Comparative genomics reveals insights into avian genome evolution and adaptation

Zhang, G. and Li, C. and Li, Q. and Li, B. and Larkin, D. M. and Lee, C. and Storz, J. F. and Antunes, A. and Greenwold, M. J. and Meredith, R. W. and Odeen, A. and Cui, J. and Zhou, Q. and Xu, L. and Pan, H. and Wang, Z. and Jin, L. and Zhang, P. and Hu, H. and Yang, W. and Hu, J. and Xiao, J. and Yang, Z. and Liu, Y. and Xie, Q. and Yu, H. and Lian, J. and Wen, P. and Zhang, F. and Li, H. and Zeng, Y. and Xiong, Z. and Liu, S. and Zhou, L. and Huang, Z. and An, N. and Wang, J. and Zheng, Q. and Xiong, Y. and Wang, G. and Wang, B. and Wang, J. and Fan, Y. and da Fonseca, R. R. and Alfaro-Nunez, A. and Schubert, M. and Orlando, L. and Mourier, T. and Howard, J. T. and Ganapathy, G. and Pfenning, A. and Whitney, O. and Rivas, M. V. and Hara, E. and Smith, J. and Farre, M. and Narayan, J. and Slavov, G. and Romanov, M. N. and Borges, R. and Machado, J. P. and Khan, I. and Springer, M. S. and Gatesy, J. and Hoffmann, F. G. and Opazo, J. C. and Hastad, O. and Sawyer, R. H. and Kim, H. and Kim, K.-W. and Kim, H. J. and Cho, S. and Li, N. and Huang, Y. and Bruford, M. W. and Zhan, X. and Dixon, A. and Bertelsen, M. F. and Derryberry, E. and Warren, W. and Wilson, R. K. and Li, S. and Ray, D. A. and Green, R. E. and O'Brien, S. J. and Griffin, D. and Johnson, W. E. and Haussler, D. and Ryder, O. A. and Willerslev, E. and Graves, G. R. and Alstrom, P. and Fjeldsa, J. and Mindell, D. P. and Edwards, S. V. and Braun, E. L. and Rahbek, C. and Burt, D. W. and Houde, P. and Zhang, Y. and Yang, H. and Wang, J. and Jarvis, E. D. and Gilbert, M. T. P. and Wang, J. and Ye, C. and Liang, S. and Yan, Z. and Zepeda, M. L. and Campos, P. F. and Velazquez, A. M. V. and Samaniego, J. A. and Avila-Arcos, M. and Martin, M. D. and Barnett, R. and Ribeiro, A. M. and Mello, C. V. and Lovell, P. V. and Almeida, D. and Maldonado, E. and Pereira, J. and Sunagar, K. and Philip, S. and Dominguez-Bello, M. G. and Bunce, M. and Lambert, D. and Brumfield, R. T. and Sheldon, F. H. and Holmes, E. C. and Gardner, P. P. and Steeves, T. E. and Stadler, P. F. and Burge, S. W. and Lyons, E. and Smith, J. and McCarthy, F. and Pitel, F. and Rhoads, D. and Froman, D. P. (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346 (6215). pp. 1311-1320. ISSN 0036-8075

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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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