DOI: 10.5061/dryad.v1h63
title: Data from: A comprehensive and dated phylogenomic analysis of butterflies

description: Butterflies (Papilionoidea), with over 18,000 described species [1], have
 captivated naturalists and scientists for centuries. They play a central
 role in the study of speciation, community ecology, biogeography, climate
 change, and plant-insect interactions and include many model organisms and
 pest species [2, 3]. However, a robust higher-level phylogenetic framework
 is lacking. To fill this gap, we inferred a dated phylogeny by analyzing
 the first phylogenomic dataset, including 352 loci (&gt; 150,000 bp)
 from 207 species representing 98% of tribes, a 35-fold increase in gene
 sampling and 3-fold increase in taxon sampling over previous studies [4].
 Most data were generated with a new anchored hybrid enrichment (AHE) [5]
 gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g.,
 [6]) informative loci, enabling direct comparison and future dataset
 merging with previous studies. Butterflies originated around 119 million
 years ago (mya) in the late Cretaceous, but most extant lineages diverged
 after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses
 support swallowtails (Papilionidae) as sister to all other butterflies,
 followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae)
 as sister to the remainder, indicating a secondary reversal from
 diurnality to nocturnality. The whites (Pieridae) were strongly supported
 as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks
 (Lycaenidae and Riodinidae). Ant association independently evolved once in
 Lycaenidae and twice in Riodinidae. This study overturns prior notions of
 the taxon’s evolutionary history, as many long-recognized subfamilies and
 tribes are para- or polyphyletic. It also provides a much-needed backbone
 for a revised classification of butterflies and for future comparative
 studies including genome evolution and ecology.
description: READMEEspeland_et_al_AHE_Illumina_DATAEspeland et al. Illumina anchored hybrid enrichment data in fastq format for each taxa inside a compressed (tar.gz) directory.Espeland_et_al_Butterfly_tribe_reads_onlyMicrosoft Excel worksheet listing the Filename, sample, # trimmed paired reads, #RAW reads, sample code, and Repository.Espeland_et_al_data_alignmentsCompressed (tar.gz) directory including 13 relaxed phylip format alignments and partition files used in analysis in Espeland et al. [13L, AA, Full_dataset, GC1, GC2, GC3, GCLE1, LE1, LE2, LE3, LE4M, PI1, PI2]Espeland_et_al_Dated_tree_Bell_2010_root_calibrationTree file in Newick formatEspeland_et_al_Dated_tree_Magallon_2015_root_calibrationTree file in Newick format.Espeland_et_al_Figure_credibility_intervalsPDF file of the time calibrated tree with credibility intervals from Espeland et al.Espeland_et_al_NEWICK_treesCompressed (tar.gz) directory including 39 phylogenetic trees estimated for Espeland et al. in newick tree format.[13L_astral.tre, 13L_astrid.tre, 13L_ML_BS.tre, AA_astral.tre, AA_astrid.tre, AA_ML_BS.tre, ALL_astral.tre, ALL_astrid.tre, ALL_ML_BS.tre, GC1_astral.tre, GC1_astrid.tre, GC1_ML_BS.tre, GC2_astral.tre, GC2_astrid.tre, GC2_ML_BS.tre, GC3_astral.tre, GC3_astrid.tre, GC3_ML_BS.tre, GCLE1_astral.tre, GCLE1_astrid.tre, GCLE1_ML_BS.tre, LE1_astral.tre, LE1_astrid.tre, LE1_ML_BS.tre, LE2_astral.tre, LE2_astrid.tre, LE2_ML_BS.tre, LE3_astral.tre, LE3_astrid.tre, LE3_ML_BS.tre, LE4M_astral.tre, LE4M_astrid.tre, LE4M_ML_BS.tre, PI1_astral.tre, PI1_astrid.tre, PI1_ML_BS.tre, PI2_astral.tre, PI2_astrid.tre, PI2_ML_BS.tre]Espeland_et_al_Alignments_used_for_BUTTERFLY1.0_probesCompressed (tar.gz) directory of the alignments in fasta format used to make BUTTERFLY1.0 probe kit.Espeland_et_al_BUTTERFLY1.0_refCompressed (tar.gz) directory of the alignments in fasta format used as the reference in IBA.py (Breinholt et al 2017) for assembly of Illumina data.genome_getprobe_BLASTPython script used to pull possible hits to probe loci from transcriptomes and genomes.Espeland_et_al_BUTTERFLY1.0_ProbeKitBUTTERFLY1.0 probe kit