Whole-genome analyses resolve early branches in the tree of life of modern birds.

Erich Jarvis; Siavash Mirarab; Andre Aberer; Bo Li; Peter Houde; Cai Li; Simon Y.W. Ho; Brant Faircloth; Benoit Nabholz; Jason Howard; Alexander Suh; Claudia Weber; Rute da Fonseca; Jianwen Li; Fang Zhang; Hui Li; Long Zhou; Nitish Narula; Liang Liu; Ganesh Ganapathy; Bastien Boussau; Md Shamsuzzoha Bayzid; Volodymyr Zavidovych; Sankar Subramanian; Toni Gabaldón; Salvador Capella-Gutiérrez; Jaime Huerta-Cepas; Bhanu Rekepalli; Kasper Munch; Mikkel Schierup; Bent Lindow; Wesley Warren; David Ray; Richard Green; Michael Bruford; Xiangjiang Zhan; Andrew Dixon; Shengbin Li; Ning Li; Yinhua Huang; Elizabeth Derryberry; Mads Frost Bertelsen; Frederick Sheldon; Robb Brumfield; Claudio Mello; Peter Lovell; Morgan Wirthlin; Maria Paula Cruz Schneider; Francisco Prosdocimi; José Alfredo Samaniego; Amhed Missael Vargas Velazquez; Alonzo Alfaro-Núñez; Paula Campos; Bent Petersen; Thomas Sicheritz-Ponten; An Pas; Tom Bailey; Paul Scofield; Michael Bunce; David Lambert; Qi Zhou; Polina Perelman; Amy Driskell; Beth Shapiro; Zijun Xiong; Yongli Zeng; Shiping Liu; Zhenyu Li; Binghang Liu; Kui Wu; Jin Xiao; Xiong Yinqi; Qiuemei Zheng; Yong Zhang; Huanming Yang; Jian Wang; Linnea Smeds; Frank Rheindt; Michael Braun; Jon Fjeldsa; Ludovic Orlando; F Keith Barker; Knud Andreas Jønsson; Warren Johnson; Klaus-Peter Koepfli; Stephen O'Brien; David Haussler; Oliver Ryder; Carsten Rahbek; Eske Willerslev; Gary Graves; Travis Glenn; John Mccormack; Dave Burt; Hans Ellegren; Per Alström; Scott Edwards; Alexandros Stamatakis; David Mindell; Joel Cracraft; Edward Braun; Tandy Warnow; Wang Jun; M Thomas P Gilbert; Guojie Zhang

doi:10.1126/science.1253451

Article dans une revue

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Erich Jarvis ^{1, 2} Siavash Mirarab ³ Andre Aberer ⁴ Bo Li ^{5, 6, 7} Peter Houde ⁸ Cai Li ^{5, 7} Simon Y.W. Ho ⁹ Brant Faircloth ¹⁰ Benoit Nabholz ¹¹ Jason Howard ^{1, 2} Alexander Suh ¹² Claudia Weber ¹² Rute da Fonseca ⁷ Jianwen Li ⁵ Fang Zhang ⁵ Hui Li ⁵ Long Zhou ⁵ Nitish Narula ^{8, 13} Liang Liu ¹⁴ Ganesh Ganapathy ^{1, 2} Bastien Boussau ¹⁵ Md Shamsuzzoha Bayzid ³ Volodymyr Zavidovych ^{1, 2} Sankar Subramanian ¹⁶ Toni Gabaldón ^{17, 18} Salvador Capella-Gutiérrez ¹⁷ Jaime Huerta-Cepas ¹⁷ Bhanu Rekepalli ^{19, 20} Kasper Munch ²¹ Mikkel Schierup ²¹ Bent Lindow ⁷ Wesley Warren ²² David Ray ^{23, 24} Richard Green ²⁵ Michael Bruford ²⁶ Xiangjiang Zhan ^{26, 27} Andrew Dixon ²⁸ Shengbin Li ⁶ Ning Li ²⁹ Yinhua Huang ²⁹ Elizabeth Derryberry ^{30, 31} Mads Frost Bertelsen ³² Frederick Sheldon ³¹ Robb Brumfield ³¹ Claudio Mello ^{33, 34} Peter Lovell ³³ Morgan Wirthlin ³³ Maria Paula Cruz Schneider ³⁴ Francisco Prosdocimi ³⁴ José Alfredo Samaniego ⁷ Amhed Missael Vargas Velazquez ⁷ Alonzo Alfaro-Núñez ⁷ Paula Campos ⁷ Bent Petersen ³⁵ Thomas Sicheritz-Ponten ³⁵ An Pas ³⁶ Tom Bailey ³⁷ Paul Scofield ³⁸ Michael Bunce ³⁹ David Lambert ¹⁶ Qi Zhou ⁴⁰ Polina Perelman ^{41, 42} Amy Driskell ⁴³ Beth Shapiro ²⁵ Zijun Xiong ⁵ Yongli Zeng ⁵ Shiping Liu ⁵ Zhenyu Li ⁵ Binghang Liu ⁵ Kui Wu ⁵ Jin Xiao ⁵ Xiong Yinqi ⁵ Qiuemei Zheng ⁵ Yong Zhang ⁵ Huanming Yang ⁵ Jian Wang ⁵ Linnea Smeds ¹² Frank Rheindt ⁴⁴ Michael Braun ⁴³ Jon Fjeldsa ⁷ Ludovic Orlando ⁷ F Keith Barker ⁴⁵ Knud Andreas Jønsson ^{7, 46} Warren Johnson ⁴⁷ Klaus-Peter Koepfli ⁴⁷ Stephen O'Brien ^{48, 49} David Haussler ⁵⁰ Oliver Ryder ⁵¹ Carsten Rahbek ^{7, 46} Eske Willerslev ⁷ Gary Graves ^{7, 43} Travis Glenn ¹⁴ John Mccormack ⁵² Dave Burt ^{53, 54, 55} Hans Ellegren ¹² Per Alström ^{56, 57} Scott Edwards ⁵⁸ Alexandros Stamatakis ^{4, 59} David Mindell ⁶⁰ Joel Cracraft ⁶¹ Edward Braun ⁶² Tandy Warnow ^{3, 63} Wang Jun ^{5, 64, 65, 66, 67} M Thomas P Gilbert ^{7, 39} Guojie Zhang ^{5, 64}

1 HHMI - Howard Hughes Medical Institute

2 Duke University Medical Center

3 University of Texas at Austin [Austin]

4 HITS - Heidelberg Institute for Theoretical Studies

5 BGI - Beijing Genomics Institute [Shenzhen]

6 Xjtu - Xi'an Jiaotong University

7 Natural History Museum of Denmark

8 New Mexico State University

9 The University of Sydney

10 University of California

11 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier

12 EBC - Evolutionary Biology Centre

13 Okinawa Institute of Science and Technology Graduate University

14 University of Georgia [USA]

15 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558

16 Griffith University [Brisbane]

17 CRG - Centre for Genomic Regulation [Barcelona]

18 ICREA - Institució Catalana de Recerca i Estudis Avançats

19 JICS - Joint Institute for Computational Sciences [Knoxville]

20 ORNL - Oak Ridge National Laboratory [Oak Ridge]

21 Aarhus University [Aarhus]

22 MGI - The McDonnell Genome Institute

23 BCH-EPP - Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA]

24 Department of Biological Sciences [Lubbock]

25 Department of Ecology and Evolutionary Biology [Santa Cruz]

26 School of Biosciences [Cardiff]

27 Kunming Institute of Zoology

28 International Wildlife Consultants Ltd

29 CAU - China Agricultural University

30 Tulane University

31 LSU - Louisiana State University

32 Copenhagen Zoo

33 OHSU - Oregon Health and Science University [Portland]

34 Federal University of Para - Universidade Federal do Para [Belem - Brésil]

35 DTU - Technical University of Denmark [Lyngby]

36 Breeding Centre for Endangered Arabian Wildlife

37 Dubai Hospital

38 Canterbury Museum

39 Curtin University [Perth]

40 IB - Department of Integrative Biology [Berkeley]

41 National Cancer Institute Frederick

42 NSU - Novosibirsk State University

43 Smithsonian Institution

44 Department of Biological Sciences [Singapore]

45 Bell Museum of Natural History

46 Department of Life Sciences

47 Smithsonian Conservation Biology Institute

48 Theodosius Dobzhansky Center for Genome Bioinformatics

49 NSU - Nova Southeastern University

50 Center for Biomolecular Science and Engineering

51 San Diego Zoo Global Institute for Conservation Research

52 Occidental College

53 The Roslin Institute

54 Royal (Dick) School of Veterinary Studies

55 University of Edinburgh

56 Key Laboratory of Zoological Systematics and Evolution

57 Swedish Species Information Centre

58 OEB - Department of Organismic and Evolutionary Biology [Cambridge]

59 Institute of Theoretical Informatics

60 Department of Biochemistry and Biophysics [San Francisco]

61 AMNH - American Museum of Natural History

62 UF - University of Florida [Gainesville]

63 University of Illinois at Urbana-Champaign [Urbana]

64 KU - University of Copenhagen = Københavns Universitet

65 King Abdulaziz University

66 MUST - Macau University of Science and Technology

67 HKU - The University of Hong Kong

Abstract : To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Type de document :

Article dans une revue

Domaine :

Sciences du Vivant [q-bio] / Génétique / Génétique animale

Sciences du Vivant [q-bio] / Biodiversité / Evolution [q-bio.PE]

Liste complète des métadonnées

https://hal.umontpellier.fr/hal-03021815
Contributeur : Anthony Herrada <>
Soumis le : mardi 24 novembre 2020 - 14:58:01
Dernière modification le : mercredi 21 juillet 2021 - 10:28:04

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