Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics

The advent of next-generation sequencing technology has allowed for the collection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target “probe” region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus anchored hybrid enrichment kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes and expressed sequence tag (EST) dat..., READMEREADME File containing list of files and script contained in this dryad packageBreinholt_et_al_Supplementary_Figure_S1Supplementary Figure S1 from Breinholt et al. (2017)Breinholt_et_al_Supplementary_Figure_S2Supplementary Figure S2 from Breinholt et al. (2017)Breinholt_et_al_Supplementary_Figure_S3Supplementary Figure S3 from Breinholt et al. (2017)Breinholt_et_al_Supplementary_Figure_S4Supplementary Figure S4 from Breinholt et al. (2017)Breinholt_et_al_Supplementary_Figure_S5Supplementary Figure S5 from Breinholt et al. (2017)Breinholt_et_al_Supplementary_File_1__S1-S11Supplementary File 1: Microsoft excel document including Supplementary Table S1-S11 from Breinholt et al. (2017)Breinholt_et_al_Supplementary_File_1_S1-S11.xlsxBreinholt_et_al_Supplementary_File_2_Lep1Specification file for the Lep1 probe set used to order probes from Agilent Technologies (http://www.agilent.com/)Breinholt_et_al_Supplementary_File_3Word document that expands discussion of Breinholt et al. (2017) ...