DOI: 10.5061/dryad.89n87
title: Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

description: 1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved
 elements or UCEs) has emerged as a promising tool for inferring
 evolutionary history in many organismal groups. Because the UCE approach
 is still relatively new, much remains to be learned about how best to
 identify UCE loci and design baits to enrich them. 2. We test an updated
 UCE identification and bait design workflow for the insect order
 Hymenoptera, with a particular focus on ants. The new strategy augments a
 previous bait design for Hymenoptera by (a) changing the parameters by
 which conserved genomic regions are identified and retained, and (b)
 increasing the number of genomes used for locus identification and bait
 design. We perform in vitro validation of the approach in ants by
 synthesizing an ant-specific bait set that targets UCE loci and a set of
 “legacy” phylogenetic markers. Using this bait set, we generate new data
 for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17
 genome-enabled taxa. We then use these data to examine UCE capture success
 and phylogenetic performance across ants. We also test the workability of
 extracting legacy markers from enriched samples and combining the data
 with published data sets. 3. The updated bait design (hym-v2) contained a
 total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing
 the number of loci relative to the original bait set (hym-v1; 1,510 loci).
 Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments
 demonstrated a high and unbiased capture success rate, with the mean locus
 enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants
 produced a robust tree that included strong support for previously
 uncertain relationships. Complementing the UCE results, we successfully
 enriched legacy markers, combined the data with published Sanger data
 sets, and generated a comprehensive ant phylogeny containing 1,060
 terminals. 4. Overall, the new UCE bait design strategy resulted in an
 enhanced bait set for genome-scale phylogenetics in ants and likely all of
 Hymenoptera. Our in vitro tests demonstrate the utility of the updated
 design workflow, providing evidence that this approach could be applied to
 any organismal group with available genomic information.
description: Raw Illumina reads (SRA
 PRJNA360290).Raw Illumina reads for
 all enriched samples included in this study. Data available from the NCBI
 Sequence Read Archive using BioProject accession
 PRJNA360290.Alignment supermatrices
 and data partitioning filesAlignment supermatrices
 and associated data partitioning files for all analyses performed in this
 study. Includes 101-sample and 1060-sample data sets. Includes
 PartitionFinder configuration file for hcluster analysis of UCE
 loci.alignment-supermatrices-&-partitioning-files.zipTables and table captions - ExcelAll tables and table captions from the main text and supporting information of this study. Provided in Excel format.all-tables-and-table-captions.xlsxAppendix 2 from study.Appendix 2 from study. Includes supplementary methods, table captions, figures, and references.appendix2-supporting-information-methods-table-captions-figures-and-references.docxExon and rDNA alignments (trimmed) - enriched samples only.Exon and rDNA alignments for all enriched samples included in this study. Alignments trimmed to remove introns and excessive flanking DNA.exon-rDNA-alignments-trimmed-enriched-taxa-only.zipExon and rDNA alignments (untrimmed) - enriched samples only.Exon and rDNA alignments for all enriched samples included in this study. Alignments untrimmed.exon-rDNA-alignments-untrimmed-enriched-taxa-only.zipHym-v2 bait set files.Hymenoptera v2 bait set files. Includes the principal and ant-specific UCE bait set files, and the ant-exon bait set files.hym-v2-bait-set-files-complete.zipPhylogenetic trees.All phylogenetic trees from study in PDF and either Newick or Nexus formats. Includes 101-terminal and 1060-terminal trees.phylogenetic-trees.zipR script to calculate locus stats.R script used to calculate mean gene-tree bootstrap and mean GC-variance among taxa for a given set of gene trees and associated alignment files.r-script-for-locus-stats.rUCE contigs - aligned, trimmed, and filtered (Ants101T-F90).All UCE contigs (aligned and trimmed) for the Ants101T-F90 data set. Contigs aligned with MAFFT and trimmed with Gblocks. Alignments filtered to include only those alignments with at least 90% taxon occupancy.uce-contigs-aligned-gblocks-trimmed-taxon-filtered-90.zipAll UCE contigs - aligned, untrimmed.All UCE contigs from enriched taxa. Data aligned, but not trimmed or filtered for taxon occupancy. Data also available from GenBank using BioProject accession PRJNA360290.uce-contigs-aligned-untrimmed-unfiltered.zipUCE contigs from genome-enabled taxa.UCE contigs extracted from genome-enabled taxa and used in some analyses. Files can be used to add genome-enabled taxa to UCE data sets. Contigs include UCE core region and 700 bp of flanking DNA.uce-contigs-for-genome-enabled-taxa.zip