Phylogenomics of the leaf-footed bug subfamily Coreinae (Hemiptera: Coreidae): applicability of ultraconserved elements at shallower depths

Abstract

Baits targeting invertebrate ultraconserved elements (UCEs) are becoming more common for phylogenetic studies. Recent studies have shown that invertebrate UCEs typically encode proteins -- and thus, are functionally different from more conserved vertebrate UCEs --can resolve deep divergences (e.g., superorder to family ranks). However, the ability of the invertebrate UCE baits to robustly resolve relationships at shallower phylogenetic scales (i.e., tribes and congeners) has been generally limited to Coleoptera and Hymenoptera. Here, we assessed the ability of a recently designed Hemiptera UCE bait set to reconstruct more recent phylogenetic relationships in the largest leaf-footed bug subfamily, the Coreinae (Hemiptera: Coreidae), using a taxon-rich sample representing 21 of the 32 coreine tribes. Many well-supported, novel relationships were congruent in maximum likelihood and summary coalescent analyses. We also found evidence for the para- and polyphyly of several tribes and genera of Coreinae, as well as the subfamilies Coreinae and Meropachyinae. Our study, along with other recent UCE studies, provides evidence that UCEs can produce robust and novel phylogenetic hypotheses at various scales in invertebrates. Additionally, we used different DNA extraction and target enrichment protocols and recovered more UCE data using a touch-down hybridization approach.