Paternal heritage of the Han Chinese in Henan province (Central China): high diversity and evidence of in situ Neolithic expansions

References

• Arunkumar G, Wei LH, Kavitha VJ, Syama A, Arun VS, Sathua S, Sahoo R, et al. 2015. A late Neolithic expansion of Y chromosomal haplogroup O2a1‐M95 from east to west. J Syt Evol. 53(6):546–560.
   Web of Science ®Google Scholar
• Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, Suchard MA, et al. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 10(4):e1003537.
   PubMed Web of Science ®Google Scholar
• Cui Y, Li H, Ning C, Zhang Y, Chen L, Zhao X, Hagelberg E, Zhou H. 2013. Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China. BMC Evol Biol. 13(1):216.
   PubMedGoogle Scholar
• Fei XT. 2003. The pattern of diversity and unity of Chinese nation. Beijing: Central University for Nationalities Press.
   Google Scholar
• Hu K, Yan S, Liu K, Ning C, Wei L-H, Li S-L, Song B, et al. 2015. The dichotomy structure of Y chromosome Haplogroup N. arXiv, 1504.06463. https://arxiv.org/abs/1504.06463
   Google Scholar
• Jin L, Su B. 2000. Natives or immigrants: modern human origin in east Asia. Nat Rev Genet. 1(2):126–133.
   PubMed Web of Science ®Google Scholar
• Karmin M, Saag L, Vicente M, Wilson Sayres MA, Jarve M, Talas UG, Rootsi S, et al. 2015. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 25(4):459–466.
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 26(5):589–595.
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics. 25(16):2078–2079.
   PubMed Web of Science ®Google Scholar
• Li H, Huang Y, Mustavich LF, Zhang F, Tan JZ, Wang LE, Qian J, et al. 2007. Y chromosomes of prehistoric people along the Yangtze River. Hum Genet. 122(3–4):383–388.
   PubMed Web of Science ®Google Scholar
• Liu L. 2004. The Chinese Neolithic: trajectories to early states. Cambridge: Cambridge University Press.
   Google Scholar
• Liu L, Chen X-C. 2012. The archaeology of China: from the late Paleolithic to the early bronze age. Cambridge: Cambridge University Press.
   Google Scholar
• Liu L, Chen X-C. 2017. The archaeology of China: From the late Paleolithic to the early bronze age. Beijing: SDX Joint Publishing Company.
   Google Scholar
• Lowe M, Shaughnessy EL. 1999. The Cambridge history of ancient China: from the origins of civilization to 22 B.C. England: Cambridge University Press.
   Google Scholar
• Members BIGDC. 2017. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res. 45:D18–D24.
   PubMed Web of Science ®Google Scholar
• Ning C, Yan S, Hu K, Cui YQ, Jin L. 2016. Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134. Eur J Hum Genet. 24(2):307–309.
   PubMed Web of Science ®Google Scholar
• Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, et al.,. 2016. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 48(6):593–599.
   PubMed Web of Science ®Google Scholar
• Qi X, Cui C, Peng Y, Zhang X, Yang Z, Zhong H, Zhang H, et al. 2013. Genetic evidence of paleolithic colonization and neolithic expansion of modern humans on the tibetan plateau. Mol Biol Evol. 30:1761–1778.
   PubMed Web of Science ®Google Scholar
• Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, Chakraborty R, et al. 2005. Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122. Am J Hum Genet. 77(3):408–419.
   PubMed Web of Science ®Google Scholar
• Sun N, Ma PC, Yan S, Wen SQ, Sun C, Du PX, Cheng HZ, et al. 2019. Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia. Ann Hum Biol. 46(3):261–266.
   PubMed Web of Science ®Google Scholar
• Tong ZC. 1998. Studies on neolithic age of China. Chengdu: Bashu Publishing House.
   Google Scholar
• Twitchett D, Loewe M. 1986. The Cambridge history of China, Vol. 1: The Ch’in and Han empires, 221 BC–AD 220. Cambridge: Cambridge University Press.
   Google Scholar
• Wang CC, Yan S, Qin ZD, Lu Y, Ding QL, Wei LH, Li SL, et al. 2013a. Late Neolithic expansion of ancient Chinese revealed by Y chromosome haplogroup O3a1c-002611. J Syt Evol. 51(3):280–286.
   Web of Science ®Google Scholar
• Wang CC, Yan S, Yao C, Huang XY, Ao X, Wang Z, Han S, et al. 2013b. Ancient DNA of emperor CAO Cao’s granduncle matches those of his present descendants: a commentary on present Y chromosomes reveal the ancestry of Emperor CAO Cao of 1800 years ago. J Hum Genet. 58(4):238–239.
   PubMed Web of Science ®Google Scholar
• Wang LX, Lu Y, Zhang C, Wei LH, Yan S, Huang YZ, Wang CC, et al. 2018. Reconstruction of Y-chromosome phylogeny reveals two neolithic expansions of Tibeto-Burman populations. Mol Genet Genomics. 293(5):1293–1300.
   PubMed Web of Science ®Google Scholar
• Wang Y, Song F, Zhu J, Zhang S, Yang Y, Chen T, Tang B, et al. 2017. GSA: genome sequence archive. Genom Proteom Bioinf. 15(1):14–18.
   PubMed Web of Science ®Google Scholar
• Wen B, Li H, Lu D, Song X, Zhang F, He Y, Li F, et al. 2004. Genetic evidence supports demic diffusion of Han culture. Nature. 431(7006):302–305.
   PubMed Web of Science ®Google Scholar
• Xu JS. 2012. The development history of Han nationality. Wuhan: Wuhan University Press.
   Google Scholar
• Y Chromosome Consortium. 2002. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12:339–348.
   PubMed Web of Science ®Google Scholar
• Yan S, Wang CC, Zheng HX, Wang W, Qin ZD, Wei LH, Wang Y, et al. 2014. Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers. PLoS One. 9(8):e105691.
   PubMed Web of Science ®Google Scholar
• Yao X, Tang S, Bian B, Wu X, Chen G, Wang CC. 2017. Improved phylogenetic resolution for Y-chromosome Haplogroup O2a1c-002611. Sci Rep. 7(1):1146.
   PubMedGoogle Scholar
• Zhang X, Kampuansai J, Qi X, Yan S, Yang Z, Serey B, Sovannary T, et al. 2014. An updated phylogeny of the human Y-chromosome lineage O2a-M95 with novel SNPs. PLoS One. 9(6):e101020.
   PubMed Web of Science ®Google Scholar
• Zhang X, Liao S, Qi X, Liu J, Kampuansai J, Zhang H, Yang Z, et al. 2015. Y-chromosome diversity suggests southern origin and Paleolithic backwave migration of Austro-Asiatic speakers from eastern Asia to the Indian subcontinent. Sci Rep. 5(1):15486.
   PubMedGoogle Scholar
• Zhang ZH, Wu JM, Huang JQ. 2003. Palaeolithic archaeology of China. Nanjing: Nanjing University Press.
   Google Scholar
• Zhao Y-B, Zhang Y, Li HJ, Cui YQ, Zhu H, Zhou H. 2014. Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago. Am J Hum Biol. 26(6):813–821.
   PubMed Web of Science ®Google Scholar
• Zhong H, Shi H, Qi XB, Xiao CJ, 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. 55(7):428–435.
   PubMed Web of Science ®Google Scholar