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. The Lepidoptera includes ~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 ESTs. Using HaMStR with a Lepidoptera specific core-ortholog set of single copy loci, we identified 2,696 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 ≥ 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 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.

蝴蝶与蛾类是最受大众喜爱且极具魅力的昆虫类群之一。鳞翅目（Lepidoptera）目前已记录约16万个已正式描述的物种，其中诸多类群为重要的模式生物。此前针对鳞翅目演化的研究无法精准确定蝴蝶的演化归属位置，且物种极为丰富的双孔亚目（Ditrysia）大支系下各总科间的多数演化关系仍不明确。本研究构建了包含46个分类单元的分子数据集，整合了33条新构建的转录组数据与13条已公开的基因组、转录组及表达序列标签（Expressed Sequence Tags, ESTs）。本研究采用适配鳞翅目特异性单拷贝基因座核心直系同源集的HaMStR分析工具，筛选得到2696个基因用于系统发育基因组学分析。基于全基因、全分类单元数据集的核苷酸序列与氨基酸序列分析，得到了拓扑结构高度一致且支持度优异的系统发育树。蝴蝶类群（凤蝶总科Papilionoidea）的单系性得到了强力支持，该类群涵盖弄蝶科（Hesperiidae）与神秘的蝶蛾科（Hedylidae）。蝴蝶被确定为其余闭轭亚目（obtectomeran）鳞翅目的姊妹群，且该类群的聚类得到了≥87%的自举法支持率。此前难以明确4个物种多样性最高的大异角亚目总科间的可靠演化关系，但本研究得到了100%自举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）))。本研究构建了首个强力推翻蝴蝶类群传统演化定位的高可信度鳞翅目系统发育树，并为这一物种丰富的昆虫目级类群的基因组学、发育生物学及生态学研究提供了演化框架。