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Exons, Introns [Upper Panel, Left to Right] and Uces [Lower Panel]) in Jarvis Et Al

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● 40 R = 0.39 , p < 2.2e−16 ● ● ● ● ● ● ● ●● ● ●● ● ●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ●●● ●● ● ●● ● ● ● ● ●● ●●● ●●●●● ●●● ●● ● ●● ● ● ●●●●●● ●●● ●●●●●●●●● ●●●● ● ●● ● ●●●●●●●●●●●●●●●● ●●●●●●●●●●●●● ● ● ●● ● ● ● ● 30 ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ● ● ● ● ● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ●●● ●●● ● ●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●● ●● ● ● ●● ●●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●● ● ● ● ● ●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●● ●●●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●●● ● ●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●●●●● ● ●● ●●● ● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ●●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ● ●●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●● ● ● ● ●● ● ● supporting nodes 20 ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ●●●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●● ●●●●● ●● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ●●●●●●●●●●●●●●●● ●● ●●●●●●●●●●●●●●● ● ● ●●●●●●●● ●● ●● 10 ●●●●● ●● ● ● 0 5000 10000 15000 alignment length Figure S1. the correlation between supporting node numbers and the alignment length for each dataset (Exons, Introns [upper panel, left to right] and UCEs [lower panel]) in Jarvis et al. (2014). Earliest Neoaves Hoatzin sister Owls sister 1. VI+VII 1. I+III+V 1. M+W 2. V 2. I 2. W 3. VII 3. S+CR 3. EHV 4. III+V+VI+VII 4. V 4. M 5. Doves 5. S Others Others 6. TB 7. II+III+S+CR Others 1500 Exon 1000 500 1000 1500 2000 0 0 1000 2000 Intron 200 400 0 0 200 400 600 0 300 600 0 500 UCE 1000 1500 2000 400 800 1200 500 2000 0 04008001200 0 12 34 5 1234 567 1234 Best supported Constraints Best supported Constraints Best supported Constraints Figure S2: The consistency of the ML gene topology with its best supported constraint. The most genes presented a different ML topology for the focal edge other than its best supporting constraints or any other testing constraints. The Greek numbers (bolded) correspond to the “magnificent seven” of Reddy et al. (2017), including I: “core” Landbirds; II: “core” Waterbirds; III: Sunbittern and Tropicbirds; IV: Cuckoos, Bustards, and Turacos; V: Nightjars, Swifts, Hummingbirds, and allies; VI: Doves, Mesites, and Sandgrouse; VII: Flamingos and Grebes. Other short codes including S: Shorebirds; CR: Cranes and Rails; TB: Turacos and Bustards; M: Mousebirds; W: Woodpeckers and allies; EHV: Eagles, Hawks, and New world Vultures. Exon Intron UCE Hummingbirds&Swifts VII Columba_livia Pterocles_gutturalis VII Cuculus_canorus Cuculus_canorus Balearica_regulorum A Balearica_regulorum Columba_livia VI+VII Chlamydotis_macqueenii pterocles_guturalis Pterocles_gutturalis Cuculus_canorus Chlamydotis_macqueenii Mesitornis_unicolor Mesitornis_unicolor unsupported Mesitornis_unicolor Tauraco_erythrolophus Earliest Neoaves Parrots V Charadrius_vociferus Picoides_pubescens Charadrius_vociferus VI+VII Phaethon_lepturus Columba_livia chlamydotis_undulata Mesites&Sandgrouses Eurypyga_helias Antrostomus_carolinensis Phaethon_lepturus unsupported Ophisthocomus_hoazin Ophisthocomus_hoazin Phaethon_lepturus Colius_striatus caprimugus_carolinensis Balearica_regulorum Colius_striatus Hummingbirds&Swifts Passeriformes Gavia_stellata Charadrius_vociferus Core landbird (I) Tauraco_erythrolophus Core waterbird (II) V Falco_peregrinus Buceros_rhinoceros Parrots Eurypyga_helias Mesites&Sandgrouse Gavia_stellata Falco_peregrinus Picoides_pubescens unsupported Merops_nubicus Passeriformes III Tyto_alba Tyto_alba Calypte_anna Apaloderma_vittatum Phalacrocorax_carbo Cariama_cristata Leptosomus_discolor Cathartes_aura Apaloderma_vittatum Cariama_cristata Chaetura_pelagica Dove&VII VII Phalacrocorax_carbo Buceros_rhinoceros Eagles Pelecanus_crispus PLeptosoodiceps_cmus_discolorristatus CathaNipponia_nipponrtes_aura FulmaEgretta_garrus_glacialiszetta VI+VII 50% supports rare resolutions found in < 10 genes rare resolutions rare resolutions found in < 10 genes found in < 10 genes Eurypyga_helias Hoatzin missing Charadrius_vociferus Hoatzin missing Eurypyga_helias Charadrius_vociferus Balearica_regulorum Charadrius_vociferus Balearica_regulorum Tauraco_erythrolophus Phaethon_lepturus chlamydotis_undulata Pterocles_gutturalis Chlamydotis_macqueenii Eurypyga_helias Columba_livia Hoatzin sister Columba_livia Antrostomus_carolinensis Columba_livia Tauraco_erythrolophus Chlamydotis_macqueenii unsupported unsupported Cuculus_canorus Phaethon_lepturus Cuculus_canorus Gavia_stellata Tauraco_erythrolophus Phaethon_lepturus unsupported Balearica_regulorum Mesitornis_unicolor Mesitornis_unicolor VII Falco_peregrinus Gavia_stellata Apaloderma_vittatum Pterocles_gutturalis caprimugus_carolinensis Gavia_stellata Hmmingbirds&Swifts Egretta_garzetta pterocles_guturalis Antrostomus_carolinensis Leptosomus_discolor All other Neoaves Phalacrocorax_carbo Mesitornis_unicolor III Cariama_cristata Cuculus_canorus VII Colius_striatus Phoenicopterus_ruber V VII Buceros_rhinoceros Core Waterbird (II)−Gavia_stellata Hummingbirds&Swifts Nipponia_nippon Tyto_alba Phalacrocorax_carbo 50% supports Colius_striatus Colius_striatus Eagles Cariama_cristata Podiceps_cristatus Fulmarus_glacialis Fulmarus_glacialis Apaloderma_vittatum Cathartes_aura Penguins Pelecanus_crispus Tyto_alba Merops_Picoides_pubescensnubicus Egretta_garzetta Penguins Falco_peregrinus Hummingbird&Swifts Eagles AlPl arrotsother Neoaves Leptosomus_discolor Calypte_annaPasseriformes Buceros_rhinoceros rare resolutions CathaNipponia_nipponrtes_aura ParrotsPicoides_pubescens rare resolutions PPodiceps_celecaPasseG (iii)nrus_ciforristatusmesrispus rare resolutions found in < 10 genes MesiteB (V)s&Sandgrouse found in < 10 genes found in < 10 genes Eagles Colius_striatus Owl missing Falco_peregrinus Owl missing Colius_striatus Leptosomus_discolor Eagles Eagles Cariama_cristata Cariama_cristata Apaloderma_vittatum Cariama_cristata Owls sister Cathartes_aura Leptosomus_discolor Falco_peregrinus Colius_striatus Falco_peregrinus Parrots Cathartes_aura Buceros_rhinoceros Apaloderma_vittatum Phaethon_lepturus Eagles&New World Vultures unsupported Antrostomus_carolinensis Leptosomus_discolor Cathartes_aura Balearica_regulorum unsupported Merops_nubicus Merops_nubicus Eurypyga_helias Parrots Charadrius_vociferus Woodpeckers&allies Picoides_pubescens Chlamydotis_macqueenii Pterocles_gutturalis Apaloderma_vittatum Parrots unsupported Mesitornis_unicolor Ophisthocomus_hoazin Passeriformes Buceros_rhinoceros Gavia_stellata Picoides_pubescens Tauraco_erythrolophus Buceros_rhinoceros Passeriformes Cuculus_canorus Charadrius_vociferus Balearica_regulorum Picoides_pubescens chlamydotis_undulata Passeriformes Columba_livia Eurypyga_helias Phalacrocorax_carbo pterocles_guturalis Podiceps_cristatus Egretta_garzetta Ophisthocomus_hoazin Fulmarus_glacialis Cuculus_canorus 50% supports Pelecanus_crispus Chaetura_pelagica Tauraco_erythrolophus Nipponia_nippon PhoenicopteAll other Neorus_avesruber Hummingbirds&Swifts Hummingbirds&Swifts Mesitornis_unicolor Eagles & New World Vultures Charadrius_vociferus caprimugus_carolinensis All other Neoaves Phaethon_lepturus Columba_livia Gavia_stellata WWoodpecoodpeckerkers&s&Bee−eaterallies s&Hornbills Eagles & New World Vultures rare resolutions rare resolutions rare resolutions found in < 10 genes found in < 10 genes found in < 10 genes Figure S3. A, Topology distribution of the ML gene trees for the three focal edges using Jarvis et al. (2014) data. unsupported: relationships shown less than 50% UFBS (ultrafast bootstrap support, we use lower support cutoff to show potential topology distributions). Situations are even worse for 95% UFBS cutoff (not shown). rare resolutions: relationships shown in less than 10 gene trees. Hoatzin missing or Owl missing: Hoatzin or Owl is missing in the gene trees. B Earliest Neoaves Hoatzin sister Owls sister New_world_vultures (condors) Sandgrouse Hoatzin missing Bustards Nightjars Cuckoo_roller Doves Bustards Falcons Polyphyletic PG Hawks+Eagles (without condors) Sunbitten Rails+Sungrebe+Trumpeter+Cranes Tropicbirds Turacos Bustards Sunbitten Coraciiformes Tropicbirds Mousebirds Nightjars Doves Cariama Trogons Trogons Frogmouth Penguins Sandgrouse Common_potoo Falcons Nightjars Frogmouths Cuckoos Oilbirds Owlet_nightjar+Treeswifts+hummingbirds+swifts yletic_Owl Turacos h Cuckoos Rails+Sungrebe+Trumpeter+Cranes Passeriformes Common_Loon Trogons Mesites Flamingo+Grebe Storks non_monop Boobies+Darter+Cormorant rare resolutions (<2 genes) Cuckoos Cuckoos+Bustards All trees Mesites Mousebirds Hoatzin Penguins Common_potoo Frigatebirds Tropicbirds Cuckoos+Passeriformes Owlet_nightjar Cariama Hornbills Common_Loon Storks Mousebirds Common_potoo Flamingo+Grebe Shorebirds rare resolutions (<2 genes) Frigatebirds Parrots Falcons Herons Pelicans Barred_owl rare resolutions (<2 genes) Northern_storm_petrel All_Neoaves Treeswifts+hummingbirds+swifts Cuckoo_roller Sandgrouse+Bustards rare resolutions (<2 genes) Doves All_Neoaves rare resolutions (<2 genes) Hoatzin missing rare resolutions
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    Pdf Available

    Animal Behaviour 179 (2021) 235e245 Contents lists available at ScienceDirect Animal Behaviour journal homepage: www.elsevier.com/locate/anbehav Differences in flight initiation distances between African and Australian birds * Michael A. Weston a, b, , Anna Radkovic a, b, Lennox Kirao c , Patrick-Jean Guay a, d, Wouter F. D. Van Dongen a, b, Philista Malaki e, Daniel T. Blumstein f , Matthew R. E. Symonds a, b a Deakin University, Geelong, Australia b School of Life and Environmental Sciences, Faculty of Science, Engineering and the Built Environment, Deakin University, Burwood, VIC, Australia c A Rocha Kenya, Nairobi, Kenya d Faculty of Arts and Education, Deakin University, Burwood, VIC, Australia e National Museums of Kenya, Nairobi, Kenya f Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, U.S.A. article info Associations between escape behaviours of birds approached by humans and life history traits differ Article history: between continents. This suggests environment and history have shaped the evolution of escape at the Received 11 October 2020 continental scale. We compared the escape behaviour of birds between eastern Australia (relatively low Initial acceptance 5 January 2021 density and shorter history of human presence) and eastern Africa (high density and substantially longer Final acceptance 31 May 2021 history of human presence), in relation to life and natural history traits known to influence escape behaviour. We examined associations between flight initiation distance (FID) and life and natural history MS. number: 20-00743R variables, using phylogenetically controlled analysis and model selection procedures, for 9372 FIDs from 516 bird species. Overall, African birds had shorter FIDs than Australian birds; however, this difference Keywords: was only observed among nonmigratory (resident) species.
  • Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds Erich D

    Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds Erich D

    AFLOCKOFGENOMES 90. J. F. Storz, J. C. Opazo, F. G. Hoffmann, Mol. Phylogenet. Evol. RESEARCH ARTICLE 66, 469–478 (2013). 91. F. G. Hoffmann, J. F. Storz, T. A. Gorr, J. C. Opazo, Mol. Biol. Evol. 27, 1126–1138 (2010). Whole-genome analyses resolve ACKNOWLEDGMENTS Genome assemblies and annotations of avian genomes in this study are available on the avian phylogenomics website early branches in the tree of life (http://phybirds.genomics.org.cn), GigaDB (http://dx.doi.org/ 10.5524/101000), National Center for Biotechnology Information (NCBI), and ENSEMBL (NCBI and Ensembl accession numbers of modern birds are provided in table S2). The majority of this study was supported by an internal funding from BGI. In addition, G.Z. was 1 2 3 4,5,6 7 supported by a Marie Curie International Incoming Fellowship Erich D. Jarvis, *† Siavash Mirarab, * Andre J. Aberer, Bo Li, Peter Houde, grant (300837); M.T.P.G. was supported by a Danish National Cai Li,4,6 Simon Y. W. Ho,8 Brant C. Faircloth,9,10 Benoit Nabholz,11 Research Foundation grant (DNRF94) and a Lundbeck Foundation Jason T. Howard,1 Alexander Suh,12 Claudia C. Weber,12 Rute R. da Fonseca,6 grant (R52-A5062); C.L. and Q.L. were partially supported by a 4 4 4 4 7,13 14 Danish Council for Independent Research Grant (10-081390); Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, and E.D.J. was supported by the Howard Hughes Medical Institute Ganesh Ganapathy,1 Bastien Boussau,15 Md.
  • Global Diversity of Birds 2015

    Global Diversity of Birds 2015

    Ornithology NREM/ZOOL 4464 Dr. Tim O’Connell Spring 2015 A Classification of Birds of the World – Laboratory Investigations As students of Ornithology, a primary objective for you is to develop a working knowledge of the diversity of birds of the world. As you internalize this information, you will develop a deep appreciation for the central role that evolution plays as the driver of biological diversity. We begin this week in Lab to really explore the diversity of birds through in-depth examination of orders and families. Avian classification is fluid: the ordering and alliance of families and orders differs according to different authorities and new information is continually becoming available that enhances our ability to discern relationships; this results in updated classifications. You are embarking on this voyage during a time of significant taxonomic revision, and much of what you will learn in Lab supersedes classification systems in your field guides. Different authorities (usually committees) often disagree in their assessment of a taxon. Where one authority might recognize a full species, another might recognize it as a subspecies of some other species. Higher-level assignments are tricky too, e.g., some place the South American rheas in their own order (Rheiformes) whereas others lump it in with other ostrich-like birds in Struthioniformes. The American Ornithologists’ Union manages two committees (North American and South American Classification Committees) that review information and render decisions on which taxonomic proposals will be recognized. Each July, the AOU publishes updates to its official checklist. That checklist is commonly accessed via a massive book containing information on distribution, evolutionary affinities, etc.
  • Vantuinen2009chap60.Pdf

    Vantuinen2009chap60.Pdf

    Advanced birds (Neoaves) Marcel van Tuinen this result is now considered an artifact of limited taxon Department of Biology and Marine Biology, 601 South College sampling (7, 15). Phylogenetic resolution among the main Road, University of North Carolina at Wilmington, Wilmington, NC divergences within Neoaves continues to remain a major 28403-5915, USA ([email protected]) hurdle (10), with most neoavian orders appearing to have diverged in close succession. 7 is “neoavian comb” (10) Abstract on the one hand has been interpreted as evidence for a real (hard) polytomy among most, if not all, neoavian Neoaves, the largest superorder of living birds (Neornithes), orders (12), indicating a rapid evolutionary radiation. consists of 16–24 orders and ~9000 species. Although recent Others have maintained that additional taxonomic and progress has been made, available molecular data continue nucleotide sampling will provide added resolution (10). to show remarkable lack of phylogenetic resolution and the At present, three molecular studies (7, 13, 14) exist basal splits within Neoaves are still uncertain. The neoavian that have included a combination of both complete timetree shows an initial divergence at ~95 million years ago neoavian ordinal sampling and nuclear gene sequen- (Ma) followed by Cretaceous (87–75 Ma) diversifi cation of cing. Two of these studies were based on nuclear gene southern hemispheric orders and younger times for north- ern and aquatic orders (Paleogene, 65–30 Ma). The time- tree thus implicates possible roles for continental breakup (Cretaceous) and climate (Paleogene) in the diversifi cation of advanced birds. Neoavian birds are included in the Subclass Neornithes, and most broadly can be deA ned as those orders with advanced Pight capabilities.
  • The Origin and Diversification of Birds

    The Origin and Diversification of Birds

    Current Biology Review The Origin and Diversification of Birds Stephen L. Brusatte1,*, Jingmai K. O’Connor2,*, and Erich D. Jarvis3,4,* 1School of GeoSciences, University of Edinburgh, Grant Institute, King’s Buildings, James Hutton Road, Edinburgh EH9 3FE, UK 2Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China 3Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA 4Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA *Correspondence: [email protected] (S.L.B.), [email protected] (J.K.O.), [email protected] (E.D.J.) http://dx.doi.org/10.1016/j.cub.2015.08.003 Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two de- cades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and became so successful. Birds evolved from theropod dino- saurs during the Jurassic (around 165–150 million years ago) and their classic small, lightweight, feathered, and winged body plan was pieced together gradually over tens of millions of years of evolution rather than in one burst of innovation. Early birds diversified throughout the Jurassic and Cretaceous, becoming capable fliers with supercharged growth rates, but were decimated at the end-Cretaceous extinction alongside their close dinosaurian relatives. After the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today. Introduction dinosaurs Dromaeosaurus albertensis or Troodon formosus.This Birds are one of the most conspicuous groups of animals in the clade includes all living birds and extinct taxa, such as Archaeop- modern world.