計算ツールにより、新しく改良された鳥類の家系図が再構築される(Computational Tools Fuel Reconstruction of New and Improved Bird Family Tree)

2024-04-022024-04-03

2024-04-01 カリフォルニア大学サンディエゴ校(UCSD)

The updated bird family tree, published in Nature, delineating 93 million years of evolutionary relationships between 363 bird species. Credit: Jon Fjeldså (drawings) and Josefin Stiller

国際的な科学者チームが、363種の鳥類を対象に、最も詳細な系統樹を構築しました。この進展は、カリフォルニア大学サンディエゴ校のエンジニアが開発した計算方法と同校のスーパーコンピューターを活用し、鳥類の進化関係を解析しました。彼らの成果はNatureとPNASに掲載され、恐竜が絶滅した後の鳥類の進化パターンを明らかにしました。

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鳥類進化の複雑さがファミリーレベルのゲノムから明らかになった Complexity of avian evolution revealed by family-level genomes

Josefin Stiller,Shaohong Feng,Al-Aabid Chowdhury,Iker Rivas-González,David A. Duchêne,Qi Fang,Yuan Deng,Alexey Kozlov,Alexandros Stamatakis,Santiago Claramunt,Jacqueline M. T. Nguyen,Simon Y. W. Ho,Brant C. Faircloth,Julia Haag,Peter Houde,Joel Cracraft,Metin Balaban,Uyen Mai,Guangji Chen,Rongsheng Gao,Chengran Zhou,Yulong Xie,Zijian Huang,Zhen Cao,… Guojie Zhang
Nature Published:01 April 2024
DOI:https://doi.org/10.1038/s41586-024-07323-1

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

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 analyzing genomes of 363 bird species ⁴ (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Paleogene (K–Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts 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 K–Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

組換えが抑制された領域がネオアビ系統学を惑わす A region of suppressed recombination misleads neoavian phylogenomics

Siavash Mirarab, Iker Rivas-González, Shaohong Feng, +15, and Edward L. Braun
Proceedings of the National Academy of Sciences Published: April 1, 2024
DOI:https://doi.org/10.1073/pnas.2319506121

Significance

Genomes are mosaics of evolutionary histories, and over time, regions of shared history shrink due to recombination. We typically observe frequent changes in evolutionary trees across the genome, especially for rapid radiations. We have found an exception across 21 Mb of neoavian genomes. Unexpectedly, this region shows a consistent history for the first divergence among Neoaves circa 65 Mya. Moreover, the history strongly supported in this region differs from the inferred species tree. We show that the cause of this surprising pattern may be an ancient rearrangement that remained polymorphic across multiple speciation events. We demonstrate that this single region can interact with limited taxon sampling to mislead phylogenomic analyses.

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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