DOI: 10.5061/dryad.r8d4q
title: Data from: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees

description: The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse
 lineage of hymenopteran insects, encompassing over 70,000 described
 species and a diversity of life history traits, including ectoparasitism,
 cleptoparasitism, predation, pollen feeding (bees [Anthophila] and
 Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1].
 The most well-studied lineages of Aculeata are the ants, which are
 ecologically dominant in most terrestrial ecosystems [2], and the bees,
 the most important lineage of angiosperm-pollinating insects [3].
 Establishing the phylogenetic affinities of ants and bees helps us
 understand and reconstruct patterns of social evolution as well as fully
 appreciate the biological implications of the switch from carnivory to
 pollen feeding (pollenivory). Despite recent advancements in aculeate
 phylogeny [4–11], considerable uncertainty remains regarding higher level
 relationships within Aculeata, including the phylogenetic affinities of
 ants and bees [5–7]. We used ultraconserved element (UCE) phylogenomics
 [7,12] to resolve relationships among stinging wasp families, gathering
 sequence data from &gt; 800 UCE loci and 187 samples, including 30 out
 of 31 aculeate families. We analyzed the 187-taxon data set using multiple
 analytical approaches, and we evaluated several alternative taxon sets. We
 also tested alternative hypotheses for the phylogenetic positions of ants
 and bees. Our results present a highly supported phylogeny of the stinging
 wasps. Most importantly, we find unequivocal evidence that ants are the
 sister group to bees+apoid wasps (Apoidea) and that bees are nested within
 a paraphyletic Crabronidae. We also demonstrate that taxon choice can
 fundamentally impact tree topology and clade support in phylogenomic
 inference.
description: Raw sequence
 reads.Raw Illumina reads for
 all newly sequenced samples from this
 study.Alignment
 supermatrices.All alignment
 supermatrices from this study. In NEXUS format. Includes UCE locus
 character set information.all-alignment-supermatrices.zipBEAST XML data files.All BEAST XML data files generated for this study.all-beast-xml-files.zipPhylogenetic trees.All phylogenetic trees generated in this study.all-phylogenetic-trees-results.zipData tables.All data tables from this study.all-tables.xlsxPartitioning files.Partitioning files for the Hym-187T-F75 alignment supermatrix. Includes bylocus, hcluster, rcluster, and kmeans partitioning schemes. In RAxML format.partition-files-for-hym-187t-f75-supermatrix.zipAlternative topologies for SH-tests.All alternative topologies used to test the position of ants and bees. SH-tests were performed using RAxML.sh-test-alternative-topologies.zipSupplemental figures S1 and S2 combined.The supplemental figures combined into a single pdf figure.supplemental-figure-complete.pdfUCE contigs - aligned, untrimmed, and unfiltered.Trinity contigs containing UCE loci. The contigs have been extracted from the bulk set of Trinity contigs using Phyluce and aligned, but they have not been trimmed to remove ambiguously aligned sites or filtered to remove loci with missing data.uce-aligments-untrimmed-unfiltered.zipUCE loci from genome-enabled samples.UCE loci extracted from available genome-enabled Hymenoptera. Each UCE locus consists of a core region plus 400 bp of flanking DNA on either side. Includes a lastz match-counts database and fasta files for use with Phyluce.uce-loci-extracted-from-genome-enabled-samples.zipTrinity assemblies - bulk.The bulk set of Trinity assemblies for all enriched samples analyzed in this study. Includes assemblies from the previous Faircloth et al. (2015) study. Cleaned reads were assembled using Trinity ver. r2013-02-25.trinity-assemblies-all-samples.zipBaCoCa resultsBaCoCa analysis results. Performed on the Hym-187T-F75 locus set.bacoca-results.xlsx