Article open access publication

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

Science, American Association for the Advancement of Science (AAAS), ISSN 0036-8075

Volume 346, 6215, 2014

DOI:10.1126/science.1253451, Dimensions: pub.1013266868, PMC: PMC4405904, PMID: 25504713,

Authors

Li, Bo (4) (5) (6)
Li, Cai (5) (6)
Li, Hui (6)
Narula, Nitish (7) (13)
Liu, Liang (14)
Gabaldón, Toni (17) (18) (19)
Ray, David (23) (24)
Zhan, Xiang-Jiang (26) (27)
Li, Ning (30)
Mello, Claudio V. (33) (34)
Pas, An (37)
Zhou, Qi (41)
Perelman, Polina (42) (43)
Wu, Kui (6)
Xiao, Jin (6)
Jønsson, Knud Andreas (5) (47) (48)
O'Brien, Stephen J (51) (52)
Rahbek, Carsten (5) (48)
Graves, Gary R (5) (44)
Burt, Dave (55)
Alström, Per (27) (56)
Warnow, Tandy (2) (62)
Jun, Wang (5) (6) (63) (64) (65)
Zhang, Guo-Jie (5) (6)

Affiliations

Organisations

  1. (1) Duke University Hospital, grid.189509.c
  2. (2) The University of Texas at Austin, grid.89336.37
  3. (3) Heidelberg Institute for Theoretical Studies, grid.424699.4
  4. (4) College of Medicine and Forensics, Xi’an Jiaotong University Xi’an 710061, China
  5. (5) University of Copenhagen, grid.5254.6, KU
  6. (6) Beijing Genomics Institute, grid.21155.32
  7. (7) New Mexico State University, grid.24805.3b
  8. (8) University of Sydney, grid.1013.3
  9. (9) University of California, Los Angeles, grid.19006.3e
  10. (10) Louisiana State University, grid.64337.35
  11. (11) Institut des Sciences de l'Evolution de Montpellier, grid.462058.d
  12. (12) Uppsala University, grid.8993.b
  13. (13) Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan
  14. (14) University of Georgia, grid.213876.9
  15. (15) Biometry and Evolutionary Biology Laboratory, grid.462854.9
  16. (16) Griffith University, grid.1022.1
  17. (17) Catalan Institution for Research and Advanced Studies, grid.425902.8
  18. (18) Centre for Genomic Regulation, grid.11478.3b
  19. (19) Pompeu Fabra University, grid.5612.0
  20. (20) Oak Ridge National Laboratory, grid.135519.a
  21. (21) Aarhus University, grid.7048.b, AU
  22. (22) Washington University in St. Louis, grid.4367.6
  23. (23) Mississippi State University, grid.260120.7
  24. (24) Texas Tech University, grid.264784.b
  25. (25) University of California, Santa Cruz, grid.205975.c
  26. (26) Cardiff University, grid.5600.3
  27. (27) Institute of Zoology, grid.458458.0
  28. (28) International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
  29. (29) College of Medicine and Forensics, Xi’an Jiaotong University Xi’an, 710061, China
  30. (30) China Agricultural University, grid.22935.3f
  31. (31) Tulane University, grid.265219.b
  32. (32) Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark
  33. (33) Oregon Health & Science University, grid.5288.7
  34. (34) Federal University of Para, grid.271300.7
  35. (35) Federal University of Rio de Janeiro, grid.8536.8
  36. (36) Technical University of Denmark, grid.5170.3, DTU
  37. (37) Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
  38. (38) Dubai Falcon Hospital, Dubai, United Arab Emirates
  39. (39) Canterbury Museum, grid.464524.5
  40. (40) Curtin University, grid.1032.0
  41. (41) University of California, Berkeley, grid.47840.3f
  42. (42) Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA
  43. (43) Novosibirsk State University, grid.4605.7
  44. (44) National Museum of Natural History, grid.453560.1
  45. (45) National University of Singapore, grid.4280.e
  46. (46) University of Minnesota, grid.17635.36
  47. (47) Natural History Museum, grid.35937.3b
  48. (48) Imperial College London, grid.7445.2
  49. (49) Smithsonian Conservation Biology Institute, grid.419531.b
  50. (50) National Zoological Park, grid.467700.2
  51. (51) Nova Southeastern University, grid.261241.2
  52. (52) Saint Petersburg State University, grid.15447.33
  53. (53) San Diego Zoo Institute for Conservation Research, grid.452788.4
  54. (54) Occidental College, grid.217156.6
  55. (55) University of Edinburgh, grid.4305.2
  56. (56) Swedish Species Information Centre, grid.484682.4
  57. (57) Harvard University, grid.38142.3c
  58. (58) Karlsruhe Institute of Technology, grid.7892.4
  59. (59) University of California, San Francisco, grid.266102.1
  60. (60) American Museum of Natural History, grid.241963.b
  61. (61) University of Florida, grid.15276.37
  62. (62) University of Illinois at Urbana Champaign, grid.35403.31
  63. (63) King Abdulaziz University, grid.412125.1
  64. (64) Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China
  65. (65) University of Hong Kong, grid.194645.b

Description

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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Dimensions Citation Indicators

Times Cited: 1000

Field Citation Ratio (FCR): 157.38

Relative Citation ratio (RCR): 36.74

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