Complexity of avian evolution revealed by family-level genomes
File(s)
Published version
Author(s)
Type
Journal Article
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 regions1,2,3. 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 Issued
2024-05-23
Date Acceptance
2024-03-15
Citation
Nature, 2024, 629, pp.851-860
ISSN
0028-0836
Publisher
Nature Research
Start Page
851
End Page
860
Journal / Book Title
Nature
Volume
629
Issue
8013
Copyright Statement
© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/38560995
PII: 10.1038/s41586-024-07323-1
Subjects
BAYESIAN-ESTIMATION
BIRDS
BRAIN SIZE
DATA SETS
DIVERGENCE TIMES
LIFE
Multidisciplinary Sciences
MULTIPLE SEQUENCE ALIGNMENT
PHYLOGENY
RESOLVE EARLY BRANCHES
Science & Technology
Science & Technology - Other Topics
TREE
Publication Status
Published
Coverage Spatial
England
Date Publish Online
2024-04-01