| Based on the molecular biology, ancient DNA research could analyze the genetic information of the ancient samples despite the time limitation in human evolution. By comparing the modern living creatures with the ancient ones, it could answer the questions of the origin, evolution and expansion of various kinds of lives including mankind. Mitochondrial DNA was most suitable for ancient DNA analysis because of high mutation rate, no recombination and multiple copies.Xinjiang Uigur Autonomous Region of China, located in northwest China, was famous for the ancient Silk Road. As an area of contact between Asia and Europe, Xinjiang had experienced a scenario of complex cultural from West and East Eurasian. The ancient civilization of China, India, Persia and Greece could all be found there, so the analysis of the ancient Xinjiang populations had always been an important research topic in the international academics. Cui et al. had analysis the mitochondrial DNA hypervariable region I of ancient Luobunouer, Turfan, Chawuhu and Yuansha populations, and provided important genetic evidences of human origin and movement.We selected three important relics which were located in Xinjiang Tarim Basin for ancient DNA analysis, including Sampula cemetery and Niya relic which were located in south route of Silk Road, and the Xiaohe cemetery was located in Luobupo. These samples were analyzed not only the mitochondrial DNA hypervariable region I, but also the RFLP of coding region, at the same time, quantification PCR was also performed in our research.The Yu Hong tomb archaeological site was located in Wangguo country of Taiyuan, Shanxi province. A well-preserved epitaph carved on the tombstone was found. The epitaph showed that Yu Hong died in 592 A.D, and the ancestors of Yu Hong lived in the ancient Yu country which was located in somewhere of Central Asian. Yu Hong came to central part of China and settled in there.SYBR green I Real-time polymerase chain reaction (PCR) was used to quantify five tooth and bone samples, which were excavated in Xiaohe cemetery, China. To evaluate the preservation of these ancient samples and to compare the DNA content of tooth and bone samples, three different fragment sizes (138 bp, 209 bp and 363 bp) within the mitochondrial DNA hypervariable region I and the AMG gene (121/115 bp) of the nuclear DNA were analyzed. The quantification results of mitochondrial DNA showed an inverse correlation between amplicon length and amplification efficiency, which was one of the criteria used to determine authenticity in ancient DNA studies. We also found that the 138 bp fragment had highest copies. Our study also showed that tooth samples had more DNA molecules than bone samples, and tooth samples were more suitable for ancient DNA analysis.Xiaohe cemetery was located about 60 kilometres to the south of the downriver of peafowl river which was located in Luobupo, dated from 3400 to 4000 years BP. Xiaohe was the earliest and easternmost cemetery which had been found in Xinjiang, which was very important for analyzing the genetic information of the earlier Xinjiang population. Of the twenty ancient Xiaohe individuals analyzed, seventeen individuals revealed reproducibly successful amplifications of mitochondrial DNA hypervariable region I. The sequences from the bone and tooth samples from each individual were identical, which strongly confirmed the authenticity of the results. Tajima's D test and the Mismatch distributions all showed that the ancient Xiaohe population had no recent demographic expansions. The distribution of ancient Xiaohe haplotypes among modern human populations showed that the genetic structure of Xiaohe people was complex, which had European and Asian origin at the same time. Comparing with the mtDNA data of 15 modern Eurasian populations, including Eastern Asian, Siberian, Central Asian, European and Southwestern Asian, Neighbour-joining tree, multidimensional scaling analysis and analysis of molecular variance all showed that ancient Xiaohe population had close relationships with Central Asian. The median joining network of the Xiaohe people and eight ancient Xinjiang and Central Asian populations showed that Xiaohe people had close relationships with Yuansha and Sampula which were located in the south route of Silk Road, and was far from the populations of north route of Silk RoadThe archaeological site of Sampula cemetery was located about 14 kilometres to the southwest of the Luo County in Xinjiang Khotan, and this cemetery dated from 217 B.C. to 283 A.D. Of the sixteen ancient Sampula individuals analyzed, thirteen individuals revealed reproducibly successful amplifications. Haplogroups were assigned based on the sequences of mitochondrial DNA hypervariable region I region and the RFLP results of coding region. The haplogroup distributions showed that Sampula was complex population of European and Asian. Tajima's D test and the Mismatch distributions all showed that the ancient Sampula population had no recent demographic expansions. Comparing with the mtDNA data of 11 modern Eurasian populations, median joining network, multidimensional scaling analysis and sequence diversity all showed that ancient Sampula peoples had close relationships with Ossetian and Iranian.Niya was located about 100 kilometres to the north of the downtown of Minfeng, deep in the Taklamakan Desert in Xinjiang, and dated to about 1,700 years BP. One sample was collected in the Niya relic, and the mtDNA lineage of this Niya sample was assigned to the haplogroup U3. Compared with the U3 lineages from modern Eurasian populations and ancient Xinjiang samples, this lineage was mainly concentrated in Iranian and Near Eastern populations. Haplogroup U3 had also been found in four ancient Sampula samples, which indicated that the ancient Niya peoples perhaps had genetic relationship with ancient Sampula peoples.Mitochondrial DNA was successfully amplified from both the bones and teeth samples of Yuhong and his wife, and the sequences from the bone and tooth samples from each individual were identical. Basing the sequences of mitochondrial DNA hypervariable region I region and the RFLP results of coding region, Yuhong was included in haplogroup U5, the West Eurasian-specific haplogroup, while his wife belonged to haplogroup G, representative of East Asian populations. Our findings indicate that a member of the oldest European-specific haplogroups, U5, arrived in Taiyuan about 1400 years ago. It is the first West Eurasian-specific haplogroup to have been found in the central part of ancient China, and Taiyuan may be the easternmost region which European lineage has been found until now in ancient China.In a word, on the basis of mtDNA data from different space-time populations in the Xinjiang Tarim Basin, our research reveals that the genetic structure and ethnologic origin of the ancient populations as well as the relationships and gene continuity between the ancient populations and extant populations. At the same time, the first West Eurasian-specific haplogroup has been found in the central part of ancient China, 1400 years ago. This article provides molecular evidences for the origin, expansion, evolution and forming process of these populations.
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