Phylogeographic Evidence for a Link of Species Divergence of <em>Ephedra</em> in the Qinghai-Tibetan Plateau and Adjacent Regions to the Miocene Asian Aridification

<div><p>The Qinghai-Tibetan Plateau (QTP) has become one of the hotspots for phylogeographical studies due to its high species diversity. However, most previous studies have focused on the effects of the Quaternary glaciations on phylogeographical structures and the locations of glacial refugia, and little is known about the effects of the aridization of interior Asia on plant population structure and speciation. Here the chloroplast DNA (cpDNA) <em>trn</em>T-<em>trn</em>F and <em>trn</em>S-<em>trn</em>fM sequences were used to investigate the differentiation and phylogeographical history of 14 <em>Ephedra</em> species from the QTP and northern China, based on a sampling of 107 populations. The phylogeographical analysis, together with phylogenetic reconstruction based on combined four cpDNA fragments (<em>rbc</em>L, <em>rpl</em>16, <em>rps</em>4, and <em>trn</em>S-<em>trn</em>fM), supports three main lineages (eastern QTP, southern QTP, and northern China) of these <em>Ephedra</em> species. Divergence of each lineage could be dated to the Middle or Late Miocene, and was very likely linked to the uplift of the QTP and the Asian aridification, given the high drought and/or cold tolerance of <em>Ephedra</em>. Most of the <em>Ephedra</em> species had low intraspecific variation and lacked a strong phylogeographical structure, which could be partially attributed to clonal reproduction and a relatively recent origin. In addition, ten of the detected 25 cpDNA haplotypes are shared among species, suggesting that a wide sampling of species is helpful to investigate the origin of observed haplotypes and make reliable phylogeographical inference. Moreover, the systematic positions of some <em>Ephedra</em> species are discussed.</p>