Revisiting the systematics of Brevipalpus flat mites (Tenuipalpidae): phylogeny, species groups and cryptic diversity

Phytophagous mites in the genus Brevipalpus (Tenuipalpidae) can be major pests, causing direct damage to their host plants or vectoring viruses. However, a phylogeny-based classification to understand their evolution and predict their bioecological aspects is lacking. Accurate species identification is crucial for studying pathosystem interactions, implementing quarantine measures, and developing control strategies. This study revisited the classification of Brevipalpus based on phylogenetic relationships, identifying cryptic species and determining genetic distance boundaries. A multi-tool exploration of DNA datasets, including mitochondrial (two COI regions) and nuclear (ITS2 and D1-D3) data combined with a detailed morphological study using light and scanning microscopy, was performed. Specimens were collected from 20 host plant families from South America, Europe, and the Middle East. Species were discriminated using three different approaches, namely, Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partition (ASAP), and a local regression to establish consistent genetic distance thresholds. Results indicate that the current species-group classification only partially matches that based on genetic lineages. Some species currently classified as belonging to the phoenicis and cuneatus species groups were found to be polyphyletic and related to species placed in other species groups. A rearrangement of the species groups to align with the observed genetic lineages is proposed, and phylogenetically informative morphological traits are defined. Cryptic diversity in certain taxa was consistently confirmed by various methods. Nuclear and mitochondrial markers were essential for identifying candidate lineages when morphology alone was insufficient. Nuclear markers detected host-associated lineages within certain species. Inconsistencies between markers and methods suggest the presence of ongoing speciation processes, and hypotheses about speciation events were explored. Intra- and interspecific genetic distances and threshold values were determined for the four studied genomic fragments and can be used for routine taxonomic identification and uncovering cryptic lineages. Further research should combine genetic data, carefully selected markers, and thorough morphological analyses before proposing new species.