Gaining a genomic perspective on phylogeny requires the collection of data
from many putatively independent loci collected 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 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 (UCE) shared among the insect order Hymenoptera. We use
in silico analyses to show that these loci accurately reconstruct relationships
among genome-enabled Hymenoptera, and we design a set of baits for enriching
these loci that researchers can use with DNA templates extracted from a variety
of sources. We use our UCE bait set to enrich an average of 721 UCE loci from
30 hymenopteran taxa, and we use these UCE loci to reconstruct phylogenetic
relationships spanning very old (≥220 MYA) to very young (≤1 MYA)
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
