ArticleProceedings of the National Academy of Sciences of the United States of America2024
A region of suppressed recombination misleads neoavian phylogenomics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 32 citations in OpenAlex.
- Recombination and Incomplete Lineage Sorting Resolve the Enigma of Lysozyme Evolution.Journal of molecular evolution · 2026Article
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- Genomic Distortion of Jawed Vertebrate Phylogeny.bioRxiv : the preprint server for biology · 2026Article
- Persistent conflict in palaeognath phylogeny revealed by quartet-based and ML analyses.Frontiers in zoology · 2026Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts).Ecology and evolution · 2025Article
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The avian respiratory system: implications for anaesthesia.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly colour pattern supergene.PLoS biology · 2025Article
- Toward a Comprehensive Anatomical Matrix for Crown Birds: Phylogenetic Insights from the Pectoral Girdle and Forelimb Skeleton.Integrative organismal biology (Oxford, England) · 2025Article
- Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation.Systematic biology · 2024Article
- Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge.Scientific reports · 2024Article
- A region of suppressed recombination misleads neoavian phylogenomics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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Authors and funding
19 authors at 11 institutions in 6 countries.
Funding
Abstract
Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.
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