DOI: 10.5061/dryad.5df18fp
title: Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

description: Background: Silkmoths and their relatives constitute the ecologically and
 taxonomically diverse superfamily Bombycoidea, which includes some of the
 most charismatic species of Lepidoptera. Despite displaying spectacular
 forms and diverse ecological traits, relatively little attention has been
 given to understanding their evolution and drivers of their diversity. To
 begin to address this problem, we created a new Bombycoidea-specific
 Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for
 117 taxa across all major lineages of the Bombycoidea, with a newly
 developed DNA extraction protocol that allows Lepidoptera specimens to be
 readily sequenced from pinned natural history collections.Results The
 well-supported tree was overall consistent with prior morphological and
 molecular studies, although some taxa (e.g., the bombycid, Arotros Schaus)
 were misplaced and here formally transferred to Apatelodidae. We
 identified important evolutionary patterns (e.g., morphology,
 biogeography, and differences in speciation and extinction), and our
 analysis of diversification rates highlights the stark increases that
 exist within the Sphingidae (hawkmoths) and Saturniidae (wild
 silkmoths).Conclusions Our study establishes a backbone for future
 evolutionary, comparative, and taxonomic studies of Bombycoidea. We
 postulate that the rate shifts identified are due to the well-documented
 bat-moth “arms race”. Our research highlights the flexibility of AHE to
 generate genomic data from a wide range of museum specimens, both age and
 preservation method, and will allow researchers to tap into the wealth of
 biological data residing in natural history collections around the globe.
description: Hamilton_et_al_READMEREADME file containing list of files and scripts contained in this dryad package.Hamilton_et_al_Supplementary_Figure_1Supplementary Figure 1 from Hamilton et al. (2019); shows the Maximum likelihood tree of Bombycoidea, based on 650 AHE loci.Hamilton_et_al_Supplementary_Figure_2Supplementary Figure 2 from Hamilton et al. (2019); shows the interfamilial relationships of the ‘CAPOPEM’ group.Hamilton_et_al_Supplementary_Figure_3Supplementary Figure 3 from Hamilton et al. (2019); shows the interfamilial relationships of the Saturniidae.Hamilton_et_al_Supplementary_Figure_4Supplementary Figure 4 from Hamilton et al. (2019); shows the most common diversification rate shifts.Hamilton_et_al_Supplementary_File_1Set of commands to run the Breinholt et al. 2017 Anchored Hybrid Enrichment bioinformatics pipeline.Hamilton_et_al_Supplementary_File_2Specification file for the BOM1 probe set used to order probes from Agilent Technologies (http://www.agilent.com/).Hamilton_et_al_Supplementary_File_3Compressed directory of SLURM rungen scripts, referenced in the pipeline instructions.Hamilton_et_al_Supplementary_File_4Compressed directory of reference files or databases used in the pipeline.Hamilton_et_al_Supplementary_File_5Compressed directory of new scripts used in the pipeline, not previously in Breinholt et al., (2018).Hamilton_et_al_Supplementary_File_6Compressed directory of all FASTA sequence files (Pr+Fl, AA, and all individual AHE loci), all partition files, and all consensus trees from each AHE locus/tree used in ASTRAL analysis.Hamilton_et_al_Supplementary_Table_1Supplementary Table 1 from Hamilton et al. (2019); describes the loci names in the BOM1 probe set.Hamilton_et_al_Supplementary_Table_2Supplementary Table 2 from Hamilton et al. (2019); lists the taxa included in the phylogenetic analyses.Hamilton_et_al_Supplementary_Tree_1Supplementary Tree 1 from Hamilton et al. (2019); the Pr+Fl phylogeny.Hamilton_et_al_Supplementary_Tree_2Supplementary Tree 2 from Hamilton et al. (2019); the AA phylogeny.Hamilton_et_al_Supplementary_Tree_3Supplementary Tree 3 from Hamilton et al. (2019); the ASTRAL phylogeny.