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306 results for “Birds (Aves)”
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>
Figure 3 in Comparative ossification and development of the skull in palaeognathous birds (Aves: Palaeognathae)
Figure 3. Evolution of embryonic and adult palatal morphology of the ratites (phylogeny sensu Bledsoe, 1988, palaeognathous characters 1–3 sensu Zusi & Livezey, 2006). Top row: adult morphology (Parker, 1869, 1891; Beddard, 1898; Simonetta, 1960; Zusi & Livezey, 2006; Silveira & Höfling, 2007). Bottom row: embryonic morphology. Gallus (Jollie, 1957), Rhea, Apteryx (Parker, 1891), and Dromaius are all stage 37; Struthio (Parker, 1866) is slightly older; Aepyornis (Balanoff & Rowe, 2007) and Eudromia (Tinamidae) are late-stage individuals. The palatine is shaded to facilitate comparison.
Figure 2 in Comparative ossification and development of the skull in palaeognathous birds (Aves: Palaeognathae)
Figure 2. Palatal view of selected palaeognath embryos. A, B, Struthio camelus (modified from Parker, 1866). C, Rhea americana, stage 37 (day 17 of incubation, RM 7219). D, Rhea americana (modified from Müller, 1963). E, Dromaius novaehollandiae, stage 37 (day 28 of incubation, RM 8026). F, Eudromia elegans, day 14 of incubation (YPM 112524). Scale bars = 5 mm. Abbreviations: bo, basioccipital; exo, exoccipital; mx, maxilla; pal, palatine; pmx, premaxilla; psl, parasphenoid lamina; psr, parasphenoid rostrum; pt, pterygoid; q, quadrate; v, vomer.
Fig. 2 in Interspecific Agression Of The Passerine Birds (Aves, Passeriformes) On Watering Places In Wood-And-Steppe Zone Of Ukraine
Fig. 2. Grouping of species distribution by demonstration of aggressive behavior at watering places in the State Arboretum "Alexandria".
Fig. 6 in Interspecific Agression Of The Passerine Birds (Aves, Passeriformes) On Watering Places In Wood-And-Steppe Zone Of Ukraine
Fig. 6. Rating of success of attack and defense of birds in biological educational and research institution "Vakalivschyna".
Fig. 3 in Interspecific Agression Of The Passerine Birds (Aves, Passeriformes) On Watering Places In Wood-And-Steppe Zone Of Ukraine
Fig. 3. Grouping of species distribution by demonstration of aggressive behavior at watering places in biological educational and research institution "Vakalivschyna".
Fig. 1 in Interspecific Agression Of The Passerine Birds (Aves, Passeriformes) On Watering Places In Wood-And-Steppe Zone Of Ukraine
Fig. 1. Grouping of species distribution by demonstration of aggressive behavior at watering places in Kaniv Nature Reserve.
Fig. 2 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist
Fig. 2. Biomes in the Horn of Africa following Fishpool & Evans (2001). SG = Sudan-Guinea Savanna biome (green); AH = Afrotropical Highlands biome (blue); SM = Somali-Masai biome (yellow).
Fig. 1 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist
Fig. 1. The National Regional State of Oromia (red) within Ethiopia and the Horn of Africa (boundaries after MapLibrary 2013).
Fig. 6 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist
Fig. 6. The White-tailed Swallow Hirundo megaensis Benson, 1942 is another endemic species to Oromia, restricted to the Borana and Guji zone (Photo: Kai Gedeon).
Fig. 5 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist
Fig. 5. The Ethiopian Bush-crow Zavattariornis stresemanni Moltoni, 1938 is restricted to the Borana zone in SE Oromia, with a total range of just 6000 km² (Photo: Kai Gedeon).
Fig. 4 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist
Fig. 4. The Black-fronted Francolin Pternistis castaneicollis atrifrons (Conover, 1930) exists in a small mountain range around Mega in southern Oromia (Borana zone). It shows a number of distinct features that may justify the split from P. castaneicollis (Photo: Kai Gedeon).
Fig. 3 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist
Fig. 3. The National Regional State of Oromia covered by 1-degree-tetrads. For the bold-red framed tetrads the data on distribution of birds was taken from the distribution atlas of Ash & Atkins (2009).
Figure 4 in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 4. Maximum clade credibility trees for three data sets obtained by BI analysis in BEAST v1.8.0. MCC genealogy based on a Yule speciation process, summarized from the output of a Markov chain Monte Carlo chain run for 10 million iterations and sampled every 1000 iterations.
Figure 3 in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 3. The ML tree for myoglobin gene (in blue) and for CHD-Z gene (in red); both trees are scaled in substitutions and the length of each tree and different topologies indicate that both of them are improper for phylogeny using a single gene.
Figure 1. Sex distribution for A. arundinaceus, A in CHD genes: a reliable marker for bird populations and phylogenetic analysis? Case study of the superfamily Sylvioidea (Aves: Passeriformes)
Figure 1. Sex distribution for A. arundinaceus, A. scirpaceus, and A. schoenobaenus, shown by sampling date.
FIGURE 2 in An ameghinornithid-like bird (Aves, Cariamae, ?Ameghinornithidae) from the early Oligocene of Egypt
FIGURE 2. The distal tibiotarsus of the Fayum ameghinornithid-like bird (DPC 5659). 1, Lateral view. 2, Cranial view. 3, Medial view. 4, Caudal view. 5, Distal view. Abbreviations: ep, elongate pit; es, extensor sulcus; fs, flattened spot; g, groove; is, intercondylar sulcus; lc, lateral condyle; mc, medial condyle; me, medial epicondyle; mf, medial flange of the tibial cartilage articulation; r, ridge; s, sand/sediment grains.
FIGURE 1 in An ameghinornithid-like bird (Aves, Cariamae, ?Ameghinornithidae) from the early Oligocene of Egypt
FIGURE 1. Maps showing the geographic range of fossil localities with ameghinornithid specimens (left panel; 1, Quercy, France; 2, Messel, Germany; 3, Geiseltal, Germany; 4, Fayum Depression, Egypt) and the location of the Fayum Depression in northern Egypt (right panel) where the ameghinornithid-like specimen was collected.
Linked collectors and determiners for: Type specimens and type localities of birds (Aves) collected during F. J. F. Meyen's circumnavigation in 1830 – 1832.
Natural history specimen data linked to collectors and determiners held within, "Type specimens and type localities of birds (Aves) collected during F. J. F. Meyen's circumnavigation in 1830 – 1832". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/ac9cc78c-c2cd-453f-8715-8f38648de567">https://bionomia.net/dataset/ac9cc78c-c2cd-453f-8715-8f38648de567</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ac9cc78c-c2cd-453f-8715-8f38648de567">https://gbif.org/dataset/ac9cc78c-c2cd-453f-8715-8f38648de567</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Type specimens and type localities of birds (Aves) collected by Gustav Adolf Fischer (1848 - 1886) in East Africa.
Natural history specimen data linked to collectors and determiners held within, "Type specimens and type localities of birds (Aves) collected by Gustav Adolf Fischer (1848 - 1886) in East Africa". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/86bd1537-578b-462b-ae18-c669bc6e0dce">https://bionomia.net/dataset/86bd1537-578b-462b-ae18-c669bc6e0dce</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/86bd1537-578b-462b-ae18-c669bc6e0dce">https://gbif.org/dataset/86bd1537-578b-462b-ae18-c669bc6e0dce</a>. Formatted as a Frictionless Data package.
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