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.