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, 513 (7518), 409-13

Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans

Iosif Lazaridis  1 Nick Patterson  2 Alissa Mittnik  3 Gabriel Renaud  4 Swapan Mallick  1 Karola Kirsanow  5 Peter H Sudmant  6 Joshua G Schraiber  7 Sergi Castellano  4 Mark Lipson  8 Bonnie Berger  9 Christos Economou  10 Ruth Bollongino  5 Qiaomei Fu  11 Kirsten I Bos  3 Susanne Nordenfelt  1 Heng Li  1 Cesare de Filippo  4 Kay Prüfer  4 Susanna Sawyer  4 Cosimo Posth  3 Wolfgang Haak  12 Fredrik Hallgren  13 Elin Fornander  13 Nadin Rohland  1 Dominique Delsate  14 Michael Francken  15 Jean-Michel Guinet  16 Joachim Wahl  17 George Ayodo  18 Hamza A Babiker  19 Graciela Bailliet  20 Elena Balanovska  21 Oleg Balanovsky  22 Ramiro Barrantes  23 Gabriel Bedoya  24 Haim Ben-Ami  25 Judit Bene  26 Fouad Berrada  27 Claudio M Bravi  20 Francesca Brisighelli  28 George B J Busby  29 Francesco Cali  30 Mikhail Churnosov  31 David E C Cole  32 Daniel Corach  33 Larissa Damba  34 George van Driem  35 Stanislav Dryomov  36 Jean-Michel Dugoujon  37 Sardana A Fedorova  38 Irene Gallego Romero  39 Marina Gubina  34 Michael Hammer  40 Brenna M Henn  41 Tor Hervig  42 Ugur Hodoglugil  43 Aashish R Jha  39 Sena Karachanak-Yankova  44 Rita Khusainova  45 Elza Khusnutdinova  45 Rick Kittles  46 Toomas Kivisild  47 William Klitz  48 Vaidutis Kučinskas  49 Alena Kushniarevich  50 Leila Laredj  51 Sergey Litvinov  52 Theologos Loukidis  53 Robert W Mahley  54 Béla Melegh  26 Ene Metspalu  55 Julio Molina  56 Joanna Mountain  57 Klemetti Näkkäläjärvi  58 Desislava Nesheva  44 Thomas Nyambo  59 Ludmila Osipova  34 Jüri Parik  55 Fedor Platonov  60 Olga Posukh  34 Valentino Romano  61 Francisco Rothhammer  62 Igor Rudan  63 Ruslan Ruizbakiev  64 Hovhannes Sahakyan  65 Antti Sajantila  66 Antonio Salas  67 Elena B Starikovskaya  36 Ayele Tarekegn  68 Draga Toncheva  44 Shahlo Turdikulova  69 Ingrida Uktveryte  49 Olga Utevska  70 René Vasquez  71 Mercedes Villena  71 Mikhail Voevoda  72 Cheryl A Winkler  73 Levon Yepiskoposyan  74 Pierre Zalloua  75 Tatijana Zemunik  76 Alan Cooper  12 Cristian Capelli  77 Mark G Thomas  78 Andres Ruiz-Linares  78 Sarah A Tishkoff  79 Lalji Singh  80 Kumarasamy Thangaraj  81 Richard Villems  82 David Comas  83 Rem Sukernik  36 Mait Metspalu  50 Matthias Meyer  4 Evan E Eichler  84 Joachim Burger  5 Montgomery Slatkin  48 Svante Pääbo  4 Janet Kelso  4 David Reich  85 Johannes Krause  86
Affiliations

Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans

Iosif Lazaridis et al. Nature.

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.

Conflict of interest statement

The authors declare competing financial interests: UH is an employee of Illumina, TL is an employee of AMGEN, and JM is an employee of 23andMe.

Figures

Extended Data Figure 1
Extended Data Figure 1
Photographs of analyzed ancient samples. (A) Loschbour skull; (B) Stuttgart skull, missing the lower right M2 we sampled; (C) excavation at Kanaljorden in Motala, Sweden; (D) Motala 1 in situ.
Extended Data Figure 2
Extended Data Figure 2
Pairwise Sequential Markovian Coalescent (PSMC) analysis. (A) Inference of population size as a function of time, showing a very small recent population size over the most recent period in the ancestry of Loschbour (at least the last 5–10 thousand years). (B) Inferred time since the most recent common ancestor from the PSMC for chromosomes 20, 21, 22 (top to bottom); Stuttgart is plotted on top and Loschbour at bottom.
Extended Data Figure 3
Extended Data Figure 3
ADMIXTURE analysis (K=2 to K=20). Ancient samples (Loschbour, Stuttgart, Motala_merge, Motala12, MA1, and LaBrana) are at left.
Extended Data Figure 4
Extended Data Figure 4
ANE ancestry is present in both Europe and the Near East but WHG ancestry is restricted to Europe, which cannot be due to a single admixture event. (x-axis) We computed the statistic f4(Test, Stuttgart; MA1, Chimp), which measures where MA1 shares more alleles with a test population than with Stuttgart. It is positive for most European and Near Eastern populations, consistent with ANE (MA1-related) gene flow into both regions. (y-axis) We computed the statistic f4(Test, Stuttgart; Loschbour, Chimp), which measures whether Loschbour shares more alleles with a test sample than with Stuttgart. Only European populations show positive values of this statistic, providing evidence of WHG (Loschbour-related) admixture only in Europeans.
Extended Data Figure 5
Extended Data Figure 5
MA1 is the best surrogate for ANE for which we have data. Europeans share more alleles with MA1 than with Karitiana, as we see from the fact that in a plot of f4(Test, BedouinB; MA1, Chimp) and f4(Test, BedouinB; Karitiana, Chimp), the European cline deviates in the direction of MA1, rather than Karitiana (the slope is >1 and European populations are above the line indicating equality of these two statistics).
Extended Data Figure 6
Extended Data Figure 6
The differential relatedness of West Eurasians to Stuttgart (EEF), Loschbour (WHG), and MA1 (ANE) cannot be explained by two-way mixture. We plot on a West Eurasian map the statistic f4(Test, Chimp; A1, A2), where A1 and A2 are a pair of the three ancient samples representing the three ancestral populations of Europe. (A) In both Europe and the Near East/Caucasus, populations from the south have more relatedness to Stuttgart than those from the north where ANE influence is also important. (B) Northern European populations share more alleles with Loschbour than with Stuttgart, as they have additional WHG ancestry beyond what was already present in EEF. (C) We observe a striking contrast between Europe west of the Caucasus and the Near East in degree of relatedness to WHG. In Europe, there is a much higher degree of allele sharing with Loschbour than with MA1, which we ascribe to the 60–80% WHG/(WHG+ANE) ratio in most Europeans that we report in SI14. In contrast, the Near East has no appreciable WHG ancestry but some ANE ancestry, especially in the northern Caucasus. (Jewish populations are marked with a square in this figure to assist in interpretation as their ancestry is often anomalous for their geographic regions.)
Extended Data Figure 7
Extended Data Figure 7
Evidence for Siberian gene flow into far northeastern Europe. Some northeastern European populations (Chuvash, Finnish, Russian, Mordovian, Saami) share more alleles with Han Chinese than with other Europeans who are arrayed in a cline from Stuttgart to Lithuanians/Estonians in a plot of f4(Test, BedouinB; Han, Mbuti) against f4(Test, BedouinB; MA1, Mbuti).
Figure 1
Figure 1. Map of West Eurasian populations and Principal Component Analysis
(a) Geographical locations of analyzed samples, with color coding matching the PCA. We show all sampling locations for each population, which results in multiple points for some (e.g., Spain). (b) PCA on all present-day West Eurasians, with ancient and selected eastern non-African samples projected. European hunter-gatherers fall beyond present-day Europeans in the direction of European differentiation from the Near East. Stuttgart clusters with other Neolithic Europeans and present-day Sardinians. MA1 falls outside the variation of present-day West Eurasians in the direction of southern-northern differentiation along dimension 2.
Figure 1
Figure 1. Map of West Eurasian populations and Principal Component Analysis
(a) Geographical locations of analyzed samples, with color coding matching the PCA. We show all sampling locations for each population, which results in multiple points for some (e.g., Spain). (b) PCA on all present-day West Eurasians, with ancient and selected eastern non-African samples projected. European hunter-gatherers fall beyond present-day Europeans in the direction of European differentiation from the Near East. Stuttgart clusters with other Neolithic Europeans and present-day Sardinians. MA1 falls outside the variation of present-day West Eurasians in the direction of southern-northern differentiation along dimension 2.
Figure 2
Figure 2. Modeling of West Eurasian population history
(a) A three-way mixture model that is a fit to the data for many populations. Present-day samples are colored in blue, ancient in red, and reconstructed ancestral populations in green. Solid lines represent descent without mixture, and dashed lines represent admixture. We print mixture proportions and one standard error for the two mixtures relating the highly divergent ancestral populations. (We do not print the estimate for the “European” population as it varies depending on the population). (b) We plot the proportions of ancestry from each of three inferred ancestral populations (EEF, ANE and WHG).
Figure 2
Figure 2. Modeling of West Eurasian population history
(a) A three-way mixture model that is a fit to the data for many populations. Present-day samples are colored in blue, ancient in red, and reconstructed ancestral populations in green. Solid lines represent descent without mixture, and dashed lines represent admixture. We print mixture proportions and one standard error for the two mixtures relating the highly divergent ancestral populations. (We do not print the estimate for the “European” population as it varies depending on the population). (b) We plot the proportions of ancestry from each of three inferred ancestral populations (EEF, ANE and WHG).

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