Research ArticleANTHROPOLOGY

Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

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Science Advances  12 Jun 2020:
Vol. 6, no. 24, eaaz0183
DOI: 10.1126/sciadv.aaz0183
  • Fig. 1 Basic information of newly reported ancient genomes.

    (A) Approximate locations of new samples and published present-day modern African populations. Same legend scheme applies to the principal components analysis (PCA) plot in Fig. 2. (B) C14 dates after calibration. Samples from Botswana (green) and Uganda (orange) are based on archaeological context dates rather than accelerator mass spectrometry (AMS) measurements.

  • Fig. 2 PCA of ancient genomic data analyzed in this and previous studies, together with published modern genetic data.

    Modern populations shown are detailed in the legend of Fig. 1 and fig. S1. A separate PCA with only present-day populations is shown in fig. S1A. Color circles highlight the key groups discussed in this paper and summarized in Fig. 3A.

  • Fig. 3 Admixture history of ancient African populations.

    (A) Overview of coexistence of distinct African ancestries through time drawing on currently available ancient genomes. (B) Ancestral components of ancient African groups/individuals according to qpAdm. We order ancient groups in the same order shown in (A) and highlight newly reported genetic groups/individuals in bold. P values and estimated ancestral proportions can be found in table S3.

  • Table 1 Summary of individuals with successful aDNA from Africa reported in this study.

    Note 1: Two samples from Lukenya Hill (LUK001 and LUK002) tend out to be genetically the same individual. We merged the genomic data for genetic analyses but report radiocarbon dates for both here. Note 2: The age of samples marked with asterisk is based on the archeological context instead of calibrated radiocarbon date. Aut. Cov., autosomal coverage; MT Cov., mitochondrial coverage.

    IDPopulation labelArcheological
    site
    CountryArcheological
    affiliation
    Aut.
    Cov.
    MT
    Cov.
    SexY haplogroupMT
    haplogroup
    Aut.
    SNPs
    SNPs
    hit on
    Human
    Origin
    dataset
    Date
    (calendar
    BP)
    Uncalibrated
    C14
    dates ± error
    (lab number)
    NYA002Kenya_
    Nyarindi_
    3500BP
    Nyarindi
    Rockshelter
    KenyaLater Stone
    Age (Kansyore)
    0.140.23FL4b2a124,06464,7853555–33753253 ± 23
    (OxA-37364)
    NYA003Kenya_
    Nyarindi_
    3500BP
    Nyarindi
    Rockshelter
    KenyaLater Stone
    Age (Kansyore)
    0.020.02ME(E-M96,E-P162)18,5869736
    LUK001Kenya_
    LukenyaHill_
    3500BP
    Lukenya Hill,
    GvJm 202
    KenyaPastoral
    Neolithic
    0.591.41ME1b1b1b2b(E-
    M293,E-
    CTS10880)
    L4b2a2b495,472222,4393610–
    3460
    3340 ± 23
    (OxA-37356),
    3296 ± 25
    (OxA-37357)
    LUK003Kenya_
    LukenyaHill_
    3500BP
    Lukenya Hill,
    GvJm 202
    KenyaPastoral
    Neolithic
    0.010.30FL0f1683035863635–
    3475
    3359 ± 23
    (OxA-37358)
    HYR002Kenya_
    HyraxHill_
    2300BP
    Hyrax Hill,
    GrJj25
    KenyaPastoral
    Neolithic
    0.770.52ME1b1b1b2b(E-
    M293,E-M293)
    L5a1b505,972260,9992365–
    2305
    2354 ± 23
    (OxA-37352)
    MOL001Kenya_
    MoloCave_
    1500BP
    Molo Cave,
    GoJi3
    KenyaPastoral
    Neolithic
    2.645.40ME1b1b1b2b(E-
    M293,E-M293)
    L3h1a2a1886,222461,7561415–
    1320
    1532 ± 21
    (OxA-37360)
    MOL003Kenya_
    MoloCave_
    1500BP
    Molo Cave,
    GoJi3
    KenyaPastoral
    Neolithic
    0.060.14F57,42629,7002110–
    1990
    2101 ± 22
    (OxA-37361)
    KPL001Kenya_
    Kakapel_
    3900BP
    KakapelKenyaLater Stone
    Age (Kansyore)
    0.923.94MCT(CT-
    M168,CT-M5695)
    L3i1572,074299,1813974–
    3831
    3584 ± 28
    [SUERC-86057
    (GU51350)]
    KPL002Kenya_
    Kakapel_
    300BP
    KakapelKenyaLater Iron Age/
    protohistoric
    1.2678.35FL2a1f684,698363,447309–145222 ± 28
    [SUERC-86058
    (GU51351)]
    KPL003Kenya_
    Kakapel_
    900BP
    KakapelKenyaLater Iron Age0.0763.21FL2a575,11339,367910–736895 ± 28
    [SUERC-86059
    (GU51352)]
    MUN001*Uganda_
    Munsa_
    500BP
    MunsaUgandaLater Iron Age0.461.57FL3b1a1377,3321400–
    1600 CE
    KIN002Congo_
    Kindoki_
    230BP
    KindokiDR CongoProtohistoric0.621.46ME1b1a1a1d1a2(E-
    CTS99,E-CTS99)
    L1c3a1b438,125229,240295–145217 ± 20
    (OxA-37353)
    KIN003Congo_
    Kindoki_
    150BP
    KindokiDR CongoProtohistoric0.020.09ME(E-M96,E-
    PF1620)
    19,69110,329285–
    modern
    172 ± 20
    (OxA-37354)
    KIN004Congo_
    Kindoki_230BP
    KindokiDR CongoProtohistoric0.962.01MR1b1(R-
    P25_1,R-M415)
    L0a1b1a1560,376291,465305–150241 ± 20
    (OxA-37355)
    NGO001Congo_
    NgongoMbata_
    220BP
    Ngongo
    Mbata
    DR CongoProtohistoric0.420.78ML1c3a328,389170,742295–145211 ± 21
    (OxA-37363)
    MTN001Congo_
    MatangaiTuru_
    750BP
    Matangai Turu
    Northwest
    DR CongoIron Age
    forager
    0.060.33F52,01228,452795–690871 ± 21
    (OxA-37362)
    NQO002*Botswana_
    Nqoma_
    900BP
    NqomaBotswanaEarly Iron Age0.020.60FL2a1f14,1897,587700-
    1090 CE
    TAU001*Botswana_
    Taukome_
    1100BP
    TaukomeBotswanaEarly Iron Age0.095.82ME1b1a1(E-
    M2,E-Z1123)
    L0d3b179,26142,998900-
    1000 CE
    XAR001*Botswana_
    Xaro_
    1400BP
    XaroBotswanaEarly Iron Age3.6437.94ME1b1a1a1c1aL3e1a2939,378494,074700-
    1000 CE
    XAR002*Botswana_
    Xaro_
    1400BP
    XaroBotswanaEarly Iron Age1.36172.94ME1b1b1b2b(E-
    M293,E-
    CTS10880)
    L0k1a2703,295375,283700-
    1000 CE

Supplementary Materials

  • Supplementary Materials

    Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

    Ke Wang, Steven Goldstein, Madeleine Bleasdale, Bernard Clist, Koen Bostoen, Paul Bakwa-Lufu, Laura T. Buck, Alison Crowther, Alioune Dème, Roderick J. McIntosh, Julio Mercader, Christine Ogola, Robert C. Power, Elizabeth Sawchuk, Peter Robertshaw, Edwin N. Wilmsen, Michael Petraglia, Emmanuel Ndiema, Fredrick K. Manthi, Johannes Krause, Patrick Roberts, Nicole Boivin, Stephan Schiffels

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