Extremely high diversity and endemism of chlorotypes in Wikstroemia monnula Hance (Thymelaeaceae) shed light on the effects of habitat heterogeneity on intraspecific differentiation in southeast China

Abstract Southeast China is one of the core areas of the Sino‐Japanese floristic region and a hotspot of biodiversity in East Asia. This region has been considered as both a museum and a cradle of woody genera in China. Why a region with highly stable topography and climate could be a cradle of species diversity remains unclear. In this study, the phylogeographic pattern and genetic structure of Wikstroemia monnula , an endemic species to southeast China, were analyzed by sequencing four chloroplast DNA fragments (4679 bp in total) of 836 individuals from 39 populations. Extremely high diversity and endemism of chlorotypes were found. Out of 54 chlorotypes, 51 (94.44%) were private, with genetic diversity index ( H T ) near 1 ( H T = 0.992), and 96.51% of the genetic variation occurring among populations, indicating that this species has undergone strong intraspecific differentiation and very limited migration. The correlational analysis showed that the population differentiation of W. monnula was driven not only via isolation by distance (IBD), but more importantly via isolation by environment (IBE). A significant phylogeographic structure was not found ( N ST = 0.979, G ST = 0.833, P > 0.05); however, the spatial pattern of the sublineages of chlorotypes was largely consistent with the biogeographic boundaries on a smaller scale in the region. These results suggest that habitat heterogeneity in southeast China not only promoted speciation on a long time‐scale, but still continues to impact population differentiation in recent times.