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Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Abstract

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1,2,3, there is no consensus with regard to which specific Old World populations they are closest to4,5,6,7,8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10,11,12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2,13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

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Figure 1: Sample locations and MA-1 genetic affinities.
Figure 2: Admixture graph for MA-1 and 16 complete genomes.
Figure 3: Evidence of gene flow from a population related to MA-1 and western Eurasians into Native American ancestors.

Accession codes

Accessions

Gene Expression Omnibus

Sequence Read Archive

Data deposits

Sequence data for MA-1 and AG-2, produced in this study, are available for download through NCBI SRA accession number SRP029640. Data from the Illumina genotyping analysis generated in this study are available through GEO Series accession number GSE50727; PLINK files can be accessed from http://www.ebc.ee/free_data. In addition, the above data and alignments for the published modern genomes, Denisova genome, Tianyuan individual and the two ancient genomes are available at http://www.cbs.dtu.dk/suppl/malta. Raw reads and alignments for the four modern genomes sequenced in this study are available for demographic research under data access agreement with E.W.

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Acknowledgements

We thank the Hermitage State Museum for providing access to the Mal’ta and Afontova Gora-2 human remains. We also thank the Danish National High-Throughput DNA Sequencing Centre and T. Reisberg for technical assistance. This work was supported by the Danish National Research Foundation and the Lundbeck Foundation (E.W. and M.R.) and the Arctic Social Sciences Program, National Science Foundation (grant PLR-1003725 to K.E.G.). R.V., M.M., M.K., E.M., K.T., S.Ro. and R.M. were supported by the European Regional Development Fund (European Union) through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu and Estonian Basic Research grant SF0270177As08. M.M. thanks the Estonian Science Foundation grant no. 8973 and Baltic-American Freedom Foundation Research Scholarship program and M.I.V. thanks the Government of Russian Federation grant no. 14.B25.31.0033 (to E. I. Rogaev). M.D. was supported by the US National Science Foundation (grant DBI-1103639). Computational analyses were carried out at the High Performance Computing Center, University of Tartu, and the Swedish National Infrastructure for Computing (SNIC-UPPMAX, project b2012063).

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E.W. and K.E.G. conceived the project. E.W. headed the project. E.W. and M.R. designed the experimental research project setup. S.D. and K.E.G. provided access to the Mal’ta and Afontova Gora-2 samples, and K.E.G. provided archaeological context for the samples. T.W.S. Jr performed AMS dating. E.B. and O.B. (Tajik individual), E.K. and S.L. (Mari and Avar individuals) provided modern DNA extracts for complete genome sequencing. E.K. and S.L. (Kazakh, Kirghiz, Uzbek and Mari individuals), L.P.O. (Selkup individuals), S.A.F. (Even, Dolgan and Yakut individuals) and M.I.V. (Altai individuals) provided access to modern DNA extracts for genotyping. R.V. carried out Illumina chip analysis on modern samples. P.F.C. performed DNA extraction from the Indian individual. M.R. performed the ancient extractions and library constructions on the modern and ancient samples —the latter with input from L.O. M.R. coordinated the sequencing. M.R. and S.Ra. performed mapping of MA-1 and AG-2 data sets with input from L.O. S.Ra., T.S.-P. and S.B. provided super-computing resources, developed the next-generation sequencing pipeline and performed mapping and genotyping for all the modern genomes. M.R. performed DNA damage analysis with input from L.O. M.M. performed the admixture analysis. M.M., E.M., K.T. and R.V. performed the mtDNA analysis. M.M., M.K., S.Ro., T.K., R.V. and R.M. performed the Y-chromosome analysis. A.A. and I.M. performed the autosomal contamination estimates, error rate estimates, D-statistics tests based on sequence reads and ngsAdmix analyses. P.S. performed biological sexing, mtDNA contamination estimates, PCA, TreeMix, MixMapper, D-statistic tests based on allele frequencies, f3-statistics and phenotypic analyses, and analysis of AG-2 using nucleotide misincorporation patterns under the supervision of R.N. and M.J. M.R., P.S. and E.W. wrote the majority of the manuscript with critical input from R.N., M.J., M.M., K.E.G., A.A., I.M. and M.D. M.M., A.A. and I.M. contributed equally to this work.

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Correspondence to Eske Willerslev.

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Raghavan, M., Skoglund, P., Graf, K. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014). https://doi.org/10.1038/nature12736

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