Integrating niches, functional traits and genomics to reveal differentiation and inform adaptive management of sympatric Rhododendron species in montane forests

Understanding how closely related woody species coexist and respond to climate change is critical for conserving species-rich montane forests. However, forest management and conservation planning often lack integrated evidence linking ecological differentiation, functional strategies and adaptive genomic variation. Here, we integrated environmental niche, functional traits, genome-wide SNPs, ensemble species distribution models and genomic vulnerability assessments to investigate adaptive differentiation and climate vulnerability of three sympatric Rhododendron species from montane forests of the Yunnan–Guizhou Plateau, China: R. delavayi , R. irroratum and R. agastum . Despite broad geographic overlap, the three species occupied non-equivalent realized niches, with differentiation driven mainly by temperature–moisture and elevational gradients. They also diverged in multivariate leaf trait space, reflecting contrasting leaf construction, water-use and resource-use strategies. Genome-wide analyses revealed strong genomic differentiation among taxa, deep within-species lineage structure and asymmetric divergence, while mixed ancestry in R. agastum and migration-edge analyses suggested limited historical genetic exchange. Climate-associated genomic variation was primarily linked to temperature, precipitation and elevation, indicating that present-day ecological differentiation is partly aligned with adaptive genomic variation. Future projections showed substantial habitat contraction, upslope shifts and increasing genomic mismatch, especially under high-emission scenarios. The Wumeng–Miaoling–Xuefeng Mountains were identified as a shared hotspot of habitat loss, climatic novelty and genomic vulnerability, whereas parts of the Hengduan Mountains may function as potential climatic refugia. Our results show that integrating niches, traits and genomics can identify vulnerable populations, potential refugia and priority regions for adaptive conservation. This framework provides practical guidance for conserving montane Rhododendron diversity and managing climate-sensitive woody species in forest ecosystems.