Summary• Numerous temperate plants now distributed across Eurasia are hypothesized to have originated and migrated from the Qinghai-Tibet Plateau (QTP) and adjacent regions. However, this hypothesis has never been tested through a phylogeographic analysis of a widely distributed species. Here, we use Hippophaë rhamnoides as a model to test this hypothesis.• We collected 635 individuals from 63 populations of the nine subspecies of H. rhamnoides. We sequenced two maternally inherited chloroplast (cp) DNA fragments and also the bi-paternally inherited nuclear ribosomal ITS.• We recovered five major clades in phylogenetic trees constructed from cpDNA and internal transcribed spacer (ITS) sequence variation. Most sampled individuals of six subspecies that are distributed in northern China, central Asia and Asia Minor ⁄ Europe, respectively, comprised monophyletic clades (or subclades) nested within those found in the QTP. Two subspecies in the QTP were paraphyletic, while the placement of another subspecies from the Mongolian Plateau differed between the ITS and cpDNA phylogenetic trees.• Our phylogeographic analyses supported an 'out-of-QTP' hypothesis for H. rhamnoides followed by allopatric divergence, hybridization and introgression. These findings highlight the complexity of intraspecific evolutions and the importance of the QTP as a center of origin for many temperate plants.

Increasing evidence suggests that geological or climatic events in the past promoted allopatric speciation of alpine plants in the Qinghai-Tibetan Plateau and adjacent region. However, few studies have been undertaken to examine whether such allopatric divergences also occurred within a morphologically uniform species. In the present study, we report the evolutionary history of an alpine shrub species, Hippophae tibetana, based on examining chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variations. We sequenced two cpDNA fragments (trnL-F and trnS-G) and the nuclear ITS region in 183 individuals collected from 21 natural populations. Ten chlorotypes and 17 ITS types were identified. Phylogenetic analyses of both chlorotypes and ITS sequence variations suggested two distinct lineages distributed in the eastern and western region, respectively. On the basis of the fast and low plant substitution rates, these two lineages were estimated to have diverged from each other between 1 and 4 million years ago, during the period of the major glaciations and orogenic processes. In addition, ITS has undergone the accelerated evolution in two populations in the southern Himalaya isolated by the high mountains with a surprising accumulation of the private variations. The east-west split was also supported by an analysis of molecular variance, which partitioned around 91% of the total cpDNA variance between these two groups of populations. A single chlorotype was found for most populations in eastern or western region, suggesting a recent postglacial expansion within each region. Star-phylogeny and mismatch analyses of all chlorotypes within the eastern group of populations suggested an earlier regional expansion before the Last Glacial Maximum (LGM). The local fixture of the different chlorotypes in multiple populations suggested more than one refugia remained for eastern or western region. Coalescent tests rejected the hypothesis that all current populations originated from a single refugium during the LGM. Instead, they supported hypothesis that two lineages diverged before the late Pleistocene. These findings, when taken together, suggested that this species had experienced long allopatric divergence and recent regional range expansions in response to orogenic processes and the climate changes. The evolutionary history of this shrub species highlights importance of geographical isolations to the intraspecific divergence of alpine plants occurring in the world's ruff.

To date, little is still known about how alpine species occurring in the Qinghai-Tibetan Plateau (QTP) responded to past climatic oscillations. Here, by using variations of the chloroplast trnT-L, we examined the genetic distribution pattern of 101 individuals of Potentilla glabra, comprising both the interior QTP and the plateau edge. Phylogenetic and network analyses of 31 recovered haplotypes identified three tentative clades (A, B and C). Analysis of molecular variance (amova) revealed that most of the genetic variability was found within populations (0.693), while differentiations between populations were obviously distinct (F(st)= 0.307). Two independent range expansions within clades A and B occurring at approximately 316 and 201 thousand years ago (kya) were recovered from the hierarchical mismatch analysis, and these two expansions were also confirmed by Fu's F(S) values and 'g' tests. However, distant distributions of clade C and private haplotypes from clades A and B suggest that they had survived the Last Glacial Maximum (LGM) and previous glaciers in situ since their origins. Our findings based on available limited samples support that multiple refugia of a few cold-enduring species had been maintained in the QTP platform during LGM and/or previous glacial stages.

Homoploid hybrid speciation, the origin of a hybrid species without change in chromosome number, is currently considered to be a rare form of speciation. In the present study, we examined the phylogenetic origin of Hippophaë gyantsensis, a diploid species occurring in the western Qinghai–Tibet Plateau. Some of its morphological and molecular traits suggest a close relationship to H. rhamnoides ssp. yunnanensis while others indicate H. neurocarpa. We conducted phylogenetic analyses of sequence data of two maternally inherited chloroplast (cp) DNA fragments and the bi‐parentally inherited nuclear ribosomal internal transcribed spacer (ITS) from 17 populations of H. gyantsensis, 15 populations of H. rhamnoides ssp. yunnanensis and 27 populations of H. neurocarpa across their distributional ranges, and modelled the niche differentiation of the three taxa. Multiple lines of evidence suggested that H. gyantsensis is a morphologically stable, genetically independent and ecologically distinct species. The inconsistent phylogenetic placements of the H. gyantsensis clade that comprised the dominant cpDNA haplotypes and ITS ribotypes suggested a probable diploid hybrid origin from multiple crosses between H. rhamnoides ssp. yunnanensis and H. neurocarpa. This tentative hypothesis is more parsimonious than alternative explanations according to the data available, although more evidence based on further testing is needed.