A Novel Specific UCE Probe Set Sheds New Light on the Phylogeny of Eriophyoid Mites

ABSTRACT Eriophyoid mites (Eriophyoidea) represent a highly diverse arthropod lineage with more than 5000 named species worldwide. Recent advances in sequence‐capture phylogenomics, particularly using ultraconserved elements (UCEs), have significantly enhanced phylogenetic and evolutionary analyses in Arachnida. However, the current probe sets are suboptimal for eriophyoid mites due to the lack of specific probes. In this study, we developed an Eriophyoidea‐specific UCE probe set (25,226 probes targeting 2172 loci) based on our newly sequenced 86 eriophyoid mite genomes and compared its performance in phylogenetic reconstruction with the Acari and Arachnida probe sets. This newly developed UCE probe set has doubled the efficiency of sequence capture and shows stronger support for certain phylogeny than previous probe sets. Our phylogenetic results recovered Eriophyoidea monophyletic whereas the monophyly of Trombidiformes and Sarcoptiformes was rejected because eriophyoid mites were placed outside of Trombidiformes and grouped with two Sarcoptiformes species. Furthermore, the monophyly of three families (i.e., Phytoptidae, Eriophyidae and Diptilomiopidae) was rejected—Eriophyidae+Diptilomiopidae nested within Phytoptidae and Diptilomiopidae nested within Eriophyidae. Our study provides a useful tool for higher‐level phylogenomics and evolutionary studies among eriophyoid mites and sheds new light on the recalcitrant relationships within Acariformes.