The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous. In this study, we reanalyzed a 7.0 Mbp region of 132 paternal Y-chromosome sequences, including 39 newly reported ones, of male samples from American aborigines and Eurasian populations. Among Eurasian samples, we identified Y-chromosome branches that are most closely related to known American aborigine founding lineages, that is, Q1-L804 links to Q1-M3, Q1-L330 links to Q1-Z780, Q1-M120 links to Q1-B143, and C2-F1756 links to C2-P39. The revised phylogenetic tree and age estimates indicate a narrow timeframe (~15.3–14.3 kya) for the upper time limit of human entry to the American continent. Our analysis suggests that the in situ differentiation of Q-M242 in Central Eurasia and South Siberia region gave rise to numerous sub-lineages older than 15.3 kya, and the founding of Paleo-Indian paternal lineages is part of the great Q1-L53 diffusion throughout the Eurasia after the Last Glacial Maximum. The results of our study will assist in future studies of the history of modern populations in Eurasia and the Americas.

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We are grateful to all sample donors. We thank the Family Tree DNA lab team including Brent Manning and Michael Sager and the Yfull team for their help and comments. The administrators of the haplogroup Q-M242 and the Nordic Q citizen science projects helped in collecting and analyzing these data. This study was supported by the National Natural Science Foundation of China (91731303 to S.X. and H.L., 31222030 and 31671297 to H.L., 31401060 to Y.S., 31271338 to L.J., 31501011 to Y.L., 31525014, 31771388 and 31711530221 to S.X.), MOE Scientific Research Project (113022A to H.L.), Shanghai Shuguang Project (14SG05 to H.L.), Ministry of Science and Technology of China (MOST) (2016YFC0900300 to H.L.). S.X. acknowledges financial support from the Strategic Priority Research Program (XDB13040100) and Key Research Program of Frontier Sciences (QYZDJ-SSW-SYS009) of the Chinese Academy of Sciences (CAS), the Program of Shanghai Academic Research Leader (16XD1404700), and the National Key Research and Development Program (2016YFC0906403). L.-H.W. was supported by Future Scientists Project of China Scholarship Council. C.-C.W was supported by the Nanqiang Outstanding Young Talents Program of Xiamen University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author contributions

L.-H.W., L.-X.W., Q.-S.W., and R.C. carried out the molecular genetic studies and drafted the manuscript. S.Y., Q.-S.W., R.C., V.G., S.W., A.B., A.O., Y.L., and C.Z. collected the samples. Q.-S.W., S.Y., Y.L., and C.Z. participated in the experiments. Y.-Z.H., V.G., A.B., A.O., C.-C.W., and L.J. participated in the statistical analysis. S.-H.X. and H.L. designed the study and revised the manuscript. All authors read and approved the final manuscript.

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Author notes

  1. These authors contributed equally: Lan-Hai Wei, Ling-Xiang Wang, Shao-Qing Wen, Shi Yan, Rebekah Canada


  1. MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 20043, China

    • Lan-Hai Wei
    • , Ling-Xiang Wang
    • , Shao-Qing Wen
    • , Shi Yan
    • , Yun-Zhi Huang
    • , Li Jin
    •  & Hui Li
  2. Collaborative Innovation Center of Genetics and Development, Shanghai, 200438, China

    • Lan-Hai Wei
    • , Ling-Xiang Wang
    • , Shao-Qing Wen
    • , Shi Yan
    • , Yun-Zhi Huang
    • , Li Jin
    • , Shuhua Xu
    •  & Hui Li
  3. Institut National des Langues et Civilisations Orientales, Paris, 75214, France

    • Lan-Hai Wei
  4. Gene by Gene, Ltd, Houston, 77008, USA

    • Rebekah Canada
    • , Alessandro Biondo
    •  & Amy O’Leary
  5. Vavilov Institute of General Genetics, Moscow, 119991, Russia

    • Vladimir Gurianov
  6. Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA

    • Swapan Mallick
  7. Department of Anthropology and Ethnology, Xiamen University, Xiamen, 361005, China

    • Chuan-Chao Wang
  8. Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    • Yan Lu
    • , Chao Zhang
    •  & Shuhua Xu
  9. University of Chinese Academy of Sciences, Beijing, 100049, China

    • Chao Zhang
    •  & Shuhua Xu
  10. School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China

    • Shuhua Xu
  11. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China

    • Shuhua Xu


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