Complexity of avian evolution revealed by family-level genomes

Josefin Stiller (), Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A. Duchêne, Qi Fang, Yuan Deng, Alexey Kozlov, Alexandros Stamatakis, Santiago Claramunt, Jacqueline M. T. Nguyen, Simon Y. W. Ho, Brant C. Faircloth, Julia Haag, Peter Houde, Joel Cracraft, Metin Balaban, Uyen Mai, Guangji Chen, Rongsheng Gao, Chengran Zhou, Yulong Xie, Zijian Huang, Zhen Cao, Zhi Yan, Huw A. Ogilvie, Luay Nakhleh, Bent Lindow, Benoit Morel, Jon Fjeldså, Peter A. Hosner, Rute R. Fonseca, Bent Petersen, Joseph A. Tobias, Tamás Székely, Jonathan David Kennedy, Andrew Hart Reeve, Andras Liker, Martin Stervander, Agostinho Antunes, Dieter Thomas Tietze, Mads F. Bertelsen, Fumin Lei, Carsten Rahbek, Gary R. Graves, Mikkel H. Schierup, Tandy Warnow, Edward L. Braun, M. Thomas P. Gilbert, Erich D. Jarvis, Siavash Mirarab () and Guojie Zhang ()
Additional contact information
Josefin Stiller: University of Copenhagen
Shaohong Feng: Zhejiang University School of Medicine
Al-Aabid Chowdhury: University of Sydney
Iker Rivas-González: Aarhus University
David A. Duchêne: University of Copenhagen
Qi Fang: BGI Research
Yuan Deng: BGI Research
Alexey Kozlov: Heidelberg Institute for Theoretical Studies
Alexandros Stamatakis: Heidelberg Institute for Theoretical Studies
Santiago Claramunt: University of Toronto
Jacqueline M. T. Nguyen: Flinders University
Simon Y. W. Ho: University of Sydney
Brant C. Faircloth: Louisiana State University
Julia Haag: Heidelberg Institute for Theoretical Studies
Peter Houde: New Mexico State University
Joel Cracraft: American Museum of Natural History
Metin Balaban: University of California San Diego
Uyen Mai: University of California San Diego
Guangji Chen: BGI Research
Rongsheng Gao: BGI Research
Chengran Zhou: BGI Research
Yulong Xie: Zhejiang University School of Medicine
Zijian Huang: Zhejiang University School of Medicine
Zhen Cao: Rice University
Zhi Yan: Rice University
Huw A. Ogilvie: Rice University
Luay Nakhleh: Rice University
Bent Lindow: University of Copenhagen
Benoit Morel: Heidelberg Institute for Theoretical Studies
Jon Fjeldså: University of Copenhagen
Peter A. Hosner: University of Copenhagen
Rute R. Fonseca: University of Copenhagen
Bent Petersen: University of Copenhagen
Joseph A. Tobias: Silwood Park
Tamás Székely: University of Bath
Jonathan David Kennedy: University of Copenhagen
Andrew Hart Reeve: University of Copenhagen
Andras Liker: University of Pannonia
Martin Stervander: Natural History Museum
Agostinho Antunes: University of Porto
Dieter Thomas Tietze: NABU
Mads F. Bertelsen: Copenhagen Zoo
Fumin Lei: Chinese Academy of Sciences
Carsten Rahbek: University of Copenhagen
Gary R. Graves: University of Copenhagen
Mikkel H. Schierup: Aarhus University
Tandy Warnow: University of Illinois Urbana-Champaign
Edward L. Braun: University of Florida
M. Thomas P. Gilbert: University of Copenhagen
Erich D. Jarvis: The Rockefeller University
Siavash Mirarab: San Diego
Guojie Zhang: Zhejiang University School of Medicine

Nature, 2024, vol. 629, issue 8013, 851-860

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41586-024-07323-1

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