| Yuansha Ruins is located in the lower reach of Keriyan River, which was dated about 2000-2500 years ago according to the features of pottery and the data of a series of 14C. Keriyan River is originated from the north of Kunlun Mountain, and flows into the center of Taklamakan Desert as a green life corridor. Based on its special geographic location and fine natural environment, the lower reach of Keriyan River growed to the cultural center of Taklamakan in the history. In the early of Han dynasty, the ancient Kermi country on the south Silk Road located in the area, which is around by many other famous ruins such as Niya. So the research on the ancient population of Yuansha Ruins have an important role on tracing the history of population origin and migration in the South of Xinjiang, even to the ones of Central Asia.In the study, 11 ancient bone samples were gathered from Yuansha Ruins. MtDNA was successfully extracted and amplified through four overlapping primers. After sequencing, we got the DNA data between site 16035 and 16398 in the hypervariable region I of mitochondrial DNA, which length is about 325bp (except the primers region). Compared with CRS, 16 polymorphic sites were detected including 1 deletion and 15 transitions, no transversion founded. 10 haplotype were obtained, and all the sequences were different except the sample 5 and 8 which were from the same individual. The mean number of pairwise differences and nucleotide diversity of the population is respectively 3.85236 ± 0.94758 and 0.0128412 ± 0.0031586.For the phylogenetic analysis, 35 modern populations in Eurasia and other ancient populations which are Chawuhu population in south of Xinjiang, Jiaohe, Yanghai, Subeixi populations in Turfan basin of Xinjiang , Xiongnu population in Mongolia, and the JiangJialiang population in Hebei province are also included. The result shows that all the ancient and modern populations in Central Asia occupy the positions between the Asian and Europe lineages. They are not only linked with the Europe branch through the populations in Turkey and Anatolian, also linked with the East Asia and north Asia branches, as well as the India branch. This suggests the important role of Central Asia in the human expansion and migration. The Yuansha population clustered with ancient Chawuhu population and Tajikistan population in High Pamirs, also the Uzbekistan population, which is mostly near the branch of INDUS valley among the compare populations in a larger region. India branch node is closer with Yuansha than the East/North Asia branch one, while those populations in Turfan basin are contrary. At the same time, Yuansha and Chawuhu population has shorter distance with the Europe compared with ancient Turfan basin populations. In addition, Luobenoer population is clustered with Europe. Moreover, the positions of the modern populations in Central Asia show a trend of geographic differentiation, while the trend is not significant and complex in special region. The multidimensional scan analysis shows a two dimensional distribution of genetic distances consistent with a geographic locations, which is similar with the results of phylogenetic population tree analysis. The relationship among Yuansha, Chawuhu and Turfan populations is closer, while the relationship between Yuansha and Yanghai is remoter. Luobenor population is close to the Europe and Iranian plateau populations. Compared with those modern populations, Yuansha population has a closer relationship with Tajikistan, Uzbekistan, and the populations in INDUS valley including Baluchistan, Karachi populations. The eastern region of Central Asia have a closer relationship with north and east Asia, which gradually decline from the east to west; the southern region shows a closer one with INDUS valley; the western region show a similar situation as the eastern one, but is relatively remoter from north and east Asia, and nearer the INDUS valley. Comparing with the above trends, the distribution of the ancient populations in eastern...
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