Data from: History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai-Tibetan Plateau (QTP) remains largely unknown. Here we report a survey of chloroplast (cp) and nuclear ribosomal (ITS) DNA variation aimed at exploring the phylogeographic history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20-rps12 intergenic spacer, the trnV intron and psbA-trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the species' range. Two distinct lineages with east and west geographical distributions respectively were identified from a phylogenetic analysis of ITS sequence variation and the divergence were estimated to be around 1.45 Ma. Nine chlorotypes that clustered into two major clades were broadly congruent in geographical distribution with the two ITS lineages, which was also supported by an analysis of molecular variance (AMOVA). Analysis of the spatial distribution of chlorotypes and coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and the four-refugia hypothesis during the LGM. Two previous phylogeographic studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south-eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.

第四纪（Quaternary）气候振荡对青藏高原（Qinghai-Tibetan Plateau, QTP）高山植物的分布范围与种内分化造成的影响，目前仍鲜为人知。本研究以青藏高原特有高山植物露蕊乌头（Aconitum gymnandrum）为研究对象，通过调查其叶绿体（chloroplast, cp）与核核糖体转录间隔区（ITS）DNA的变异情况，旨在解析该物种的谱系生物地理学历史。我们对覆盖该物种完整分布范围的23个种群共245个个体，开展了3个叶绿体DNA（cpDNA）片段（rpl20-rps12基因间隔区、trnV内含子及psbA-trnH基因间隔区）与核基因组ITS区的测序工作。基于ITS序列变异的系统发育分析，共鉴定出两个分化显著的支系，二者分别呈东、西地理分布，其分化时间估算为约145万年前。共获得9种叶绿体单倍型，可聚类为两大支系，其地理分布格局与两个ITS支系大体一致，该结果亦得到分子方差分析（analysis of molecular variance, AMOVA）的支持。对叶绿体单倍型空间分布的分析，以及叶绿体单倍型谱系的溯祖模拟结果，均支持两大叶绿体DNA支系起源于早更新世，以及末次盛冰期（Last Glacial Maximum, LGM）的四重避难所假说。此前两项针对青藏高原高山植物的谱系生物地理学研究表明，此类植物在末次盛冰期及/或此前的冰盛期，会退缩至高原东部/东南部边缘的避难所中。但本研究针对露蕊乌头的结果显示，至少部分此类耐寒物种，在整个第四纪时期均可在青藏高原腹地存活。