Divergent Phylogeographic Responses to Quaternary Climate Change in Two Alpine‐Subalpine Sister Rhododendrons in Northeast Asia

ABSTRACT Aim This study aimed to explore how Pleistocene climatic oscillations influenced the demographic histories of two closely related alpine‐subalpine species in a region that has not been extensively studied. Additionally, the study sought to evaluate whether closely related species might respond differently to similar environmental pressures, leading to distinct demographic patterns. Taxon Rhododendron aureum Georgi and R. brachycarpum D. Don ex G. Don (Ericaceae). Location The study area, located in Northeast Asia, encompasses the Russian Far East, northeastern China, the Korean Peninsula, and the Japanese Archipelago. Methods We analysed 44 complete chloroplast genomes spanning their ranges and nuclear microsatellite genotypes from 19 populations, and applied ecological niche modelling (ENM) to infer past habitat shifts. We further inferred phylogenetic relationships, divergence times, genetic diversity, population structure, and historical range dynamics. Results Rhododendron aureum exhibited weak spatial structure, shallow plastid divergence, and low nuclear divergence among populations, alongside high diversity within populations. This pattern aligns with the idea of glacial niche tracking and historical connectivity. In contrast, R. brachycarpum showed pronounced regional differentiation, reduced diversity within populations, and clear signals of bottlenecks and founder effects. These characteristics are consistent with postglacial recolonization following southward shifts in glacial climatic suitability. ENM further suggested differing glacial responses: R. aureum retained broad suitable areas in northern regions, whereas suitable areas for R. brachycarpum were projected mainly farther south. Additionally, instances of cytonuclear discordance in sympatric populations are consistent with localized historical introgression. Main Conclusions Our results indicate that even closely related alpine species can follow different demographic paths despite experiencing similar Quaternary climatic pressures, highlighting the role of Northeast Asia as a natural laboratory for evolutionary diversification.