Data from: A comprehensive and dated phylogenomic analysis of butterflies

Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]. Most data were generated with a new anchored hybrid enrichment (AHE) [5] gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g., [6]) informative loci, enabling direct comparison and future dataset merging with previous studies. Butterflies originated around 119 million years ago (mya) in the late Cretaceous, but most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses support swallowtails (Papilionidae) as sister to all other butterflies, followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae) as sister to the remainder, indicating a secondary reversal from diurnality to nocturnality. The whites (Pieridae) were strongly supported as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks (Lycaenidae and Riodinidae). Ant association independently evolved once in Lycaenidae and twice in Riodinidae. This study overturns prior notions of the taxon’s evolutionary history, as many long-recognized subfamilies and tribes are para- or polyphyletic. It also provides a much-needed backbone for a revised classification of butterflies and for future comparative studies including genome evolution and ecology.蝴蝶（凤蝶总科Papilionoidea）已被描述的物种超过18000个[1]，数个世纪以来一直吸引着自然学家与科学家的关注。它们在物种形成、群落生态学、生物地理学、气候变化以及植物-昆虫互作的研究中占据核心地位，同时包含诸多模式生物与害虫类群[2, 3]。然而，目前仍缺乏一套严谨的高阶系统发育框架。 为填补这一空白，本研究通过分析首个系统基因组数据集构建了时间校准的系统发育树：该数据集涵盖了代表98%现生族级类群的207个物种的352个基因座（序列总长超150000 bp），与既往研究相比，基因采样量提升了35倍，类群采样量提升了3倍[4]。本研究大部分数据依托全新的锚定杂交富集（anchored hybrid enrichment, AHE）[5]基因试剂盒（BUTTERFLY1.0）生成，该试剂盒整合了新开发与常用（如[6]）的信息性基因座，可实现与既往研究的直接比对及后续数据集合并。 蝴蝶起源于约1.19亿年前的白垩纪晚期，但绝大多数现生支系是在6500万年前的白垩纪-古近纪（K-Pg）大灭绝事件之后分化而来。本研究的分析结果支持凤蝶科（Papilionidae）为其余所有蝴蝶的姊妹群，随后弄蝶科（Hesperiidae）与夜蝶科（Hedylidae）构成剩余类群的姊妹群，这表明夜行性是由昼行性二次逆转而来。粉蝶科（Pieridae）被强力支持为蛱蝶科（Nymphalidae）以及灰蝶科（Lycaenidae）+蚬蝶科（Riodinidae）的姊妹群。与蚂蚁的共生关系在灰蝶科独立演化一次，在蚬蝶科独立演化两次。 本研究推翻了学界此前对该类群演化历史的认知，因为诸多长期被认可的亚科与族级类群均为并系群或多系群。本研究同时为蝴蝶的修订分类系统以及未来包括基因组演化与生态学在内的比较研究提供了亟需的系统发育主干框架。