Phylogenetic relationships of and within non-photosynthetic parasitic lineages are notoriously poorly known, which negatively affects our understanding of parasitic plants. This is also the case for Cistanche (Orobanchaceae), an Old World genus with about two dozen species, whose relationships have not yet been addressed using molecular phylogenetic approaches. Here we infer phylogenetic relationships within the genus, employing a taxonomically and geographically broad sampling covering all previously distinguished infrageneric groups and most of the currently recognized species. A combined matrix of three plastid markers (trnL-trnF, including the trnL intron and the intergenic spacer (IGS), trnS-trnfM IGS and psbA-trnH IGS) and one nuclear marker (ITS) was analyzed using maximum parsimony, maximum likelihood and Bayesian inference. Cistanche falls into four well-supported and geographically differentiated clades: East Asian Clade, Northwest African Clade, Southwest Asian Clade and Widespread Clade. Of those, only the East Asian Clade corresponds to a previously recognized taxonomic section, whereas the others either contain members of two or three sections (Widespread Clade and Southwest Asian Clade, respectively) or have not been taxonomically recognized so far (Northwest African Clade). Whereas the Southwest Asian Clade exhibits strong phylogenetic structure among and partly within species (the East Asian Clade and the Northwest African Clade are monospecific), phylogenetic resolution within the Widespread Clade is often low and hampered by discrepancies between nuclear and plastid markers. Both molecular and morphological data indicate that species diversity in Cistanche is currently underestimated.

众所周知，非光合寄生谱系及其内部的亲缘关系众所周知，这不利于我们对寄生植物的理解。肉stan蓉属（Orobanchaceae）也是如此，这是一种旧世界属，大约有二十多种，其关系尚未使用分子系统发育方法解决。在这里，我们通过分类学和地理上广泛的采样来推断属内的系统发育关系，这些采样涵盖了所有先前杰出的次基因组和大多数当前公认的物种。三种质体标记物（trnL-trnF，包括trn L内含子和基因间隔子（IGS），trnS - trnfM使用最大简约，最大似然和贝叶斯推断分析了IGS和psbA - trnH IGS）和一个核标记（ITS）。肉stan蓉分为四个有良好支持和地理差异的进化枝：东亚进化枝，西北非洲进化枝，西南亚进化枝和广泛进化进化枝。其中，仅东亚进化枝对应于先前公认的分类学部分，而其他则包含两个或三个部分的成员（分别为宽泛进化枝和西南亚进化枝）或到目前为止尚未被分类学认识（西北非洲进化枝） 。西南亚进化枝在种间和种内表现出很强的系统发育结构（东亚进化枝和西北非洲进化枝是单特异性的），而广泛进化枝内的系统发育分辨率通常很低，并且受核和质体标记之间的差异所阻碍。分子和形态学数据均表明肉stan蓉目前被低估了。