To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

Abstract

Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference, or if tailored probe design will be desirable. Here we investigate the utility of eight different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (1) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (2) breadth of phylogenetic inference probe set was designed for, and (3) method of probe design. As part of this study, two new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We find that, predictably, probe set utility decreases with increasing phylogenetic distance of design taxa from focal taxa, as well as with narrower breadth of phylogenetic inference probes were designed for. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design and reinforce previous proposed methods for maximizing UCE probe design to improve phylogenomic inference.