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Comparative genomics reveals insights into avian genome evolution and adaptation

Science2014Vol. 346(6215), pp. 1311–1320

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Guojie Zhang, Cai Li, Qiye Li, Bo Li, Denis M. Larkin, Chul Lee, Jay F. Storz, Agostinho Antunes, Matthew J. Greenwold, Robert W. Meredith, Anders Ödeen, Jie Cui, Qi Zhou, Luohao Xu, Hailin Pan, Zongji Wang, Lijun Jin, Pei Zhang, Haofu Hu, Wei Yang, Jiang Hu, Jin Xiao, Zhikai Yang, Yang Liu, Qiaolin Xie, Hao Yu, Jinmin Lian, Ping Wen, Fang Zhang, Hui Li, Yongli Zeng, Zijun Xiong, Shiping Liu, Long Zhou, Zhiyong Huang, Na An, Jie Wang, Qiumei Zheng, Yingqi Xiong, Guangbiao Wang, Bo Wang, Jingjing Wang, Yu Fan, Rute R. da Fonseca, Alonzo Alfaro‐Núñez, Mikkel Schubert, Ludovic Orlando, Tobias Mourier, Jason T. Howard, Ganeshkumar Ganapathy, Andreas R. Pfenning, Osceola Whitney, Miriam Rivas, Erina Hara, Julia Smith, Marta Farré, Jitendra Narayan, Gancho Slavov, Michael N Romanov, Rui Borges, João Paulo Machado, Imran Khan, Mark S. Springer, John Gatesy, Federico G. Hoffmann, Juan C. Opazo, Olle Håstad, Roger H. Sawyer, Heebal Kim, Kyu-Won Kim, Hyeon Jeong Kim, Seoae Cho, Ning Li, Yinhua Huang, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Mads F. Bertelsen, Elizabeth P. Derryberry, Wesley C. Warren, Richard K. Wilson, Shengbin Li, David A. Ray, Richard E. Green, Stephen J. O’Brien, Darren Griffin, Warren E. Johnson, David Haussler, Oliver A. Ryder, Eske Willerslev, Gary R. Graves, Per Alström, Jon Fjeldså, David P. Mindell, Scott V. Edwards, Edward L. Braun, Carsten Rahbek, David W. Burt, Peter Houde, Yong Zhang, Huanming Yang, Jian Wang, Erich D. Jarvis, M. Thomas P. Gilbert, Jun Wang, Chen Ye, Shaoguang Liang, Zengli Yan, M. Lisandra Zepeda, Paula F. Campos, Amhed Missael Vargas Velazquez, José Alfredo Samaniego Castruita, María C. Ávila‐Arcos, Michael D. Martin, Ross Barnett, Ângela M. Ribeiro, Claudio V. Mello, Peter V. Lovell, Daniela Almeida, Emanuel Maldonado, Joana Pereira, Kartik Sunagar, Siby Philip, María Gloria Domínguez-Bello, Michael Bunce, David M. Lambert, Robb T. Brumfield, Frederick H. Sheldon, Edward C. Holmes, Paul P. Gardner, Tammy E. Steeves, Peter F. Stadler, Sarah Burge, Eric Lyons, Jacqueline Smith, Fiona McCarthy, Frédérique Pitel, Douglas D. Rhoads, D. P. Froman

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.

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Abstract

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