Genomic analysis of population structure and target-site mutations of Tetranychus truncatus in China

Tetranychus truncatus is a dominant mite pest in China, yet its population structure and pesticide resistance status remain poorly characterized. To address this, we performed whole-genome resequencing of 176 individuals, integrating them with previous data to analyze 343 individuals from 44 populations. We investigated the population genetic structure, screened for 22 target-site resistance mutations across ten genes, and reconstructed the evolutionary origins of resistance mutations in acetylcholinesterase (AChE).

Phylogenetic analysis identified four geography-based clades. The southeast China (SEC) lineage emerged as the most genetically distinct, characterized by high differentiation yet low nucleotide diversity. However, deviations from strict geographic clustering were observed; TreeMix and admixture analyses revealed that phylogenetic outliers resulted from extensive gene flow bridging distant lineages. While resistance mutations were generally rare, high frequencies of AChE mutations were detected. Evolutionary analysis revealed contrasting patterns: the widespread F331W mutation and the derived G328A mutation (confined to northern regions) shared a single evolutionary origin, whereas the F331Y mutation, which dominated the isolated SEC lineage, arose via multiple independent origins.

Resistance evolution in T. truncatus is tightly coupled with population history. The strong isolation of the SEC lineage maintains a distinct, independently evolved resistance profile (F331Y), limiting the ingress of northern haplotypes. Conversely, extensive anthropogenic gene flow in northern China has facilitated the widespread dispersal of the single-origin F331W and G328A mutations. These findings highlight that both historical divergence and human-mediated dispersal shape local resistance landscapes, necessitating region-specific management strategies. © 2026 Society of Chemical Industry.