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.