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Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Open accessAbstract
The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, 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-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. 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 Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, 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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In the citing paper
“We combined our data with previously published ancient data7,8,9,10,8,10-15 to form a dataset of 281 ancient individuals.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [15]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Application of this methods highlights the impact of Ancient North Eurasian (ANE) ancestry related to the ~22,000 BCE Mal'ta 1 and ~15,000 BCE Afontova Gora 215 on populations living in Europe, the Americas, and Eastern Eurasia.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [15]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal′ta individual5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened prior to 12,600 years BP.”
From The genome of a Late Pleistocene human from a Clovis burial site in western Montana (2014) · cites this paper as [5]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“A second regional population with roots in western Eurasia (Ancient North Eurasians (ANE)) expanded into Northeast Asia before 30 ka and contributed to the East Asian genome and—both indirectly and directly—to the Native American genome.”
From Beringia and the peopling of the Western Hemisphere (2023) · cites this paper as [78]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Eastern Eurasians can be modelled as arrayed along a cline with different proportions of ANE ancestry (Supplementary Information, section 11; Extended Data Fig. 8), ranging from ~40% ANE in Native Americans matching previous findings13,15, to no less than ~5-10% ANE in diverse East Asian groups including Han Chinese (Extended Data Fig. 5; Extended Data Fig. 7f).”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [15]
The cited source says what the claim attributes to it.
In the citing paper
“We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal′ta individual5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened prior to 12,600 years BP.”
From The genome of a Late Pleistocene human from a Clovis burial site in western Montana (2014) · cites this paper as [5]
The cited source says what the claim attributes to it.
In the citing paper
“f3 statistics can reveal unambiguous evidence for situations in which one individual (or population) is formed by the admixture of two others 219 , but they can also provide a measure of shared genetic drift when an outgroup is included 220 .”
From Ancient DNA analysis (2021) · cites this paper as [220]
The cited source says what the claim attributes to it.
In the citing paper
“The ANE population is present in southern Siberia during middle and late Upper Palaeolithic times at Mal'ta (24 ka) and Afontova Gora (17 ka), and their immediate ancestors (see below) are found in the Arctic and western Beringia as early as 33 ka [39,61,78].”
From Beringia and the peopling of the Western Hemisphere (2023) · cites this paper as [78]
In the citing paper
“This finding provided an explanation for some of the western Eurasian genetic signatures in present-day Native Americans, previously thought to be from post-Columbian admixture [30].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [30]
In the citing paper
“Analysis showed that at least three different ancient populations contributed to the genetics of present-day Europeans: (1) West European hunter-gatherers, (2) ancient north Eurasians related to Upper Paleolithic Siberians, and (3) early European farmers, who were mainly of Near Eastern origin [29].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [30]
In the citing paper
“The Mal’ta boy genome showed that Upper Paleolithic West Eurasians had a more north-easterly distribution and were genetically related to modern-day Native Americans, contributing significantly to their ancestry.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [30]
In the citing paper
“A second regional population with roots in western Eurasia (Ancient North Eurasians (ANE)) expanded into Northeast Asia before 30 ka and contributed to the East Asian genome and—both indirectly and directly—to the Native American genome.”
From Beringia and the peopling of the Western Hemisphere (2023) · cites this paper as [78]
In the citing paper
“The ANE population is present in southern Siberia during middle and late Upper Palaeolithic times at Mal'ta (24 ka) and Afontova Gora (17 ka), and their immediate ancestors (see below) are found in the Arctic and western Beringia as early as 33 ka [39,61,78].”
From Beringia and the peopling of the Western Hemisphere (2023) · cites this paper as [78]
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Metadata
- Authors
- Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford Jr, T. W., Orlando, L., Metspalu, E., Karmin, M., Tambets, K., Rootsi, S., Mägi, R., Campos, P. F., Balanovska, E., Balanovsky, O., Khusnutdinova, E., Litvinov, S., Osipova, L. P., Fedorova, S. A., Voevoda, M. I., DeGiorgio, M., Sicheritz-Ponten, T., Brunak, S., Demeshchenko, S., Kivisild, T., Villems, R., Nielsen, R., Jakobsson, M., & Willerslev, E.
- Affiliations
- University of Copenhagen (DK)
- Uppsala University (SE)
- Texas A&M University (US)
- Estonian Biocentre (EE)
- Technical University of Denmark (DK)
- University of Tartu (EE)
- Research Centre for Medical Genetics (RU)
- Russian Academy of Sciences (RU)
- Institute of Cytology and Genetics (RU)
- University of California, Berkeley (US)
- Novo Nordisk Foundation (DK)
- University of Cambridge (GB)
- Estonian Academy of Sciences (EE)
- Corresponding author
- Willerslev, Eske
- ORCID
- Raghavan, Maanasa
- Skoglund, Pontus
- Graf, Kelly E.
- Metspalu, Mait
- Albrechtsen, Anders
- Moltke, Ida
- Rasmussen, Simon
- Orlando, Ludovic
- Metspalu, Ene
- Karmin, Monika
- Tambets, Kristiina
- Mägi, Reedik
- Campos, Paula F.
- Balanovska, Elena
- Balanovsky, Oleg
- Litvinov, Sergey
- Osipova, Ludmila P.
- Voevoda, Mikhail I.
- Brunak, Søren
- Kivisild, Toomas
- Villems, Richard
- Nielsen, Rasmus
- Jakobsson, Mattias
- Willerslev, Eske
- Venue
- Nature
- Published
- 2013-11-20
- Volume
- 505
- Issue
- 7481
- Pages
- 87-91
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4105016
- OpenAlex
- W2050927297
- Cited by
- 963
- References
- 66
- Citations by year
- 2026: 27 · 2025: 97 · 2024: 44 · 2023: 53 · 2022: 80 · 2021: 113 · 2020: 97 · 2019: 81 · 2018: 83 · 2017: 98 · 2016: 64 · 2015: 61 · 2014: 60 · 2013: 3
- FWCI
- 41.17
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
- Scopus (Elsevier) (submittedVersion)
- Griffith Research Online (submittedVersion)
- Funders
- Villum Fonden (00007171)
- Lundbeckfonden (R109-2012-9995, R70-2010-6286, R155-2013-16338, R38-2008-3048, R24-2008-2527)
- Novo Nordisk Fonden (NNF10CC1016517)
- National Human Genome Research Institute (R01HG003229)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Upper Palaeolithic, Native American ancestry, East Asian ancestry, gene flow, population divergence time, human migration history, Denisovans, Neanderthals
- MeSH terms
- Animals, Asia, DNA, Mitochondrial, Emigration and Immigration, Haplotypes, Humans, Indians, North American, Male, Phylogeny, Siberia, Skeleton, Genome, Human, Chromosomes, Human, Y, White People, Asian People, Gene Flow, Genome, Mitochondrial, Phylogeography
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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