Data from: Phylogeography of the arid shrub Atraphaxis frutescens (Polygonaceae) in northwestern China, evidence from cpDNA sequences

Climatic fluctuations during the Pleistocene are usually considered a significant factor in shaping intraspecific genetic variation and influencing demography histories. To well understand these processes in desert northwest China, we selected arid adapted Atraphaxis frutescens as the study species. Two cpDNA regions (psbK-psbI, psbB-psbH) were sequenced in 272 individuals from 33 natural populations across the range of this species, and 10 haplotypes were identified. High levels of total gene diversity (HT=0.858), and low levels of within-population diversity (HS=0.092) were detected. Analysis of molecular variance (AMOVA) indicated that genetic differentiation primarily occurred among groups of populations. Based on BEAST analysis, we conclude that intraspecific differentiation of the species, resulting from isolated populations, accompanied enhanced desertification during the late Pleistocene. The expansion of the Gurbantunggut and Kumtag deserts in this area appears to have triggered divergence among populations of the western, central and eastern portions of the region and shaped genetic differentiation among them. Two independent glacial refugia were identified, the Ili Valley and the northern Junggar Basin. Extensive development of arid habitats (desert margin and arid piedmont grassland) coupled with a more equable climate since the early Holocene has promoted recent expansion of A. frutescens.