A first ultraconserved elements phylogeny of Diaspidinae armored scale insects from genomic data

Abstract

Diaspidinae is the largest group of armored scale insects (Hemiptera: Coccomorpha: Diaspididae), with more than 200 genera and considerable ecological and economic impact. Despite their importance, relationships within Diaspidinae and the placement of its earliest lineages are still not well understood. Here, we analyze ultraconserved elements (UCEs) data to clarify the phylogeny of the group. Our dataset includes 24 genomic samples, covering all 2 tribes and 3 subtribes of the ingroup currently known from China. We employed a broad and hierarchically structured outgroup sampling to provide both proximate and distant comparative lineages, creating a stable phylogenetic framework for evaluating the internal relationships and monophyly of Diaspidinae. Using a taxon-specific Coccoidea-v4 probe set, we recovered 3,995 UCE loci, ranging from 1,093 to 3,238 loci per genome (average 2,928) for the ingroup genomic datasets alone, and 289 to 3,238 UCE loci were recovered with an average of 2,566 UCE loci with the outgroup included. Phylogenetic analyses with maximum likelihood, Bayesian inference, and maximum parsimony all strongly supported the monophyly of Diaspidinae. To our knowledge, our study is the first to use UCE data for Diaspidinae, and it also demonstrates both the applicability of UCE and the feasibility of a hierarchically structured outgroup strategy.