Intraspecific genetic variation and biogeographic history of the arid relict shrub Amygdalus pedunculata (Rosaceae) in northwest China

We studied the arid shrub Amygdalus pedunculata to better understand biogeographic histories and the impact of climate fluctuations during the Quaternary in shaping genetic variation and in northwest China. Three chloroplast DNA intergenic spacers (psbK‐psbI, trnL‐trnF and trnV) were sequenced in 129 individuals from 10 populations across the range of A. pedunculata, and 17 haplotypes were identified, with one haplotype that was distributed across all sampled populations. High levels of total gene diversity (HT = 0.965) and within‐population diversity (HS = 0.669) were identified. Analysis of molecular variance (AMOVA) indicated that most genetic variation occurred within populations. Neutrality tests and mismatch distribution analysis suggested past range expansions of A. pedunculata. As such, A. pedunculata has likely undergone a substantial postglacial range expansion northward and southward along the margins of the northern Yin Mountains and Mu Us Desert, respectively. Principal coordinate analyses, median‐joining network analysis and Beast analysis revealed that 17 haplotypes mainly formed three clusters, corresponding to the Northern (Damao Banner) and Central (Wula Mountains and Guyang County) regions of Inner Mongolia and the Southern region (Bulang Township) in northern Shannxi. The local adaptative differentiation is speculated to have occurred among the three regions mainly resulting from geographical isolation caused by the uplift and extension of the Yinshan Mountains during the Quaternary.