Supplementary material - A novel set of ultraconserved element (UCE) probes for lacewings and allies (Insecta: Neuropterida)

Target-enrichment of ultra-conserved elements (UCE) has proven advantageous in recovering large quantities of phylogenetically informative data even from specimens with suboptimal DNA preservation. It is also possible to develop UCE probe sets with minimal exemplar taxa, enabling the resolution of recalcitrant nodes in the Tree of Life even of rare groups. Unfortunately, probe sets are still lacking for multiple groups of insects, such as the three orders in Neuropterida (Insecta: Holometabola): Megaloptera, Neuroptera and Raphidioptera. Additionally, a well-curated probe set for neuropterids makes it possible for the investigation of their evolution, including reconstructing the ancestral state of characters and examining their life-history transitions. In this study, we developed the first openly available probe set targeting UCEs of Neuropterida. We in-silico tested different parameters to design an optimized probe set that efficiently captures conserved loci of the three orders of Neuropterida. After comparing taxonomically tailored and universal probes, our study suggests that the latter recovers higher number of shared UCEs for the superorder. Accordingly, we provide an optimized probe set that successfully targets 5,577 loci across all Neuropterida lineages.