DOI: 10.5061/dryad.qd27g
title: Data from: Phylogenomics provides strong evidence for the relationships of butterflies and moths

description: 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.
description: README.txtThis file contains descriptions of all the files associated with this Dryad package.LEP1-COS.tar.gzThis compressed directory contains the HaMStR (Ebersberger et al. 2009: http://sourceforge.net/projects/hamstr/) formatted core-ortholog set we compiled to analyze the phylogeny of Lepidoptera in Kawahara and Breinholt (2014). See the file Taxon_list_readme.txt inside the compressed directory and Kawahara and Breinholt (2014) for more information about this core-ortholog set.taxa_list.txttaxa_list.txt: List of Sample ID's used in nexus files, species names, Assembly File Name, and Genbank SRA in tab-delimited textfinal_soap_SW130206final_soap_SW130206.fa: Assembly of Nemophora sp. from Genbank SRA accession #SRR1299782, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120096Bfinal_soap_FG120096B.fa: Assembly of Eacles sp. from Genbank SRA accession #SRR1299435, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120016final_soap_FG120016.fa: Assembly of Therinia lactucina from Genbank SRA accession #SRR1299418, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120049Bfinal_soap_FG120049B.fa: Assembly of Adhemarius daphne from Genbank SRA accession #SRR1299394, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_Xter2final_soap_Xter2.fa: Assembly of Xylophanes tersa from Genbank SRA accession #SRR1298384, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_Callidfinal_soap_Callid.fa: Assembly of Pterodecta felderi from Genbank SRA accession #SRR1299369, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120022final_soap_FG120022.fa: Assembly of Morpheis mathani from Genbank SRA accession #SRR1299214, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SW130197final_soap_SW130197.fa: Assembly of Dichomeris sp. from Genbank SRA accession #SRR1299773, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SW130007final_soap_SW130007.fa: Assembly of Thubana sp. from Genbank SRA accession #SRR1300991, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV120029final_soap_GNV120029.fa: Assembly of Macaria distribuaria from Genbank SRA accession #SRR1299213, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV120032final_soap_GNV120032.fa: Assembly of Nemoria lixaria from Genbank SRA accession #SRR1299347, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120055Bfinal_soap_FG120055B.fa: Assembly of Nothus lunus from Genbank SRA accession #SRR1299318, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SW130126final_soap_SW130126.fa: Assembly of Lyssa zampa from Genbank SRA accession #SRR1299769, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_Pcit2final_soap_Pcit2.fa: Assembly of Phyllocnistis citrella from Genbank SRA accession #SRR1299751, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120028Bfinal_soap_FG120028B.fa: Assembly of Aepytus sp. from Genbank SRA accession #SRR1299317, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120070Bfinal_soap_FG120070B.fa: Assembly of Artace sp. from Genbank SRA accession #SRR1299316, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120046Bfinal_soap_FG120046B.fa: Assembly of Lacosoma ludolpha from Genbank SRA accession #SRR1299212, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SW130232final_soap_SW130232.fa: Assembly of Eudocima salaminia from Genbank SRA accession #SRR1300148, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SW130103final_soap_SW130103.fa: Assembly of Anigraea sp. from Genbank SRA accession #SRR1299755, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SW130224final_soap_SW130224.fa: Assembly of Manoba major from Genbank SRA accession #SRR1300145, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120015final_soap_FG120015.fa: Assembly of Notoplusia minuta from Genbank SRA accession #SRR1299746, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120122final_soap_FG120122.fa: Assembly of Macrosoma sp. from Genbank SRA accession #SRR1299306, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV120020final_soap_GNV120020.fa: Assembly of Hylephila phyleus from Genbank SRA accession #SRR1299296, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV139000final_soap_GNV139000.fa: Assembly of Megathymus yuccae from Genbank SRA accession #SRR1299752, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV120025final_soap_GNV120025.fa: Assembly of Hemiargus ceraunus from Genbank SRA accession #SRR1299274, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120077final_soap_FG120077.fa: Assembly of Semomesia campanea from Genbank SRA accession #SRR1299211, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SRR850324final_soap_SRR850324.fa: Assembly of Papilio glaucus from Genbank SRA accession #SRR850324 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SRR850327final_soap_SRR850327.fa: Assembly of Papilio polytes from Genbank SRA accession #SRR850327 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV120027final_soap_GNV120027.fa: Assembly of Lantanophaga pusillidactyla from Genbank SRA accession #SRR1299210, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SRR64791_final_soap_SRR64791_.fa: Assembly of Cnaphalocrocis medinalis from Genbank SRA accession #SRR647910 - SRR647915 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120071Bfinal_soap_FG120071B.fa: Assembly of Myelobia sp. from Genbank SRA accession #SRR1299267, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV139006final_soap_GNV139006.fa: Assembly of Pseudothyris sepulchralis from Genbank SRA accession #SRR1299495, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120079final_soap_FG120079.fa: Assembly of Zeuzerodes maculata from Genbank SRA accession #SRR1299209, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_SRR803483final_soap_SRR803483.fa: Assembly of Grapholita dimorpha from Genbank SRA accession #SRR803483 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_GNV129007final_soap_GNV129007.fa: Assembly of Urodus parvula from Genbank SRA accession #SRR1299750, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120035final_soap_FG120035.fa: Assembly of Dalcera abrasa from Genbank SRA accession #SRR1299208, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.final_soap_FG120024final_soap_FG120024.fa: Assembly of Megalopyge tharops from Genbank SRA accession #SRR1299217, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details.Kawahara_Breinholt_2014_26taxa_465loci_aa.nexKawahara_Breinholt_2014_26taxa_465loci_aa.nex: Nexus file containing 465 genes for 26 taxa. See taxa_list.txt for species names of each taxon, this is an amino acid nexus file with a CHARSET that defines each gene. The data was trimmed using ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html). Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this DRAYD package. For further information see text and supplementary tables in Kawahara and Breinholt (2014).Kawahara_Breinholt_2014_26taxa_465loci_aa.model.txtKawahara_Breinholt_2014_26taxa_465loci_aa.model.txt: RAxML formatted partitioning and model file. This partitioning file was used to analyze data in Kawahara_Breinholt_2014_26taxa_465loci_aa.nex. 198 partitions and amino acid models defined by partitionfinder (Lanfear et al 2012). See text and supplementary text in Kawahara and Breinholt (2014) for more details.Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nexKawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nex: Nexus file containing codon position 1 & 2 for 465 genes for 26 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. The nucleotide data was trimmed 3 codons at a time with ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html), synonymous signal removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this Dryad package. For further information see text and supplementary tables in Kawahara and Breinholt (2014).Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.model.txtKawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.model.txt: RAxML formatted partitioning file. This partitioning file was used to analyze data in Kawahara_Breinholt_2014_26taxa_465loci_Degen_nt12.nex. 178 partitions defined by partionfinder (Lanfear et al 2012). See text and supplementary text in Kawahara and Breinholt (2014) for more details.Kawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.nexKawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.nex: Nexus file containing codon position 1 & 2 for 2969 genes for 46 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. The nucleotide data was trimmed 3 codons at a time with ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html), synonymous signal removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this Dryad package. For further information see text and supplementary tables in Kawahara and Breinholt (2014).Kawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.model.txtKawahara_Breinholt_2014_46taxa_2696loci_Degen_nt12.model.txt: RAxML formatted partitioning and model file. This partitioning file was used to analyze data in Kawahara_Breinholt_2014_47taxa_2696loci_Degen_nt12.nex. Two partitions by codon position. See text and supplementary text in Kawahara and Breinholt (2014) for more details.Kawahara_Breinholt_2014_46taxa_2696loci_aa.nexKawahara_Breinholt_2014_46taxa_2696loci_aa.nex: Nexus file containing 2969 genes for 46 taxa. See taxa_list.txt for species names of each taxon, this is a amino acid nexus file with a CHARSET that defines each gene. The data was trimmed using ALICUT/ALISCORE (http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/Aliscore/index.en.html). Gene names correspond to gene numbers in the LEP1-COS core ortholog database included in this Dryad package. For further information see text and supplementary tables in Kawahara and Breinholt (2014).