Genetic structure and demographic history of Allium mongolicum based on SSR markers

The population genetic structure was proved to be influenced by both historical events and gene flow, which can be examined by analyzing intraspecific differentiation and spatiotemporal population dynamics of a species at large spatial scale. In this study, we surveyed the population structure and evolutionary dynamics of 38 natural populations of a desert plant, Allium mongolicum Regel (Liliaceae), in northwestern China, using nine microsatellite loci. High genetic diversity was observed within populations, with mean allele diversity and the expected heterozygosity values of 0.689 and 0.655, respectively. The value of expected heterozygosity ( H e = 0.655) was higher than that of observed heterozygosity ( H o = 0.317), which indicated an excess of homozygosity within populations, which could be due to inbreeding. The gene flow among populations was high ( N m = 1.245) while the genetic differentiation among populations was low ( F st = 0.169). However, a distinct regional-scale differentiation was discerned among three geographical regions. Our results further detected considerably restricted but asymmetric gene flow among the three regions. The demographic dynamic analysis also detected an ancient population contraction and subsequent expansion during 0.11–0.33 Ma. These results suggested that both gene flow and population contraction/expansion caused by climate oscillations in ancient time played an important role in forming the population structure and accelerating the regional-scale differentiation of the desert plant. Our results further enforce the idea that the aridification and subsequent desert expansion/contraction since Pleistocene have greatly promoted the habitat fragmentation, and subsequent plant differentiation in northwestern China.