Abstract Climate change and human activities alter habitat suitability and connectivity, significantly affecting plant species distribution. The complex topography and variable climate of the Yunnan–Guizhou Plateau provide an ideal system for studying species differentiation in heterogeneous habitats. In this study, restriction site-associated DNA sequencing was employed to assess the genetic characteristics of the endemic shrub Morella nana. Using genetic structure analysis, phylogenetic reconstruction, genotype–environment association, and approximate Bayesian computation, we investigated the species’ geographic structure and evolutionary history. Results revealed moderate genetic diversity, low differentiation, and incomplete divergence. Populations from the Guizhou and Yunnan Plateaus diverged from a common ancestor, with subsequent dispersal of Yunnan populations to south-western and north-western regions. Landscape genomic analysis demonstrated that climatic factors contributed more to genetic variation than geographical factors, with temperature and precipitation identified as key drivers of adaptive differentiation in M. nana. Furthermore, predicted candidate adaptive genes suggested that genes involved in cell wall remodelling and precipitation regulation may play important roles in local adaptation. These findings indicate that, while the species has retained moderate genetic diversity despite recent habitat loss and fragmentation, future climate change may pose a significant threat to its survival. Our findings hold significant implications for the conservation and management of M. nana.
Lu et al. (Thu,) studied this question.