Whole sequence analysis indicates a recent southern origin of Mongolian Y-chromosome C2c1a1a1-M407

Abstract

The Y-chromosome haplogroup C2c1a1a1-M407 is a predominant paternal lineage in Mongolic-speaking populations, especially in Buryats and Kalmyks. However, the origin and internal phylogeny of C2c1a1a1-M407 have not been investigated in detail. In this study, we analyzed twenty-three Y-chromosome sequences of haplogroup C2c1a1a1-M407 and its most closely related clades. We generated a high-resolution phylogenetic tree of haplogroup C2c1a1a1-M407 and its upstream clade C2c1a1-CTS2657, including 32 subclades and 144 non-private Y-chromosome polymorphisms. We discover that all available C2c1a1a1-M407 samples from Mongolic-speaking populations belong to its newly defined downstream clade C2c1a1a1b-F8465, whereas all samples of C2c1a1-CTS2657(xF8465) come from northern Han Chinese, Korean, and Japanese. Furthermore, we observe that C2c1a1a1b-F8465 and its subclade C2c1a1a1b1-F8536 expanded at approximately 0.86 and 0.44 thousand years ago, respectively. Therefore, we conclude that C2c1a1a1-M407 in Mongolic-speaking populations has originated from northeastern Asia. C2c1a1a1b1-F8536, the newly defined subclade of C2c1a1a1-M407, probably represents the genetic relationships between ancient Oyrats, modern Kalmyks, Mongolians, and Buryats.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  1. Adamov D, Guryanov V, Karzhavin S, Tagankin V, Urasin V (2015) Defining a new rate constant for Y-chromosome SNPs based on full sequencing data. Russ J Genet Geneal 1:3–36

    Google Scholar 

  2. Batbayar K, Sabitov ZM (2012) The genetic origin of the Turko-Mongols and review of the genetic legacy of the Mongols. Part 1: the Y-chromosomal lineages of Chinggis Khan. Russ J Genet Geneal 4:1–8

    Google Scholar 

  3. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: a software platform for bayesian evolutionary analysis. PLoS Comput Biol 10:1–6. https://doi.org/10.1371/journal.pcbi.1003537

    Article  Google Scholar 

  4. Derenko M, Maliarchuk B, Wozniak M, Denisova G, Dambueva I, Dorzhu C, Grzybowski T, Zakharov I (2007) Distribution of the male lineages of Genghis Khan’s descendants in northern Eurasian populations. Genetika 43:422–426

    CAS  PubMed  Google Scholar 

  5. Di Cristofaro J, Pennarun E, Mazieres S, Myres NM, Lin AA, Temori SA, Metspalu M, Metspalu E, Witzel M, King RJ, Underhill PA, Villems R, Chiaroni J (2013) Afghan Hindu Kush: Where Eurasian sub-continent gene flows converge. PLoS One. https://doi.org/10.1371/journal.pone.0076748

    Google Scholar 

  6. Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, Johnson PLF, Aximu-Petri A, Prüfer K, de Filippo C, Meyer M, Zwyns N, Salazar-García DC, Kuzmin YV, Keates SG, Kosintsev PA, Razhev DI, Richards MP, Peristov NV et al (2014) Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514:445–449. https://doi.org/10.1038/nature13810

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. Karmin M, Saag L, Vicente M, Sayres MAW, Järve M, Talas UG, Rootsi S, Ilumäe A, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G et al (2015) A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 25:459–466. https://doi.org/10.1101/gr.186684.114

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595. https://doi.org/10.1093/bioinformatics/btp698

    Article  PubMed  PubMed Central  Google Scholar 

  10. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352

    Article  PubMed  PubMed Central  Google Scholar 

  11. Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M (2014) Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investig Genet 5:13. https://doi.org/10.1186/2041-2223-5-13

    Article  PubMed  PubMed Central  Google Scholar 

  12. Lu D, Lou H, Yuan K, Wang X, Wang Y, Zhang C, Lu Y, Yang X, Deng L, Zhou Y, Feng Q, Hu Y, Ding Q, Yang Y, Li S, Jin L, Guan Y, Su B, Kang L et al (2016) Ancestral origins and genetic history of Tibetan Highlanders. Am J Hum Genet 99:580–594. https://doi.org/10.1016/j.ajhg.2016.07.002

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A, Skoglund P, Lazaridis I, Sankararaman S, Fu Q, Rohland N, Renaud G, Erlich Y, Willems T, Gallo C et al (2016) The simons genome diversity project: 300 genomes from 142 diverse populations. Nature 538:201–206. https://doi.org/10.1038/nature18964

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. Malyarchuk B, Derenko M, Denisova G, Wozniak M, Grzybowski T, Dambueva I, Zakharov I (2010) Phylogeography of the Y-chromosome haplogroup C in northern Eurasia. Ann Hum Genet 74:539–546. https://doi.org/10.1111/j.1469-1809.200.00601.1x

    CAS  Article  PubMed  Google Scholar 

  15. Malyarchuk B, Derenko M, Denisova G, Khoyt S, Woźniak M, Grzybowski T, Zakharov I (2013) Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels. J Hum Genet 58:804–811. https://doi.org/10.1038/jhg.2013.108

    CAS  Article  PubMed  Google Scholar 

  16. Malyarchuk BA, Derenko M, Denisova G, Woźniak M, Rogalla U, Dambueva I, Grzybowski T (2016) Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407. J Hum Genet 61:491–496. https://doi.org/10.1038/jhg.2016.14

    CAS  Article  PubMed  Google Scholar 

  17. Members BIGDC. (2017) The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 45:D18–D24. https://doi.org/10.1093/nar/gkw1060

    Article  Google Scholar 

  18. Nasidze I, Quinque D, Dupanloup I, Cordaux R, Kokshunova L, Stoneking M (2005) Genetic evidence for the Mongolian ancestry of Kalmyks. Am J Phys Anthropol 128:846–854. https://doi.org/10.1002/ajpa.20159

    Article  PubMed  Google Scholar 

  19. Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R et al (2016) Punctuated bursts in human male demography inferred from 1244 worldwide Y-chromosome sequences. Nat Genet 48:593–599. https://doi.org/10.1038/ng.3559

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Ramakrishnan U, Mountain JL (2004) Precision and accuracy of divergence time estimates from STR and SNPSTR variation. Mol Biol Evol 21:1960–1971. https://doi.org/10.1093/molbev/msh212

    CAS  Article  PubMed  Google Scholar 

  21. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow C-ET, Lin AA, Mitra M, Sil SK, Ramesh A, Rani MVU, Thakur CM, Cavalli-Sforza LL, Majumder PP, Underhill PA (2006) Polarity and temporality of high-resolution Y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet 78:202–221

    CAS  Article  PubMed  Google Scholar 

  22. Wang Y, Song F, Zhu J, Zhang S, Yang Y, Chen T, Tang B, Dong L, Ding N, Zhang Q, Bai Z, Dong X, Chen H, Sun M, Zhai S, Sun Y, Yu L, Lan L, Xiao J et al (2017) GSA: Genome Sequence Archive *. Genom Proteom Bioinform 15:14–18. https://doi.org/10.1016/j.gpb.2017.01.001

    Article  Google Scholar 

  23. Wei L-H, Yan S, Yu G, Huang Y-Z, Yao D-L, Li S-L, Jin L, Li H (2016) Genetic trail for the early migrations of Aisin Gioro, the imperial house of the Qing dynasty. J Hum Genet 1–5. https://doi.org/10.1038/jhg.2016.142

  24. Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339–348. https://doi.org/10.1101/gr.217602

    Article  Google Scholar 

  25. Yan S, Wang C-C, Zheng H-X, Wang W, Qin Z-D, Wei L-H, Wang Y, Pan X-D, Fu W-Q, He Y-G, Xiong L-J, Jin W-F, Li S-L, An Y, Li H, Jin L (2014) Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers. PLoS One 9:e105691. https://doi.org/10.1371/journal.pone.0105691

    Article  PubMed  PubMed Central  Google Scholar 

  26. Zerjal T, Wells RS, Yuldasheva N, Ruzibakiev R, Tyler-Smith C (2002) A genetic landscape reshaped by recent events: Y-chromosomal insights into central Asia. Am J Hum Genet 71:466–482. https://doi.org/10.1086/342096

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. Zhivotovsky L (2001) Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow. Mol Biol Evol 18:700

    CAS  Article  PubMed  Google Scholar 

  28. Zhong H, Shi H, Qi X-B, Xiao C-J, Jin L, Ma RZ, Su B (2010) Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet 5540:428–435

    Article  Google Scholar 

Download references

Acknowledgements

This study was supported by the National Natural Science Foundation of China (31222030 and 31671297 to H.L., 31401060 to Y.S., 31271338 to L.J., 31501011 to Y.L., 91331204 to S.H.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.) and Science and Technology Commission of Shanghai Municipality (STCSM) (14YF1406800 to Y.L.). 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. We also thank all the sample donors and the laboratory assistants.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Hui Li.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Research involving human participants and/or animals

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Additional information

Yun-Zhi Huang and Lan-Hai Wei contributed equally to this work.

Communicated by S. Hohmann.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Huang, YZ., Wei, LH., Yan, S. et al. Whole sequence analysis indicates a recent southern origin of Mongolian Y-chromosome C2c1a1a1-M407. Mol Genet Genomics 293, 657–663 (2018). https://doi.org/10.1007/s00438-017-1403-4

Download citation

Keywords

  • C2c1a1a1-M407
  • Mongolic-speaking
  • Han Chinese
  • Y-chromosome sequence