DOI: 10.5061/dryad.425vg4m
title: Data from: Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources

description: Target enrichment of conserved genomic regions facilitates collecting
 sequences of many orthologous loci from non-model organisms to address
 phylogenetic, phylogeographic, population genetic, and molecular evolution
 questions. Bait sets for sequence capture can simultaneously target
 thousands of loci, which opens new avenues of research on speciose groups.
 Current phylogenetic hypotheses on the &gt;103,000 species of
 Hemiptera have failed to unambiguously resolve major nodes, suggesting
 that alternative datasets and more thorough taxon sampling may be required
 to resolve relationships. We here use a recently designed ultraconserved
 element (UCE) bait set for Hemiptera, with a focus on the suborder
 Heteroptera, or the true bugs, to test previously proposed relationships.
 We present newly generated UCE data for 36 samples representing three
 suborders, all seven heteropteran infraorders, 23 families, and 34 genera
 of Hemiptera and one thysanopteran outgroup. To improve taxon sampling, we
 also mined additional UCE loci in silico from published hemipteran genomic
 and transcriptomic data. We obtained 2,271 UCE loci for newly sequenced
 hemipteran taxa, ranging from 265 to 1,696 (average 904) per sample. These
 were similar in number to the data mined from transcriptomes and genomes,
 but with fewer loci overall. The amount of missing data correlates with
 greater phylogenetic divergence from taxa used to design the baits. This
 bait set hybridizes to a wide range of hemipteran taxa and specimens of
 varying quality, including dried specimens as old as 1973. Our estimated
 phylogeny yielded topologies consistent with other studies for most nodes
 and was strongly-supported. We also demonstrate that UCE loci are almost
 exclusively from the transcribed portion of the genome, thus data can be
 successfully integrated with existing genomic and transcriptomic resources
 for more comprehensive phylogenetic sampling, an important feature in the
 era of phylogenomics. UCE approaches can be used by other researchers for
 additional studies on hemipteran evolution and other research that
 requires well resolved phylogenies.
description: scriptsZip file of scripts used in PHYLUCE pipeline from assembly through RAxML trees. Scripts include those for the "empirical" data set and those for the "empirical + in silico" data set with the extension "_empIns added to each script name.config_filesZip file of configuration files used in the PHYLUCE pipeline. Files included for assembly, Illuminiprocessor, taxonomic sets, and incomplete matrix. Taxon-set2.conf and all_empIns-taxa-incomplete.conf are for the "empirical + in silico" data sets.UCE_lociZip of .fasta and .incomplete files of UCE loci identified. Output from extract_fasta.sh and extract_fasta_empIns.sh scripts. Used as input for internal_trim.sh and internal_trim_empIns.sh scripts respectively.RAxML_alignment_input_&_Trees_outputZip of UCE loci and character set files used as input for RAxML for both the "empirical" and "empirical + in silico" (empIns) data sets for the 60% data matrix. The output reconciled tree from RAxML for each data set.RAxML_alignInput_&_Trees.zipphyluce_workflowText file of script usage workflow of the analyses performed in PHYLUCE and RAxML.UCE_alignmentsZip of individual UCE loci alignments from MAFFT in nexus format, output of internal_trim.sh and internal_trim_empIns.sh scripts, for input into Gblocks.