open access publication

Article, 2024

Complexity of avian evolution revealed by family-level genomes

Nature, ISSN 0028-0836, 1476-4687, Volume 629, 8013, Pages 851-860, 10.1038/s41586-024-07323-1

Contributors

Stiller, Josefin 0000-0001-6009-9581 (Corresponding author) [1] Feng, Shao-Hong 0000-0002-2462-7348 [2] [3] Chowdhury, Al-Aabid [4] Rivas-González, Iker 0000-0002-0515-0628 [5] Duchêne, David A 0000-0002-5479-1974 [1] Fang, Qi [6] Deng, Yuan [6] [7] Kozlov, Alexey M [8] Stamatakis, Alexandros P 0000-0003-0353-0691 [8] [9] [10] Claramunt, Santiago 0000-0002-8926-5974 [11] [12] Nguyen, Jacqueline M T 0000-0002-3076-0006 [13] [14] Ho, Simon Y W [4] Faircloth, Brant C 0000-0002-1943-0217 [15] Haag, Julia 0000-0002-7493-3917 [8] Houde, Peter W [16] Cracraft, Joel [17] Balaban, Metin 0000-0002-6947-5915 [18] Mai, Uyen [18] Chen, Guangji 0000-0002-9441-1155 [7] [19] Gao, Rongsheng [7] [19] Zhou, Chengran [7] Xie, Yulong [3] Huang, Zijian [3] Cao, Zhen [20] Yan, Zhi [20] Ogilvie, Huw A 0000-0003-1589-6885 [20] Nakhleh, Luay K [20] Lindow, Bent Erik Kramer [1] Morel, Benoit 0000-0001-6286-4419 [8] [10] Fjeldså, Jon [1] Hosner, Peter Andrew 0000-0001-7499-6224 [1] Da Fonseca, Rute R 0000-0002-2805-4698 [1] Petersen, Bent Ole 0000-0002-2472-8317 [1] [21] Tobias, Joseph Andrew 0000-0003-2429-6179 [22] Székely, Tama'S 0000-0003-2093-0056 [23] [24] Kennedy, Jonathan David [1] Reeve, Andrew Hart [1] Liker, András 0000-0001-8545-4869 [25] Stervander, Martin 0000-0002-6139-7828 [26] Antunes, Agostinho 0000-0002-1328-1732 [27] Tietze, Dieter Thomas 0000-0001-6868-227X [28] Bertelsen, Mads Frost 0000-0001-9201-7499 [29] Lei, Fu-Min 0000-0001-9920-8167 [19] [30] Rahbek, Carsten 0000-0003-4585-0300 [1] [31] [32] Graves, Gary R [1] [33] Schierup, Mikkel Heide 0000-0002-5028-1790 [5] Warnow, Tandy J 0000-0001-7717-3514 [34] Braun, Edward Louis 0000-0003-1643-5212 [35] Gilbert, Marcus Thomas Pius 0000-0002-5805-7195 [1] [36] Jarvis, Erich David [37] [38] Mirarab, Siavash 0000-0001-5410-1518 (Corresponding author) [18] Zhang, Guo-Jie 0000-0001-6860-1521 (Corresponding author) [1] [3] [7]

Affiliations

  1. [1] University of Copenhagen
    2. [NORA names: KU University of Copenhagen; University; Denmark; Europe, EU; Nordic; OECD];
  2. [2] Sir Run Run Shaw Hospital
    3. [NORA names: China; Asia, East];
  3. [3] Zhejiang University
    4. [NORA names: China; Asia, East];
  4. [4] The University of Sydney
    5. [NORA names: Australia; Oceania; OECD];
  5. [5] Aarhus University
    6. [NORA names: AU Aarhus University; University; Denmark; Europe, EU; Nordic; OECD];

Abstract

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1–3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Keywords

Cretaceous–Palaeogene, Cretaceous–Palaeogene boundary, DNA, DNA composition, Neoaves, ancient hybridization, assessment, avian evolution, avian lineages, backbone tree, birds, boundaries, brain, brain size, choice, coalescent methods, comparative study, complex, complex evolutionary events, composition, decades, degree, degree of discordance, discordance, discrepancy, diversification, diversification of modern birds, diversity, diversity of species, ecological opportunity, effect, effective population size, estimation, events, evolution, evolutionary events, extinction event, fresh insights, genome, genome partitioning, heterogeneity, hybrid, hypothesis, increase, insights, intergenic region, issues, lineage sorting, lineages, loci, method, modern birds, nodes, opportunities, partitioning, phylogenetic estimates, phylogenetic methods, population size, radiation, rapid radiation, rate, recalcitrant nodes, region, regions1, relationship, resolution, samples, size, sorting, species, species4, study, substitution, substitution rates, taxa, taxon sampling, trees, variable substitution rates, well-supported tree

Funders

  • Klaus Tschira Foundation
  • Directorate for Computer & Information Science & Engineering
  • Carlsberg Foundation
  • Royal Society
  • Chinese Academy of Sciences
  • Natural Sciences and Engineering Research Council
  • Howard Hughes Medical Institute
  • Directorate for Biological Sciences
  • National Natural Science Foundation of China
  • Deutsche Forschungsgemeinschaft
  • National Research, Development and Innovation Office
  • Australian Research Council
  • European Commission
  • The Velux Foundations

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