浙江大学张国捷等研究人员合作发现，科级基因组揭示鸟类演化的复杂性。相关论文于2024年4月1日在线发表在《自然》杂志上。

研究人员表示，尽管在过去的几十年中做出了巨大的努力，但主要鸟类世系之间的关系仍然争论不休，没有一个明确的解决方案。差异主要归因于采样物种的多样性、系统发育方法以及基因组区域的选择。

研究人员通过分析363个鸟类物种（218个分类科，占总数的92%）的基因组来解决了这些问题。通过使用基因间区和聚合方法，研究人员发现了一棵支持度很高的树，但同时也发现了明显的不一致性。该树证实，新鸟小纲在白垩纪-古近纪（K-Pg）边界或附近经历了快速辐射。在解决困难节点方面，充足的位点比广泛的类群取样更有效。剩余的难以解决的节点涉及因极端的GC含量、可变的替换率、不完整的世系分类或复杂的演化事件（如远古杂交）而对建模提出挑战的物种。对不同基因组分区影响的评估显示了整个基因组的高度异质性。

研究人员发现，在K-Pg灭绝事件之后，有效种群规模、替代率和相对脑容量都急剧增加，这支持了新出现的生态机会催化了现代鸟类多样化的假说。由此得出的系统发育估计结果为现代鸟类的快速辐射提供了新的见解，并为未来的比较研究提供了一个类群丰富的骨干树。

附：英文原文

Title: Complexity of avian evolution revealed by family-level genomes

Author: Stiller, Josefin, Feng, Shaohong, Chowdhury, Al-Aabid, Rivas-Gonzlez, Iker, Duchne, David A., Fang, Qi, Deng, Yuan, Kozlov, Alexey, Stamatakis, Alexandros, Claramunt, Santiago, Nguyen, Jacqueline M. T., Ho, Simon Y. W., Faircloth, Brant C., Haag, Julia, Houde, Peter, Cracraft, Joel, Balaban, Metin, Mai, Uyen, Chen, Guangji, Gao, Rongsheng, Zhou, Chengran, Xie, Yulong, Huang, Zijian, Cao, Zhen, Yan, Zhi, Ogilvie, Huw A., Nakhleh, Luay, Lindow, Bent, Morel, Benoit, Fjelds, Jon, Hosner, Peter A., da Fonseca, Rute R., Petersen, Bent, Tobias, Joseph A., Szkely, Tams, Kennedy, Jonathan David, Reeve, Andrew Hart, Liker, Andras, Stervander, Martin, Antunes, Agostinho, Tietze, Dieter Thomas, Bertelsen, Mads, Lei, Fumin, Rahbek, Carsten, Graves, Gary R., Schierup, Mikkel H., Warnow, Tandy, Braun, Edward L., Gilbert, M. Thomas P., Jarvis, Erich D., Mirarab, Siavash, Zhang, Guojie

Issue&Volume: 2024-04-01

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.

DOI: 10.1038/s41586-024-07323-1

Source: https://www.nature.com/articles/s41586-024-07323-1