Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Phylogenetic analysis of the Y-chromosome haplogroup C2b-F1067, a dominant paternal lineage in Eastern Eurasia

Abstract

Human Y-chromosome haplogroup C2b-F1067 is one of the dominant paternal lineages of populations in Eastern Eurasia. In order to explore the origin, diversification, and expansion of this haplogroup, we generated 206 new Y-chromosome sequences from C2b-F1067 males and coanalyzed 220 Y-chromosome sequences of this haplogroup. BEAST software was used to reconstruct a revised phylogenetic tree of haplogroup C2b-F1067 with age estimates. The revised phylogeny of C2b-F1067 included 155 sublineages, 1986 non-private variants, and >6000 private variants. The age estimation suggested that the initial splitting of C2b-F1067 happened at about 32.8 thousand years ago (kya) and the major sublineages of this haplgroup experienced continuous expansion in the most recent 10,000 years. We identified numerous sublineages that were nearly specific for Korean, Mongolian, Chinese, and other ethnic minorities in China. In particular, we evaluated the candidate-specific lineage for the Dayan Khan family and the Confucius family, the descendants of the ruling family of the Chinese Shang dynasty. These findings suggest that ancient populations with varied C2b-F1067 sublineages played an important role during the formation of most modern populations in Eastern Eurasia, and thus eventually became the founding paternal lineages of these populations.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1
Fig. 2

References

  1. 1.

    Zhong H, Shi H, Qi XB, Xiao CJ, Jin L, Ma RZ, et al. Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet. 2010;55:428–35.

    Article  PubMed  Google Scholar 

  2. 2.

    Karmin M, Saag L, Vicente M, Wilson Sayres MA, Jarve M, Talas UG, et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 2015;25:459–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Wei LH, Huang YZ, Yan S, Wen SQ, Wang LX, Du PX, et al. Phylogeny of Y-chromosome haplogroup C3b-F1756, an important paternal lineage in Altaic-speaking populations. J Hum Genet. 2017;62:915–8.

    Article  CAS  PubMed  Google Scholar 

  4. 4.

    Wei LH, Wang LX, Wen SQ, Yan S, Canada R, Gurianov V, et al. Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences. Eur J Hum Genet. 2018;26:1687–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Malyarchuk B, Derenko M, Denisova G, Wozniak M, Grzybowski T, Dambueva I, et al. Phylogeography of the Y-chromosome haplogroup C in northern Eurasia. Ann Hum Genet. 2010;74:539–46.

    Article  CAS  PubMed  Google Scholar 

  6. 6.

    Wei LH, Yan S, Lu Y, Wen SQ, Huang YZ, Wang LX, et al. Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan. Eur J Hum Genet. 2018;26:230–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Kwon SY, Lee HY, Lee EY, Yang WI, Shin KJ. Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups. Forensic science international. Genetics. 2015;19:42–6.

    CAS  Google Scholar 

  8. 8.

    Yan S, Wang CC, Zheng HX, Wang W, Qin ZD, Wei LH, et al. Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers. PloS ONE 2014;9:e105691.

    Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Huang YZ, Wei LH, Yan S, Wen SQ, Wang CC, Yang YJ, et al. Whole sequence analysis indicates a recent southern origin of Mongolian Y-chromosome C2c1a1a1-M407. Mol Genet Genom. 2018;293:657–63.

    Article  CAS  Google Scholar 

  10. 10.

    Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, et al. Insights into human genetic variation and population history from 929 diverse genomes. Science. 2020;367. https://science.sciencemag.org/content/367/6484/eaay5012.full.

  11. 11.

    Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 2016;48:593–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Zhang Y, Wu X, Li J, Li H, Zhao Y, Zhou H. The Y-chromosome haplogroup C3*-F3918, likely attributed to the Mongol Empire, can be traced to a 2500-year-old nomadic group. J Hum Genet. 2018;63:231–8.

    Article  CAS  PubMed  Google Scholar 

  13. 13.

    Wang Y, Song F, Zhu J, Zhang S, Yang Y, Chen T, et al. GSA: Genome Sequence Archive. Genom Proteom Bioinforma. 2017;15:14–8.

  14. 14.

    Members BIGDC. The BIG Data Center: from deposition to integration to translation. Nucleic acids Res. 2017;45:D18–24.

    Article  CAS  Google Scholar 

  15. 15.

    Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016;538:201–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Y Chromosome Consortium. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 2002;12:339–48.

    Article  CAS  Google Scholar 

  19. 19.

    Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014;10:e1003537.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr. et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 2014;506:225–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67:901–04.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Rambaut A. http://tree.bio.ed.ac.uk/software/figtree/ (2018). Accessed 1 Feb 2018.

  23. 23.

    Song S, Tian D, Li C, Tang B, Dong L, Xiao J, et al. Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic acids Res. 2018;46:D944–9.

    Article  CAS  PubMed  Google Scholar 

  24. 24.

    Pinotti T, Bergstrom A, Geppert M, Bawn M, Ohasi D, Shi W, et al. Y chromosome sequences reveal a short beringian standstill, rapid expansion, and early population structure of Native American Founders. Curr Biol. 2019;29:149–57.e3.

    Article  CAS  PubMed  Google Scholar 

  25. 25.

    Yang X, Wan Z, Perry L, Lu H, Wang Q, Zhao C, et al. Early millet use in northern China. Proc Natl Acad Sci USA. 2012;109:3726–30.

    Article  PubMed  Google Scholar 

  26. 26.

    Tong ZC. Studies on Neolithic Age of China. Chengdu: Bashu Publishing House; 1998.

  27. 27.

    Lowe M, Shaughnessy EL. The Cambridge History of Ancient China: From the Origins of Civilization to 22 B.C. England: Cambridge University Press; 1999.

  28. 28.

    Hou W-G, Wang C-C, Jiang S-H, Liu H-D, Li H. Genetic diversity of seventeen Y-STR loci among the people with the surname Kong from Qufu Prefecture. Acta Anthropologica Sin. 2015;35:125–31.

    Google Scholar 

  29. 29.

    Kaizuka S. Confucius. Mineola: Dover Publications; 2002.

  30. 30.

    Loewe M, Shaughnessy EL. The Cambridge History of Ancient China: From the Origins of Civilization to 221 BC. Cambridge: Cambridge University Press; 1999.

  31. 31.

    Batbayar K, Sabitov ZM. The Genetic Origin of the Turko-Mongols and Review of The Genetic Legacy of the Mongols. Part 1: Y-chromosomal Lineages Chinggis Khan Russian J Genet Geneal. 2012;4:1–8.

    Google Scholar 

  32. 32.

    Balinova N, Post H, Kushniarevich A, Flores R, Karmin M, Sahakyan H, et al. Y-chromosomal analysis of clan structure of Kalmyks, the only European Mongol people, and their relationship to Oirat-Mongols of Inner Asia. Eur J Hum Genet. 2019;27:1466–74.

    Article  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Malyarchuk BA, Derenko M, Denisova G, Wozniak M, Rogalla U, Dambueva I, et al. Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407. J Hum Genet. 2016;61:491–6.

    Article  CAS  PubMed  Google Scholar 

  34. 34.

    Zhao BF. Archaeology of the stone age in Northeast China. Changchuan: Jilin University Press; 2003.

  35. 35.

    Zhao BF. Study on Archaeological Culture of Xia Dynasty to Warring States in Northeast Region of China. Beijing: Science Press; 2009.

  36. 36.

    Zhang W. Study on the Hongmashan Culture (in Chinese). Northern Cultural Relics; 2007.

  37. 37.

    Lin G. A history of Donghu (in Chinese). Hohhot: Inner Mongolian People’s Publishing House; 2007.

  38. 38.

    Wang CY, Luo W. A brief history of Tusi families of Tujia population (in Chinese). Beijing: Minzu University of China Press; 1991.

  39. 39.

    Xia Z-Y, Yan S, Wang C-C, Zheng H-X, Zhang F, Liu Y-C, et al. Inland-coastal bifurcation of southern East Asians revealed by Hmong-Mien genomic history. 2019. https://www.biorxiv.org/content/10.1101/730903v1.

Download references

Acknowledgements

We thank all donors for providing DNA samples and/or DNA sequences. This work was supported by the National Natural Science Foundation of China (31900406 to LHW). LHW was also supported Fundamental Research Funds for the Central Universities (20720191047). This study was also supported by the Scientific and Technology Committee of Shanghai Municipality (18490750300).

Author information

Affiliations

Authors

Contributions

The authors are responsible for the content and writing of the paper.

Corresponding author

Correspondence to Lan-Hai Wei.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Wu, Q., Cheng, HZ., Sun, N. et al. Phylogenetic analysis of the Y-chromosome haplogroup C2b-F1067, a dominant paternal lineage in Eastern Eurasia. J Hum Genet 65, 823–829 (2020). https://doi.org/10.1038/s10038-020-0775-1

Download citation

Search

Quick links