Ancient east-west divergence, recent admixture, and multiple marginal refugia shape genetic structure of a widespread oak species (Quercus acutissima) in China

The interactions of major topographic features with climate fluctuations over time are key factors that influence the spatial genetic structure of trees species. As an important characteristic of China’s terrain, the boundary between the mountainous West China and the lowland East China has been found to contribute to the divergence of many species. In this study, we examined whether the stepped geomorphology of China has shaped the genetic structure of Quercus acutissima, a widespread oak species native to East Asia, at a much larger geographic scale. Thirty natural populations of the species were sampled across the entire distribution in China and genotyped using ten nuclear microsatellite markers. To determine the genetic structure and demographic history, we conducted Bayesian cluster analysis and approximate Bayesian computation. A significant east-west divergence was detected at the species level, with western populations presenting much stronger differentiation and lower genetic diversity than eastern populations. The divergence between the groups of Southwest China and East China was estimated to have occurred 3.55–2.37 million years ago (Ma), closely associated with the recent uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes during the late Pliocene to the early Pleistocene. The Central China group may arise from the admixture of these two groups, which was dated to 0.83–0.55 Ma, a period covering several interglacial intervals with unusually warm and wet climate in Central China. The spatial genetic structure of Q. acutissima indicates the possibility of central-marginal dispersal dynamics along latitude and existence of multiple refugia at distribution edges. Our findings highlight that the stepped geomorphology in China and climatic changes since the Pliocene play an important role in shaping the intraspecific genetic structure of widespread species in East Asia.