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 UC - 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 - Centre de Regulació Genòmica [Barcelona]
18 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
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 KIZ - 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 UFPA - Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil]
35 DTU - Danmarks Tekniske Universitet = Technical University of Denmark
36 Breeding Centre for Endangered Arabian Wildlife
37 Dubai Hospital
38 Canterbury Museum
39 Curtin University
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 Edin. - 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 [New York, USA] = Musée américain d'histoire naturelle [New York, USA]
62 UF - University of Florida [Gainesville]
63 UIUC - University of Illinois at Urbana-Champaign [Urbana]
64 UCPH - University of Copenhagen = Københavns Universitet
65 King Abdulaziz University
66 MUST - Macau University of Science and Technology
67 HKU - The University of Hong Kong
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 UC - 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 - Centre de Regulació Genòmica [Barcelona]
18 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
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 KIZ - 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 UFPA - Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil]
35 DTU - Danmarks Tekniske Universitet = Technical University of Denmark
36 Breeding Centre for Endangered Arabian Wildlife
37 Dubai Hospital
38 Canterbury Museum
39 Curtin University
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 Edin. - 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 [New York, USA] = Musée américain d'histoire naturelle [New York, USA]
62 UF - University of Florida [Gainesville]
63 UIUC - University of Illinois at Urbana-Champaign [Urbana]
64 UCPH - University of Copenhagen = Københavns Universitet
65 King Abdulaziz University
66 MUST - Macau University of Science and Technology
67 HKU - The University of Hong Kong
Siavash Mirarab
- Fonction : Auteur
- PersonId : 1167126
- ORCID : 0000-0001-5410-1518
Benoit Nabholz
- Fonction : Auteur
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- IdHAL : benoit-nabholz
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Alexander Suh
- Fonction : Auteur
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- ORCID : 0000-0002-8979-9992
Fang Zhang
- Fonction : Auteur
- PersonId : 772635
- IdRef : 18430038X
Bastien Boussau
- Fonction : Auteur
- PersonId : 178402
- IdHAL : bastienboussau
- ORCID : 0000-0003-0776-4460
- IdRef : 131807625
Ning Li
- Fonction : Auteur
- PersonId : 759918
- ORCID : 0000-0001-6009-6831
Qi Zhou
- Fonction : Auteur
- PersonId : 801317
- ORCID : 0000-0002-7419-2047
Beth Shapiro
- Fonction : Auteur
- PersonId : 786457
- ORCID : 0000-0002-2733-7776
- IdRef : 158997832
Yong Zhang
- Fonction : Auteur
- PersonId : 758537
- ORCID : 0000-0003-3988-5961
Ludovic Orlando
- Fonction : Auteur
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- IdHAL : ludovicorlando
- ORCID : 0000-0003-3936-1850
- IdRef : 080106951
Knud Andreas Jønsson
- Fonction : Auteur
Alexandros Stamatakis
- Fonction : Auteur
- PersonId : 775080
- ORCID : 0000-0003-0353-0691
Résumé
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.
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