Low hybridization temperatures improve target capture success of invertebrate loci

Target capture approaches are widely used in phylogenomic studies, yet only four experimental comparisons of a critical parameter, hybridization temperature, have been published. These studies provide conflicting conclusions regarding the benefits of lower temperatures during target capture, and none include invertebrates where bait-target divergences may be higher than seen in vertebrate capture studies. Most capture studies use a fixed hybridization temperature of 65{degrees}C to maximize the proportion of on-target data, but many invertebrate capture studies report low locus recovery. Lower hybridization temperatures, which might improve locus recovery, are not commonly employed in invertebrate capture studies. We used leaf-footed bugs and relatives (Hemiptera: Coreoidea) to investigate the effect of hybridization temperature on capture success of ultraconserved elements (UCE) targeted by previously published baits derived from divergent hemipteran genomes and other loci targeted by newly designed baits derived from less divergent coreoid transcriptomes. We found touchdown capture approaches with lower hybridization temperatures generally resulted in lower proportions of on-target reads and lower read depth but were associated with more contigs and improved recovery of UCE loci. Low temperatures were also associated with increased numbers of putative paralogs of UCE loci. Hybridization temperatures did not generally affect recovery of newly targeted loci, which we attributed to their lower bait-target divergences (compared to higher divergences between UCE baits and targets) and greater bait tiling density. Thus, optimizing in vitro target capture conditions to accommodate low hybridization temperatures can provide a cost-effective, widely applicable solution to improve recovery of protein-coding loci in invertebrates.