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Cited by 459Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenetic diversity and population structure

Dense sampling of bird diversity increases power of comparative genomics

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Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji +142 more·2020·Nature
DOI 10.1038/s41586-020-2873-9PMC PMC7759463
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Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

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  • The problem of non-independence is complicated even further by how unrepresentative most genomic datasets are of natural communities, owing to biases in which species have been sequenced more frequently.

    “The problem of non-independence is complicated even further by how unrepresentative most genomic datasets are of natural communities, owing to biases in which species have been sequenced more frequently (Fig. 2)27–29.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [28]

    The Abstract says sparse taxon sampling captures only a fraction of genomic diversity, supporting the concern that genomic datasets can be unrepresentative. It does not establish that most datasets are unrepresentative of natural communities because some species are sequenced more frequently, or explain how that bias compounds non-independence. No page numbers are available in our copy. (LLM, conf=0.81)

    Experimental — accuracy not yet measured

  • Genomic databases are biased towards taxonomic groups that have been sequenced more frequently.

    “This problem is made worse because genomic databases are biased towards taxonomic groups that have been sequenced more frequently27–29 (Fig. 2).”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [28]

    The Abstract (page not provided) says sparse taxon sampling captures only a fraction of genomic diversity, and the Methods describe adding 267 newly sequenced bird genomes to 96 publicly available ones. This supports a concern about limited taxonomic representation, but the paper does not establish the broader claim that genomic databases are biased toward taxonomic groups sequenced more frequently. (LLM, conf=0.74)

    Experimental — accuracy not yet measured

  • Applying TOGA with chicken (18,039 genes, RefSeq annotation) as reference to 501 assemblies of 476 distinct bird species annotated a median of 14,058 orthologous genes.

    “To demonstrate TOGA’s applicability to non-mammalian genomes, we used chicken (18,039 genes, RefSeq annotation (21)) as the reference and applied TOGA with default models and parameters to 501 assemblies of 476 distinct bird species (28, 32) (Tables S11,S14). Across all assemblies, TOGA annotated a median of 14,058 orthologous genes (Fig. 5C, Table S14).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [28]

  • TOGA provides a general strategy to cope with the annotation and orthology inference bottleneck.

    “With the tree of life becoming more densely populated with genomes, thanks to great efforts of large-scale projects and numerous laboratories (26–28, 39), TOGA provides a general strategy to cope with the annotation and orthology inference bottleneck.”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [28]

  • The amniote-wide alignment combines two smaller alignments: one for the Zoonomia project including 242 placental mammals representing most eutherian mammal families, and one for the Bird 10,000 genomes (B10K) project including 363 avians representing most bird families.

    “The amniote-wide alignment combines two smaller alignments: one created for the initial release of the Zoonomia project31, which includes 242 placental mammals representing most eutherian mammal families, and one for the Bird 10,000 genomes (B10K) project32, which includes 363 avians, also representing most bird families.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [32]

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Authors
Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A. H., Xie, D., Chen, G., Guo, C., Faircloth, B. C., Petersen, B., Wang, Z., Zhou, Q., Diekhans, M., Chen, W., Andreu-Sánchez, S., Margaryan, A., Howard, J. T., Parent, C., Pacheco, G., Sinding, M.-H. S., Puetz, L., Cavill, E., Ribeiro, Â. M., Eckhart, L., Fjeldså, J., Hosner, P. A., Brumfield, R. T., Christidis, L., Bertelsen, M. F., Sicheritz-Ponten, T., Tietze, D. T., Robertson, B. C., Song, G., Borgia, G., Claramunt, S., Lovette, I. J., Cowen, S. J., Njoroge, P., Dumbacher, J. P., Ryder, O. A., Fuchs, J., Bunce, M., Burt, D. W., Cracraft, J., Meng, G., Hackett, S. J., Ryan, P. G., Jønsson, K. A., Jamieson, I. G., da Fonseca, R. R., Braun, E. L., Houde, P., Mirarab, S., Suh, A., Hansson, B., Ponnikas, S., Sigeman, H., Stervander, M., Frandsen, P. B., van der Zwan, H., van der Sluis, R., Visser, C., Balakrishnan, C. N., Clark, A. G., Fitzpatrick, J. W., Bowman, R., Chen, N., Cloutier, A., Sackton, T. B., Edwards, S. V., Foote, D. J., Shakya, S. B., Sheldon, F. H., Vignal, A., Soares, A. E. R., Shapiro, B., González-Solís, J., Ferrer-Obiol, J., Rozas, J., Riutort, M., Tigano, A., Friesen, V., Dalén, L., Urrutia, A. O., Székely, T., Liu, Y., Campana, M. G., Corvelo, A., Fleischer, R. C., Rutherford, K. M., Gemmell, N. J., Dussex, N., Mouritsen, H., Thiele, N., Delmore, K., Liedvogel, M., Franke, A., Hoeppner, M. P., Krone, O., Fudickar, A. M., Milá, B., Ketterson, E. D., Fidler, A. E., Friis, G., Parody-Merino, Á. M., Battley, P. F., Cox, M. P., Lima, N. C. B., Prosdocimi, F., Parchman, T. L., Schlinger, B. A., Loiselle, B. A., Blake, J. G., Lim, H. C., Day, L. B., Fuxjager, M. J., Baldwin, M. W., Braun, M. J., Wirthlin, M., Dikow, R. B., Ryder, T. B., Camenisch, G., Keller, L. F., DaCosta, J. M., Hauber, M. E., Louder, M. I. M., Witt, C. C., McGuire, J. A., Mudge, J., Megna, L. C., Carling, M. D., Wang, B., Taylor, S. A., Del-Rio, G., Aleixo, A., Vasconcelos, A. T. R., Mello, C. V., Weir, J. T., Haussler, D., Li, Q., Yang, H., Wang, J., Lei, F., Rahbek, C., Gilbert, M. T. P., Graves, G. R., Jarvis, E. D., Paten, B., & Zhang, G.
Affiliations
  • BGI Group (China) (CN)
  • University of Copenhagen (DK)
  • University of California, Santa Cruz (US)
  • Louisiana State University (US)
  • University of Vienna (AT)
  • Duke Medical Center (US)
  • Medical University of Vienna (AT)
  • Southern Cross University (AU)
  • Copenhagen Zoo (DK)
  • Universität Hamburg (DE)
  • University of Otago (NZ)
  • Griffith University (AU)
  • University of Maryland, College Park (US)
  • University of Toronto (CA)
  • Cornell University (US)
  • Department of Biodiversity, Conservation and Attractions (AU)
  • National Museums of Kenya (KE)
  • California Academy of Sciences (US)
  • University of California San Diego (US)
  • Centre National de la Recherche Scientifique (FR)
  • Curtin University (AU)
  • The University of Queensland (AU)
  • American Museum of Natural History (US)
  • China National GeneBank (CN)
  • Field Museum of Natural History (US)
  • University of Cape Town (ZA)
  • University of Florida (US)
  • New Mexico State University (US)
  • University of East Anglia (GB)
  • Lund University (SE)
  • University of Oregon (US)
  • Brigham Young University (US)
  • University of Pretoria (ZA)
  • East Carolina University (US)
  • Archbold Biological Station (US)
  • University of Rochester (US)
  • Harvard University (US)
  • Howard Hughes Medical Institute (US)
  • Institut de Recerca de la Biodiversitat de la Universitat de Barcelona (ES)
  • University of New Hampshire (US)
  • Queen's University (CA)
  • Swedish Museum of Natural History (SE)
  • Instituto de Ecología (MX)
  • University of Bath (GB)
  • Sun Yat-sen University (CN)
  • Smithsonian Institution (US)
  • New York Genome Center (US)
  • Carl von Ossietzky Universität Oldenburg (DE)
  • Max Planck Institute for Evolutionary Biology (DE)
  • Christian-Albrechts-Universität zu Kiel (DE)
  • Leibniz Institute for Zoo and Wildlife Research (DE)
  • Indiana University Bloomington (US)
  • Consejo Superior de Investigaciones Científicas (ES)
  • University of Auckland (NZ)
  • New York University Abu Dhabi (AE)
  • Massey University (NZ)
  • Universidade Federal do Ceará (BR)
  • University of Nevada, Reno (US)
  • Smithsonian Tropical Research Institute (PA)
  • University of Mississippi (US)
  • Brown University (US)
  • Max Planck Institute for Ornithology (DE)
  • Carnegie Mellon University (US)
  • University of Zurich (CH)
  • Boston College (US)
  • University of Illinois Urbana-Champaign (US)
  • University of New Mexico (US)
  • Museum of Vertebrate Zoology (US)
  • National Center for Genome Resources (US)
  • University of Wyoming (US)
  • The University of Melbourne (AU)
  • University of Colorado Boulder (US)
  • University of Helsinki (FI)
  • Laboratório Nacional de Computação Científica (BR)
  • Oregon Health & Science University (US)
  • Chinese Academy of Sciences (CN)
Corresponding author
  • Paten, Benedict
  • Zhang, Guojie
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2020-11-11
Volume
587
Issue
7833
Pages
252-257
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-020-2873-9
PMC
PMC7759463
OpenAlex
W3042072141
Cited by
459
References
8
Citations by year
2026: 56 · 2025: 69 · 2024: 93 · 2023: 63 · 2022: 86 · 2021: 85 · 2020: 7
FWCI
19.63
Type
journal article
Language
en
Update notices
correction (2021-04-08)
Open access
Licence
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  • Griffith Research Online (submittedVersion, other-oa)
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  • University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
  • Zurich Open Repository and Archive (University of Zurich)
Funders
  • Howard Hughes Medical Institute
  • University of Otago
  • Louisiana State University
  • Villum Fonden (25900, 00025900, 00015560)
  • National Natural Science Foundation of China (25900, 31901214)
  • Chinese Academy of Sciences (XDB31020000, 152453KYSB20170002)
  • Danish e-Infrastructure Cooperation
  • Danmarks Tekniske Universitet
  • National Institutes of Health
  • National Heart, Lung, and Blood Institute (U01HL137183)
  • National Human Genome Research Institute (R01HG010485, T32HG008345, R01HG010053, U54HG007990, U24HG007234)
  • National Institute of General Medical Sciences (R35GM133412)
  • H2020 European Research Council (681396)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
bird genome, avian phylogeny, comparative genomics, ortholog identification, selection signatures, non-coding DNA, genome conservation
MeSH terms
Animals, Birds, Chickens, Conservation of Natural Resources, Humans, Phylogeny, Selection, Genetic, Genome, Genomics, Synteny, Finches, Datasets as Topic

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