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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>
FIGURES 7 9. 7 8, Brachypterodina gonzalezi. 7 in New flightless Eumolpinae of the genera Apterodina Bechyné and Brachypterodina n. gen. (Coleoptera: Chrysomelidae) from the Neotropics
FIGURES 7 9. 7 8, Brachypterodina gonzalezi. 7. female, dorsal view; 8. humeral area enlarged; 9. Apterodina bucki, pygidium.
FIGURES 3 – 6. Apterodina spp. 3 – 4 in New flightless Eumolpinae of the genera Apterodina Bechyné and Brachypterodina n. gen. (Coleoptera: Chrysomelidae) from the Neotropics
FIGURES 3 – 6. Apterodina spp. 3 – 4, Apterodina bechynei: 3. male, dorsal view; 4. female, dorsal view. 5; A. bucki female, dorsal view; 6. A. ruminyahui female, dorsal view.
FIGURE 2 in Flightless litter-dwelling Cotasterosoma (Coleoptera: Curculionidae: Cossoninae) found outside of Japan, with mtDNA phylogeography of a new species from Southwest China
FIGURE 2. Cotasterosoma coronus sp. n., paratype, female, specimen # 1110 from Mt. Emei. A – D: habitus; E – F: head and prothorax (E: ventral, F: lateral); G – I: distal part of right legs (G: fore-, H: mid-, I: hind-); J: genitalia, ventral; K: spermatheca.
FIGURE 1 in Flightless litter-dwelling Cotasterosoma (Coleoptera: Curculionidae: Cossoninae) found outside of Japan, with mtDNA phylogeography of a new species from Southwest China
FIGURE 1. Cotasterosoma coronus sp. n., holotype, male. A – D: habitus; E: genitalia and abdominal tergites 7 and 8, ventral; F – H: genitalia (F: dorsal, G: ventral, H: lateral).
Fig. 5 in METAPOCYRTUS MADAYAW SP. N. (COLEOPTERA: CURCULIONIDAE, ENTIMINAE), A NEW FLIGHTLESS WEEVIL FROM EASTERN MINDANAO, PHILIPPINES
Fig. 5. Habitats of Metapocyrtus (Artapocyrtus) madayaw sp. n. A – Lamiawan, Davao Oriental; B – Maragusan, Davao de Oro.
Fig. 7. A in Contribution to the knowledge of Batrachideini (Orthoptera: Tetrigidae): description of two new flightless genera, Naskreckiana and Procellator, and revision of the status of Eotetrix
Fig. 7. A nymph of Procellator kai gen. & sp. nov. photographed in its natural habitat by Kai Squires.
Fig. 3. A in Contribution to the knowledge of Batrachideini (Orthoptera: Tetrigidae): description of two new flightless genera, Naskreckiana and Procellator, and revision of the status of Eotetrix
Fig. 3. A living female individual of Naskreckiana, potentially representing an undescribed species of the genus. Photographed by Piotr Naskrecki.
Fig. 6 in Contribution to the knowledge of Batrachideini (Orthoptera: Tetrigidae): description of two new flightless genera, Naskreckiana and Procellator, and revision of the status of Eotetrix
Fig. 6. An adult female of Procellator kai gen. & sp. nov. photographed in its natural habitat by Kai Squires.
Fig. 2 in Contribution to the knowledge of Batrachideini (Orthoptera: Tetrigidae): description of two new flightless genera, Naskreckiana and Procellator, and revision of the status of Eotetrix
Fig. 2. The holotype of Naskreckiana kosemeni gen. & sp. nov. A – hind tarsus; B – body in lateral view; C – body in dorsal view; D–E – head in anterior view; F – head in dorsal view; G – knee of the hind leg, showing the antegenicular and the genicular teeth. Photographs by Filippo Maria Buzzetti, Josip Skejo and Jadranka Škorput.
Fig. 5 in Contribution to the knowledge of Batrachideini (Orthoptera: Tetrigidae): description of two new flightless genera, Naskreckiana and Procellator, and revision of the status of Eotetrix
Fig. 5. The holotype of Procellator kai gen. & sp. nov. with key diagnostic characters marked. Photographed by Kai Squires.
Fig. 1 in Contribution to the knowledge of Batrachideini (Orthoptera: Tetrigidae): description of two new flightless genera, Naskreckiana and Procellator, and revision of the status of Eotetrix
Fig. 1. Illustrations of some of the characters used in the key. A – shape of the eyes; B – elevation of the median carina of the pronotum; C – undulations of the median carina of the pronotum. The drawings were made after photographs taken by Josef Tumbrinck, Daniela Silva, Marcelo Pereira, Josip Skejo, Jadranka Škorput, Filippo Maria Buzzetti, and Holger Braun, available on the Orthoptera Species File website (CIGLIANO et al. 2023).
Fig. 4 in Contribution to the knowledge of Batrachideini (Orthoptera: Tetrigidae): description of two new flightless genera, Naskreckiana and Procellator, and revision of the status of Eotetrix
Fig. 4. Living male (top) and female (bottom) individuals of Naskreckiana kosemeni gen. & sp. nov. in their natural habitat. Photographed in Braulio Carrillo National Park in Costa Rica by Roland Lupoli.
Fig. 4 in Two New Flightless Species Of Lacon Laporte, 1838 From Yunnan, China, With Discovery Of The Female Of L. Habashanensis Platia Et Al., 2023 (Coleoptera: Elateridae: Agrypninae)
Fig. 4. Morphology of Lacon yejiei sp. n., female: A = abdominal tergite VIII, dorsal view; B = abdominal sternite VIII, ventral view; C = ovipositor, ventral view; D = part of female genital tract (sac-like spermatophores removed). Scale bar: 1 mm
Fig. 1 in Two New Flightless Species Of Lacon Laporte, 1838 From Yunnan, China, With Discovery Of The Female Of L. Habashanensis Platia Et Al., 2023 (Coleoptera: Elateridae: Agrypninae)
Fig. 1. Habitus of Lacon species, dorsal view: A = L. taotie sp. n., holotype, male; B = L. taotie sp. n., paratype, male; C = L. yejiei sp. n., holotype, male; D = L. yejiei sp. n., paratype, female; E = L. lijiangensis Prosvirov, 2016, holotype, female; F = L. diqingensis Prosvirov, 2016,
Fig. 6 in Two New Flightless Species Of Lacon Laporte, 1838 From Yunnan, China, With Discovery Of The Female Of L. Habashanensis Platia Et Al., 2023 (Coleoptera: Elateridae: Agrypninae)
Fig. 6. Morphology of Lacon habashanensis Platia, Mertlik et Dušánek, 2023 from Lanping, Nujiang: A = female antenna; B = aedeagus, dorsal view; C = part of female genital tract; D =
Fig. 3 in Two New Flightless Species Of Lacon Laporte, 1838 From Yunnan, China, With Discovery Of The Female Of L. Habashanensis Platia Et Al., 2023 (Coleoptera: Elateridae: Agrypninae)
Fig. 3. Morphology of Lacon species, male: A–D. L. taotie sp. n., holotype; E–H. L. yejiei sp. n., holotype. A, E = Abdominal sternite IX, ventral view; B, F = abdominal tergites IX–X,
Fig. 2 in Two New Flightless Species Of Lacon Laporte, 1838 From Yunnan, China, With Discovery Of The Female Of L. Habashanensis Platia Et Al., 2023 (Coleoptera: Elateridae: Agrypninae)
Fig. 2. Morphology of Lacon species: A–D = pronotum, dorsal view; E–H = antennae. A, E = L. taotie sp. n., holotype, male; B, F = L. taotie sp. n., paratype, male; C, G = L. yejiei sp. n.,
Fig. 5 in Two New Flightless Species Of Lacon Laporte, 1838 From Yunnan, China, With Discovery Of The Female Of L. Habashanensis Platia Et Al., 2023 (Coleoptera: Elateridae: Agrypninae)
Fig. 5. Habitus of Lacon habashanensis Platia, Mertlik et Dušánek, 2023 from Lanping, Nujiang: A = male, dorsal view; B = female, dorsal view; C = female, lateral view. Scale bar: 2 mm
Fig. 3 in METAPOCYRTUS MADAYAW SP. N. (COLEOPTERA: CURCULIONIDAE, ENTIMINAE), A NEW FLIGHTLESS WEEVIL FROM EASTERN MINDANAO, PHILIPPINES
Fig. 3. Metapocyrtus (Artapocyrtus) spp. A, B – M. (A.) pardalis Heller, 1912 (female paratype): A – rostrum, dorsal view, B – same, lateral view; C, D – M. (A.) madayaw sp. n.: C – rostrum, dorsal view; D – idem, lateral view.
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