Comparative genomics reveals insights into avian genome evolution and adaptation

Authors

Guojie Zhang, Beijing Genomics Institute (BGI)–ShenzhenFollow
Cai Li, Beijing Genomics Institute (BGI)–Shenzhen
Qiye Li, Beijing Genomics Institute (BGI)–Shenzhen
Bo Li, Beijing Genomics Institute (BGI)–Shenzhen
Dennis M. Larkin, Royal Veterinary College, University of London
Chul Lee, Seoul National University, Korea
Jay F. Storz, University of Nebraska-LincolnFollow
Agostinho Antunes, Universidade do Porto, Portugal
Matthew J. Greenwold, University of South Carolina - Columbia
Robert W. Meredith, Montclair State University
Anders Ödeen, Uppsala University, Sweden
Jie Cui, The University of Sydney, Australia
Qi Zhou, University of California, Berkeley
Luohao Xu, Wuhan University, China
Hailin Pan, Beijing Genomics Institute (BGI)–Shenzhen
Zongji Wang, South China University of Technology, Guangzhou
Lijun Jin, Beijing Genomics Institute (BGI)–Shenzhen
Pei Zhang, Beijing Genomics Institute (BGI)–Shenzhen
Haofu Hu, Beijing Genomics Institute (BGI)–Shenzhen
Wei Yang, Beijing Genomics Institute (BGI)–Shenzhen
Jiang Hu, Beijing Genomics Institute (BGI)–Shenzhen
Jin Xiao, Beijing Genomics Institute (BGI)–Shenzhen
Zhikai Yang, Beijing Genomics Institute (BGI)–Shenzhen
Yang Liu, Beijing Genomics Institute (BGI)–Shenzhen
Qiaolin Xie, Beijing Genomics Institute (BGI)–Shenzhen
Hao Yu, Beijing Genomics Institute (BGI)–Shenzhen
Jinmin Lian, Beijing Genomics Institute (BGI)–Shenzhen
Ping Wen, Beijing Genomics Institute (BGI)–Shenzhen
Fang Zhang, Beijing Genomics Institute (BGI)–Shenzhen
Hui Li, Beijing Genomics Institute (BGI)–Shenzhen
Yongli Zeng, Beijing Genomics Institute (BGI)–Shenzhen
Zijun Xiong, Beijing Genomics Institute (BGI)–Shenzhen
Shiping Liu, Beijing Genomics Institute (BGI)–Shenzhen
Long Zhou, Beijing Genomics Institute (BGI)–Shenzhen
Zhiyong Huang, Beijing Genomics Institute (BGI)–Shenzhen
Na An, Beijing Genomics Institute (BGI)–Shenzhen
Jie Wang, Beijing Genomics Institute (BGI)–Shenzhen
Quimei Zheng, Beijing Genomics Institute (BGI)–Shenzhen
Yingqi Xiong, Beijing Genomics Institute (BGI)–Shenzhen
Guangbiao Wang, Beijing Genomics Institute (BGI)–Shenzhen
Bo Wang, Beijing Genomics Institute (BGI)–Shenzhen
Jingjing Wang, Beijing Genomics Institute (BGI)–Shenzhen
Yu Fan, Kunming Institute of Zoology, China
Rute R. da Fonseca, University of Copenhagen
Alonzo Alfaro-Núñez, University of Copenhagen
Mikkel Schubert, University of Copenhagen
Ludovic Orlando, University of Copenhagen
Tobias Mourier, University of Copenhagen
Jason T. Howard, Duke University Medical Center, Durham
Ganeshkumar Ganapathy, Duke University Medical Center, Durham
Andreas Pfenning, Duke University Medical Center, Durham
Osceola Whitney, Duke University Medical Center, Durham
Miriam V. Rivas, Duke University Medical Center, Durham
Erina Hara, Duke University Medical Center, Durham
Julia Smith, Duke University Medical Center, Durham
Marta Farré, Royal Veterinary College, University of London
Jitendra Narayan, Aberystwyth University
Gancho Slavov, Aberystwyth University
Michael N. Romanov, University of Kent at Canterbury - U.K.
Rui Borges, Universidade do Porto
João Paulo Machado, Universidade do Porto
Imran Khan, Universidade do Porto
Mark S. Springer, University of California, Riverside
John Gatesy, University of California, Riverside
Federico G. Hoffmann, Mississippi State University
Juan C. Opazo, Universidad Austral de Chile, Valdivia
Olle Håstad, Swedish University of Agricultural Sciences
Roger H. Sawyer, University of South Carolina - Columbia
Heebal Kim, Seoul National University, Korea
Kyu-Won Kim, Seoul National University, Korea
Hyeon Jeong Kim, Cho and Kim Genomics, Seoul National University Research Park, Seoul
Seoae Cho, Cho and Kim Genomics, Seoul National University Research Park, Seoul
Ning Li, China Agricultural University, Beijing
Yinhua Huang, China Agricultural University, Beijing
Michael W. Bruford, Cardiff University, Wales
Xiangjiang Zhan, Cardiff University, Wales
Andrew Dixon, International Wildlife Consultants, Carmarthen, Wales
Mads F. Bertelsen, Copenhagen Zoo, Denmark
Elizabeth Derryberry, Tulane University, New Orleans
Wesley Warren, Washington University, St. Louis
Richard K. Wilson, Washington University, St. Louis
Shengbin Li, Xi’an Jiaotong University, China
David A. Ray, Mississippi State University
Richard E. Green, University of California, Santa CruzFollow
Stephen J. O'Brien, St. Petersburg State University, Russia
Darren Griffin, University of Kent, England
Warren E. Johnson, Smithsonian Conservation Biology Institute, National Zoological Park
David Haussler, University of California, Santa Cruz
Oliver A. Ryder, San Diego Zoo Institute for Conservation Research
Eske Willerslev, Natural History Museum of Denmark, University of Copenhagen
Gary R. Graves, National Museum of Natural History, Smithsonian Institution
Per Alström, Swedish University of Agricultural Sciences
Jon Fjeldså, Natural History Museum of Denmark, University of Copenhagen
David P. Mindell, University of California, San Francisco
Scott V. Edwards, Harvard University
Edward L. Braun, University of Florida, Gainesville
Carsten Rahbek, Natural History Museum of Denmark, University of Copenhagen
David W. Burt, University of Edinburgh, Scotland
Peter Houde, New Mexico State University
Yong Zhang, Beijing Genomics Institute (BGI)–Shenzhen
Huanming Yang, Beijing Genomics Institute (BGI)–Shenzhen
Jian Wang, Beijing Genomics Institute (BGI)–Shenzhen
Avian Genome Consortium, Avian Genome Consortium
Erich D. Jarvis, Duke University Medical Center, DurhamFollow
M. Thomas P. Gilbert, Natural History Museum of Denmark, University of CopenhagenFollow
Jun Wang, Beijing Genomics Institute (BGI)–ShenzhenFollow

Date of this Version

12-2014

Citation

Published in Science 346:6215 (2014), pp. 1311-1320; doi: 10.1126/science.1251385

Comments

Copyright (c) 2014 AAAS. Used by permission.

Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.