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Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

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Science  04 May 2018:
Vol. 360, Issue 6388, pp. 548-552
DOI: 10.1126/science.aar8380
  • Fig. 1 Spatiotemporal locations of the Taforalt and other ancient genomes.

    (A and B) Geographic locations of representative ancient genomes from West Eurasia and Africa included in our analysis. The Pleistocene Taforalt site is denoted by a red circle. (C) The date range of each ancient group is marked by black bars, representing the range of 95% confidence intervals of radiocarbon dates across all dated individuals (cal. yr B.P. on the x axis). Group labels are taken from previous studies reporting each ancient genome (4, 16, 27). N, Neolithic; WHG, Western European hunter-gatherers; EHG, Eastern European hunter-gatherers; CHG, Caucasus hunter-gatherers.

  • Fig. 2 Summary of the genetic profile of the Taforalt individuals.

    (A) The top two principal components (PCs) calculated from present-day African, Near Eastern, and Southern European individuals from 72 populations. The Taforalt individuals are projected thereon (red inverted triangles), and selected present-day populations are denoted by various colored symbols. Labels for other populations (denoted by small gray squares) are provided in fig. S8. (B) ADMIXTURE analysis results of chosen African and Middle Eastern populations (K = 10). Ancient individuals are labeled in red. Major ancestry components in Taforalt individuals are maximized in early Holocene Levantines (green), West Africans (purple), and East African Hadza (brown). The ancestry component prevalent in pre-Neolithic Europeans (beige) is absent in Taforalt.

  • Fig. 3 Geographic distribution of the genetic affinity of the Taforalt group with worldwide populations.

    (A) Mean shared genetic drift with the Taforalt group, as measured by outgroup f3 statistics in the form f3(Taforalt, X; Mbuti). Warm colors denote populations genetically close to Taforalt. Large diamonds and squares represent the 10 highest and lowest f3 values, respectively. Early Holocene Levantine groups (Natufians and Neolithic Levantines) show the highest affinity with Taforalt. The statistics and their associated SEs for the top 30 signals are presented in fig. S14. (B) Extra genetic affinity with the Taforalt group in comparison to Natufians, as measured by f4 statistics in the form f4(Chimpanzee, X; Natufian, Taforalt). Large diamonds and squares represent the 10 most positive and negative f4 values, respectively. Sub-Saharan Africans show high positive values, with West African Yoruba and Mende having the highest values, supporting the presence of sub-Saharan African ancestry in Taforalt individuals. In contrast, all Eurasian populations are genetically closer to Natufians than to the Taforalt group. The statistics and their associated SEs for the top 30 signals are presented in fig. S16.

  • Fig. 4 Relative genetic affinity of representative sub-Saharan African groups to a mixture of Yoruba and Natufians in comparison to the Taforalt group.

    We measured f4 statistics in the form f4(Chimpanzee, African; Yoruba+Natufian, Taforalt) by using (A) aSouthAfrica, (B) Mbuti, and (C) Hadza as the African group. The f4 statistics were calculated for the proportions of Natufian-related ancestry ranging from 0 to 100% in increments of 1%. The blue rectangle marks a plausible range of Natufian ancestry proportion, estimated by our qpAdm modeling [0.637 ± (2 × 0.069)]. Gray solid and dotted lines represent ±1 and −3 SE ranges, respectively. SEs were calculated by 5-centimorgan block jackknife method.

Supplementary Materials

  • Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

    Marieke van de Loosdrecht, Abdeljalil Bouzouggar, Louise Humphrey, Cosimo Posth, Nick Barton, Ayinuer Aximu-Petri, Birgit Nickel, Sarah Nagel, El Hassan Talbi, Mohammed Abdeljalil El Hajraoui, Saaïd Amzazi, Jean-Jacques Hublin, Svante Pääbo, Stephan Schiffels, Matthias Meyer, Wolfgang Haak, Choongwon Jeong, Johannes Krause

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Supplementary Text
    • Figs. S1 to S26
    • Tables S1 to S16
    • References

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