Ancient human genomes suggest three ancestral populations for present-day Europeans
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Abstract
We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
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PCA on present-day West Eurasian populations replicates previous findings of a Europe-Near East contrast along the horizontal Principal Component 1 (PC1) and parallel clines (PC2) in both Europe and the Near East.
“PCA on present-day West Eurasian populations (Methods) (Extended Data Fig. 1) on which we projected the ancient individuals (Fig. 1b) replicates previous findings of a Europe-Near East contrast along the horizontal Principal Component 1 (PC1) and parallel clines (PC2) in both Europe and the Near East (Extended Data Fig. 1)7,8,13.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [13]
The PCA results passage (labeled Abstract in our copy; page unavailable) reports a Europe–Near East discontinuity and north–south clines in both regions, supporting the main pattern. It does not specify that the contrast lies on horizontal PC1 or that the clines lie on PC2, so those axis assignments are not verified by our copy. (LLM, conf=0.82)
Experimental — accuracy not yet measuredEastern Eurasians can be modelled as arrayed along a cline with different proportions of ANE ancestry, ranging from ~40% ANE in Native Americans to no less than ~5-10% ANE in diverse East Asian groups including Han Chinese.
“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 [13]
The Online Methods ('Ancestry estimates from f4-ratios'; page not supplied) describe estimating ANE ancestry in Karitiana, and Extended Data report that Native Americans are closer to ANE than to WHG. Neither passage gives the claimed ~40% estimate. The passages found also do not establish an Eastern Eurasian ANE cline or ~5–10% ANE ancestry in East Asian groups, including Han Chinese. (LLM, conf=0.78)
Experimental — accuracy not yet measuredScandinavian hunter-gatherers (SHG) are a mix of EHG and WHG.
“Scandinavian hunter-gatherers7,8,13 (SHG) are a mix of EHG and WHG;”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [13]
The paper identifies Scandinavian hunter-gatherers (SHG) and reports that Motala12 (SHG) fits a mixture of WHG and Ancient North Eurasian (ANE) ancestry (Abstract; page not provided). It does not identify the second component as EHG, so the specific EHG–WHG mixture attributed to it is not supported. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe dataset further merges with 2,583 present-day people genotyped on the Affymetrix Human Origins array, including 238 new individuals.
“We then further merged with 2,583 present-day people genotyped on the Affymetrix Human Origins array13,16 (238 new) (Supplementary Data Table 2; Supplementary Information, section 2).”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [13]
The dataset combines the newly reported ancient individuals with previously published ancient data to form a dataset of 281 ancient individuals.
“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 [13]
The study genotyped 238 present-day individuals from 17 diverse West Eurasian populations on the Affymetrix Human Origins array and applied quality control analyses as previously described.
“We genotyped 238 present-day individuals from 17 diverse West Eurasian populations on the Affymetrix Human Origins array16, and applied quality control analyses as previously described13 (Supplementary Data Table 2).”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [13]
The newly generated present-day genotyping data were merged with data from 2,345 individuals previously genotyped on the same array.
“We merged the newly generated data with data from 2,345 individuals previously genotyped on the same array13.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [13]
Previously, the West Eurasian population known to be the best proxy for East African West Eurasian ancestry was present-day Sardinians, who resemble Neolithic Europeans genetically.
“Previously, the West Eurasian population known to be the best proxy for this ancestry was present-day Sardinians32, who resemble Neolithic Europeans genetically13,33.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [13]
At least three different ancient populations contributed to the genetics of present-day Europeans: West European hunter-gatherers, ancient north Eurasians related to Upper Paleolithic Siberians, and early European farmers mainly of Near Eastern origin.
“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 [29]
A 7,000-year-old Early European farmer was homozygous for the skin-lightening SLC24A5 allele.
“A 7,000-y-old Early European farmer was found to be homozygous for the skinlightening SLC24A5 allele (25), suggesting that light skin was relatively prevalent by 7,000 y ago and could have originated much earlier.”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [25]
The ROH trend suggests an unusually restricted ancestral population size for KO1, supporting the inference that he represents an exogenous individual in a farming settlement.
“This suggests an unusually restricted ancestral population size for KO1 (we note that low heterozygosity was also found within a 8,000 year old hunter-gatherer from Luxembourg5), supporting the inference that he represents an exogenous individual in a farming settlement.”
From Genome flux and stasis in a five millennium transect of European prehistory (2014) · cites this paper as [5]
Both SLC24A5 and SLC45A2 exhibited an ancestral homozygous state in Mesolithic specimens of Central and Western Europe, while SLC24A5 had the derived state in a Central European Neolithic individual.
“Both SLC24A5 and SLC45A2 exhibited an ancestral homozygous state in Mesolithic specimens of Central5 and Western Europe7, while SLC24A5 had the derived state in a Central European Neolithic individual5.”
From Genome flux and stasis in a five millennium transect of European prehistory (2014) · cites this paper as [5]
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Benefits and limitations of genome-wide association studies
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Self-citation
- Authors
- Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., Berger, B., Economou, C., Bollongino, R., Fu, Q., Bos, K. I., Nordenfelt, S., Li, H., de Filippo, C., Prüfer, K., Sawyer, S., Posth, C., Haak, W., Hallgren, F., Fornander, E., Rohland, N., Delsate, D., Francken, M., Guinet, J.-M., Wahl, J., Ayodo, G., Babiker, H. A., Bailliet, G., Balanovska, E., Balanovsky, O., Barrantes, R., Bedoya, G., Ben-Ami, H., Bene, J., Berrada, F., Bravi, C. M., Brisighelli, F., Busby, G. B. J., Cali, F., Churnosov, M., Cole, D. E. C., Corach, D., Damba, L., van Driem, G., Dryomov, S., Dugoujon, J.-M., Fedorova, S. A., Gallego Romero, I., Gubina, M., Hammer, M., Henn, B. M., Hervig, T., Hodoglugil, U., Jha, A. R., Karachanak-Yankova, S., Khusainova, R., Khusnutdinova, E., Kittles, R., Kivisild, T., Klitz, W., Kučinskas, V., Kushniarevich, A., Laredj, L., Litvinov, S., Loukidis, T., Mahley, R. W., Melegh, B., Metspalu, E., Molina, J., Mountain, J., Näkkäläjärvi, K., Nesheva, D., Nyambo, T., Osipova, L., Parik, J., Platonov, F., Posukh, O., Romano, V., Rothhammer, F., Rudan, I., Ruizbakiev, R., Sahakyan, H., Sajantila, A., Salas, A., Starikovskaya, E. B., Tarekegn, A., Toncheva, D., Turdikulova, S., Uktveryte, I., Utevska, O., Vasquez, R., Villena, M., Voevoda, M., Winkler, C. A., Yepiskoposyan, L., Zalloua, P., Zemunik, T., Cooper, A., Capelli, C., Thomas, M. G., Ruiz-Linares, A., Tishkoff, S. A., Singh, L., Thangaraj, K., Villems, R., Comas, D., Sukernik, R., Metspalu, M., Meyer, M., Eichler, E. E., Burger, J., Slatkin, M., Pääbo, S., Kelso, J., Reich, D., & Krause, J.
- Affiliations
- Broad Institute (US)
- University of Tübingen (DE)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Johannes Gutenberg University Mainz (DE)
- University of Washington (US)
- Massachusetts Institute of Technology (US)
- Stockholm University (SE)
- Harvard University (US)
- The University of Adelaide (AU)
- Musée national d'histoire naturelle Luxembourg (LU)
- Senckenberg Centre for Human Evolution and Palaeoenvironment (DE)
- Sultan Qaboos University (OM)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Research Centre for Medical Genetics (RU)
- Universidad de Costa Rica (CR)
- Universidad de Antioquia (CO)
- University of Pecs (HU)
- Al Akhawayn University (MA)
- Università Cattolica del Sacro Cuore (IT)
- Centre for Human Genetics (GB)
- Belgorod National Research University (RU)
- University of Toronto (CA)
- Universidad de Buenos Aires (AR)
- Russian Academy of Sciences (RU)
- Centre National de la Recherche Scientifique (FR)
- University of Arizona (US)
- Stony Brook University (US)
- University of Bergen (NO)
- University of Chicago (US)
- Medical University of Sofia (BG)
- University of Cambridge (GB)
- University of California, Berkeley (US)
- Vilnius University (LT)
- Estonian Biocentre (EE)
- Institut de génétique et de biologie moléculaire et cellulaire (FR)
- University College London (GB)
- Gladstone Institutes (US)
- University of Tartu (EE)
- 23andMe (United States) (US)
- University of Oulu (FI)
- Muhimbili University of Health and Allied Sciences (TZ)
- University of Palermo (IT)
- University of Tarapacá (CL)
- University of Edinburgh (GB)
- Academy of Sciences Republic of Uzbekistan (UZ)
- Institute of Molecular Biology (AM)
- University of Helsinki (FI)
- Universidade de Santiago de Compostela (ES)
- V. N. Karazin Kharkiv National University (UA)
- Universidad Mayor de San Andrés (BO)
- National Institutes of Health (US)
- University of Split (HR)
- University of Oxford (GB)
- University of Pennsylvania (US)
- Centre for Cellular and Molecular Biology (IN)
- Estonian Academy of Sciences (EE)
- Universitat Pompeu Fabra (ES)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Reich, David
- Krause, Johannes
- ORCID
- Lazaridis, Iosif
- Patterson, Nick
- Mittnik, Alissa
- Renaud, Gabriel
- Mallick, Swapan
- Sudmant, Peter H.
- Schraiber, Joshua G.
- Castellano, Sergi
- Lipson, Mark
- Berger, Bonnie
- Fu, Qiaomei
- Bos, Kirsten I.
- Li, Heng
- Prüfer, Kay
- Sawyer, Susanna
- Posth, Cosimo
- Haak, Wolfgang
- Hallgren, Fredrik
- Fornander, Elin
- Rohland, Nadin
- Delsate, Dominique
- Francken, Michael
- Wahl, Joachim
- Ayodo, George
- Babiker, Hamza A.
- Bailliet, Graciela
- Balanovska, Elena
- Bedoya, Gabriel
- Bene, Judit
- Brisighelli, Francesca
- Busby, George B. J.
- Churnosov, Mikhail
- Corach, Daniel
- Damba, Larissa
- Dugoujon, Jean-Michel
- Gubina, Marina
- Hammer, Michael
- Henn, Brenna M.
- Hervig, Tor
- Jha, Aashish R.
- Karachanak-Yankova, Sena
- Khusainova, Rita
- Kittles, Rick
- Kivisild, Toomas
- Kučinskas, Vaidutis
- Kushniarevich, Alena
- Litvinov, Sergey
- Mahley, Robert W.
- Melegh, Béla
- Metspalu, Ene
- Mountain, Joanna
- Näkkäläjärvi, Klemetti
- Nesheva, Desislava
- Nyambo, Thomas
- Osipova, Ludmila
- Posukh, Olga
- Romano, Valentino
- Rothhammer, Francisco
- Rudan, Igor
- Sahakyan, Hovhannes
- Sajantila, Antti
- Salas, Antonio
- Starikovskaya, Elena B.
- Toncheva, Draga
- Turdikulova, Shahlo
- Utevska, Olga
- Voevoda, Mikhail
- Winkler, Cheryl A.
- Yepiskoposyan, Levon
- Zalloua, Pierre
- Zemunik, Tatijana
- Cooper, Alan
- Capelli, Cristian
- Thomas, Mark G.
- Tishkoff, Sarah A.
- Singh, Lalji
- Villems, Richard
- Comas, David
- Sukernik, Rem
- Metspalu, Mait
- Meyer, Matthias
- Eichler, Evan E.
- Slatkin, Montgomery
- Pääbo, Svante
- Kelso, Janet
- Reich, David
- Krause, Johannes
- Venue
- Nature
- Published
- 2014-09
- Volume
- 513
- Issue
- 7518
- Pages
- 409-413
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4170574
- OpenAlex
- W2050967443
- Cited by
- 1,357
- References
- 126
- Citations by year
- 2026: 67 · 2025: 96 · 2024: 108 · 2023: 114 · 2022: 112 · 2021: 148 · 2020: 109 · 2019: 120 · 2018: 127 · 2017: 126 · 2016: 108 · 2015: 96 · 2014: 22 · 2012: 1
- FWCI
- 76.14
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (acceptedVersion, other-oa)
- arXiv (Cornell University) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- Open Access Repository (Belgorod State National Research University) (submittedVersion)
- El Servicio de Difusión de la Creación Intelectual (National University of La Plata) (submittedVersion, cc-by-nc-sa)
- RePEc: Research Papers in Economics (submittedVersion)
- Americanae (AECID Library) (submittedVersion, cc-by-nc-sa)
- BORIS (University Library Bern) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- Nova Science Publishers (Nova Science Publishers, Inc.) (submittedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- RUNE (Research UNE) (submittedVersion)
- arXiv (Cornell University)
- PMC
- The University of Adelaide (cc-by)
- Open Access CRIS of the University of Bern
- Funders
- National Science Foundation (0827436, 1053575, 1032255)
- Howard Hughes Medical Institute
- U.S. Department of Health and Human Services
- Children's Hospital of Philadelphia
- Wellcome Trust (100719/Z/12/Z)
- European Commission
- Deutsche Forschungsgemeinschaft (KR 4015/1-1)
- Eesti Teadusfondi
- Russian Foundation for Basic Research (13-06-00670)
- Hungarian Scientific Research Fund (73430, 103983)
- Max-Planck-Gesellschaft
- Tartu Ülikool
- National Institutes of Health (OCI-1053575, HHSN26120080001E)
- U.S. Public Health Service (HHSN 26120080001E)
- Natural Sciences and Engineering Research Council of Canada
- Russian Academy of Sciences
- National Human Genome Research Institute (HG002385, P01HG004120, R01HG006399, HG004120, R01HG002385)
- National Cancer Institute (HHSN26120080001E)
- National Institute of General Medical Sciences (GM-40282, R01GM040282, GM100233, R01GM100233)
- National Institute of Environmental Health Sciences (DP1ES022577)
- National Center for Chronic Disease Prevention and Health Promotion (8 DP1 ES022577-04)
- European Social Fund (VP1-3.1-ŠMM-07-K-01-013, 62,63)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- ancient human genomes, European ancestry, hunter-gatherers, genetic differentiation, transition to agriculture
- MeSH terms
- Workforce, Agriculture, Asia, Europe, Humans, Population Dynamics, Genome, Human, Principal Component Analysis, White People, History, Ancient
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