Complexity of avian evolution revealed by family-level genomes

Authors

Josefin Stiller, Københavns Universitet
Shaohong Feng, Zhejiang University School of Medicine
Al Aabid Chowdhury, The University of Sydney
Iker Rivas-González, Aarhus Universitet
David A. Duchêne, Københavns Universitet
Qi Fang, BGI Research
Yuan Deng, BGI Research
Alexey Kozlov, Heidelberg Institute for Theoretical Studies (HITS GmbH)
Alexandros Stamatakis, Heidelberg Institute for Theoretical Studies (HITS GmbH)
Santiago Claramunt, University of Toronto
Jacqueline M.T. Nguyen, College of Science and Engineering
Simon Y.W. Ho, The University of Sydney
Brant C. Faircloth, Louisiana State University
Julia Haag, Heidelberg Institute for Theoretical Studies (HITS GmbH)
Peter Houde, New Mexico State University
Joel Cracraft, American Museum of Natural History
Metin Balaban, University of California, San Diego
Uyen Mai, Department of Computer Science and Engineering
Guangji Chen, BGI-Shenzhen
Rongsheng Gao, BGI-Shenzhen
Chengran Zhou, BGI-Shenzhen
Yulong Xie, Zhejiang University School of Medicine
Zijian Huang, Zhejiang University School of Medicine
Zhen Cao, George R. Brown School of Engineering and Computing
Zhi Yan, George R. Brown School of Engineering and Computing
Huw A. Ogilvie, George R. Brown School of Engineering and Computing
Luay Nakhleh, George R. Brown School of Engineering and Computing
Bent Lindow, Statens Naturhistoriske Museum
Benoit Morel, Heidelberg Institute for Theoretical Studies (HITS GmbH)
Jon Fjeldså, Statens Naturhistoriske Museum
Peter A. Hosner, Statens Naturhistoriske Museum
Rute R. da Fonseca, Københavns Universitet
Bent Petersen, Københavns Universitet

Document Type

Article

Publication Date

5-23-2024

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 regions^1–3. 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.

Publication Source (Journal or Book title)

Nature

First Page

851

Last Page

860

Recommended Citation

Stiller, J., Feng, S., Chowdhury, A., Rivas-González, I., Duchêne, D., Fang, Q., Deng, Y., Kozlov, A., Stamatakis, A., Claramunt, S., Nguyen, J., Ho, S., Faircloth, B., Haag, J., Houde, P., Cracraft, J., Balaban, M., Mai, U., Chen, G., Gao, R., Zhou, C., Xie, Y., Huang, Z., Cao, Z., Yan, Z., Ogilvie, H., Nakhleh, L., Lindow, B., Morel, B., Fjeldså, J., Hosner, P., da Fonseca, R., & Petersen, B. (2024). Complexity of avian evolution revealed by family-level genomes. Nature, 629 (8013), 851-860. https://doi.org/10.1038/s41586-024-07323-1