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Cited by 1,055Chromosomal and Genetic VariationsGenomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Comparative genomics reveals insights into avian genome evolution and adaptation

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Zhang, Guojie, Li, Cai, Li, Qiye, Li, Bo, Larkin, Denis M., Lee, Chul, Storz, Jay F., Antunes, Agostinho +132 more·2014·Science
DOI 10.1126/science.1251385PMC PMC4390078
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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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  • The higher proportion of sequence for avians is consistent with a more conservative mode of genome evolution in avians that is influenced by lower repeat counts and denser gene content.

    “consistent with a more conservative mode of genome evolution in avians that is influenced by lower repeat counts and denser gene content33.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [33]

    The Results sections on selective constraints and conservative genome evolution report more slowly evolving regions and less genome shuffling in birds than in mammals. The broad-patterns Results also report fewer repeats and increased gene density, but the paper does not establish that those features influence the conservative mode of evolution. Page numbers are unavailable in our copy. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Multi-species genome alignments are a useful tool for analysis of species homology in large-scale comparative genomic projects.

    “Multi-species genome alignments are a useful tool for analysis of species homology in large-scale comparative genomic projects [12,13].”

    From halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments (2020) · cites this paper as [13]

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Authors
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., Ödeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W., Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., da Fonseca, R. R., Alfaro-Núñez, A., Schubert, M., Orlando, L., Mourier, T., Howard, J. T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M. V., Hara, E., Smith, J., Farré, M., Narayan, J., Slavov, G., Romanov, M. N., Borges, R., Machado, J. P., Khan, I., Springer, M. S., Gatesy, J., Hoffmann, F. G., Opazo, J. C., Håstad, O., Sawyer, R. H., Kim, H., Kim, K.-W., Kim, H. J., Cho, S., Li, N., Huang, Y., Bruford, M. W., Zhan, X., Dixon, A., Bertelsen, M. F., Derryberry, E., Warren, W., Wilson, R. K., Li, S., Ray, D. A., Green, R. E., O’Brien, S. J., Griffin, D., Johnson, W. E., Haussler, D., Ryder, O. A., Willerslev, E., Graves, G. R., Alström, P., Fjeldså, J., Mindell, D. P., Edwards, S. V., Braun, E. L., Rahbek, C., Burt, D. W., Houde, P., Zhang, Y., Yang, H., Wang, J., Avian Genome Consortium, Jarvis, E. D., Gilbert, M. T. P., Wang, J., Ye, C., Liang, S., Yan, Z., Zepeda, M. L., Campos, P. F., Velazquez, A. M. V., Samaniego, J. A., Avila-Arcos, M., Martin, M. D., Barnett, R., Ribeiro, A. M., Mello, C. V., Lovell, P. V., Almeida, D., Maldonado, E., Pereira, J., Sunagar, K., Philip, S., Dominguez-Bello, M. G., Bunce, M., Lambert, D., Brumfield, R. T., Sheldon, F. H., Holmes, E. C., Gardner, P. P., Steeves, T. E., Stadler, P. F., Burge, S. W., Lyons, E., Smith, J., McCarthy, F., Pitel, F., Rhoads, D., & Froman, D. P.
Affiliations
  • BGI Group (China) (CN)
  • University of London (GB)
  • Seoul National University (KR)
  • University of Nebraska–Lincoln (US)
  • Universidade do Porto (PT)
  • University of South Carolina (US)
  • Montclair State University (US)
  • Uppsala University (SE)
  • The University of Sydney (AU)
  • University of California, Berkeley (US)
  • China National GeneBank, Beijing Genomics Institute (BGI)–Shenzhen, Shenzhen, 518083, China.
  • Kunming Institute of Zoology (CN)
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
  • University of Copenhagen (DK)
  • Howard Hughes Medical Institute (US)
  • Aberystwyth University (GB)
  • University of Kent (GB)
  • University of California, Riverside (US)
  • Mississippi State University (US)
  • Austral University of Chile (CL)
  • Swedish University of Agricultural Sciences (SE)
  • Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea.
  • Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea.
  • China Agricultural University (CN)
  • Cardiff University (GB)
  • Chinese Academy of Sciences (CN)
  • International Wildlife Consultants (United Kingdom) (GB)
  • Copenhagen Zoo (DK)
  • Tulane University (US)
  • Washington University in St. Louis (US)
  • Xi'an Jiaotong University (CN)
  • University of California, Santa Cruz (US)
  • St Petersburg University (RU)
  • Smithsonian Conservation Biology Institute (US)
  • San Diego Zoo Institute for Conservation Research (US)
  • Smithsonian Institution (US)
  • University of California, San Francisco (US)
  • Harvard University (US)
  • University of Florida (US)
  • Roslin Institute (GB)
  • New Mexico State University (US)
Corresponding author
  • Zhang, Guojie
  • Li, Cai
  • Jarvis, Erich D.
  • Gilbert, M. Thomas P.
  • Wang, Jun
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2014-12-12
Volume
346
Issue
6215
Pages
1311-1320
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.1251385
PMC
PMC4390078
OpenAlex
W2167406239
Cited by
1,055
References
22
Citations by year
2026: 63 · 2025: 58 · 2024: 72 · 2023: 78 · 2022: 83 · 2021: 129 · 2020: 95 · 2019: 114 · 2018: 89 · 2017: 90 · 2016: 83 · 2015: 80 · 2014: 20
FWCI
97.39
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Kent Academic Repository (University of Kent) (acceptedVersion)
  • Civil War Book Review (submittedVersion)
  • RVC Research Online (Royal Veterinary College) (submittedVersion, cc-by)
  • Lincoln (University of Nebraska) (submittedVersion)
  • NSUWorks (Nova Southeastern University) (submittedVersion)
  • HAL (submittedVersion)
  • DukeSpace (Duke University) (submittedVersion)
  • DukeSpace (Duke University) (submittedVersion, cc-by-nc-nd)
  • eScholarship (California Digital Library) (submittedVersion)
  • eSpace (Curtin University) (submittedVersion)
  • ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
  • DSpace Repository (Smithsonian) (submittedVersion)
  • Griffith Research Online (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • Villum Fonden (00007370)
  • National Research Foundation
  • Danmarks Grundforskningsfond (DNRF94)
  • Lundbeckfonden (R109-2012-9995, R70-2010-6286, R155-2013-16338, R52‐A5062, R38-2008-3048, R24-2008-2527)
  • Danmarks Frie Forskningsfond (10‐081390)
  • H. Lundbeck A/S
  • National Institutes of Health (DP1OD000448)
  • Biotechnology and Biological Sciences Research Council (BB/J010170/2, BB/K008226/2, BB/J010170/1, BB/K008226/1)
  • National Heart, Lung, and Blood Institute (R01HL087216)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
avian genome evolution, comparative genomics, genome size reduction, segmental deletion, gene loss, evolutionary stasis, synteny, chromosome structure, non-neutral evolution, non-coding regions, convergent evolution, lifestyle adaptation, genomic diversity
MeSH terms
Adaptation, Physiological, Animals, Birds, Diet, Biological Evolution, Female, Flight, Animal, Genes, Male, Phylogeny, Reproduction, Selection, Genetic, Genetic Variation, Vision, Ocular, Vocalization, Animal, Genome, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular, Genomics, Synteny, Biodiversity, Molecular Sequence Annotation

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