Abstract
Aim Exploring the divergence and speciation processes is central to understanding the origin and maintenance of biodiversity. The dry valley mosaic in the Hengduan Mountains and its southern extension range is one of the special landscapes globally and harbours a high level of endemic plants of tropical margin nature. The dry valleys and lowlands‐adapted plants constitute a unique system to explore how the geological and ecological effects have shaped the speciation processes here. Location Subtropical China. Taxon Diospyros dumetorum and Diospyros saxatilis. Methods We surveyed patterns of genetic variation from 33 populations spanning their distribution ranges using three chloroplast DNA fragments and eight nuclear microsatellite loci. Approximate Bayesian computation was conducted to compare population demographic models considering gene flow and to estimate key parameters. We used Ecological Niche Models (ENMs) to reconstruct changes in range distribution during glacial and interglacial periods and evaluate their niche differentiation. Results Plastid and nuclear data strongly support divergence between the two species occurring during the Pliocene/Pleistocene period followed by secondary contact in response to climatic oscillations. ENMs predicted drastic distribution range changes during the Quaternary and identified significant differences in climatic conditions at the set of locations occupied by these two species. Correlation analyses were conducted, and the results suggest that geographical isolation rather than environmental heterogeneity shapes the current population genetic structure within the two species. Main Conclusion Phylogeographical patterns revealed in our results document that geographic vicariance associated with tectonic uplifts initiated allopatric species divergence between the two dry valleys and lowlands‐adapted Diospyros species, and niche differentiation perhaps further accelerated the speciation processes with limited subsequent gene flow. Our findings could contribute to the knowledge of forces that drive speciation processes in the unique landscape of dry valleys, as well as the evolution of the flora in subtropical China.