DOI: 10.5061/dryad.46195
title: Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

description: Gaining a genomic perspective on phylogeny requires the collection of data
 from many putatively independent loci across the genome. Among insects, an
 increasingly common approach to collecting this class of data involves
 transcriptome sequencing, because few insects have high-quality genome
 sequences available; assembling new genomes remains a limiting factor; the
 transcribed portion of the genome is a reasonable, reduced subset of the
 genome to target; and the data collected from transcribed portions of the
 genome are similar in composition to the types of data with which
 biologists have traditionally worked (e.g. exons). However, molecular
 techniques requiring RNA as a template, including transcriptome
 sequencing, are limited to using very high-quality source materials, which
 are often unavailable from a large proportion of biologically important
 insect samples. Recent research suggests that DNA-based target enrichment
 of conserved genomic elements offers another path to collecting
 phylogenomic data across insect taxa, provided that conserved elements are
 present in and can be collected from insect genomes. Here, we identify a
 large set (n = 1510) of ultraconserved elements (UCEs) shared among the
 insect order Hymenoptera. We used in silico analyses to show that these
 loci accurately reconstruct relationships among genome-enabled
 hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching
 these loci that researchers can use with DNA templates extracted from a
 variety of sources. We used our UCE bait set to enrich an average of 721
 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to
 reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very
 young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a
 recent study addressing hymenopteran phylogeny using transcriptome data,
 we found ants to be sister to all remaining aculeate lineages with
 complete support, although this result could be explained by factors such
 as taxon sampling. We discuss this approach and our results in the context
 of elucidating the evolutionary history of one of the most diverse and
 speciose animal orders.
description: hymenoptera-uce-probes.fastaFASTA file containing target enrichment bait sequences for UCE loci in hymenoptera.in-silico-NOTESNOTES describing the pipeline steps used to analyze the in silico data.in-silico-contigs.tar.gzUCE contigs sliced from available hymenopteran genomes.in-silico-uce-probes-to-contigs.lastz.tar.gzLASTZ files showing mapping of UCE probes onto in silico genome slices AND probe.matches.sqlite database.in-silico-taxon-set-alignment-data.tar.gzArchive file containing nested directories of in-silico alignment and analysis data. See overall README or file-specific README.hymenoptera-data-sets.confTop level file defining taxon sets used in analyses (e.g. ABYSS and TRINITY, with and without sawflies.abyss-NOTESNOTES describing the pipeline steps used to analyze the ABYSS data.abyss-contigs.tar.gzUCE contigs enriched from hymenopteran taxa and assembled using ABySS.abyss-uce-probes-to-contigs.lastz.tar.gzLASTZ files showing mapping of UCE probes onto in ABySS contigs AND probe.matches.sqlite database.abyss-probe-alignment-logs.tar.gzLog files from ABySS probe alignment.abyss-taxon-set-alignment-data.tar.gzArchive file containing nested directories of ABySS alignment and analysis data. See overall README or file-specific README.trinity-NOTESNOTES describing the pipeline steps used to analyze the TRINITY data.trinity-contigs.tar.gzUCE contigs enriched from hymenopteran taxa and assembled using TRINITY.trinity-uce-probes-to-contigs.lastz.tar.gzLASTZ files showing mapping of UCE probes onto TRINITY contigs AND probe.matches.sqlite database.trinity-assembly-and-probe-alignment-logs.tar.gzLog files from TRINITY probe alignment.trinity-taxon-set-alignment-data.tar.gzArchive file containing nested directories of TRINITY alignment and analysis data. See overall README or file-specific README.in-silico-RENAMED-TIPS.treeIn silico tree with tips renamed to full species binomial.abyss-WITH-SAWFLIES-100-bootrep-RENAMED-TIPS.treeABySS (with sawfly taxa) tree with tips renamed to full species binomial.trinity-WITH-SAWFLIES-100-bootrep-RENAMED-TIPS.treeTrinity (with sawfly taxa) tree with tips renamed to full species binomial.trinity-WITHOUT-SAWFLIES-100-bootrep-RENAMED-TIPS.treeTrinity (*without* sawfly taxa) tree with tips renamed to full species binomial.Tables.xlsxExcel file of tables in manuscript.figure-1-hymenoptera-with-sawfliesIllustrator file of Figure 1, sources of Figure 1 images, and an archive of photoshop cartoon images used in Figure 1 are located in figshare at doi:10.6084/m9.figshare.1173286supplemental-figures.tar.gzArchive of supplemental figures (Illustrator documents).pycogent-distance-estimates.xlsxDistances estimates output by PyCogent as xlsx file.r-steps-and-data.tar.gzSteps and data used in R for barplots and glms.READMEOverall description of files/project with additional information on code used, SRA accessions, etc.