Complexity of avian evolution revealed by family-level genomes

• 成果类型: Article
• 署名作者: Stiller, Josefin; Feng, Shaohong; Chowdhury, Al-Aabid; Rivas-Gonzalez, Iker; Duchene, David A.; Fang, Qi; Deng, Yuan; Kozlov, Alexey; Stamatakis, Alexandros; Claramunt, Santiago; Nguyen, Jacqueline M. T.; Ho, Simon Y. W.; Faircloth, Brant C.; Haag, Julia; Houde, Peter; Cracraft, Joel; Balaban, Metin; Mai, Uyen; Chen, Guangji; Gao, Rongsheng; Zhou, Chengran; Xie, Yulong; Huang, Zijian; Cao, Zhen; Yan, Zhi; Ogilvie, Huw A.; Nakhleh, Luay; Lindow, Bent; Morel, Benoit; Fjeldsa, Jon; Hosner, Peter A.; da Fonseca, Rute R.; Petersen, Bent; Tobias, Joseph A.; Szekely, Tamas; Kennedy, Jonathan David; Reeve, Andrew Hart; Liker, Andras; Stervander, Martin; Antunes, Agostinho; Tietze, Dieter Thomas; Bertelsen, Mads F.; Lei, Fumin; Rahbek, Carsten; Graves, Gary R.; Schierup, Mikkel H.; Warnow, Tandy; Braun, Edward L.; Gilbert, M. Thomas P.; Jarvis, Erich D.; Mirarab, Siavash; Zhang, Guojie
• 署名单位: University of Copenhagen; Zhejiang University; Zhejiang University; Zhejiang University; University of Sydney; Aarhus University; University of Copenhagen; Beijing Genomics Institute (BGI); Heidelberg Institute for Theoretical Studies; Foundation for Research & Technology - Hellas (FORTH); Helmholtz Association; Karlsruhe Institute of Technology; University of Toronto; Royal Ontario Museum; Flinders University South Australia; Australian Museum; Louisiana State University System; Louisiana State University; Louisiana State University System; Louisiana State University; New Mexico State University; American Museum of Natural History (AMNH); University of California System; University of California San Diego; University of California System; University of California San Diego; Chinese Academy of Sciences; University of Chinese Academy of Sciences, CAS; Rice University; University of Copenhagen; University of Copenhagen; AIMST University; Imperial College London; University of Bath; University of Debrecen; HUN-REN; Office for Supported Research Groups (ELKH); University of Copenhagen; University of Pannonia; University of Pannonia; Natural History Museum London; Universidade do Porto; Universidade do Porto; Chinese Academy of Sciences; Institute of Zoology, CAS; Chinese Academy of Sciences; University of Chinese Academy of Sciences, CAS; Peking University; University of Southern Denmark; Smithsonian Institution; Smithsonian National Museum of Natural History; University of Illinois System; University of Illinois Urbana-Champaign; State University System of Florida; University of Florida; Norwegian University of Science & Technology (NTNU); Rockefeller University; Howard Hughes Medical Institute; University of California System; University of California San Diego; University of Copenhagen
• 刊物名称: Nature
• ISSN/ISSBN: 0028-4417
• DOI: 10.1038/s41586-024-07323-1
• 发表日期: 2024-05-23
• 页码: 851-860
• 关键词: multiple sequence alignment; resolve early branches; bayesian-estimation; divergence times; brain size; data sets; TREE; phylogeny; birds; LIFE

摘要

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 regions(1-3). Here we address these issues by analysing the genomes of 363bird species(4) (218taxonomic 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.