Phylogeography and population dynamics of an endemic oak (Quercus fabri Hance) in subtropical China revealed by molecular data and ecological niche modeling

Abstract

High numbers of endemic plants exist in subtropical China, but there have been few investigations of the phylogeography and dynamic history for endemic tree species in this region. In this study, we explored the phylogeographic pattern of Quercus fabri, an endemic oak species in subtropical China, to assess the effects of past geographical and climatic changes on the evolutionary history of this deciduous species using three chloroplast DNA (cpDNA) fragments and the internal transcribed spacer region (ITS) and ecological niche modeling (ENM). The cpDNA fragments differentiated three phylogeographical groups among Q. fabri populations. A BEAST-derived chronogram based on the cpDNA haplotypes indicated that the initial divergence of Q. fabri probably occurred during the late Miocene (12.33 Ma), whereas haplotype divergence time could date back to the late Pliocene to early Pleistocene. ENM showed that the suitable areas contracted during the last glacial maximum (LGM) and expanded in the warm period during the Pleistocene. Consistently, both the cpDNA and ITS datasets suggested that population expansion occurred after the LGM period (ca. 13–14 kyr) for Q. fabri. Demographical analyses based on multiple genetic datasets and a coalescent-based method also suggested a shrinkage–expansion trend for the effective population sizes of Q. fabri during the glacial–interglacial periods in the Quaternary. Our results suggest that the Neogene and Pleistocene were important periods for triggering species differentiation and intraspecific diversification in Q. fabri, thereby providing insights into the effects of environmental changes in the Quaternary on the population dynamics of endemic tree species in subtropical China.