Research ArticleANTHROPOLOGY

Ancient DNA sheds light on the genetic origins of early Iron Age Philistines

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Science Advances  03 Jul 2019:
Vol. 5, no. 7, eaax0061
DOI: 10.1126/sciadv.aax0061
  • Fig. 1 Overview of locations and ages of analyzed individuals.

    (A) Locations of newly reported and other selected published genomes. The newly reported Ashkelon populations are annotated in the upper corner. (B) The range of average ages of the ancient groups is given in thousands of years (ka) BCE.

  • Fig. 2 PCA and ADMIXTURE analysis.

    (A) Ancient genomes (marked with color-filled symbols) projected onto the principal components inferred from present-day west Eurasians (gray circles) (fig. S2). The newly reported Ashkelon populations are annotated in the upper corner. (B) ADMIXTURE analysis. A selected set of ancient individuals (as well as present-day Sardinians) is plotted (K = 9 was chosen since it is the cluster number that maximizes components correlated to the most differentiated populations in the west Eurasian PCA).

  • Fig. 3 European-related admixture detected in ASH_IA1.

    (A) ASH_IA1 shares access affinity with European-related populations compared to ASH_LBA. We plot the top and bottom 40 values of f4 (ASH_IA1, ASH_IA2; X, Mbuti) on the map. Circles mark the ancient populations and triangles the present-day ones. Z-scores calculated by 5-centimorgan block jackknifing are represented by the size of the symbols. “X” share more alleles with ASH_IA1 when values are positive and with ASH_IA2 when negative. The five groups with the most positive values are annotated on the map (Z > 2.3). (B) We plot the ancestral proportions of the Ashkelon individuals inferred by qpAdm using Iran_ChL, Levant_ChL, and WHG as sources ±1 SEs. P values are annotated under each model. In cases when the three-way model failed (χ2P < 0.05), we plot the fitting two-way model. The WHG ancestry is necessary only in ASH_IA1.

  • Table 1 An overview of the Ashkelon genomes reported in this study.

    For each individual, the analysis group is given (ASH_LBA, Ashkelon Late Bronze Age; ASH_IA1, Ashkelon Iron Age 1; ASH_IA2, Ashkelon Iron Age 2). 14C dating results are given in cal BCE in two-sigma range (NA, not available). Detailed dating information is provided in text S1 and table S1. The proportion of human DNA and the mean coverage on 1240 K target sites in the “1240 K” enriched libraries are given. The assigned genetic sex is listed (F, Female; M, Male). Uniparental haplogroups (mt, mitochondrial; Ychr, Y chromosome) are listed.

    IDAnalysis
    group
    Sampled
    tissue
    Mean
    coverage
    (fold)
    Carbon
    date
    Archeological
    date
    Total
    sequenced
    reads (×106)
    Human
    DNA (%)
    Genetic
    sex
    mtYchr
    ASH029.A0101ASH_LBAPetrous0.141622–1522MBIIC–LBII86.66.9FH66a
    ASH033.A0101ASH_LBAPetrous0.111746–1643MBIIC–LBII84.82FN
    ASH034.A0101ASH_LBAPetrous0.42NAMBIIC–LBII81.913.7FU3b1a
    ASH066.A0101ASH_IA1Petrous0.181371–1129Iron I–Post Ramses III10.511.0MT2c1cJ
    ASH067.A0101ASH_IA1Petrous0.171379–1131Iron I–Post Ramses III10.911.2MH92R1
    ASH002/3.A0101ASH_IA1Petrous0.081378–1134Iron I–Post Ramses III26.913FI1
    ASH068.A0101ASH_IA1Petrous0.271284–1126Iron I–Post Ramses III11.217.6FT1a1
    ASH008.A0101ASH_IA2Petrous0.71257–1042Iron IIA126.717.2MH2cBT
    ASH087.A0101ASH_IA2Petrous0.22NAIron IIA12.815.6MH4a1cL
    ASH135.A0101ASH_IA2Molar0.09NAIron IIA13.33.9FJT

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/7/eaax0061/DC1

    Text S1. Description of individuals excavated in Ashkelon and archeological information

    Fig. S1. Pairwise mismatch rate.

    Fig. S2. PCA plot of present-day west Eurasian populations.

    Fig. S3. ADMIXTURE CV errors for each cluster number (K).

    Fig. S4. The Bronze Age Ashkelon population shares a higher genetic affinity with Caucasus/Iranian-related populations when compared to the Neolithic Levantines.

    Fig. S5. The Bronze Age Ashkelon population shares a marginal higher genetic affinity with populations related to ancient Caucasus/Iran when compared to Chalcolithic Levantines.

    Fig. S6. The Bronze Age Ashkelon population is symmetrically related to Lebanon_MBA.

    Fig. S7. The Bronze Age Ashkelon population is mostly symmetrically related to Jordan_EBA but shares a slightly higher genetic affinity with populations related to ancient Caucasus/Iran.

    Fig. S8. Variation in differential affinities between the Ashkelon groups.

    Fig. S9. The proportion of Mesolithic European WHG ancestry in ASH_IA1 individuals correlates with their position in the west Eurasian PCA.

    Fig. S10. ASH_IA1 shares more alleles with European-related populations compared to ASH_IA2.

    Fig. S11. ASH_IA2 is symmetrically related to ASH_LBA.

    Fig. S12. Map of the Bronze Age necropolis.

    Fig. S13. Relative stratigraphy of grid 38.

    Fig. S14. Relative stratigraphy of N5. Square 14.

    Fig. S15. Relative stratigraphy of N5. Square 24.

    Table S1. 14C radiocarbon dating performed for this study.

    Table S2. Nuclear and mitochondrial contamination estimates.

    Table S3. qpADM admixture models of the ASH_LBA group.

    Table S4. Fligner-Killeen test based on [f4 (Ashkelon ind 1, Ashkelon ind 2; test, Mbuti)]2 statistics.

    Table S5. Ashkelon individuals and groups modeled using qpADM by “Levant_ChL,” “Iran_ChL,” and WHG as sources.

    Table S6. Bronze Age and Iron Age individuals and groups modeled by the three maximized populations on the west Eurasian PCA (using qpADM).

    Table S7. qpADM admixture models of the ASH_IA1 group.

    Table S8. qpADM admixture models of the ASH_IA2 group.

    Table S9. Phenotypic analysis.

    Table S10. Archeological context.

    Data file S1. An overview of skeletal material screened for aDNA in this study.

    Data file S2. An overview of the main analysis groups used in this study.

    Data file S3. Sequencing statistics of negative controls.

    References (2866)

  • Supplementary Materials

    The PDF file includes:

    • Text S1. Description of individuals excavated in Ashkelon and archeological information
    • Fig. S1. Pairwise mismatch rate.
    • Fig. S2. PCA plot of present-day west Eurasian populations.
    • Fig. S3. ADMIXTURE CV errors for each cluster number (K).
    • Fig. S4. The Bronze Age Ashkelon population shares a higher genetic affinity with Caucasus/Iranian-related populations when compared to the Neolithic Levantines.
    • Fig. S5. The Bronze Age Ashkelon population shares a marginal higher genetic affinity with populations related to ancient Caucasus/Iran when compared to Chalcolithic Levantines.
    • Fig. S6. The Bronze Age Ashkelon population is symmetrically related to Lebanon_MBA.
    • Fig. S7. The Bronze Age Ashkelon population is mostly symmetrically related to Jordan_EBA but shares a slightly higher genetic affinity with populations related to ancient Caucasus/Iran.
    • Fig. S8. Variation in differential affinities between the Ashkelon groups.
    • Fig. S9. The proportion of Mesolithic European WHG ancestry in ASH_IA1 individuals correlates with their position in the west Eurasian PCA.
    • Fig. S10. ASH_IA1 shares more alleles with European-related populations compared to ASH_IA2.
    • Fig. S11. ASH_IA2 is symmetrically related to ASH_LBA.
    • Fig. S12. Map of the Bronze Age necropolis.
    • Fig. S13. Relative stratigraphy of grid 38.
    • Fig. S14. Relative stratigraphy of N5. Square 14.
    • Fig. S15. Relative stratigraphy of N5. Square 24.
    • Table S1. 14C radiocarbon dating performed for this study.
    • Table S2. Nuclear and mitochondrial contamination estimates.
    • Table S3. qpADM admixture models of the ASH_LBA group.
    • Table S4. Fligner-Killeen test based on f4 (Ashkelon ind 1, Ashkelon ind 2; test, Mbuti)2 statistics.
    • Table S5. Ashkelon individuals and groups modeled using qpADM by “Levant_ChL,” “Iran_ChL,” and WHG as sources.
    • Table S6. Bronze Age and Iron Age individuals and groups modeled by the three maximized populations on the west Eurasian PCA (using qpADM).
    • Table S7. qpADM admixture models of the ASH_IA1 group.
    • Table S8. qpADM admixture models of the ASH_IA2 group.
    • Table S9. Phenotypic analysis.
    • Table S10. Archeological context.
    • References (2866)

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • Data file S1 (Microsoft Excel format). An overview of skeletal material screened for aDNA in this study.
    • Data file S2 (Microsoft Excel format). An overview of the main analysis groups used in this study.
    • Data file S3 (Microsoft Excel format). Sequencing statistics of negative controls.

    Files in this Data Supplement:

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