Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree.

Plant phylogeographic studies in East Asia have provided support for the biogeographic hypothesis that the complex landforms and climate of this region have provided substantial opportunities for allopatric speciation. However, most of these studies have been based on maternally inherited chloroplast DNA (cpDNA) markers and were therefore unable to reveal the role of pollen-mediated gene flow in preventing population divergence. Here, we investigate the phylogeography of the Chinese walnut Juglans cathayensis, a temperate deciduous tree widely distributed across disjunct montane sites in subtropical China. We genotyped 19 populations using seven cpDNA fragments and ten nuclear microsatellite loci and modeled the ecological niche of J. cathayensis. CpDNA analysis identified a total of nine haplotypes, and each of the 19 sampled populations was fixed for a single haplotype, displaying a prominent phylogeographic structure. The results of ecological niche modeling indicated that J. cathayensis populations survived the last glaciation in situ, although they were probably more fragmented than today. In contrast, we detected a much weaker, but nonetheless clear, genetic structure based on nuclear microsatellite data. Our study demonstrates how extensive pollen flow can erase the genetic imprint of long-term refugial isolation in maternal lineages, effectively preventing population differentiation in temperate, particularly wind-pollinated, forest trees in subtropical China.