Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia

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Abstract

The genetic variation in Northern Asian populations is currently undersampled. To address this, we generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The cataloged variation in the panel shows strong population stratification among these tribes, which correlates with the diverse demographic histories in the region. Incorporating our results with the 1000 Genomes Project panel identifies derived alleles shared between Finns and Mongolians/Siberians, suggesting that substantial gene flow between northern Eurasian populations has occurred in the past. Furthermore, we highlight that North, East, and Southeast Asian populations are more aligned with each other than these groups are with South Asian and Oceanian populations.

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Fig. 1: Sampling, variants, and imputation.
Fig. 2: Population genetic structure.
Fig. 3: Inference of population demographic history.
Fig. 4: Gene flow between Mongolians and global human populations of 1000G.
Fig. 5: Phylogenetic relatedness of East Asian groups with other people.

Data availability

Raw sequencing data and variant sets have been deposited to the CNGB (China National Genebank) Nucleotide Sequence Archive (CNSA) with accession CNP0000063 (https://db.cngb.org/cnsa/).

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Acknowledgements

We sincerely thank the Mongolian volunteers who agreed to contribute blood samples and participate in this study. We thank D. Reich for sharing genotype data on populations from Siberia and South Asia, and J. Fekecs for graphical assistance. We acknowledge F.S. Collins and C.D. Bustamante for their helpful discussions and comments on the manuscript, as well as Shuangshan Shuangshan, Y. Bao, and S. Ba for contributing to the sample collection process. This study was supported by Shenzhen Municipal Government of China (CXB201108250094A), Inner Mongolia University for Nationalities Scientific Research Project (MD2012038), the National Science Foundation of China (81560176, 81511130050), China National Genebank, Foundation of the Inner Mongolia Department of Science and Technology (2015MS0875, 201502103), Science and Technology Planning Project of Inner Mongolia, China (20120409), and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301010). C.R.G. is supported by the US National Institutes of Health (4U01HG007419-04) and National Science Foundation (1201234). N.N., S.R.B., and L.C.B are supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health.

Author information

Y.Y., H.Z., B.B., and H.B. initiated and supervised the project. H.B., Q.W., Y.X., Z.P., J.J., X.Y., M.M., B.G., D.W., Y.G., H.H., S.S., Y.C., YanruZ., L.Z., YiyiL., C.L., F.M., K.W., L.L., and YingchunL. surveyed and collected the samples. Y.X., YanruZ., DongZ., J.C., S.W., X.Li, and T.Li performed extraction of the genomic DNA. H.B., X.G., Q.W., M.J., and B.W. did the genome sequencing. YongZ., L.F., H.W., and T.Lan did the mapping and variation calling. T.Lan, X.G., H.L., W.L., Z.W., and B.W. performed experimental validation. X.G., T.Lan, and B.D. did the construction of the haplotype reference panel. X.G., T.Lan, DandanZ., H.X., N.D., X.Luo, W.X., and L.Y. performed the analysis of population diversity and genetic structure. T.Lan, X.G., N.N., B.D., and X.N. did the inferences of population demographic history. N.N., S.R.B., K.L., and C.R.G. did the analysis of phylogeny of East Asians. X.G., N.N., T.Lan, and S.R.B. wrote the manuscripts. X.G., C.Y., X.Luo, and T.Li were in charge of data submission. N.N., X.G., T.Lan, S.R.B., N.D., C.R.G., X.X., X.Liu, H.Y., L.C.B., J.W., and K.K. revised the manuscript.

Correspondence to Burenbatu Burenbatu or Huanmin Zhou or Ye Yin.

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Bai, H., Guo, X., Narisu, N. et al. Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia. Nat Genet 50, 1696–1704 (2018) doi:10.1038/s41588-018-0250-5

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