Unveiling phylogenetic relationships of Brachypylina (Acari: Oribatida) using whole-genome sequencing data

The ecologically important oribatid mites are soil arthropods widely used as bioindicators in environmental monitoring. Several major oribatid lineages are considered to be monophyletic; however, internal relationships within the species-rich Brachypylina remain poorly resolved. To fill this knowledge gap, new whole-genome sequences were generated for 43 species of oribatid mites in this study, and they were combined with genomic data from 42 additional oribatid species and two outgroup taxa retrieved from NCBI. Based on thousands of universal single-copy orthologs (USCOs), a robust higher-level phylogeny was reconstructed using concatenated and coalescent methods based on multiple data matrices (USCO_DVMC70/80/90). The resulting topologies were highly congruent, although the placement of some unstable taxa, such as Allodamaeus sp., differed between inference methods. While a comprehensive assessment of early-diverging lineages (e.g., Enarthronota and Mixonomata) was not possible due to limited sampling, core groups including Hypochthonioidea, Phthiracaroidea, and Euphthiracaroidea were consistently recovered as monophyletic. Within Brachypylina, Opsiopheredermata was recovered as monophyletic, whereas Eupheredermata, Pycnonotic Apheredermata, and Dorsodeficient Apheredermata were non-monophyletic, showing extensive nesting among constituent superfamilies such as Ameroidea, Oppioidea, and Gustavioidea. A broadly circumscribed Poronota, including Tectocepheus velatus , was consistently recovered as monophyletic. This study enriched genome-scale resources for Oribatida and provided a robust framework for understanding long-standing phylogenetic and taxonomic problems in this group.