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）气候振荡如何影响青藏高原（Qinghai-Tibetan Plateau, QTP）高寒植物的分布范围与种内分化，目前仍不甚明晰。本研究针对叶绿体（chloroplast, cp）与核核糖体内转录间隔区（Internal Transcribed Spacer, ITS）DNA的变异开展调查，旨在解析青藏高原特有高寒植物露蕊乌头（Aconitum gymnandrum）的谱系地理学历史。我们对该物种全分布范围内23个种群的245个个体，进行了3段cpDNA片段（rpl20-rps12基因间区、trnV内含子与psbA-trnH基因间区）以及核ITS区域的测序。基于ITS序列变异的系统发育分析，我们鉴定出两个地理分布分别呈东、西格局的支系，其分化时间经估算约为1.45 Ma。9个聚类为两大分支的叶绿体单倍型（chlorotype），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（coalescent simulation），均支持两大cpDNA分支的早更新世（Pleistocene）起源，以及末次盛冰期（Last Glacial Maximum, LGM）的四避难所假说。此前两项针对青藏高原高寒植物的谱系地理学研究表明，这类耐寒植物在末次盛冰期及更早的冰期极盛期时，均退缩至高原东部/东南部边缘的避难所中。然而，本研究中露蕊乌头的结果则显示，至少有部分这类耐寒物种，在整个第四纪时期也可在青藏高原腹地存活。