Castanopsis sclerophylla (Lindl.) Schott. is a canopy tree species of evergreen broad-leaved forests in subtropical China. In this study, the genetic diversity and population structure of C. sclerophylla were investigated by using chloroplast DNA sequences and nuclear microsatellite markers. Permutation tests with chloroplast DNA sequences indicated the presence of phylogeographic structure in C. sclerophylla. Based on nuclear microsatellite markers, Bayesian clustering analysis revealed eastern-to-western differentiation in C. sclerophylla, and the analysis of molecular variance suggested population divergence has arisen along the Xuefeng, Luoxiao, and Wuyi mountain ranges. The approximate Bayesian computation demonstrated that the genetic diversity pattern of C. sclerophylla could be explained by geographic isolation followed by secondary contact. Ecological niche modelling showed that distribution of C. sclerophylla shrank southward at the Last Glacial Maximum and expanded northward at the Mid Holocene. These results suggested that the uplift of the Xuefeng, Luoxiao, and Wuyi mountain ranges and the interglacial–glacial climate change shaped the genetic diversity of C. sclerophylla. The Luoxiao mountain range should be considered as a key conservation unit of C. sclerophylla due to its higher level of genetic diversity. Our study supplies important information for prioritizing the conservation and sustainable utilization of C. sclerophylla, and provides insight on the dynamics of evergreen broad-leaved forests in subtropical China.

Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units.