Data from: Phylotranscriptomics resolves ancient divergences in the Lepidoptera

Classic morphological studies of the oldest, so-called nonditrysian
lineages of Lepidoptera yielded a well-resolved phylogeny, supported by
the stepwise origin of the traits characterizing the clade Ditrysia, which
contains over 98% of extant lepidopterans. Subsequent polymerase chain
reaction (PCR)-based molecular studies have robustly supported many
aspects of the morphological hypothesis and strongly contradicted others,
while leaving some relationships unsettled. Here we bring the greatly
expanded gene sampling of RNA-Seq to bear on nonditrysian phylogeny,
especially those aspects that were not conclusively resolved by the
combination of morphology and previous PCR-based multi-gene studies. We
analysed up to 2212 genes in each of 28 species representing all 12
superfamilies and 15 of 21 families of nonditrysians, plus trichopteran
outgroups and representative Ditrysia. Our maximum likelihood phylogeny
estimates used both nonsynonymous changes only (degen1 coding) and all
nucleotides (nt123) partitioned by codon position, recovering a novel
hypothesis for early glossatan relationships that is the most strongly
supported to date. We find strong support for Micropterigidae alone as the
sister group to all other Lepidoptera, in agreement with morphology and
early molecular evidence, but in contrast to recent PCR-based studies.
Also very strongly supported are the previously recognized clades
Angiospermivora, Heteroneura, Eulepidoptera and Euheteroneura. Finally, we
find strong support for paraphyly of the southern hemisphere family
Palaephatidae, with the South American genus Palaephatus Butler forming
the previously undetermined sister group to Ditrysia. The remaining
palaephatids, Australian and South American, form the sister group to
Tischeriidae.