Abstract: Phylogeographic studies on alpine plants endemic to the Hengduan Mountains of the southeastern Qinghai–Tibet Plateau are still limited in number. In this study, we used sequence variation of one nuclear gene (ncpGS, which encodes the chloroplastic glutamine synthetase) and in two chloroplast DNA segments to investigate the phylogeographic structure and population demographic history of Cyananthus delavayi, a narrow-range species endemic to this region. We identified eight chlorotypes and 16 nuclear genotypes in a survey of 10 populations sampled throughout the range of the species. The results of both phylogenetic and network analyses suggested that the genealogical relationships of both chlorotypes and nuclear genotypes showed a clear geographical correlation. High total genetic diversity, low levels of within-population diversity, and strong population differentiation (chloroplast DNA: h_T= 0.827, h_S= 0.087, N_ST= 0.899, G_ST= 0.895; nuclear DNA: h_T= 0.910, h_S= 0.348, N_ST= 0719, G_ST= 0.618) were identified. Based on the mismatch distribution analyses, no evidence of recent demographic population expansion was found for this species. Nested clade analyses of both chlorotypes and nuclear genotypes indicated that restricted gene flow resulting from isolation by distance and allopatric fragmentation were likely to have been the major processes that shaped their present-day spatial distribution. Our dating of the genetic divergences between three major geographic lineages suggested that the largest glaciation of the early Quaternary developed in the Qinghai–Tibet Plateau and mountainous isolation may have together led to deep intraspecific vicariance within this species.

Key words: chloroplast DNA, Cyananthus delavayi, Hengduan Mountains, ncpGS, phylogeography, vicariance.