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Early Neolithic genomes from the eastern Fertile Crescent

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Science  29 Jul 2016:
Vol. 353, Issue 6298, pp. 499-503
DOI: 10.1126/science.aaf7943
  • Fig. 1 Map of prehistoric Neolithic and Iron Age Zagros genome locations.

    Colors indicate isochrones, with numbers giving approximate arrival times of the Neolithic culture (in years BCE).

  • Fig. 2 PCA plot of Zagros, European, and Near and Middle Eastern ancient genomes.

    Comparison of ancient and modern genomes shows that Neolithic Zagros genomes form a discrete genetic cluster close to modern Pakistani and Afghan genomes but distinct from the genomes of other Neolithic farmers and European hunter-gatherers. See animation S1 for an interactive three-dimensional version of the PCA, including the third principal component.

  • Fig. 3 Level and structure of ancient genomic diversity.

    (A) Total length of the genome in different ROH classes; shades indicate the range observed among modern samples from different populations, and lines indicate the distributions for ancient samples. (B) The total length of short (<1.6 Mb) versus long (≥1.6 Mb) ROH. (C) Distribution of heterozygosity (θ) inferred in 1-Mb windows along a portion of chromosome 3 showing the longest ROH segment in WC1. Solid lines represent the MLE estimate, shades indicate the 95% confidence intervals, and dashed lines represent the genome-wide median for each sample. (D) Distribution of heterozygosity (θ) estimated in 1-Mb windows across the autosomes for modern and ancient samples. (E) Similarity in the pattern of heterozygosity (θ) along the genome as obtained by a PCA on centered Spearman correlations. Ancient—Bich: Bichon, Upper Palaeolithic forager from Switzerland; KK1: Kotias, Mesolithic forager from Georgia; WC1: Wezmeh Cave, Early Neolithic farmer from Zagros; Mota: 4500-year-old individual from Ethiopia; BR2: Ludas-Varjú-dúló, Late Bronze Age individual from Hungary. Modern—YRI: Yoruban, West Africa; TSI: Tuscan, Italy; PJL: Punjabi, Pakistan; GBR: British.

  • Fig. 4 Modern-day peoples with affinity to WC1.

    Modern groups with an increasingly higher (respectively lower) inferred proportion of haplotype sharing with the Iranian Neolithic Wezmeh Cave (WC1, 7455 to 7082 cal BCE, blue triangle) compared to the Anatolian Neolithic Barcın genome (Bar8; 6212 to 6030 cal BCE, red triangle) are depicted with an increasingly stronger blue or red color, respectively. Circle sizes illustrate the relative absolute proportion of this difference between WC1 versus Bar8. The key for the modern group labels is provided in table S24.

Supplementary Materials

  • Early Neolithic genomes from the eastern Fertile Crescent

    Farnaz Broushaki, Mark G Thomas, Vivian Link, Saioa López, Lucy van Dorp, Karola Kirsanow, Zuzana Hofmanová, Yoan Diekmann, Lara M. Cassidy, David Díez-del-Molino, Athanasios Kousathanas, Christian Sell, Harry K. Robson, Rui Martiniano, Jens Blöcher, Amelie Scheu, Susanne Kreutzer, Ruth Bollongino, Dean Bobo, Hossein Davudi, Olivia Munoz, Mathias Currat, Kamyar Abdi, Fereidoun Biglari, Oliver E. Craig, Daniel G Bradley, Stephen Shennan, Krishna R Veeramah, Marjan Mashkour, Daniel Wegmann, Garrett Hellenthal, Joachim Burger

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

    Download Supplement
    • Supplementary Text
    • Figs. S1 to S52
    • Tables S1 to S19, S21 to S23, and S26 to S37
    • Captions for tables S20, S24, and S25
    • Caption for animation S1
    • Full reference list
    Table S1
    Detailed results of the f3 and D statistics.(Available online as a separate excel file).
    Table S2
    Ancestry proportions. Inferred proportions of ancestry for all ancient individuals and modern populations (Lazaridis merge) under Analysis I, II, II-, and III as described in supplementary section 9 (Available online as a separate excel file)
    Table S3
    Ancestry proportions. Inferred proportions of ancestry for all ancient individuals and modern populations (Busby merge) under Analysis I, II, II-, and III as described in supplementary section 9 (Available online as a separate excel file).

    Additional Data

    Animation S1
    Interactive 3D version of the PCA of modern and projected ancient samples shown in Fig. 2

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