Yuelushan Laboratory, College of Plant Protection, Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, Hunan, China; Tropical Biodiversity and Bioresource Utilization Laboratory, College of Science, Qiongtai Normal University, Haikou 571127, Hainan, China.
Yuelushan Laboratory, College of Plant Protection, Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, Hunan, China; Qiannan Polytechnic for Nationality, Duyun 558022, Guizhou, China.
Mol Phylogenet Evol. 2024 Aug;197:108113. doi: 10.1016/j.ympev.2024.108113. Epub 2024 May 23.
A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order in the world following Coleoptera and Diptera, Lepidoptera (butterflies and moths) play a central role in almost every terrestrial ecosystem as indicators of environmental change and serve as important models for biologists exploring questions related to ecology and evolutionary biology. However, for such a charismatic insect group, the higher-level phylogenetic relationships among its superfamilies are still poorly resolved. Compared to earlier phylogenomic studies, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa) and acquired a series of large amino-acid datasets from 69,680 to 400,330 for phylogenomic reconstructions. Using these datasets, we explored the effect of different taxon sampling with significant increases in the number of included genes on tree topology by considering a series of systematic errors using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness in topology robustness among the three ML-based models. The results showed that taxon sampling is an important determinant in tree robustness of accurate lepidopteran phylogenetic estimation. Long-branch attraction (LBA) caused by site-wise heterogeneity is a significant source of bias giving rise to unstable positions of ditrysian groups in phylogenomic reconstruction. Phylogenetic inference showed the most comprehensive framework to reveal the relationships among lepidopteran superfamilies, and presented some newly relationships with strong supports (Papilionoidea was sister to Gelechioidea and Immoidea was sister to Galacticoidea, respectively), but limited by taxon sampling, the relationships within the species-rich and relatively rapid radiation Ditrysia and especially Apoditrysia remain poorly resolved, which need to increase taxon sampling for further phylogenomic reconstruction. The present study demonstrates that taxon sampling is an important determinant for an accurate lepidopteran tree of life and provides some essential insights for future lepidopteran phylogenomic studies.
一个强大而稳定的系统发育框架是进化生物学的基本目标。鳞翅目（蝴蝶和蛾类）是世界上第三大昆虫目，在几乎所有陆地生态系统中都扮演着重要的角色，是环境变化的指示物，并作为生物学家探索与生态学和进化生物学相关问题的重要模型。然而，对于这样一个具有魅力的昆虫群体，其超科之间的高级系统发育关系仍然没有得到很好的解决。与早期的基因组系统发育研究相比，我们增加了鳞翅目（37 个超科和 68 个科，包含 263 个分类群）的分类群采样，并从 69680 到 400330 个氨基酸数据集用于基因组系统发育重建。利用这些数据集，我们通过考虑最大似然（ML）和贝叶斯推断（BI）方法中的一系列系统误差，探讨了增加包含基因数量的分类群采样对树拓扑结构的影响。此外，我们还测试了三种基于 ML 的模型中拓扑稳健性的有效性。结果表明，分类群采样是准确鳞翅目系统发育估计树稳健性的一个重要决定因素。基于位点异质性的长枝吸引（LBA）是导致系统发育重建中双翅目群体不稳定位置的一个重要偏差来源。系统发育推断显示了最全面的框架来揭示鳞翅目超科之间的关系，并呈现了一些新的具有强烈支持的关系（鳞翅目与 Gelechioidea 是姐妹群，Immoidea 与 Galacticoidea 是姐妹群），但受限于分类群采样，物种丰富且相对快速辐射的双翅目，特别是 Apoditrysia 内部的关系仍然没有得到很好的解决，需要增加分类群采样以进行进一步的基因组系统发育重建。本研究表明，分类群采样是准确鳞翅目生命之树的一个重要决定因素，并为未来的鳞翅目基因组系统发育研究提供了一些重要的见解。
