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203 results for “Bird Island”
Data associated with the publication "The origin of the world's smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)"
<p><strong>DESCRIPTION OF FILES</strong><br> These are files including data and additional results, that support the paper "The origin of the world's smallest flightless bird, the Inaccessible Island Rail Atlantisia rogersi (Aves: Rallidae)", by Stervander et al. 2018, published in Molecular Phylogenetics and Evolution (doi: 10.1016/j.ympev.2018.10.007).</p> <p>The phylogenetic analyses focus on rails (Aves: Rallidae) and outgroups based on (1) a dataset, 'MtProt' comprising the coding sequences (cds) from full mitochondrial genome assemblyes, and (2) a mixed-marker dataset, '2Nc3Mt', comprising the mitochondrial markers cytochrome <em>b</em> (cyt<em>b</em>), cytochrome oxidase subunit I (COI), and 16S ribosomal RNA (16S), and the nuclear markers β-fibrinogen intron 7 (bFib7) and recombination activating gene 1 (RAG1). The latter dataset i largely based on data from Garcia-R et al. (2014), with additions of the Inaccessible Island Rail <em>Atlantisia rogersi</em> and some further sequences (see our paper).</p> <p>Trees mentioned in our paper as "results not shown" can be found below.</p> <p><br> <strong>This deposition contains five groups of data:</strong><br> 1. Beast input xml files for phylogenetic analyses<br> 2. Beast output: log files<br> 3. Beast output: raw tree files<br> 4. Beast output: Maximum Clade Credibility trees<br> 5. Tree figures (pdf format)</p> <p><strong>The above are available for the following analyses:</strong><br> A. Mixed-marker dataset ‘2Nc3Mt’, one tree <br> B. Mixed-marker dataset ‘2Nc3Mt’, one tree; Micropygia schomburgkii excluded<br> C. Mixed-marker dataset ‘2Nc3Mt’, separate mitochondrial (‘3Mt’) and nuclear marker trees (RAG1 and bFib7)<br> D. Protein coding dataset ‘MtProt’ from entire mitochondrial genomes</p> <p>The files are thus the following, sorted according to dataset:<br> A1 Beast_input_2Nc3Mt_1tree.xml<br> A2 Beast_output_2Nc3Mt_1tree.log<br> A3 Beast_output_2Nc3Mt_1tree.raw.trees<br> A4 Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees<br> A5 Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf<br> B1 Beast_input_2Nc3Mt_exclMicropygia_1tree.xml<br> B2 Beast_output_2Nc3Mt_exclMicropygia_1tree.log<br> B3 Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees<br> B4 Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees<br> B5 Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf<br> C1 Beast_input_2Nc3Mt_separate_trees.xml<br> C2 Beast_output_2Nc3Mt_separate_trees.log<br> C3 Beast_output_2Nc3Mt_RAG1.raw.trees<br> C3 Beast_output_2Nc3Mt_bFib7.raw.trees<br> C3 Beast_output_2Nc3Mt_mt.raw.trees<br> C4 Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees<br> C4 Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees<br> C4 Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees<br> C5 Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf<br> C5 Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf<br> C5 Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf<br> D1 Beast_input_MtProt_1tree.xml<br> D2 Beast_output_MtProt_1tree.log<br> D3 Beast_output_MtProt_1tree.raw.trees<br> D4 Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees<br> D5 Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf</p> <p>Or, sorted according to file type:<br> 1A Beast_input_2Nc3Mt_1tree.xml<br> 1B Beast_input_2Nc3Mt_exclMicropygia_1tree.xml<br> 1C Beast_input_2Nc3Mt_separate_trees.xml<br> 1D Beast_input_MtProt_1tree.xml<br> 2A Beast_output_2Nc3Mt_1tree.log<br> 2B Beast_output_2Nc3Mt_exclMicropygia_1tree.log<br> 2C Beast_output_2Nc3Mt_separate_trees.log<br> 2D Beast_output_MtProt_1tree.log<br> 3A Beast_output_2Nc3Mt_1tree.raw.trees<br> 3B Beast_output_2Nc3Mt_exclMicropygia_1tree.raw.trees<br> 3C Beast_output_2Nc3Mt_RAG1.raw.trees<br> 3C Beast_output_2Nc3Mt_bFib7.raw.trees<br> 3C Beast_output_2Nc3Mt_mt.raw.trees<br> 3D Beast_output_MtProt_1tree.raw.trees<br> 4A Beast_output_2Nc3Mt_1tree.max_clade_cred_burnin10M.trees<br> 4B Beast_output_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.trees<br> 4C Beast_output_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees<br> 4C Beast_output_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees<br> 4C Beast_output_2Nc3Mt_mt.max_clade_cred_burnin10M.trees<br> 4D Beast_output_MtProt_1tree.max_clade_cred_burnin1M.trees<br> 5A Tree_2Nc3Mt_1tree.max_clade_cred_burnin10M.pdf<br> 5B Tree_2Nc3Mt_exclMicropygia_1tree.max_clade_cred_burnin10M.pdf<br> 5C Tree_2Nc3Mt_RAG1.max_clade_cred_burnin10M.trees.pdf<br> 5C Tree_2Nc3Mt_bFib7.max_clade_cred_burnin10M.trees.pdf<br> 5C Tree_2Nc3Mt_mt.max_clade_cred_burnin10M.trees.pdf<br> 5D Tree_MtProt_1tree.max_clade_cred_burnin1M.pdf</p> <p><strong>Note about the tree figures (pdf format): </strong>Nodes marked with a black circle are supported by a posterior probability (PP) of 1.0, for lower PP the number is given at the node. Blue bars represent the 95% highest posterior density intervals of the node age. MYA = Million years ago.</p> <p>/Martin Stervander (martin@stervander.com)</p>
Surveys of salt marsh wading birds and shorebirds in Massachusetts at Plum Island Sound, PIE LTER and portions of Essex Bay
This data set is part of a study of how wading birds, primarily Great and Snowy Egrets are using different estuarine habitats at Plum Island Sound. It contains the results of count surveys of wading birds in the salt marshes of the Plum Island Estuary and parts of adjacent Essex Bay. Surveys were carried out from May to October in 2012 and 2013, additional sampling occurred in July 2014 and summer of 2018. Bird counts took place from 37 observation points around the bay and documented species, estimated distance from observer, habitat of each individual bird counted and its behavior (feeding, resting, etc.).
High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
<p>Raw sequence data from two amplicon libraries of MHC class I exon 3 of Raso Lark <em>Alauda razae</em>, sequenced on an Illumina Miseq. The two different libraries (two different Illumina runs) are collected in separat tar archive (.tar). Within each of those are individual sequence reads as gzipped fastq files (.fastq.gz). Each sample has two files, one for read 1 (R1) and one for read 2 (R2), with file names structured as follows. Delimited by underscore (_) are:</p> <ol> <li>sample name as referred to in the data and paper (“RingNo” in the Supporting data table);</li> <li>formal ID (also referred to in data table, often corresponding to full ring number);</li> <li>Illumina sample number (i.e. based on the order that samples are listed in the sample sheet);</li> <li>Illumina lane number (static as L001, as Miseq instruments have a single lane on their flow cells);</li> <li>read number (R1 [forward] or R2 [reverse]);</li> <li>static identifier from Illumina (001).</li> </ol> <p>Thus, the file 83304_TJ83304_S163_L001_R2_001.fastq.gz is the reverse (read 2) MHC class I exon 3 sequence of individual 83304 (ring number TJ83304).</p>
Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?
<p>When populations colonise new environments they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes, and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (> 22X coverage) in Berthelot's pipit (<em>Anthus berthelotii</em>), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. Firstly, we quantify how genomic divergence accumulates across the speciation continuum, i.e., among Berthelot's pipit populations, between subspecies across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (<em>Anthus campestris</em>). Across these colonisation timeframes (2.1 million – <em>ca.</em> 8,000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism, and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism, and immune defence.</p>
Data and scripts for Co-phylogeny, narrow host breadth and local conditions drive highly specialized bird-haemosporidian associations in West-Central African sky islands
<p>This document includes the raw datafiles, host and parasite phylogenies and r-code use to conduct analyses for "Co-phylogeny, narrow host breadth and local conditions drive highly specialized bird-haemosporidian associations in West-Central African sky islands". Please see the readme file to get more detailed information about each file.</p>
Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species
<p>We present evidence for and investigate potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km<sup>2</sup> island. The island scrub-jay (<em>Aphelocoma insularis</em>) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.</p>
Data from: The Subantarctic Rayadito (Aphrastura subantarctica), a new bird species on the southernmost islands of the Americas. Scientific Reports
<p><strong>Description of the dataset</strong><br> This dataset contains morphological and genetic information of Aphrastura populations in different sample sites in Chile and Argentina. This dataset was analysed in: Rozzi R, Quilodrán CS, Botero-Delgadillo E, Napolitano C, Torres-Mura JC, Barroso O, Crego RD, Bravo C, Ippi S, Quirici V, Mackenzie R, Suazo CG, Rivero-de-Aguilar J, Goffinet B, Kempenaers B, Poulin E and RA Vásquez. 2022. The Subantarctic Rayadito (<em>Aphrastura subantarctica</em>), a new bird species on the southernmost islands of the Americas. Scientific Reports.</p> <p>There are three files: </p> <ul> <li>Subantarctic_Rayadito_Morphology.txt: morphological information used for differentiating <em>Aphrastura subantarctica</em> from <em>Aphrastura spinicauda</em>. The former was sampled in the Diego Ramirez archipelago. The date of sampling is included in the last column. </li> <li>Subantarctic_Rayadito_Microsatellite.txt: all captured and genotyped adults from five populations. The band (ring) number is used as an ID for each individual bird. The matrix includes information regarding the locality of origin (MA: Manquehue; BA: Bariloche; TF: Tierra del Fuego; NI: Navarino Island; DR: Diego Ramírez Archipelago), and allele size (number of repeats) at 12 polymorphic microsatellite loci.</li> <li>Subantarctic_Rayadito_mtDNA.nex: mtDNA information for all <em>Aphrastura</em> individuals sequenced and used in our analysis. The labels denote the code number and location for each individual (DR: Diego Ramirez Archipelago; CH: Cape Horn Island ; Navarino : Navarino Island; TdelFuego : Tierra del Fuego; PtoNatales : Puerto Natales ; ElChalten : El Chalten; CalTortel : Caleta Tortel ; Coihayque : Coihayque ; Chaiten : Chaiten ; LosAlerces : Los Alerces ; Chiloe : Chiloé Island ; IslaMocha : Mocha Island ; Curacautin : Curacautin ; Rinihue : Rinihue ; Epulauquen : Epu Lauquen ; Constitucion : Constitución ; Manquehue : Manquehue ; FrayJorge : Fray Jorge National Park). </li> </ul> <p><strong>Acknowledgments </strong><br> This study was funded with Grants from the Sub-Antarctic Biocultural Conservation Program of the University of North Texas, University of Magallanes, the Cape Horn International Center (ANID CHIC-FB210018), the Institute of Ecology and Biodiversity of Chile (CONICYT PFB-23), and the Patagonia Mar y Tierra Working Group (The Pew Charitable Trust - Chile). We thank the support of the Omora Foundation, and FONDECYT 1140548 to RAV. C.N. thank support from ANID PAI 77190064, and ANID/BASAL FB210006. CSQ acknowledges support from the Swiss National Science Foundation (N° P400PB_183930 and P5R5PB_203169). We are grateful to Sylvia Kuhn and Alexander Girg from the Max Planck Institute for Ornithology for help in the laboratory, and to Jaime A. Cursach and Maximiliano Daigre during fieldwork and ornithological records in Gonzalo Island. Fieldwork in protected areas was possible thanks to people from Parque Nacional Bosque Fray Jorge, Minera Los Pelambres, Estación Biológica Senda Darwin, Parque Nacional Nahuel Huapi, and Parque Natural Karukinka. We also express our gratitude for logistical and personnel support from the 3rd Naval Zone of the Chilean Navy.</p> <p> </p>
Figure 2 in First record of the Ashy Minivet (Pericrocotus divaricatus), a passerine bird, for Saipan, Commonwealth of the Northern Mariana Islands
Figure 2. Ashy Minivets (Pericrocotus divaricatus) mistnetted on Saipan. A. and B. Female, C. Female wing, D. Male (photos A-C, K. Beer; D. J. Chojnacki).
Figure 1. A in Survey of the Non-Migratory Birds of the Rock Islands Southern Lagoon World Heritage Site in Palau
Figure 1. A. Map of Palau. B. Map of the island groups of the Rock Islands Southern Lagoon World Heritage Site study area (inset). Our survey included all 10 island groups. Scale marker = 5 km..
Figure 1 in First record of the Ashy Minivet (Pericrocotus divaricatus), a passerine bird, for Saipan, Commonwealth of the Northern Mariana Islands
Figure 1. Map showing location of new record for Ashy Minivets in Saipan, Commonwealth of the Northern Mariana Islands. Top left - Location of the CNMI in the Western Pacific, Bottom left - Location of Saipan within the CNMI, Right - Satellite image from 2013 of the northern part of Saipan including the capture and resight locations marked with a white X.
FIGURE 10 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 10. Paleoenvironmental reconstruction of the Ypresian continental communities of Seymour Island. A large Cariamiform hunting a medium-sized ungulate and staring at Notiolofos regueroi (Mammalia: Sparnotheriodontidae), a couple of marsupials on a tree, Antarctoboenus carlinii (Aves, Falconiformes) flying on the sky, and a flightless Ratites in the back.
FIGURE 7 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 7. Ungual phalanx of representatives of the most relevant groups compared with the Antarctic specimens described in this study. A, Antarctic fossil MLP-PV 13-XI-28-546; B, Chunga incerta (Cariamiformes); C, Vultur gryphus (Cathartiformes); D, Caracara plancus (Falconiformes); E, Geranoaetus melanoleucus (Accipitriformes); F, Ninox novaeseelandiae (Strigiformes); G, Casuarius casuarius (Casuariformes); H, Dromaius novaehollandiae (Struthioniformes); I, Rhea americana (Rheiformes); J, Tinamus solitarius (Tinamiformes); K, Penelope obscura and L, Crax fasciolata (Galliformes); M, Otis tarda (Otidiformes); N, Chauna torquata (Anseriformes); O, Macronectes giganteus (Procellariiformes); P, Anthropornis grandis (giant Antartic Sphenisciformes); and Q, Pygoscelis antarctica (modern Sphenisciformes). Scale bar: 10 mm.
FIGURE 4 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 4. Fossil cariamiforms examined here. Ungual phalanx of the second right digit MLP-PV 13-XI-28-546 (A, C, E, G) in lateral (A), dorsal (C), medial (E), and proximal (G) views, and ungual phalanx of second digit MLP-PV 14-I- 10-199 (B, D, F) in lateral or medial (B, F) and dorsal (D) views. Scale bar: 10 mm.
FIGURE 3 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 3. Linear and angular measurements taken on the schematic ungual phalanges in A-B lateral, and C, proximal views. Abbreviations: BH, basal height; HAF, maximum height of the articular facet; ICA, inner curvature angle; LFT, flexor tubercle length; OCA, outer curvature angle; TL, total length; and WAF, maximum width of articular facet.
FIGURE 6 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 6. Biplot of the Principal Component Analyses (PCA). A, Analysis without normalization of data; B, Analysis with variables converted into indexes. Abbreviations: BH, basal height; HAF, maximum height of the articular facet; ICA, inner curvature angle; LFT, flexor tubercle length; OCA, outer curvature angle; TL, total length; and WAF, maximum width of articular facet.
FIGURE 2 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 2. Anatomical terms used for descriptions and comparisons (after Baumel et al., 1993) in A, dorsal; B, lateral; and C, proximal views. Abbreviations: ap. phal., apex phalanx; corp. phal., corpus phalangis; cot. art., cotyla articularis (articular or proximal face); cot. art. lat., cotyla articularis lateralis; cot. art. med., cotyla articularis medialis; sulc. neur., sulcus neurovascularis (neurovascular sulcus); tuberc. ext., tuberculum extensorium (extensor tubercle); tuberc. flex., tuberculum flexorium (flexor tubercle).
FIGURE 5 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 5. Morphological differences between the ungual phalanges of each digit (I, II, II, and IV) of Cariama cristata (A-D) and Psilopterus colzecus (E) in A, lateral; B, dorsal; C, plantar; D and E, proximal (articular) views (not scaled).
FIGURE 1 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 1. Geological map of the Seymour Island showing the fossiliferous sites where MLP-PV 13-XI-28-546 and MLP-PV 14-I-10-199 were found (A) and the corresponding stratigraphy of the locality IAA 2/13 (B), in the James Ross Basin (C), West Antarctica (D). Modified from Montes et al. (2019).
FIGURE 9 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 9. Three-dimensional reconstructions (not scaled) of different ungual phalanges. The dotted lines indicate the transversal cut areas shown below each phalanx. The arrowheads mark the path of the neurovascular sulcus and/or neurovascular canal along the phalanx. A, Patagornis marshi (MLP-PV 20-85, digit III); B, Patagornis marshi (MLP-PV 20-86, digit III); C, Psilopterus colzecus (MLP-PV 76-VI-12-2, digit II); D, Brontornis burmeisteri (MLP-PV 20-570, digit III); E, Phorusrhacos longissimus (MLP-PV 67-VIII-28-1, digit II); F, Andrewsornis abbotti MLP-PV 59-II-26-83 (digit II).
FIGURE 8 in Were terror birds the apex continental predators of Antarctica? New findings in the early Eocene of Seymour Island
FIGURE 8. Antarctic ungual phalanx compared with different Phorusrhacidae species in lateral view. A, MLP-PV 13- XI-28-546; B, Phorusrhacos longissimus (AMNH 9497 taken from Sinclair and Farr 1932 and mirrored); C, Procariama simplex MACN 8275; D, Phorusrhacus (MLP-PV 20-572); E, Paraphysornis brasiliensis; F, Patagornis marshi MLP-PV 20-184; G, Procariama simplex MACN 8225; H, Devincenzia pozzi MACN Pv 6681; I, Titanis walleri (calcotype UF 10417); J, Psilopterinae indet. MLP-PV 90-III-5-56; K, Mesembriornis milneedwardsi MACN Pv 5944; L, Patagornis marshi MLP-PV 20-164; M, Psilopterus colzecus MLP-PV 76-VI-12-2; N, Psilopterinae indet. MPEF-PV 12256; O, MMP s/n Phorusrhacidae (re-drawn from Cenizo et al., 2012). Scales bar: 10 mm (except for C, G, M, and N where the scale represents 20 mm).
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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