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.LEP62 amino acid custom substitution rate matrix for LepidopteraLEP62 custom amino acid substitution matrix constructed from the 5,152-gene moth+min-one-butterfly databaseLEP62List of 2,212 genes (orthologous groups) included in the final data matrixList of the 2,212 genes in the final data matrix, which have survived the PTP paralogy filter and are represented in at least 21 taxa. The gene numbers in this list were assigned arbitrarily during construction of our 5,152-gene moth+min-one-butterfly database. Each of these numbers, however, also corresponds to a Bombyx gene number taken from Ensembl (and hence SilkDB), as shown in the file 'bombyx_annotation_5152_OGs.txt'.non_ditrysia_OGs_21_or_more_taxa_represented_post_lep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_degen1Data matrix in fasta format for degen1 analysislep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_degen1Data matrix in Phylip format for degen1 analysis.lep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_nt123Data matrix in fasta format for all-nucleotides (nt123) analyis.lep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_nt123Data matrix in Phylip format for all-nucleotides (nt123) analysis.raxml_partition_by_codon_positionRaxml code for partitioning by codon position.lep_ensembl_bombyx_plus_min_one_butterfly_lowsimremoved_plus_plutella_manduca_HaMStR_databaseThe 5,152-gene moth+min-one-butterfly database, together with gene identifiers, available annotations, and profile hidden Markov models for use in ortholog searchpost_PTP_consensus_cds_alignments_28_taxa_2212The individual alignments for each of the 2,212 genes which survived the PTP paralog screen and are represented in at least 21 taxa.bombyx_annotation_5152_OGs.txtShows the correspondence between our gene numbers (left column), arbitrarily assigned during construction of our moth+min-one-butterfly database, and the Bombyx gene numbers in Ensemble/SilkD. Gene ontologies from SilkDB are included when they are available. This file is duplicated in the folder 'lep_ensembl_bombyx_plus_min_one_butterfly_lowsimremoved_plus_plutella_manduca_HaMStR_database'.Trinity_assemblies_unfilteredComplete raw Trinity assembliesnon-ditrysia_Trinity_assemblies_unfiltered.zipABySS_assemblies_unfilteredComplete raw ABySS assemblies (a subset of taxa only)non-ditrysia_ABySS_assemblies_unfiltered.zipFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB135502