Data from: Phylogenomics provides strong evidence for the relationships of butterflies and moths

Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly–moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order.

蝴蝶与蛾类是最具人气与魅力的昆虫类群之一。鳞翅目（Lepidoptera）现有已描述物种约16万种，其中诸多类群为重要的模式生物。既往针对鳞翅目演化的研究均未能明确界定蝴蝶的系统发育位置，且该超多样化演化支——双孔亚目（Ditrysia）——内多个总科间的亲缘关系仍基本不明朗。本研究构建了包含46个类群的分子数据集：将33组新生成的转录组（transcriptome）与13组已公开的基因组（genome）、转录组及表达序列标签（EST）进行整合。研究采用基于鳞翅目特异性单拷贝位点核心直系同源基因集的HaMStR方法，共筛选出2696个基因用于系统发育组学分析。对全基因、全类群数据集的核苷酸序列与氨基酸序列分别开展分析，得到的系统发育树结果高度一致且支持度优异。蝴蝶总科（Papilionoidea）的单系性得到强力支持，该类群包含弄蝶科（Hesperiidae）以及神秘的蝶蛾科（Hedylidae）类群。系统发育分析显示蝴蝶为其余被脉类鳞翅目（obtectomeran Lepidoptera）的姐妹群，后者的聚类得到了≥87%的自展支持率。此前学界难以明确四大多样性最高的大鳞翅类总科间的亲缘关系，但本研究得到了100%自展支持率的以下聚类关系：((尺蛾总科（Geometroidea）, 夜蛾总科（Noctuoidea）), (蚕蛾总科（Bombycoidea）, 枯叶蛾总科（Lasiocampoidea）))。本研究首次构建了基于转录组数据的高鲁棒性鳞翅目系统发育树，其结果与蝴蝶类群的传统分类定位存在显著冲突，同时为该多样性昆虫类群的基因组学、发育生物学及生态学研究提供了演化框架。