Insight from an Ultraconserved Element Bait Set Designed for Hemipteran Phylogenetics Integrated with Genomic Resources

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 large groups of species. Hemiptera are one such group with unresolved evolutionary relationships based on previous studies. We empirically test a recently designed ultraconserved element (UCE) bait set for Hemiptera, with a focus on the suborder Heteroptera, or the true bugs. We present newly generated UCE data for 36 samples representing three suborders, seven heteropteran infraorders, 23 families, and 34 genera of Hemiptera and one thysanopteran outgroup. For better clade sampling, we also utilized additional UCE loci in silico from published hemipteran genomes and transcriptomic data. We obtained 2,271 UCE loci for empirically tested hemipteran taxa, ranging from 265 to 1,696 (average 904) per sample. These were similar in number with the in silico data, but with fewer loci overall than expected. The amount of missing data correlates with greater phylogenetic divergence from taxa used to design the baits. Empirically, 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 was generally strongly-supported, yielding phylogenies consistent with other studies based on fewer loci. We also demonstrate that these 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. These tools can be used by other researchers for additional studies on hemipteran evolution and other research that requires well resolved phylogenies.