Research ArticleANTHROPOLOGY

Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard

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Science Advances  05 Sep 2018:
Vol. 4, no. 9, eaao1262
DOI: 10.1126/sciadv.aao1262
  • Fig. 1 Burial site reconstructions and location.

    (Left) Burial orientation of human and horse graves at Niederstotzingen. (Right) Location of burial site in southwest Germany.

  • Fig. 2 PCA plot of Niederstotzingen individuals, modern west Eurasians, and selected ancient Europeans.

    Genome-wide ancient data were projected against modern west Eurasian populations. Colors on PCA indicate more general Eurasian geographic boundaries than countries: dark green, Caucasus; bright green, eastern Europe; yellow, Sardinia and Canary Islands; bright blue, Jewish diaspora; bright purple, western and central Europe; red, southern Europe; dark brown, west Asia; light purple, Spain; dark purple, Russia; pale green, Middle East; orange, North Africa. The transparent circles serve to highlight the genetic overlap between regions of interest.

  • Fig. 3 Reconstruction of first- and second-degree relatedness among all related individuals.

    Bold black lines and blue lines indicate first- and second-degree relatedness, respectively. Dark blue squares are identified males with age-at-death estimates years old (y.o.), mtDNA haplotypes, and NRY haplogroups. Red circles represent unidentified females that passed maternal haplotypes to their offspring. The light square represents one male infant that shares its maternal haplotype with individuals 12B and 9. N.D., not determined.

  • Table 1 Archeological context, karyotype sex estimates, haplotypes, contamination estimates, and isotopic data from Niederstotzingen.

    Strontium values that indicate provenance outside of the region. Full list of mtDNA and NRY haplotypes is given in tables S8 and S9. Complete summary of contamination estimates for mitochondrial and X chromosome on 1240K capture and SE is given in tables S6 and S7. Genetic sex estimates are based on shotgun and 1240K capture. Individuals highlighted in red and green are from two multiple burials, graves 3 and 12 (Fig. 1).

    IndividualArcheological
    context
    Age at
    death
    estimate
    (years)
    Genetic sexMtDNA/NRY haplotypeMedian mtDNA/X
    (SE) contamination
    Strontium 87Sr/86Sr
    140–50MaleK1a/R1b1a2a1a1c2b2b1a10.03/0.002 (0.003)0.7089
    29–11Male? *K1a1b2a1a/-0.15/—0.7093
    3aByzantine20–30MaleK1a/R1b1a2a1a1c2b2b1a10.02/0.0145 (0.007)0.709
    3b50–60MaleI5a1b/G2a2b10.03/0.0009 (0.0024)0.7104
    3c20–30MaleT2/R1b1a20.03/0.0404 (0.0203)0.7089
    42MaleX2b4/-0.03/—0.7094
    50.5–2Male?*K1a1b2a1a/-0.04/—0.7096
    6Lombardian14–17MaleH65a/R1b1a2a1a1c2b2b0.02/−0.0007 (0.00117)0.7093
    9Franconian40–50MaleX2b4/R1b1a2a1a1c2b2b1a10.04/−0.0047 (0.00466)0.7089
    1020–25Male*H1b/R10.06/—0.7105
    12a25–35Male*H10e1/R1b10.09/—0.7087
    12bByzantine30–40MaleX2b4/R1b1a2a1a1c2b2b1a10.03/0.0128 (0.0136)0.709
    12c20–30MaleU5a1a1/R1b1a2a1a1c2b2b1a10.03/0.0010 (0.0078)0.7093

    *Statistically insignificant sex estimate but consistent with maleness (table S10 and fig. S4).

    †After PMD filtering, individuals 2 and 5 had insufficient reads for accurate sex estimation (table S13).

    Supplementary Materials

    • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/9/eaao1262/DC1

      Supplementary Materials and methods

      Fig. S1. Photographs of burial goods with most specific cultural identifying markers.

      Fig. S2. Isotope 86Sr/87Sr and δ18O values for enamel from teeth.

      Fig. S3. Overlaying shotgun and mtDNA deamination plots from mapDamage quantification against the reference genome.

      Fig. S4. Genetic sex estimates from genome-wide capture.

      Fig. S5. Admixture estimates for west Eurasians, Niederstotzingen, and selected ancient individuals.

      Fig. S6. F3 outgroup statistics for Niederstotzingen 1 using Mbuti as an outgroup.

      Fig. S7. F3 outgroup statistics for Niederstotzingen 3A using Mbuti as an outgroup.

      Fig. S8. F3 outgroup statistics for Niederstotzingen 3B using Mbuti as an outgroup.

      Fig. S9. F3 outgroup statistics for Niederstotzingen 3C using Mbuti as an outgroup.

      Fig. S10. F3 outgroup statistics for Niederstotzingen 6 using Mbuti as an outgroup.

      Fig. S11. F3 outgroup statistics for Niederstotzingen 9 using Mbuti as an outgroup.

      Fig. S12. F3 outgroup statistics for Niederstotzingen 12B using Mbuti as an outgroup.

      Fig. S13. F3 outgroup statistics for Niederstotzingen 12C using Mbuti as an outgroup.

      Table S1. PCR-based haplotyping of DNA extracts from previous study.

      Table S2. Archeological context and isotopes.

      Table S3. Shotgun sequencing output and mapping data.

      Table S4. mtDNA capture sequencing output data and mapping.

      Table S5. 1240K sequencing output data and mapping.

      Table S6. Schmutzi estimation of mtDNA contamination.

      Table S7. ANGSD X chromosome contamination estimate on 1240K libraries.

      Table S8. Haplogroups and private mutations for each mtDNA capture (phylotree 17).

      Table S9. Complete list of NRY haplogroups with identifying ISOGG markers for 1240K capture sequences.

      Table S10. Sex estimates from shotgun and genome-wide capture data.

      Table S11. Sex estimates from shotgun data based on Rx values.

      Table S12. Admixture CV error values for each component and individual.

      Table S13. Shotgun reads with PMDtools threshold 3 filtered and skoglund sex estimate of filtered reads.

      Table S14. Haplogroup calling of selected individuals before and after PMD (threshold 3) filtering.

      Table S15. READ pairwise kinship-based estimate.

      Table S16. Pairwise estimate of kinship and coefficient of relatedness.

      References (5258)

    • Supplementary Materials

      This PDF file includes:

      • Supplementary Materials and methods
      • Fig. S1. Photographs of burial goods with most specific cultural identifying markers.
      • Fig. S2. Isotope 86Sr/87Sr and δ18O values for enamel from teeth.
      • Fig. S3. Overlaying shotgun and mtDNA deamination plots from mapDamage quantification against the reference genome.
      • Fig. S4. Genetic sex estimates from genome-wide capture.
      • Fig. S5. Admixture estimates for west Eurasians, Niederstotzingen, and selected ancient individuals.
      • Fig. S6. F3 outgroup statistics for Niederstotzingen 1 using Mbuti as an outgroup.
      • Fig. S7. F3 outgroup statistics for Niederstotzingen 3A using Mbuti as an outgroup.
      • Fig. S8. F3 outgroup statistics for Niederstotzingen 3B using Mbuti as an outgroup.
      • Fig. S9. F3 outgroup statistics for Niederstotzingen 3C using Mbuti as an outgroup.
      • Fig. S10. F3 outgroup statistics for Niederstotzingen 6 using Mbuti as an outgroup.
      • Fig. S11. F3 outgroup statistics for Niederstotzingen 9 using Mbuti as an outgroup.
      • Fig. S12. F3 outgroup statistics for Niederstotzingen 12B using Mbuti as an outgroup.
      • Fig. S13. F3 outgroup statistics for Niederstotzingen 12C using Mbuti as an outgroup.
      • Table S1. PCR-based haplotyping of DNA extracts from previous study.
      • Table S2. Archeological context and isotopes.
      • Table S3. Shotgun sequencing output and mapping data.
      • Table S4. mtDNA capture sequencing output data and mapping.
      • Table S5. 1240K sequencing output data and mapping.
      • Table S6. Schmutzi estimation of mtDNA contamination.
      • Table S7. ANGSD X chromosome contamination estimate on 1240K libraries.
      • Table S8. Haplogroups and private mutations for each mtDNA capture (phylotree 17).
      • Table S9. Complete list of NRY haplogroups with identifying ISOGG markers for 1240K capture sequences.
      • Table S10. Sex estimates from shotgun and genome-wide capture data.
      • Table S11. Sex estimates from shotgun data based on Rx values.
      • Table S12. Admixture CV error values for each component and individual.
      • Table S13. Shotgun reads with PMDtools threshold 3 filtered and skoglund sex estimate of filtered reads.
      • Table S14. Haplogroup calling of selected individuals before and after PMD (threshold 3) filtering.
      • Table S15. READ pairwise kinship-based estimate.
      • Table S16. Pairwise estimate of kinship and coefficient of relatedness.
      • References (5258)

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