Global Diversity of Birds 2015
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Dense Sampling of Bird Diversity Increases Power of Comparative Genomics
Article Dense sampling of bird diversity increases power of comparative genomics https://doi.org/10.1038/s41586-020-2873-9 A list of authors and affiliations appears at the end of the paper. Received: 9 August 2019 Whole-genome sequencing projects are increasingly populating the tree of life and Accepted: 27 July 2020 characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed Published online: 11 November 2020 to confound phylogenetic inference5, and captures only a fraction of the genomic Open access diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird Check for updates families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confdently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specifc variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will ofer new perspectives on evolutionary processes in cross-species comparative analyses and assist in eforts to conserve species. -
Prezentace Aplikace Powerpoint
PTÁCI 1.část Systém ptáků Systém ptáků -zatím stále velmi nestabilní Passerimorphae - Psittaciformes, Passeriformes Falconiformes - Coliiformes, Trogoniformes, Coraciimorphae Bucerotiformes, Strigiformes Piciformes, Coraciiformes Accipitrimorphae - Accipitriformes - Pelecaniformes Suliformes Pelecanimorphae Ciconiiformes Procellariimorphae - Sphenisciformes, Procellariiformes Gaviimorphae - Gaviiformes Phaethontimorphae Cursorimorphae - Gruiformes, Charadriiformes Passerea Opisthocomiformes - Caprimulgiformes, Neoaves Caprimulgimorphae Apodiformes - Cuculiformes, Musophagifomes, Otidimorphae Otidiformes Columbimorphae - Columbiformes, Pterocliformes, Columbea Mesitornithiformes Phoenicopterimorphae - Podicipediformes, Phoenicopteriformes PTÁCI • opeření, přední končetiny- křídla, kostrční žláza • pneumatizace kostí, heterocélní obratle • bipední pohyb (palec dozadu, ostatní prsty dopředu) • srůsty kostí, srůsty na lebce, zobák (ramfotéka) • srůst klíčních kostí (furcula) • zvětšení koncového mozku, zdokonalení oka a ucha • malé plíce se vzdušnými vaky, endotermie • vejce s vápenitou skořápkou, péče o mláďata Avifauna ČR • dnes známo asi 10 000 druhů (druhá nejpočetnější „třída“) • u nás 403 druhů ptáků (k 12.12.2018) • u nás asi 200 hnízdících druhů • Česká společnost ornitologická (www.birdlife.cz) Létaví - Neognathae Řád: HRABAVÍ (Galliformes) - zavalití ptáci, pozemní (ale spí na větvích) - noha anizodaktylní (kráčivá), silná – hrabavá, silné tupé drápy, často ostruha - krátký zobák, na hlavě časté kožené výrůstky - pohlaví často odlišně -
Dieter Thomas Tietze Editor How They Arise, Modify and Vanish
Fascinating Life Sciences Dieter Thomas Tietze Editor Bird Species How They Arise, Modify and Vanish Fascinating Life Sciences This interdisciplinary series brings together the most essential and captivating topics in the life sciences. They range from the plant sciences to zoology, from the microbiome to macrobiome, and from basic biology to biotechnology. The series not only highlights fascinating research; it also discusses major challenges associated with the life sciences and related disciplines and outlines future research directions. Individual volumes provide in-depth information, are richly illustrated with photographs, illustrations, and maps, and feature suggestions for further reading or glossaries where appropriate. Interested researchers in all areas of the life sciences, as well as biology enthusiasts, will find the series’ interdisciplinary focus and highly readable volumes especially appealing. More information about this series at http://www.springer.com/series/15408 Dieter Thomas Tietze Editor Bird Species How They Arise, Modify and Vanish Editor Dieter Thomas Tietze Natural History Museum Basel Basel, Switzerland ISSN 2509-6745 ISSN 2509-6753 (electronic) Fascinating Life Sciences ISBN 978-3-319-91688-0 ISBN 978-3-319-91689-7 (eBook) https://doi.org/10.1007/978-3-319-91689-7 Library of Congress Control Number: 2018948152 © The Editor(s) (if applicable) and The Author(s) 2018. This book is an open access publication. Open Access This book is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made. -
Modern Birds Classification System Tinamiformes
6.1.2011 Classification system • Subclass: Neornites (modern birds) – Superorder: Paleognathae, Neognathae Modern Birds • Paleognathae – two orders, 49 species • Struthioniformes—ostriches, emus, kiwis, and allies • Tinamiformes—tinamous Ing. Jakub Hlava Department of Zoology and Fisheries CULS Tinamiformes • flightless • Dwarf Tinamou • consists of about 47 species in 9 genera • Dwarf Tinamou ‐ 43 g (1.5 oz) and 20 cm (7.9 in) • Gray Tinamou ‐ 2.3 kg (5.1 lb) 53 cm (21 in) • small fruits and seeds, leaves, larvae, worms, and mollusks • Gray Tinamou 1 6.1.2011 Struthioniformes Struthioniformes • large, flightless birds • Ostrich • most of them now extinct • Cassowary • chicks • Emu • adults more omnivorous or insectivorous • • adults are primarily vegetarian (digestive tracts) Kiwi • Emus have a more omnivorous diet, including insects and other small animals • kiwis eat earthworms, insects, and other similar creatures Neognathae Galloanserae • comprises 27 orders • Anseriformes ‐ waterfowl (150) • 10,000 species • Galliformes ‐ wildfowl/landfowl (250+) • Superorder Galloanserae (fowl) • Superorder Neoaves (higher neognaths) 2 6.1.2011 Anseriformes (screamers) Anatidae (dablling ducks) • includes ducks, geese and swans • South America • cosmopolitan distribution • Small group • domestication • Large, bulky • hunted animals‐ food and recreation • Small head, large feet • biggest genus (40‐50sp.) ‐ Anas Anas shoveler • mallards (wild ducks) • pintails • shlhovelers • wigeons • teals northern pintail wigeon male (Eurasian) 3 6.1.2011 Tadorninae‐ -
AOU Classification Committee – North and Middle America
AOU Classification Committee – North and Middle America Proposal Set 2016-C No. Page Title 01 02 Change the English name of Alauda arvensis to Eurasian Skylark 02 06 Recognize Lilian’s Meadowlark Sturnella lilianae as a separate species from S. magna 03 20 Change the English name of Euplectes franciscanus to Northern Red Bishop 04 25 Transfer Sandhill Crane Grus canadensis to Antigone 05 29 Add Rufous-necked Wood-Rail Aramides axillaris to the U.S. list 06 31 Revise our higher-level linear sequence as follows: (a) Move Strigiformes to precede Trogoniformes; (b) Move Accipitriformes to precede Strigiformes; (c) Move Gaviiformes to precede Procellariiformes; (d) Move Eurypygiformes and Phaethontiformes to precede Gaviiformes; (e) Reverse the linear sequence of Podicipediformes and Phoenicopteriformes; (f) Move Pterocliformes and Columbiformes to follow Podicipediformes; (g) Move Cuculiformes, Caprimulgiformes, and Apodiformes to follow Columbiformes; and (h) Move Charadriiformes and Gruiformes to precede Eurypygiformes 07 45 Transfer Neocrex to Mustelirallus 08 48 (a) Split Ardenna from Puffinus, and (b) Revise the linear sequence of species of Ardenna 09 51 Separate Cathartiformes from Accipitriformes 10 58 Recognize Colibri cyanotus as a separate species from C. thalassinus 11 61 Change the English name “Brush-Finch” to “Brushfinch” 12 62 Change the English name of Ramphastos ambiguus 13 63 Split Plain Wren Cantorchilus modestus into three species 14 71 Recognize the genus Cercomacroides (Thamnophilidae) 15 74 Split Oceanodroma cheimomnestes and O. socorroensis from Leach’s Storm- Petrel O. leucorhoa 2016-C-1 N&MA Classification Committee p. 453 Change the English name of Alauda arvensis to Eurasian Skylark There are a dizzying number of larks (Alaudidae) worldwide and a first-time visitor to Africa or Mongolia might confront 10 or more species across several genera. -
Wqfm: Statistically Consistent Genome-Scale Species Tree Estimation from Weighted Quartets
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.30.403352; this version posted December 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. wQFM: Statistically Consistent Genome-scale Species Tree Estimation from Weighted Quartets Mahim Mahbub1;y, Zahin Wahab1;y, Rezwana Reaz1;y, M. Saifur Rahman1, and Md. Shamsuzzoha Bayzid1,* 1Department of Computer Science and Engineering Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh yThese authors contributed equally to this work *Corresponding author: shams [email protected] Abstract Motivation: Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incom- plete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collec- tion of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree allows for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging. Results: We propose wQFM, a highly accurate method for species tree es- timation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. -
Highly Conservative Pattern of Sex Chromosome Synapsis and Recombination in Neognathae Birds
G C A T T A C G G C A T genes Article Highly Conservative Pattern of Sex Chromosome Synapsis and Recombination in Neognathae Birds Anna Torgasheva 1,2 , Lyubov Malinovskaya 1,2, Kira S. Zadesenets 1, Anastasia Slobodchikova 1,2, Elena Shnaider 3, Nikolai Rubtsov 1,2 and Pavel Borodin 1,2,* 1 Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; [email protected] (A.T.); [email protected] (L.M.); [email protected] (K.S.Z.); [email protected] (A.S.); [email protected] (N.R.) 2 Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia 3 Bird of Prey Rehabilitation Centre, 630090 Novosibirsk, Russia; [email protected] * Correspondence: [email protected] Abstract: We analyzed the synapsis and recombination between Z and W chromosomes in the oocytes of nine neognath species: domestic chicken Gallus gallus domesticus, grey goose Anser anser, black tern Chlidonias niger, common tern Sterna hirundo, pale martin Riparia diluta, barn swallow Hirundo rustica, European pied flycatcher Ficedula hypoleuca, great tit Parus major and white wagtail Motacilla alba using immunolocalization of SYCP3, the main protein of the lateral elements of the synaptonemal complex, and MLH1, the mismatch repair protein marking mature recombination nodules. In all species examined, homologous synapsis occurs in a short region of variable size at the ends of Z and W chromosomes, where a single recombination nodule is located. The remaining Citation: Torgasheva, A.; parts of the sex chromosomes undergo synaptic adjustment and synapse non-homologously. In 25% Malinovskaya, L.; Zadesenets, K.S.; of ZW bivalents of white wagtail, synapsis and recombination also occur at the secondary pairing Slobodchikova, A.; Shnaider, E.; Rubtsov, N.; Borodin, P. -
Volume 2 Book with NUMBER 1-402
FLORA OF KARNATAKA A Checklist Volume - 2 : Gymnosperms & Angiosperms CITATION Karnataka Biodiversity Board, 2019. FLORA OF KARNATAKA, A Checklist, Volume – 2: Gymnosperms and Angiosperms. 1 - 1002 (Published by Karnataka Biodiversity Board) Published: December, 2019. ISBN - 978-81-939228-1-1 © Karnataka Biodiversity Board, 2019 ALL RIGHTS RESERVED • No part of this book, or plates therein, may be reproduced, stored in a retrieval system or transmitted, in any form or by any means, electronic, mechanical, photocopying recording or otherwise without the prior permission of the publisher. • This book is sold subject to the condition that it shall not, by way of trade, be lent, re-sold, hired out or otherwise disposed of without the publisher’s consent, in any form of binding or cover other than that in which it is published. • The correct price of this publication is the price printed on this page. Any revised price indicated by a rubber stamp or by a sticker or by any other means is incorrect and should be unacceptable. DISCLAIMER • THE CONTENTS INCLUDING TEXT, PLATES AND OTHER INFORMATION GIVEN IN THE BOOK ARE SOLELY THE AUTHOR’S RESPONSIBILITY AND BOARD DOES NOT HOLD ANY LIABILITY. PRICE: ` 2000/- (Two thousand rupees only). Printed by : Peacock Advertising India Pvt Ltd. # 158 & 159, 3rd Main, 7th Cross, Chamarajpet, Bengaluru – 560 018 | Ph: 080 - 2662 0566 Web: www.peacockgroup.in FOREWORD About 60% of the Western Ghats is present in Karnataka State, with this large part of the peninsular green cover coupled with inland forest plateau enriched by the seven river systems, the State of Karnataka showcases a wider floral wealth harboring highest number of apex predators all of which is conserved by a framework of various statutes. -
Verbalizing Phylogenomic Conflict: Representation of Node Congruence Across Competing Reconstructions of the Neoavian Explosion
bioRxiv preprint doi: https://doi.org/10.1101/233973; this version posted December 14, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Tempe, December 12, 2017 RESEARCH ARTICLE (1st submission) Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion Nico M. Franz1*, Lukas J. Musher2, Joseph W. Brown3, Shizhuo Yu4, Bertram Ludäscher5 1 School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America 2 Richard Gilder Graduate School and Department of Ornithology, American Museum of Natural History, New York, New York, United States of America 3 Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom 4 Department of Computer Science, University of California at Davis, Davis, California, United States of America 5 School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America * Corresponding author E-mail: [email protected] Short title: Verbalizing phylogenomic conflict Abstract Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the novel products of phylogenomic inference – such as newly supported clade concepts – have not kept pace. However, the ability to verbalize both node concept congruence and conflict across multiple, (in effect) simultaneously endorsed phylogenomic hypotheses, is a critical prerequisite for building synthetic data environments for biological systematics, thereby also benefitting other domains impacted by these (conflicting) inferences. -
ECDC/EFSA Joint Report: Avian Influenza Overview October
SCIENTIFIC REPORT APPROVED: 29 September 2017 doi: 10.2903/j.efsa.2017.5018 Avian influenza overview October 2016–August 2017 European Food Safety Authority, European Centre for Disease Prevention and Control, European Union Reference Laboratory for Avian influenza, Ian Brown, Paolo Mulatti, Krzysztof Smietanka, Christoph Staubach, Preben Willeberg, Cornelia Adlhoch, Denise Candiani, Chiara Fabris, Gabriele Zancanaro, Joana Morgado and Frank Verdonck Abstract The A(H5N8) highly pathogenic avian influenza (HPAI) epidemic occurred in 29 European countries in 2016/2017 and has been the largest ever recorded in the EU in terms of number of poultry outbreaks, geographical extent and number of dead wild birds. Multiple primary incursions temporally related with all major poultry sectors affected but secondary spread was most commonly associated with domestic waterfowl species. A massive effort of all the affected EU Member States (MSs) allowed a descriptive epidemiological overview of the cases in poultry, captive birds and wild birds, providing also information on measures applied at the individual MS level. Data on poultry population structure are required to facilitate data and risk factor analysis, hence to strengthen science-based advice to risk managers. It is suggested to promote common understanding and application of definitions related to control activities and their reporting across MSs. Despite a large number of human exposures to infected poultry occurred during the ongoing outbreaks, no transmission to humans has been identified. Monitoring the avian influenza (AI) situation in other continents indicated a potential risk of long-distance spread of HPAI virus (HPAIV) A(H5N6) from Asia to wintering grounds towards Western Europe, similarly to what happened with HPAIV A(H5N8) and HPAIV A(H5N1) in previous years. -
Dinosaurs Free Download
DINOSAURS FREE DOWNLOAD Jenna Winterberg,Diana Fisher | 24 pages | 27 Jan 2006 | Walter Foster Publishing | 9781560109518 | English | Laguna Hills, CA, United States A Complete A to Z List of Dinosaurs Othniel Charles Marsh. Silvisaurus - This primitive Dinosaurs was discovered in Kansas. Some of the other interesting dinosaurs in this list include the tiny Pravicursor, the four-winged Microraptor, and the Parasaurolophus which is thought to be the loudest of all dinosaurs. Balaur - This "stocky dragon" was recently discovered in Romania. Despite their unrefined methods, the contributions of Cope and Marsh to paleontology were vast: Marsh unearthed 86 Dinosaurs species of dinosaur and Cope discovered 56, a total of new species. Cambridge : University of Cambridge Press. The entry of the word "dinosaur" into the common vernacular reflects the animals' cultural importance: in English, "dinosaur" is Dinosaurs used to describe anything that is impractically large, obsolete, or bound for extinction. InDinosaurs estimated number of dinosaur species that existed in the Mesozoic was estimated to be 1,—2, Phenomena - A Science Salon. Main article: Chicxulub crater. Dinosaurs Mantell recognized similarities between his fossils and the bones of modern iguanas. But if you see something that doesn't look right, click here to contact us! Tianyuraptor - A small, long-legged raptor from eastern Asia. Company Credits. Tornieria - This Dinosaurs has a complicated taxonomic history. Columbea Columbimorphae Columbiformes doves and pigeons Mesitornithiformes mesites Pterocliformes sandgrouse. This was a revolutionary discovery as, until that point, most scientists had believed dinosaurs walked on four feet, like other lizards. Perseus 4. Autumn Dinosaurs of the longer sections of our dinosaur collection, you'll discover a number of interesting finds here. -
Sixteen Vetted Fossil Calibrations for Divergence Dating of Charadriiformes (Aves, Neognathae)
Palaeontologia Electronica palaeo-electronica.org Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae) N. Adam Smith ABSTRACT The Charadriiformes (shorebirds and allies) are an ecologically and morphologi- cally diverse clade with a global geographic distribution. The perceived antiquity of this lineage and the cryptic plumage and morphology of some charadriiforms have made them a frequent focus of study by ornithologists. Likewise, with the relatively recent advent of molecular sequence based divergence estimation methods, no less than seven studies have estimated the timing of cladogenetic events in Charadriiformes. Unfortunately, all of those studies have suffered from poor choice and characterization (i.e., age and taxonomic assignment) of fossil calibrations used for divergence time analysis. Given that studies of both real and simulated data have demonstrated the potential for calibration choice to bias node age estimates, the results of previously published analyses of divergence times for Charadriiformes must, accordingly, be viewed with caution. To alleviate introduction of fossil calibration bias with respect to future analyses of divergence times including Charadriiformes, 16 rigorously evaluated charadriiform fossil calibrations are reported herein. N. Adam Smith. The National Evolutionary Synthesis Center, 2024 W. Main St., Suite A200, Durham, NC, 27705, U.S.A., [email protected] KEYWORDS: Charadrii; minimum age constraints; Pan-Alcidae; Lari; Scolopaci; seabirds and shorebirds INTRODUCTION forms were previously considered a basal neorni- thine lineage and were influential in the Charadriiformes (shorebirds and allies) are a development of the largely refuted ‘transitional globally distributed clade including more than 360 shorebird’ hypothesis (Olson, 1985; Feduccia, morphologically and ecologically diverse species 1996), dating cladogenetic events in Charadrii- (del Hoyo et al., 1996).