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Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity

Wang, Wenjun, Ding, Manyu, Gardner, Jacob D., Wang, Yongqiang, Miao, Bo, Guo, Wu, Wu, Xinhua, Ruan, Qiurong, Yu, Jianjun, Hu, Xingjun, Wang, Bo, Wu, Xiaohong, Tang, Zihua, Niyazi, Alipujiang, Zhang, Jie, Chang, Xien, Tang, Yunpeng, Ren, Meng, Cao, Peng, Liu, Feng, Dai, Qingyan, Feng, Xiaotian, Yang, Ruowei, Zhang, Ming, Wang, Tianyi, Ping, Wanjing, Hou, Weihong, Li, Wenying, Ma, Jian, Kumar, Vikas, Fu, Qiaomei·2021·Science Advances
DOI 10.1126/sciadv.abd6690PMC PMC8011967
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Abstract

The 237 ancient mitochondrial genomes from Xinjiang reveal highly admixed populations from the Bronze Age to Historical Era.

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Fig. 1 Geographic locations and haplogroups of ancient Xinjiang samples. (A) Geographic locations and haplogroups of BA and IA/HE samples from eastern (E), western (W), southern (S), and northern (N) Xinjiang (XJ). The different colored and shaped symbols overlaying Xinjiang represent different sites (group names in the map are consistent with those in the manuscript). We merged haplogroup information of our one Nanwan (NW) individual with 29 previously published Tianshanbeilu (TSBL) individuals to comprise the E_BA group. Colored bar plots represent the frequencies of various haplogroups, shown on the bottom right. (B) Timeline of Xinjiang sites with the number of individuals in parentheses. NS, NC, and NWA_EMBA are the abbreviations of NSSG_EMBA, NChemur_EMBA, and NWAfana_EMBA, respectively.
Fig. 1 Geographic locations and haplogroups of ancient Xinjiang samples. (A) Geographic locations and haplogroups of BA and IA/HE samples from eastern (E), western (W), southern (S), and northern (N) Xinjiang (XJ). The different colored and shaped symbols overlaying Xinjiang represent different sites (group names in the map are consistent with those in the manuscript). We merged haplogroup information of our one Nanwan (NW) individual with 29 previously published Tianshanbeilu (TSBL) individuals to comprise the E_BA group. Colored bar plots represent the frequencies of various haplogroups, shown on the bottom right. (B) Timeline of Xinjiang sites with the number of individuals in parentheses. NS, NC, and NWA_EMBA are the abbreviations of NSSG_EMBA, NChemur_EMBA, and NWAfana_EMBA, respectively.CC BY-NC · PubMed Central
Fig. 2 The genetic results for the ancient Xinjiang samples and other ancient and present-day Eurasians. (A) DAPC based on haplogroup frequency; the eigenvalues of the first and second PCs are shown on the top right. The different colors on the plot represent different groups made under unsupervised classification. The shapes with black frames represent the ancient Xinjiang samples with the BA samples in dark red and the IA/HE samples in dark blue. The populations plotted as triangles are ancient populations, and the circles are present-day humans. NEA, northern East Asian (upward pointing triangles), and Siberia (triangles pointing to the right); SEA, southeastern Asia; Euro, Europe; CS, central Steppe populations in BA (CS_BA; upward pointing triangles) and IA (CS_IA; triangles pointing to the right); pdCA/XJ, present-day populations in and around Xinjiang. (B) The genetic distance (FST) heatmap plot of ancient Xinjiang samples and ancient Eurasians. The different labels represent genetically distinctive groups corresponding to those in the DAPC. Values with FST ≈ 0.00 are in white, representing a close genetic relationship. SEXiaohe_BA was removed from the FST heatmap, considering the significantly large genetic distances (FST > 0.10) between them and other groups.
Fig. 2 The genetic results for the ancient Xinjiang samples and other ancient and present-day Eurasians. (A) DAPC based on haplogroup frequency; the eigenvalues of the first and second PCs are shown on the top right. The different colors on the plot represent different groups made under unsupervised classification. The shapes with black frames represent the ancient Xinjiang samples with the BA samples in dark red and the IA/HE samples in dark blue. The populations plotted as triangles are ancient populations, and the circles are present-day humans. NEA, northern East Asian (upward pointing triangles), and Siberia (triangles pointing to the right); SEA, southeastern Asia; Euro, Europe; CS, central Steppe populations in BA (CS_BA; upward pointing triangles) and IA (CS_IA; triangles pointing to the right); pdCA/XJ, present-day populations in and around Xinjiang. (B) The genetic distance (FST) heatmap plot of ancient Xinjiang samples and ancient Eurasians. The different labels represent genetically distinctive groups corresponding to those in the DAPC. Values with FST ≈ 0.00 are in white, representing a close genetic relationship. SEXiaohe_BA was removed from the FST heatmap, considering the significantly large genetic distances (FST > 0.10) between them and other groups.CC BY-NC · PubMed Central
Fig. 3 Median-joining haplogroup networks. The median-joining network of the haplogroups C4 (A), R1b (B), HV (C), U4 (D), and D4 (E) related to ancient northeastern Asian (NEA), Botai/Dali, European (Euro), Turan, and BA and IA populations from the central Steppe (CS_BA and CS_IA). The Euro group consists mainly of western Steppe–related individuals, and the CS_IA group contains the Saka, Hun, and Nomad populations. The size of the circles represents the proportion of each haplotype. The lengths of lines between nodes represent the number of mutations between two haplotypes. The different population groups are shown by different colors that are consistent with those groups in DAPC and FST heatmap. Some ancient Xinjiang samples are annotated with black labels.
Fig. 3 Median-joining haplogroup networks. The median-joining network of the haplogroups C4 (A), R1b (B), HV (C), U4 (D), and D4 (E) related to ancient northeastern Asian (NEA), Botai/Dali, European (Euro), Turan, and BA and IA populations from the central Steppe (CS_BA and CS_IA). The Euro group consists mainly of western Steppe–related individuals, and the CS_IA group contains the Saka, Hun, and Nomad populations. The size of the circles represents the proportion of each haplotype. The lengths of lines between nodes represent the number of mutations between two haplotypes. The different population groups are shown by different colors that are consistent with those groups in DAPC and FST heatmap. Some ancient Xinjiang samples are annotated with black labels.CC BY-NC · PubMed Central
Fig. 4 Inferred maternal population movements around Xinjiang. Depictions of the main population movements in the BA (A), IA (B), HE (C), and present day (D). The dashed line in (A) represents the connection between SEXiaohe_BA and ancient Siberian (Sib) populations. The shades of green, blue, brown, and turquois in (A) to (C) represent the ancient European-, NEA-, central Steppe–, and Turan-specific ancestries, respectively. The shades of light green, blue, and yellow represent lineages found in present-day Europeans and West Asians, NEA, and populations in and around Xinjiang (pdCA/XJ). NS, NC, and NWA in (A) are the abbreviations of NSSG_EMBA, NChemur_EMBA, and NWAfana_EMBA, respectively.
Fig. 4 Inferred maternal population movements around Xinjiang. Depictions of the main population movements in the BA (A), IA (B), HE (C), and present day (D). The dashed line in (A) represents the connection between SEXiaohe_BA and ancient Siberian (Sib) populations. The shades of green, blue, brown, and turquois in (A) to (C) represent the ancient European-, NEA-, central Steppe–, and Turan-specific ancestries, respectively. The shades of light green, blue, and yellow represent lineages found in present-day Europeans and West Asians, NEA, and populations in and around Xinjiang (pdCA/XJ). NS, NC, and NWA in (A) are the abbreviations of NSSG_EMBA, NChemur_EMBA, and NWAfana_EMBA, respectively.CC BY-NC · PubMed Central

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Metadata

Authors
Wang, W., Ding, M., Gardner, J. D., Wang, Y., Miao, B., Guo, W., Wu, X., Ruan, Q., Yu, J., Hu, X., Wang, B., Wu, X., Tang, Z., Niyazi, A., Zhang, J., Chang, X., Tang, Y., Ren, M., Cao, P., Liu, F., Dai, Q., Feng, X., Yang, R., Zhang, M., Wang, T., Ping, W., Hou, W., Li, W., Ma, J., Kumar, V., & Fu, Q.
Affiliations
  • College of Life Sciences, Northwest University, Xi’an 710069, China.
  • Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
  • Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China.
  • Institute of Archaeology, Chinese Academy of Social Sciences, Beijing 100710, China.
  • Xinjiang Uygur Autonomous Region Museum, Urumqi 830002, China.
  • School of Archaeology and Museology, Peking University, Beijing 100871, China.
  • Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China.
  • School of Cultural Heritage, Northwest University, Xi’an 710069, China.
ORCID
Venue
Science Advances
Publisher
American Association for the Advancement of Science (AAAS)
Published
2021-04-02
Volume
7
Issue
14
ISSN
2375-2548
DOI
10.1126/sciadv.abd6690
PMC
PMC8011967
Cited by
38
References
6
Language
en
Licence
creativecommons.org/licenses/by-nc/4.0/ (vor)
Funders
  • Howard Hughes Medical Institute (55008731)
  • Ministry of Science and Technology (2016YFE0203700)
  • National Natural Science Foundation of China (91731303, 41925009, 41672021, 41630102,)
  • Chinese Academy of Sciences (XDA1905010, QYZDB-SSW-DQC003, CAS, XDB26000000)
  • Tencent Foundation

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