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  • Review Article
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Phylogenomics and comparative genomic perspective on the avian radiation

Nature Reviews Biodiversity volume 1, pages 439–460 (2025)Cite this article

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Abstract

Adaptive radiation is a pivotal driver of macroevolution, substantially contributing to the diversity of life by promoting rapid phenotypic and ecological adaptations. In birds, neoavian species account for over 95% of modern avian diversity, emerging from an explosive radiation event near the Cretaceous–Palaeogene boundary. In this Review, we explore the current challenges in resolving the avian tree of life and examine the key drivers of their radiation. We discuss the emerging consensus from phylogenomic studies using whole-genome data to illuminate the early diversification of Neoaves. Additionally, we discuss how the radiation of birds has influenced their diversity, emphasizing the interconnected macroevolution of phenotypic traits and genomic characteristics. Finally, we discuss the multiple impacts of climate change on bird populations, highlighting how evolutionary history informs and enhances our understanding of avian resilience to environmental change. This Review underscores the critical importance of integrating genomic data with trait-based analysis to explore unresolved questions pertaining to the adaptive radiation of birds, and sets the stage for future research on how contemporary ecological pressures might continue to shape avian diversity.

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Fig. 1: Phylogenomic incongruence in the avian tree.
Fig. 2: Evolutionary scenarios that contribute to gene trees and species tree conflicts.
Fig. 3: Radiation hypotheses and ecological factors associated with the evolution of avian life history traits.
Fig. 4: Morphological and genomic innovations contributing to the avian radiation.
Fig. 5: Tempo and mode of avian morphological evolution.
Fig. 6: Trends in avian genomic evolution.
Fig. 7: Lineage-specific responses to climate change can aid in predicting avian demographic sensitivity.

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Authors and Affiliations

  1. Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China

    Guangji Chen  (陈光霁), Yulong Xie  (谢宇龙) & Guojie Zhang  (张国捷)

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  1. Guangji Chen  (陈光霁)
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  2. Yulong Xie  (谢宇龙)
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  3. Guojie Zhang  (张国捷)
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G.Z. contributed substantially to discussion of content. All authors wrote the article and reviewed and/or edited the manuscript before submission.

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Correspondence to Guojie Zhang  (张国捷).

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Animal Genome Size Database: https://www.genomesize.com

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Glossary

Avialan

Any member of the clade Avialae, which includes all modern birds and their most immediate extinct relatives among non-avian dinosaurs; the term has been extensively used in studies of Mesozoic avian evolution.

Coalesce

The process by which alleles merge into a single ancestral lineage when traced backwards in evolutionary time.

Crown group

A crown group is a monophyletic clade that contains the most recent common ancestor of all extant members, and all of that ancestor’s descendants.

Exaptation

The evolutionary process by which a trait that originally evolved for one function is subsequently co-opted for a different purpose; exaptations differ from adaptations in that the latter are directly shaped by natural selection for their current role.

Loci

A locus refers to a specific, defined position on a chromosome, typically corresponding to a gene or other functional DNA element.

Phalanges

The bones that constitute the digits of the limbs — specifically, the fingers in the forelimbs (wings) and the toes in the hindlimbs (feet) of vertebrates, including birds.

Polytomy

A condition in a phylogenetic tree in which a single node gives rise to three or more lineages, indicating either simultaneous divergence or unresolved evolutionary relationships.

Protobirds

Also referred to as stem birds, this term denotes transitional forms in the evolutionary continuum from non-avian theropod dinosaurs to crown-group birds; it has been frequently used in palaeontological literature to describe early avialan-grade taxa.

Rhamphotheca

The keratinous sheath covering the bony structure of a bird’s beak.

Syngameon

A group of closely related taxa that frequently engage in natural hybridization and lack complete reproductive isolation; the concept has been applied to various avian groups exhibiting reticulate evolution and gene flow across species boundaries.

Syntenic structure

The conserved order and orientation of genes or genomic segments on chromosomes, either across different species or within duplicated regions of the same genome; syntenic relationships provide insight into chromosomal evolution, genome rearrangements and deep homology.

Target capture

A targeted DNA enrichment technique designed to isolate and sequence specific genomic regions of interest; it enables the retrieval of relatively long DNA fragments — often up to tens of thousands of base pairs — for downstream analyses such as phylogenomics or comparative genomics.

Transposable elements

(TEs). Mobile genetic elements capable of changing their position within the genome.

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Chen, G., Xie, Y. & Zhang, G. Phylogenomics and comparative genomic perspective on the avian radiation. Nat. Rev. Biodivers. 1, 439–460 (2025). https://doi.org/10.1038/s44358-025-00062-9

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