Comparative genomics reveals insights into avian genome evolution and adaptation
Guojie Zhang(University of Copenhagen), Cai Li(University of Copenhagen), Qiye Li(University of Copenhagen), Bo Li(China National GeneBank), Denis M. Larkin(University of London), Chul Lee(Seoul National University), Jay F. Storz(University of Nebraska–Lincoln), Agostinho Antunes(Universidade do Porto), Matthew J. Greenwold(University of South Carolina), Robert W. Meredith(Montclair State University), Anders Ödeen(Uppsala University), Jie Cui(The University of Sydney), Qi Zhou(University of California, Berkeley), Luohao Xu(Wuhan University), Hailin Pan(China National GeneBank), Zongji Wang(China National GeneBank), Lijun Jin(China National GeneBank), Pei Zhang(China National GeneBank), Haofu Hu(China National GeneBank), Wei Yang(China National GeneBank), Jiang Hu(China National GeneBank), Jin Xiao(China National GeneBank), Zhikai Yang(China National GeneBank), Yang Liu(China National GeneBank), Qiaolin Xie(China National GeneBank), Hao Yu(China National GeneBank), Jinmin Lian(China National GeneBank), Ping Wen(China National GeneBank), Fang Zhang(China National GeneBank), Hui Li(China National GeneBank), Yongli Zeng(China National GeneBank), Zijun Xiong(China National GeneBank), Shiping Liu(China National GeneBank), Long Zhou(China National GeneBank), Zhiyong Huang(China National GeneBank), Na An(China National GeneBank), Jie Wang(Macau University of Science and Technology), Qiumei Zheng(China National GeneBank), Yingqi Xiong(China National GeneBank), Guangbiao Wang(China National GeneBank), Bo Wang(China National GeneBank), Jingjing Wang(Macau University of Science and Technology), Yu Fan(Kunming Institute of Zoology), 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(Howard Hughes Medical Institute), Ganeshkumar Ganapathy(Howard Hughes Medical Institute), Andreas R. Pfenning(Howard Hughes Medical Institute), Osceola Whitney(Howard Hughes Medical Institute), Miriam Rivas(Howard Hughes Medical Institute), Erina Hara(Howard Hughes Medical Institute), Julia Smith(Howard Hughes Medical Institute), Marta Farré(University of London), Jitendra Narayan(Aberystwyth University), Gancho Slavov(Aberystwyth University), Michael N Romanov(University of Kent), 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(Austral University of Chile), Olle Håstad(Swedish University of Agricultural Sciences), Roger H. Sawyer(University of South Carolina), Heebal Kim(Seoul National University), Kyu-Won Kim(Seoul National University), Hyeon Jeong Kim(Seoul National University), Seoae Cho(Seoul National University), Ning Li(China Agricultural University), Yinhua Huang(China Agricultural University), Michael W. Bruford(Cardiff University), Xiangjiang Zhan(Institute of Zoology), Andrew Dixon(International Wildlife Consultants (United Kingdom)), Mads F. Bertelsen(Copenhagen Zoo), Elizabeth P. Derryberry(Tulane University), Wesley C. Warren(Washington University in St. Louis), Richard K. Wilson(Washington University in St. Louis), Shengbin Li(Xi'an Jiaotong University), David A. Ray(Mississippi State University), Richard E. Green(University of California, Santa Cruz), Stephen J. O’Brien(St Petersburg University), Darren Griffin(University of Kent), Warren E. Johnson(Smithsonian Conservation Biology Institute), David Haussler(University of California, Santa Cruz), Oliver A. Ryder(San Diego Zoo Institute for Conservation Research), Eske Willerslev(University of Copenhagen), Gary R. Graves(National Museum of Natural History), Per Alström(Chinese Academy of Sciences), Jon Fjeldså(Natural History Museum Aarhus), David P. Mindell(University of California, San Francisco), Scott V. Edwards(Harvard University), Edward L. Braun(University of Florida), Carsten Rahbek(Natural History Museum Aarhus), David W. Burt(Roslin Institute), Peter Houde(New Mexico State University), Yong Zhang(China National GeneBank), Huanming Yang(Macau University of Science and Technology), Jian Wang(Macau University of Science and Technology), Erich D. Jarvis(Howard Hughes Medical Institute), M. Thomas P. Gilbert(University of Copenhagen), Jun Wang(Macau University of Science and Technology), 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(Howard Hughes Medical Institute), Fiona McCarthy, Frédérique Pitel, Douglas D. Rhoads, D. P. Froman
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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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