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Ancient human genome sequence of an extinct Palaeo-Eskimo
Open accessAbstract
We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit. For the first time, the sequence of a near-complete nuclear genome has been obtained from the tissue of an ancient human. It comes from permafrost-preserved hair, about 4,000 years old, of a male palaeo-Eskimo of the Saqqaq culture, the earliest known settlers in Greenland. Functional single-nucleotide polymorphism (SNP) assessment was used to assign possible phenotypic characteristics. The analysis provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of the migration that gave rise to the modern Native Americans and Inuit. Elsewhere in the issue we profile the paper's last author Eske Willerslev, who headed the project and found the lock of hair in a Copenhagen museum basement — after a fruitless search among the archaeological sites of Peary Land. The first genome sequence of an ancient human is reported. It comes from an approximately 4,000-year-old permafrost-preserved hair from a male from the first known culture to settle in Greenland. Functional single-nucleotide polymorphism (SNP) assessment is used to assign possible phenotypic characteristics and high-confidence SNPs are compared to those of contemporary populations to find those most closely related to the individual.
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“As the Anzick-1 individual was found to be male, we were also able to quantify contamination levels based on the heterozygosity levels seen on the X chromosome19, which resulted in similarly low contamination estimates (<1.2%, SI11).”
From The genome of a Late Pleistocene human from a Clovis burial site in western Montana (2014) · cites this paper as [19]
Experimental — accuracy not yet measuredIn the citing paper
“Subsequent migration of the ancestors of the Inuit is evident from the genome sequence of ~4000-year-old Saqqaqman [39].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [39]
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Self-citation
Metadata
- Authors
- Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, M. T. P., Wang, Y., Raghavan, M., Campos, P. F., Kamp, H. M., Wilson, A. S., Gledhill, A., Tridico, S., Bunce, M., Lorenzen, E. D., Binladen, J., Guo, X., Zhao, J., Zhang, X., Zhang, H., Li, Z., Chen, M., Orlando, L., Kristiansen, K., Bak, M., Tommerup, N., Bendixen, C., Pierre, T. L., Grønnow, B., Meldgaard, M., Andreasen, C., Fedorova, S. A., Osipova, L. P., Higham, T. F. G., Ramsey, C. B., Hansen, T. V. O., Nielsen, F. C., Crawford, M. H., Brunak, S., Sicheritz-Pontén, T., Villems, R., Nielsen, R., Krogh, A., Wang, J., & Willerslev, E.
- Affiliations
- University of Copenhagen (DK)
- BGI Group (China) (CN)
- Estonian Biocentre (EE)
- University of Cambridge (GB)
- Technical University of Denmark (DK)
- University of California, Berkeley (US)
- University of Bradford (GB)
- Australian Federal Police (AU)
- Murdoch University (AU)
- Lyon 1 Université (FR)
- Aarhus University (DK)
- National Museum of Denmark (DK)
- Greenland National Museum & Archives (GL)
- Institute of Cytology and Genetics (RU)
- University of Oxford (GB)
- University of Kansas (US)
- Corresponding author
- Wang, Jun
- Willerslev, Eske
- ORCID
- Rasmussen, Morten
- Li, Yingrui
- Lindgreen, Stinus
- Pedersen, Jakob Skou
- Albrechtsen, Anders
- Moltke, Ida
- Metspalu, Mait
- Metspalu, Ene
- Kivisild, Toomas
- Gupta, Ramneek
- Nielsen, Kasper
- Gilbert, M. Thomas P.
- Wang, Yong
- Raghavan, Maanasa
- Campos, Paula F.
- Kamp, Hanne Munkholm
- Wilson, Andrew S.
- Bunce, Michael
- Lorenzen, Eline D.
- Zhao, Jing
- Zhang, Xiuqing
- Zhang, Hao
- Li, Zhuo
- Chen, Minfeng
- Orlando, Ludovic
- Kristiansen, Karsten
- Bak, Mads
- Tommerup, Niels
- Bendixen, Christian
- Grønnow, Bjarne
- Meldgaard, Morten
- Andreasen, Claus
- Osipova, Ludmila P.
- Higham, Thomas F. G.
- Ramsey, Christopher Bronk
- Hansen, Thomas v. O.
- Nielsen, Finn C.
- Brunak, Søren
- Villems, Richard
- Nielsen, Rasmus
- Krogh, Anders
- Wang, Jun
- Willerslev, Eske
- Venue
- Nature
- Published
- 2010-02
- Volume
- 463
- Issue
- 7282
- Pages
- 757-762
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3951495
- OpenAlex
- W2135016593
- Cited by
- 849
- References
- 42
- Citations by year
- 2026: 18 · 2025: 22 · 2024: 36 · 2023: 47 · 2022: 38 · 2021: 61 · 2020: 32 · 2019: 67 · 2018: 60 · 2017: 58 · 2016: 52 · 2015: 63 · 2014: 62 · 2013: 60 · 2012: 52
- FWCI
- 41.87
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Murdoch University Research Portal (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Bradford Scholars (University of Bradford) (submittedVersion)
- eSpace (Curtin University) (submittedVersion)
- KU ScholarWorks (The University of Kansas) (submittedVersion, cc-by-nc-sa)
- Ministry of Culture Research Portal (submittedVersion, other-oa)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
- DigitalGeorgetown (Georgetown University Library) (submittedVersion)
- Funders
- National Science Foundation (0327676)
- European Commission (205419)
- National Research Foundation
- Danmarks Grundforskningsfond
- National Natural Science Foundation of China (30725008)
- Eesti Teadusfondi
- Lundbeckfonden (R70-2010-6286, R24-2008-2527, R13-2007-1172)
- Novo Nordisk
- Danmarks Frie Forskningsfond
- Danmarks Tekniske Universitet
- Novo Nordisk Fonden
- H. Lundbeck A/S
- Forsknings- og Innovationsstyrelsen
- Natural Environment Research Council (NRCF010002)
- Australian Research Council
- Danish Agency for Science and Higher Education
- Strategic Research Council
- 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
- Social Sciences › Arts and Humanities › Archeology (arts and humanities) › Paleopathology and ancient diseases
- Keywords
- ancient human genomes, single nucleotide polymorphisms, Inuit, Native Americans
- MeSH terms
- Emigration and Immigration, Inuit, Genetics, Population, Genotype, Greenland, Hair, Humans, Male, Phenotype, Phylogeny, Siberia, Genome, Human, Cryopreservation, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genomics, History, Ancient, Extinction, Biological
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