Research ArticleEVOLUTIONARY GENETICS

Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago

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Science Advances  01 Feb 2017:
Vol. 3, no. 2, e1601877
DOI: 10.1126/sciadv.1601877
  • Fig. 1 Regional reference panel, PCA, and ADMIXTURE analysis.

    (A) Map of Asia showing the location of Devil’s Gate (black triangle) and of modern populations forming the regional panel of our analysis. (B) Plot of the first two principal components as defined by our regional panel of modern populations from East Asia and central Asia shown on (A), with the two samples from Devil’s Gate (black triangles) projected upon them (18). (C) ADMIXTURE analysis (19) performed on Devil’s Gate and our regional panel, for K = 5 (lowest cross-validation error) and K = 8 (appearance of Devil’s Gate–specific cluster).

  • Fig. 2 Outgroup f3 statistics.

    Outgroup f3 measuring shared drift between Devil’s Gate (black triangle shows sampling location) and modern populations with respect to an African outgroup (Khomani). (A) Map of the whole world. (B) Fifteen populations with the highest shared drift with Devil’s Gate, color-coded by regions as in Fig. 1. Error bars represent 1 SE.

  • Fig. 3 Spatial pattern of outgroup f3 statistics.

    Relationship between outgroup f3(X, Devil’s Gate; Khomani) and distance on land from Devil’s Gate using DevilsGate1 and all single-nucleotide polymorphisms (SNPs). Populations up to 9000 km away from Devil’s Gate were considered when computing correlation. The highest distance considered was chosen to acquire the highest Pearson correlation in steps of 500 km. Best linear fit (r2 = 0.772, F1,108 = 368.4, P < 0.001) is shown as blue line, with 95% CI indicated by the shaded area.

  • Fig. 4 Admixture f3 statistics.

    Admixture f3 representing modern Koreans and Japanese as a mixture of two populations, X and Y, color-coded by regions as in Fig. 1. (A) Thirty pairs with the lowest f3 score for the Koreans as the target, out of those giving a significant (z < −2) value. (B) All four pairs giving a significantly (z < −2) negative score for the Japanese as the target. Error bars represent 1 SE.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/2/e1601877/DC1

    Supplementary Materials and Methods

    fig. S1. Calibrated age range of the two human specimens from Devil’s Gate (OxCal version 4.2.4).

    fig. S2. Damage patterns for samples from Devil’s Gate.

    fig. S3. Sequence length distribution for samples from Devil’s Gate.

    fig. S4. Outgroup f3 statistics on PMDtools-filtered data.

    fig. S5. PCA on all SNPs using the worldwide panel.

    fig. S6. PCA on transversion SNPs using the worldwide panel.

    fig. S7. PCA on all SNPs using the regional panel.

    fig. S8. PCA on transversion SNPs using the regional panel.

    fig. S9. ADMIXTURE analysis cross-validation (CV) error as a function of the number of clusters (K) for the regional panel using all SNPs (top row) or transversions only (bottom row) and with (left column) or without (right column) MapDamage treatment.

    fig. S10. ADMIXTURE analysis CV error as a function of the number of clusters (K) for the world panel using all SNPs (top row) or transversions only (bottom row) and with (left column) or without (right column) MapDamage treatment.

    fig. S11. Outgroup f3 scores of the form f3(X, MA1; Khomani), with modern populations and selected ancient samples (DevilsGate1, DevilsGate2, Ust’-Ishim, Kotias, Loschbour, and Stuttgart), using all SNPs, with f3 > 0.15 displayed.

    fig. S12. D scores of the form D(X, Khomani; MA1, DevilsGate1), with all modern populations in our panel and selected ancient samples, using all SNPs.

    fig. S13. D scores of the form D(X, Khomani; MA1, DevilsGate1), with all modern populations in our panel and selected ancient samples, using all SNPs.

    fig. S14. Outgroup f3 scores of the form f3(X, Ust’-Ishim; Khomani), with modern populations and selected ancient samples (MA1, Kotias, Loschbour, and Stuttgart), using all SNPs, with f3 > 0.15 displayed.

    fig. S15. D scores of the form D(X, Khomani; Ust’-Ishim, DevilsGate1), with all modern populations in our panel and selected ancient samples, using all SNPs.

    fig. S16. D scores of the form D(X, Khomani; Ust’-Ishim, DevilsGate2), with all modern populations in our panel and selected ancient samples, using all SNPs.

    fig. S17. Comparison of Devil’s Gate–related ancestry in the Ulchi and European hunter-gatherer–related ancestry in European populations.

    fig. S18. Comparison of Devil’s Gate–related ancestry in the Ulchi and Early European farmer–related ancestry in European populations.

    fig. S19. Comparison of Devil’s Gate–related ancestry in the Ulchi and Bronze Age Steppe–related ancestry in European populations.

    table S1. Details of sample preparation and sequencing.

    table S2. mtDNA contamination estimates.

    table S3. Admixture f3(Source1, Source2; Target) for the Ulchi with z < −1 using all SNPs.

    table S4. Admixture f3(Source1, Source2; Target) for the Ulchi with z < −1 using only transversion SNPs.

    table S5. Admixture f3(Source1, Source2; Target) for the Sardinians using all SNPs and showing the 10 most significantly negative pairs.

    table S6. Admixture f3(Source1, Source2; Target) for the Lithuanians using all SNPs and showing the 10 most significantly negative pairs.

    extended data fig. S1. Results from ADMIXTURE analysis using the regional panel, all SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.

    extended data fig. S2. Results from ADMIXTURE analysis using the regional panel, transversion SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.

    extended data fig. S3. Results from ADMIXTURE analysis using the regional panel, all SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.

    extended data fig. S4. Results from ADMIXTURE analysis using the regional panel, transversion SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.

    extended data fig. S5. Results from ADMIXTURE analysis using the total panel, all SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.

    extended data fig. S6. Results from ADMIXTURE analysis using the total panel, transversion SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.

    extended data fig. S7. Results from ADMIXTURE analysis using the total panel, all SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.

    extended data fig. S8. Results from ADMIXTURE analysis using the total panel, transversion SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.

    extended data table S1. Sample information.

    extended data table S2. ADMIXTURE proportions.

    extended data table S3. Outgroup f3 statistics for Devil’s Gate.

    extended data table S4. Outgroup f3 and space.

    extended data table S5. Outgroup f3 for MA1 and Ust’-Ishim.

    extended data table S6. D scores for MA1 and Ust’-Ishim.

    extended data table S7. D scores for the Ulchi.

    extended data table S8. Admixture f3 for the Koreans and the Japanese.

    extended data table S9. Phenotypes of interest.

    References (5584)

  • Supplementary Materials

    This PDF file includes:

    • Supplementary Materials and Methods
    • fig. S1. Calibrated age range of the two human specimens from Devil’s Gate (OxCal version 4.2.4).
    • fig. S2. Damage patterns for samples from Devil’s Gate.
    • fig. S3. Sequence length distribution for samples from Devil’s Gate.
    • fig. S4. Outgroup ƒ3 statistics on PMDtools-filtered data.
    • fig. S5. PCA on all SNPs using the worldwide panel.
    • fig. S6. PCA on transversion SNPs using the worldwide panel.
    • fig. S7. PCA on all SNPs using the regional panel.
    • fig. S8. PCA on transversion SNPs using the regional panel.
    • fig. S9. ADMIXTURE analysis cross-validation (CV) error as a function of the number of clusters (K) for the regional panel using all SNPs (top row) or transversions only (bottom row) and with (left column) or without (right column) MapDamage treatment.
    • fig. S10. ADMIXTURE analysis CV error as a function of the number of clusters (K) for the world panel using all SNPs (top row) or transversions only (bottom row) and with (left column) or without (right column) MapDamage treatment.
    • fig. S11. Outgroup ƒ3 scores of the form ƒ3(X, MA1; Khomani), with modern populations and selected ancient samples (DevilsGate1, DevilsGate2, Ust’-Ishim, Kotias, Loschbour, and Stuttgart), using all SNPs, with ƒ3 > 0.15 displayed.
    • fig. S12. D scores of the form D(X, Khomani; MA1, DevilsGate1), with all modern populations in our panel and selected ancient samples, using all SNPs.
    • fig. S13. D scores of the form D(X, Khomani; MA1, DevilsGate1), with all modern populations in our panel and selected ancient samples, using all SNPs.
    • fig. S14. Outgroup ƒ3 scores of the form ƒ3(X, Ust’-Ishim; Khomani), with modern populations and selected ancient samples (MA1, Kotias, Loschbour, and Stuttgart), using all SNPs, with ƒ3 > 0.15 displayed.
    • fig. S15. D scores of the form D(X, Khomani; Ust’-Ishim, DevilsGate1), with all modern populations in our panel and selected ancient samples, using all SNPs.
    • fig. S16. D scores of the form D(X, Khomani; Ust’-Ishim, DevilsGate2), with all modern populations in our panel and selected ancient samples, using all SNPs.
    • fig. S17. Comparison of Devil’s Gate–related ancestry in the Ulchi and European hunter-gatherer–related ancestry in European populations.
    • fig. S18. Comparison of Devil’s Gate–related ancestry in the Ulchi and Early European farmer–related ancestry in European populations.
    • fig. S19. Comparison of Devil’s Gate–related ancestry in the Ulchi and Bronze Age Steppe–related ancestry in European populations.
    • table S1. Details of sample preparation and sequencing.
    • table S2. mtDNA contamination estimates.
    • table S3. Admixture ƒ3(Source1, Source2; Target) for the Ulchi with z < −1 using all SNPs.
    • table S4. Admixture ƒ3(Source1, Source2; Target) for the Ulchi with z < −1 using only transversion SNPs.
    • table S5. Admixture ƒ3(Source1, Source2; Target) for the Sardinians using all SNPs and showing the 10 most significantly negative pairs.
    • table S6. Admixture ƒ3(Source1, Source2; Target) for the Lithuanians using all SNPs and showing the 10 most significantly negative pairs.
    • Legends for extended data figs. S1 to S8
    • Legends for extended data tables S1 to S9
    • References (55–84)

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • extended data fig. S1 (.pdf format). Results from ADMIXTURE analysis using the regional panel, all SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.
    • extended data fig. S2 (.pdf format). Results from ADMIXTURE analysis using the regional panel, transversion SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.
    • extended data fig. S3 (.pdf format). Results from ADMIXTURE analysis using the regional panel, all SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.
    • extended data fig. S4 (.pdf format). Results from ADMIXTURE analysis using the regional panel, transversion SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 10.
    • extended data fig. S5 (.pdf format). Results from ADMIXTURE analysis using the total panel, all SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.
    • extended data fig. S6 (.pdf format). Results from ADMIXTURE analysis using the total panel, transversion SNPs, and MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.
    • extended data fig. S7 (.pdf format). Results from ADMIXTURE analysis using the total panel, all SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.
    • extended data fig. S8 (.pdf format). Results from ADMIXTURE analysis using the total panel, transversion SNPs, and no MapDamage treatment on samples from Devil’s Gate and setting the number of clusters to K = 2 to 20.
    • extended data table S1 (Microsoft Excel format). Sample information.
    • extended data table S2 (Microsoft Excel format). ADMIXTURE proportions.
    • extended data table S3 (Microsoft Excel format). Outgroup ƒ3 statistics for Devil’s Gate.
    • extended data table S4 (Microsoft Excel format). Outgroup ƒ3 and space.
    • extended data table S5 (Microsoft Excel format). Outgroup ƒ3 for MA1 and Ust’-Ishim.
    • extended data table S6 (Microsoft Excel format). D scores for MA1 and Ust’-Ishim.
    • extended data table S7 (Microsoft Excel format). D scores for the Ulchi.
    • extended data table S8. Admixture ƒ3 for the Koreans and the Japanese.
    • extended data table S9 (Microsoft Excel format). Phenotypes of interest.

    Download Extended Figures

    Download Extended Data Tables

    Files in this Data Supplement:

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