Regional-scale differentiation and phylogeography of a desert plant <Emphasis Type="Italic">Allium mongolicum</Emphasis> (Liliaceae) inferred from chloroplast DNA sequence variation

Past geological and climatic changes have promoted regional-scale intraspecific differentiation and range contraction/expansion in many temperate plants. However, little is known about how the desert species in central Asia responded to past geological and climatic changes, especially for a few widespread desert plants. In the present study, we aimed to survey the population structure and phylogeographical history of Allium mongolicum, which is widely distributed in the deserts of northwestern China. We sequenced two chloroplast DNA fragments (accD-psaI and psbA-trnH) for 418 individuals from 38 populations across the whole range of the species. Fourteen chlorotypes were identified, and three out of them were dominant. All populations were divided into three larger distinct groups by SAMOVA, which was largely congruent with the geographical division based on the Monmonier’s maximum-difference algorithm. Each of the groups occupied a distinct geographical region with a specific dominant chlorotype. Analysis of molecular variance showed that a high proportion of the total genetic variation (70.05%) existed among the three regions. The demographic dynamic tests indicated that the desert species had experienced a sudden regional-scale range expansion/recolonization in the Quaternary glaciers, which was further identified by the ecological niche modeling. These results suggest that the species has a distinct regional-scale differentiation as well as multiple geographically isolated refugia. Our results further enforce the idea that the environmental changes since the late Miocene greatly promoted differentiation of desert plants in northwestern China, and the Quaternary climatic oscillations played an important role in structuring the current populations of these species.