Mountain corridors and Sichuan Basin jointly shape the circum-basin diversification of Rhopalus latus (Hemiptera: Rhopalidae) in China

Mountain corridors may facilitate range expansion, whereas lowland basins may restrict dispersal and promote lineage divergence in cold-adapted species. How these contrasting topographic processes jointly shape phylogeographic structure remains poorly understood. Here, we investigated the evolutionary history of the cold-adapted montane stink bug Rhopalus latus, a species exhibiting a distribution along China’s second topographic step and around the Sichuan Basin. Population genomic analyses revealed four geographically structured clades: Northeast (NE), Northern Sichuan Basin (SN), Southern Sichuan Basin (SS), and Western Sichuan Basin (SW). The SN, SS, and SW clades formed a characteristic circum-Sichuan Basin pattern. Demographic analyses indicated that the NE clade diverged first (~588 ka), followed by divergence between the SN and SS clades (~344 ka). The SW clade originated more recently (~44 ka) through secondary contact and admixture between the SN and SS clades. Genetic diversity declined from southwest to northeast, with the NE clade retaining the lowest diversity and showing evidence of bottlenecks and elevated inbreeding. ENM suggested that southwestern China provided climatically stable refugial habitats throughout the Late Pleistocene, whereas northeastern populations experienced greater habitat instability. Landscape genetic analyses showed that geographic distance explained genetic differentiation better than environmental differences, supporting isolation by distance as the primary driver of divergence. Together, our results reveal a circum-basin phylogeographic pattern driven by the Sichuan Basin as an ecological barrier and by isolation-by-distance along the species’ range. This pattern illustrates how regional barriers and geographic distance, rather than environmental adaptation, can jointly shape lineage diversification and secondary contact in montane organisms.