The Pamirs, among the world’s highest mountains in Central Asia, are one of homelands with the most extreme high altitude for several ethnic groups. The settlement history of modern humans on the Pamirs remains still opaque. Herein, we have sequenced the mitochondrial DNA (mtDNA) genomes of 382 individuals belonging to eight populations from the Pamirs and the surrounding lowlands in Central Asia. We construct the Central Asian (including both highlanders and lowlanders) mtDNA haplogroup tree at the highest resolution. All the matrilineal components are assigned into the defined mtDNA haplogroups in East and West Eurasians. No basal lineages that directly emanate from the Eurasian founder macrohaplogroups M, N, and R are found. Our data support the origin of Central Asian being the result of East–West Eurasian admixture. The coalescence ages for more than 93% mtDNA lineages in Central Asians are dated after the last glacial maximum (LGM). The post-LGM and/or later dispersals/admixtures play dominant roles in shaping the maternal gene pool of Central Asians. More importantly, our analyses reveal the mtDNA heterogeneity in the Pamir highlanders, not only between the Turkic Kyrgyz and the Indo-European Tajik groups, but also among three highland Tajiks. No evidence supports positive selection or relaxation of selective constraints in the mtDNAs of highlanders as compared to that of lowlanders. Our results suggest a complex history for the peopling of Pamirs by multiple waves of migrations from various genetic resources during different time scales.

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We are grateful to all volunteers and samplers. We thank Ni-Ni Shi, Quan-Kuan Shen, Ya-Jiang Wu, Mu-Yang Wang, Yao-Ming Li, and Feng Xu for the technical assistance. This study was supported by grants from National Natural Science Foundation of China (31301026), Science & Technology Department of Xinjiang Uygur Autonomous Region (201491188), Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, and Bureau of Science and Technology of Yunnan Province. M.-S.P. thanks the support from the Youth Innovation Promotion Association, Chinese Academy of Sciences.

Author information

Author notes


    1. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China

      • Min-Sheng Peng
      • , Jiao-Jiao Song
      • , Xing Chen
      • , He-Qun Liu
      • , Shi-Fang Wu
      • , Yun Gao
      •  & Ya-Ping Zhang
    2. Key Laboratory of the Chinese Ministry of Education and Xinjiang Uighur Autonomous Region for High-Incident Diseases in Uighur Ethnic Population, Xinjiang Medical University, Urumqi, 830011, China

      • Weifang Xu
      •  & Halmurat Upur
    3. Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, 830000, China

      • Weifang Xu
    4. Institute of Health Sciences, Anhui University, Hefei, 230601, China

      • Jiao-Jiao Song
    5. College of Uighur Medicine, Xinjiang Medical University, Urumqi, 830011, China

      • Xierzhatijiang Sulaiman
    6. The Second People’s Hospital of Kashi, Kashi, 844000, China

      • Liuhong Cai
    7. E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan

      • Najmudinov Tojiddin Abdulloevich
      • , Manilova Elena Afanasevna
      •  & Khudoidodov Behruz Ibrohimovich
    8. Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China

      • Xi Chen
      • , Wei-Kang Yang
      •  & Miao Wu
    9. Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China

      • Xi Chen
      • , Wei-Kang Yang
      •  & Miao Wu
    10. Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China

      • Gui-Mei Li
    11. State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China

      • Xing-Yan Yang
      •  & Ya-Ping Zhang
    12. Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China

      • Allah Rakha
      •  & Yong-Gang Yao
    13. Department of Forensic Sciences, University of Health Sciences, Lahore, 54600, Pakistan

      • Allah Rakha
    14. KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China

      • Yong-Gang Yao
      •  & Ya-Ping Zhang
    15. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China

      • Yong-Gang Yao
      •  & Ya-Ping Zhang


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