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309 results for “finch”
Sex-specific relationships between urbanization, parasitism, and plumage coloration in house finches
Historically, studies of condition-dependent signals in animals have been male-centric, but recent work suggests that female ornaments can also communicate individual quality (e.g., disease state, fecundity). There also has been a surge of interest in how urbanization alters signaling traits, but we know little about if and how cities affect signal expression in female animals. We present data of carotenoid-based plumage coloration and coccidian (Isospora spp.) parasite burden in desert and city populations of house finches Haemorhous mexicanus to examine links between urbanization, health state, and feather pigmentation in males and females. In earlier work, we showed that male house finches are less colorful and more parasitized in the city, and we again detected such patterns in this study for males; however, urban females were less colorful, but not more parasitized, than rural females. Moreover, contrary to rural populations, we found that urban birds (regardless of sex) with larger patches of carotenoid coloration were also more heavily infected with coccidia. These results show that urban environments can disrupt condition-dependent color expression and highlight the need for more studies on how cities affect disease and signaling traits in both male and female animals.
Distributional data for Lined Seedeaters (Sporophila lineola) and Saffron Finches (Sicalis flaveola)
<p><span>Distributional data for Lined Seedeaters (Sporophila lineola) and Saffron Finches (Sicalis flaveola). Data compiled from the literature, zoological collections, and community science platforms. </span></p>
Does water-bath cleaning affect the health of visiting birds? A study of parasite loads in house finches (Haemorhous mexicanus) in the Phoenix, Arizona, USA metropolitan area (2018)
There is evidence that urban animals have higher parasite and pathogen burdens than those from natural areas, but the mechanism behind this pattern is unclear. One possibility for yard-visiting birds is that they drink from bird baths that have not been regularly cleaned and thus they have elevate infection risks and rates by consuming unusually soiled water. We experimentally tested this idea in house finches (Haemorhous mexicanus) – a common backyard visitor in North America – by implementing a rotating bath-cleaning regime, where we either left baths uncleaned for 5 weeks or cleaned them daily with dilute bleach for 5 weeks, and did so at both an urban and rural study site. We found that coccidian endoparasitism decreased in urban birds when they drank from clean baths, but the same was not true for rural birds. These results reveal a habitat-specific effect of feeder cleaning on disease status in an abundant yard-visiting songbird.
Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
Zebra finches increase social behavior in traffic noise: implications for urban songbirds
<p>Statistical code & datasets for "Zebra finches increase social behavior in traffic noise: implications for urban songbirds" manuscript submitted to <em>Acta ethologica. </em>Also includes audio file for traffic noise playback in described experiment. </p>
Monitor predation on zebra finch nest
<p>Here, we report a detailed predation sequence, captured on film, of a sand goanna (<i>Varanus gouldii</i>) predating six zebra finch nestlings from a single nestbox in arid western New South Wales, Australia. The sand goanna made nine attempts to reach the nestbox by first climbing an adjacent bush and jumping onto the nestbox and eventually also by climbing up the steel post on which the box was attached. </p>
Zebra finch dataset for the paper: Benchmarking nearest neighbor retrieval of zebra finch vocalizations across development
<p>This is the dataset created in the paper "Benchmarking nearest neighbor retrieval of zebra finch vocalizations across development".</p>
Brightness cues affect gap negotiation behaviour in zebra finches
<p>Flying animals have had to evolve robust and effective guidance strategies for dealing with habitat clutter. Birds and insects use optic flow cues to sense and avoid obstacles, but orchid bees have also been shown to use brightness cues during gap negotiation. Brightness cues might therefore be of general importance in structuring visually guided flight. To test the hypothesis that brightness cues affect gap negotiation behaviours in birds, we presented captive zebra finches <em>Taeniopygia guttata</em> with a symmetric or asymmetric background brightness distribution on the other side of a tunnel. The background brightness conditions influenced both the birds' decision to enter the tunnel aperture, and their flight direction upon exit. Zebra finches were more likely to initiate flight through the tunnel if they could see a bright background through it; they were also more likely to fly to the bright side upon exiting. We found no evidence of the centring response that would be expected if optic flow cues were balanced bilaterally during gap negotiation. Instead, the birds entered the tunnel by targeting a clearance of approximately one wing length from its near edge. Brightness cues therefore affect how zebra finches structure their flight when negotiating gaps in enclosed environments.</p>
Genomic signatures of isolation, hybridization, and selection during speciation of island finches
<p><strong>Data associated</strong> to the study <em>Genomic signatures of isolation, hybridization, and selection during speciation of island finches</em></p> <p><strong>Contents</strong></p> <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch <em>Taeniopygia guttata</em> is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> <p>Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx).</p> </li> </ul> <p> </p> <p><strong>Study summary</strong></p> <p>Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.</p>
Where did the finch go? Insights from radio telemetry of the medium ground finch (Geospiza fortis)
<p><span>Movement patterns and habitat selection of animals have important implications for ecology and evolution. Darwin's finches are a classic model system for ecological and evolutionary studies, yet their spatial ecology remains poorly studied. We tagged and radio-tracked five (three females, two males) medium ground finches (<em>Geospiza fortis</em>) to examine the feasibility of telemetry for understanding their movement and habitat use. Based on 143 locations collected during a three-week period, we analysed, for the first time, home-range size and habitat selection patterns of finches at El Garrapatero, an arid coastal ecosystem on Santa Cruz Island (Galápagos). The average 95% home range and 50% core area for <em>G. fortis</em> in the breeding season were 20.54 ha ± 4.04 ha SE and 4.03 ha ± 1.11 ha SE, respectively. For most of the finches, their home range covered a diverse set of habitats. Three finches positively selected the dry-forest habitat, while the other habitats seemed to be either negatively selected or simply neglected by the finches. In addition, we noted a communal roosting behaviour in an area close to the ocean, where the vegetation is greener and denser than the more inland dry-forest vegetation. We show that telemetry on Darwin's finches provides valuable data to understand the movement ecology of the species. Based on our results, we propose a series of questions about the ecology and evolution of Darwin's finches that can be addressed using telemetry.</span></p>
Fig. 1 in Apparent effect of chronic Plasmodium infections on disease severity caused by experimental infections with Mycoplasma gallisepticum in house finches
Fig. 1. Mean severity of eye lesions ± SE (circles), and M. gallisepticum-load (log (qPCR+1)) (triangles) of birds infected through horizontal transmission with the CA2015 strain of M. gallisepticum. Birds in which Plasmodium was detected by PCR (grey symbols) developed more severe disease than birds in which Plasmodium was not found (white symbol). As there is no significant interaction between M. gallisepticum ‾strain and Plasmodium infection (Table 2) the results for the other M. gallisepticum strains are qualitatively similar and therefore not shown.
Figures 1-4 in Reproductive behavior of the Red-crested Finch Coryphospingus cucullatus (Aves: Thraupidae) in southeastern Brazil
Figures 1-4. Nests, eggs, and young Red-creasted Finch. (1) Nest lateral view depicting nest placement and lichens in the outer wall. (2) Female incubating eggs. (3) Eggs and incubation chamber. (4) Nestlings.
Recordings of zebra finch group behaviors with manually annotated vocal segments
<div> <div>This dataset contains recording files and manually annotated vocal segments of freely behaving zebra finches in the BirdPark. The files contain animal-borne accelerometer, microphone and video channels. Birds are housed in groups of different sizes (2, 4, or 8 birds, (one 7-mins file per group). The dataset contains 112 mins of recordings from 4 different experiments.</div> </div> <p>The dataset is published as an appendix of the following paper:</p> <p><a href="https://doi.org/10.1101/2022.09.23.509166">Rüttimann, L., Wang, Y., Rychen, J., Tomka, T., Hörster, H., Rocha, M. D., & Hahnloser, R. H. (2024). Multimodal system for recording individual-level behaviors in songbird groups. bioRxiv.</a></p> <p>See the README.pdf file for a detailed description.</p>
Figure 9 in The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa
Figure 9. Distribution of measurements of the angle of the mandibular symphysis to the internal ramus. See character 31.
Figure 8 in The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa
Figure 8. Method of measuring the angle of the mandibular symphysis to the internal ramus. Mandibles, in lateral view, are of Telespiza ypsilon USNM 254736 – subparallel (A), Vangulifer mirandus USNM 445808 – deflected (B), and Aidemedia zanclops BBM-X 155160 holotype – deflected (C). See character 31.
Figure 11 in The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa
Figure 11. Illustration of states for mandible characters 38, 40, 43, and 44. Mandibles of Passer domesticus USNM 561838 (A) and Telespiza cantans USNM 289278 (B) in lateral view, illustrating the concave vs. straight dorsal profile (character 38). The articular end of the mandible in Oreomystis bairdi USNM 553183 (C) and Sicalis flaveola USNM 556091 (D) in dorsal view, illustrating presence (D) vs. absence (C) of lateral inflation anterior to the lateral cotyla (character 40). The articular end of the mandible in Pooecetes gramineus USNM 555444 (E) and Leucosticte tephrocotis USNM 501466 (F) in dorsal view, illustrating the deep vs. shallow development of bone below the lateral cotyla (character 43). The articular end of the mandible in Cardinalis cardinalis USNM 554219 (G) and Telespiza cantans USNM 561510 (H) in anterodorsal view, illustrating a prominent intercotylar tubercle vs. a weakly developed one (character 44).
Figure 4 in The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa
Figure 4. Method of measuring degrees of arc of the premaxilla, illustrated on the skull of Himatione sanguinea (MVZ 118858). See character 5.
Figure 14 in The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa
Figure 14. Phylogram showing one of two optimal trees for matrix B (length 193 steps, consistency index 0.42). Eleven clades are identified, and illustrated in Figures 14 and 15. Bremer support (roman numbers) and bootstrap support>50% (italic numbers in parentheses) are indicated. Daggers identify taxa that became extinct in historic times; double daggers identify extinct fossil taxa. The branch lengths were determined with accelerated transformation of states. *These taxa may also be extinct.
Figure 7 in The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa
Figure 7. Distribution of logarithmic ratios of the length to height of the narial opening. See character 22.
Figure 2 in The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa
Figure 2. Osteological terminology illustrated on the skull and mandible of Loxops stejnegeri (USNM 502195).
ScienceDex guides
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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.