and how naturally occurring hybridization and genome-wide heterozygosity can relate to telomere lengths and telomere dynamics.

opencc-zeroJul 2024View details →

opencc-by-4.0Jul 2024View details →

Datasets: Laser scarecrows reduce avian corn-foraging propensity but not bout length in aviary trials

This archive is comprised of 3 files: (1) Archive Metadata: a description of the data collection, behavioral sampling, and datafile structure (variables); (2) An excel file containing scan sample data used in 2 analyses; and  (3) An excel file containing focal foraging bout data for a 3rd analysis for the named manuscript.

opencc-by-4.0Dec 2022View details →

Fig. 3 in Avian Assemblages in Forest Fragments do not Sum to the Expected Regional Community in the Brazilian Atlantic Forest.

Fig. 3. The number of local Atlantic Forest species by forest fragment size (log10 scales), showing that the number increases with fragment size (F = 13.4, r2 = 0.625, p = 0.0065).

opencc-by-4.0Dec 2022View details →

Fig. 2 in Avian Assemblages in Forest Fragments do not Sum to the Expected Regional Community in the Brazilian Atlantic Forest.

Fig. 2. Numbers of species and similarities (PCoA) among the 10 Atlantic Forest fragments in southern Bahia, Brazil. A) Species accumulation curves, illustrating that with over 5000 sightings, the predicted total number of species had not been reached in any fragment, or in all fragments combined. Also, the similarity of the curves and their lack of a relationship with fragment size suggests that all fragments are similar with respect to accumulation of species. Note that both axes are log10 scaled. B) Principal Coordinate Analysis, using Bray similarities, illustrating that similarity among fragments was always low. Larger symbols indicate fragment centroids, and each smaller point indicates a sample list of species (see text). No particular pattern is evident, and all fragments are variable and do not form groups based on fragment size.

opencc-by-4.0Dec 2022View details →

Fig. 4 in Avian Assemblages in Forest Fragments do not Sum to the Expected Regional Community in the Brazilian Atlantic Forest.

Fig. 4. Functional diversity analysis comparing different-sized fragments and functional evenness, dispersion, and divergence. A–C: Black squares and lines indicate the Atlantic Forest expected regional assemblage, circles and lines indicate the observed assemblages, with blue indicated only the Atlantic Forest species, and the open circle indicates all observed species (all based on presence-absence). D–F: estimated from presence-absence data of the expected local assemblage that were absent from the fragment. Regression results are presented in table 3.

opencc-by-4.0Dec 2015View details →

Fig. 1 in Manifold habitat effects on the prevalence and diversity of avian blood parasites

Fig. 1. Diagram illustrating how conditions of the vector, parasite, host and habitat must all be permissive for pathogen transmission to occur. The outer layer depicts some factors that are currently causing rapid environmental change, which will affect host‾parasite dynamics.

Fig. 4 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids

Fig. 4. Geographic distribution of the phylogenetic groups of avian piroplasmids (based on the 18S rRNA gene). Map prepared based on information provided in Criado et al. (2006), Yabsley et al. (2006, 2009), Jefferies et al. (2008), Paparini et al. (2014), Quillfeldt et al. (2014), Martínez et al. (2015), Montero et al. (2016) and Chavatte et al. (2017).

Fig. 2 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids

Fig. 2. Maximum likelihood phylogenetic tree of the ITS-1 (445 bp) and ITS-2 regions sequences (290 bp) of select avian-infecting Babesia lineages. Sequences identified in this study are emphasized in red, and those of other avian-infecting lineages are shown in blue. For each sequence, the following information is provided: morphospecies (individual identification or Genbank code) host species. Branch lengths are drawn proportionally to evolutionary distance (scale bar shown corresponds to both trees). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 3 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids

Fig. 3. Distribution of the phylogenetic groups of avian piroplasmids (based on the 18S rRNA gene) in relation to the phylogeny of avian orders (based on multiple nuclear genes). Avian orders investigated in this study are shown in red, and other avian orders known to host piroplasmids are shown in blue. Avian phylogeny was adapted from Yuri et al. (2013). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 1 in Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids

Fig. 1. Maximum likelihood phylogenetic tree of the 18S rRNA gene sequences (1450 bp) of the studied Babesia lineages. Sequences obtained in this study are emphasized in red, and those of other avian-infecting lineages are shown in blue. For each sequence, the following information is provided: morphospecies (individual identification or GenBank code) host species. For avian-infecting lineages, the host order is indicated with colored circles (see legend). Branch lengths are drawn proportionally to evolutionary distance. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

opencc-by-4.0Apr 2019View details →

Fig. 3 in Persistent low avian malaria in a tropical species despite high community prevalence

Fig. 3. Maximum likelihood phylogenetic inference of (A) Haemoproteus and (B) Plasmodium from the Australasian region. Sequences were included if they were at least 479 nucleotides in length and were found to be unique from a pairwise distance analysis (see methods). Bootstrap support values are shown if greater than 50. Dots indicate the 14 lineages that were detected in this study and their colour denotes the bird species they occurred within [Purple = PCFW (M. c. coronatus), Red = RBFW (M. melanocephalus), Yellow = BSR (P. cerviniventris), Grey = WGH (L. unicolor)]. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opencc-by-4.0Apr 2019View details →

Fig. 2 in Persistent low avian malaria in a tropical species despite high community prevalence

Fig. 2. (A) Malarial parasite prevalence across years in four bird species, buff-sided robin (BSR, n = 66), purple-crowned fairy-wren (PCFW, n = 731), red-backed fairy-wren (RBFW, n = 78), white-gaped honeyeater (WGH, n = 25). Fisher's exact P-values test for annual differences in infection within each bird species. (B) Longitudinal sampling of infected PCFW adults (individuals presented were sampled more than twice and were identified as infected with Haemoproteus or Plasmodium). Dotted lines indicate uncertainty in years when no sample was available. Each individual was infected with a single lineage. (C) Percentage of individual PCFW infected within each age category. (D) Local phylogenetic relationship between parasite lineages, colours refer to host species as for (A). Maximum likelihood tree was inferred using GTR + G + I with 1000 bootstrap replicates; novel lineages are indicated by *. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opencc-by-4.0Apr 2019View details →

Fig. 1 in Persistent low avian malaria in a tropical species despite high community prevalence

Fig. 1. Map of Australia and the Kimberly region. Sampling was conducted at the Australian Wildlife Conservancy's Mornington Wildlife Sanctuary (17̊31′S, 126̊6'E). Star indicates the location of the field site where samples were collected.

Fig. 5 in Avian trichomonosis mortality events in band-tailed pigeons (Patagioenas fasciata) in California during winter 2014-2015

Fig. 5. Haemotoxylin and eosin staining (left) of the oral tissue of a band-tailed pigeon (Patagioenas fasciata monilis) recovered during an avian trichomonosis mortality event showing a diffuse thick layer of necrosis extending through the submucosa and multifocally into the deeper soft tissue layers and skeletal muscle; scale bar is 200 μm. Immunohistochemical staining (right) of trichomonad antigen (red) of the same bird demonstrating large numbers of trichomonads in the oral tissue; scale bar is 50 μm. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Avian trichomonosis mortality events in band-tailed pigeons (Patagioenas fasciata) in California during winter 2014-2015

Fig. 2. Examples of caseonecrotic lesions (white arrowheads) in the oral cavity and upper digestive tracts of band-tailed pigeons (Patagioenas fasciata monolis) collected during an avian trichomonosis mortality event in California, U.S.A., between November 2014 and June 2015. Birds collected from Contra Costa County (A), Marin County (B), and Monterey County (D) in January 2015 and Placer County (E) in February 2015.

Fig. 4 in Avian trichomonosis mortality events in band-tailed pigeons (Patagioenas fasciata) in California during winter 2014-2015

Fig. 4. Body cavity with no adipose (white arrowheads) reserves (A.1) and the caseonecrotic lesions (white arrowheads) in the oral cavity (A.2) of a band-tailed pigeon (Patagioenas fasciata monolis) collected during an avian trichomonosis mortality event in Ventura County, California, U.S.A., in January 2015. Body cavity with abundant adipose (white arrowheads) reserves (B.1) and the caseonecrotic lesions (white arrowheads) in the oral cavity and upper digestive tract (B.2) of a band-tailed pigeon collected during an avian trichomonosis mortality event in Santa Clara County, California, U.S.A., in January 2015.

Fig. 3 in Avian trichomonosis mortality events in band-tailed pigeons (Patagioenas fasciata) in California during winter 2014-2015

Fig. 3. Caseonecrotic lesions (white arrowheads) in the right eye socket (A) and oral cavity (B) of a band-tailed pigeon (Patagioenas fasciata monolis) collected during an avian trichomonosis mortality event in Santa Clara County, California, U.S.A., in January 2015.