Genome-wide species delimitation and quantification of the extent of introgression in eriophyoid mite Epitrimerus sabinae complex (Acariformes: Eriophyoidea).

Species complex hinders the exploration of terrestrial species diversity, particularly in small arthropod lineages that are morphologically indistinguishable from each other. The Epitrimerus sabinae complex in the Eriophyoidea provides a valuable case study in species complex delimitation, as they exhibit limited morphological variations. In this study, we obtained thousands of nuclear genomic single-nucleotide polymorphisms via whole-genome sequencing from 55 E. sabinae complex specimens, covering their potential all known distribution ranges. We implemented a framework to infer cryptic speciation, which involved phylogenetic and genetic clustering to identify potential species, followed by population demographic assessment to confirm lineage independence (and thus species status). Our results demonstrate that the E. sabinae complex comprises ten distinct species. These species range from highly divergent, genetically isolated lineages, to differentiated populations involving gene flow. This gene flow is widespread across species boundaries, indicating potential genetic introgression among them. Additionally, demographic analyses revealed that the ten species have followed unique trajectories in size change during the Quaternary period. Time-calibrated phylogenies further showed that speciation in the E. sabinae complex occurred rapidly, resulting in a rapid radiation during the Neogene period. Collectively, parallelism/convergence and recent divergence involving multiple gene flows may explain the homoplasy of E. sabinae complex. Our results highlight the integrated approach in species complex delimitation.