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This study has mainly focused on ecological issues of Section Heterobalanus, which contains about nine sclerophyllous alpine species and occurs mainly in the China Mountains. To investigate the population history and demography of an endemic oak species (Quercus aquigolioides, Fagaceae) from the Himalaya-Hengduan Mountains region, and elucidate how the unique climatic conditions and heterogeneous topography resulted the uplift of the QTP shaped the genetic diversity and evolutionary history of the species. We sequenced and analyzed a total 1406 base pairs from chloroplast DNA (cpDNA) trnT-L sequences for 296 individuals from 19 populations across the species' geographic range. Based on these data, we constructed the genealogical relationships and coalescent analysis was used to test demographic hypotheses. 38 haplotypes were identified based on cpDNA variation, and of overall 38 haplotypes, 33 hyplotypes are restricted to single population. High levels of haplotype diversity (Hd=0.948) and low levels of nucleotide diversity (p=0.1976) were detected within the whole species, and a great amount of variation occurred among populations within groups (57.3%). The phylogenetic result demonstrated that Q. aquifolioides cpDNA hyplotypes have three main genetic lineages with distinct distribution. And these genetic lineages resulted by two main bottlenecks in the species took place at 9.37Ma and 8.41Ma, and they have undergone several genetic bottlenecks for a time span of ca. 9 million years. Significant interpopulation differentiation and phylogeopgraphic structure were also detected (G(ST)=0.629, N-ST=0.946, N-ST>G(ST), P<0.01), and the mismatch distribution analyses indicated a demographic equilibrium for Q. aquifolioides. But as a result of its complex topography, the overall network gave no clear indication regarding demographic process. Together with fossil evidence, the results strongly suggested that multiple microrefugia of Q. aquifolioides existing and the microrefugia were scattered throughout the present geographical range before the Last Glacial Maximum (LGM). Although this species seems to have post-glacial expansion, Q. aquifolioides did not undergo marked changes in population sizes from the late Miocene. And the uplift of the QTP contributed to the phylogeny of cpDNA hyplotypes and differentiation among the population by heterogeneous topographies and climatic change formed the uplift. The two main genetic bottlenecks at ca. 9Ma could contribute to the uplift of eastern and southern QTP at 13-8Ma and strengthen of Asian Summer monsoon at same time causing by the uplift. And several genetic differentiations at ca. 3Ma could confirm with the uplift of the QTP since 3.6Ma. It was reasonable to conclude that the Mio-Pliocene growth of the QTP and the accompanied climatic changes could account for the modern pattern of Q. aquifolioides phylogenetic structure in the HHMs region: first, the center and northern QTP drought and the different evaluation in south and east margin at 13-8Ma made the three main different lineages (NW group and other all). Then the asynchronous and heterogeneous uplifting of QTP in different regions during 9-0.7 Ma resulted to the difference time of the bottleneck in the different lineages. These findings have wide implications for understanding plant species' responses to the uplift of QTP and climatic change with it.