Research ArticleANTHROPOLOGY

The genetic prehistory of the Andean highlands 7000 years BP though European contact

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Science Advances  08 Nov 2018:
Vol. 4, no. 11, eaau4921
DOI: 10.1126/sciadv.aau4921
  • Fig. 1 ƒ3 statistics.

    (A to C) Left: Heat map represents the outgroup ƒ3 statistics estimating the amount of shared genetic drift between the ancient Andean individuals and each of 156 contemporary populations since their divergence with the African Yoruban population. Right: Ranked ƒ3 statistics showing the greatest affinity of the ancient Andeans with respect to 45 indigenous populations of the Americas.

  • Fig. 2 Principal components analysis.

    Principal components analysis projecting the ancient Andeans (IL2, IL3, IL4, IL5, IL7, K1, and SMP5), USR1 (Alaska) (19), Anzick-1 (Montana) (61), Saqqaq (Greenland) (62), and Kennewick Man (Washington) (63) onto a set of non-African populations from Raghavan et al. (16), with Native American populations masked for non-native ancestry. PC, principal component.

  • Fig. 3 Genetic affinity of ancient Andeans to global and regional indigenous populations.

    (A to C) Maximum likelihood trees generated by TreeMix (18) using whole-genome sequencing data from the Simons Genome Diversity Project (46). (D) Cluster analysis generated by ADMIXTURE (15) for a set of indigenous populations from Siberia, the Americas, Anzick-1, Kennewick, Saqqaq, USR1, and the ancient Andeans. The number of displayed clusters is K = 8, which was found to have the best predictive accuracy given the lowest cross-validation index value. Native American populations masked for non-native ancestry. SE, standard error.

  • Fig. 4 Demographic model of the Andes.

    ILA, Rio Uncallane.

  • Fig. 5 Selection scans.

    (A) PBS scans testing for differentiation along the Ancient Andean branch, with respect to the lowland population of the Huilliche-Pehuenche. (B) PBS scan testing for differentiation along the modern Aymara branch (post-European contact), with respect to the precontact ancient population of the Rio Uncallane. Selected global SNP frequencies (Frq) (64) and histone modifications (38) are shown on the right, which are relevant to the strongest selection signals. “*” indicates closest gene. GI, gastrointestinal tract; NK, natural killer.

  • Table 1 Ancient sample sequencing results.

    mtDNA, mitochondrial DNA; NA, not applicable.

    ID14C BPMode
    calibrated
    BP*
    95%
    calibrated
    BP*
    mtDNA
    Haplo-
    group
    SexSiteEndogenous
    DNA (%)
    Mapped
    reads
    Average
    read
    depth
    Whole-
    genome
    coverage
    IL2Not datedNANAD1XXRio
    Uncallane
    38.61933160506.510.99
    IL31830 + 2017111783–1616B2XXRio
    Uncallane
    29.91753480095.890.92
    IL41630 + 2015141529–1426C1bXYRio
    Uncallane
    17.1675443462.310.75
    IL51805 + 2017031722–1611C1cXXRio
    Uncallane
    25.2889910363.340.94
    IL71885 + 2018061825–1730C1bXYRio
    Uncallane
    44.91841507205.620.98
    K1Insufficient
    collagen
    NANAC1bXXKaillachuro2.60128152921.440.26
    SMP56030 + 2068226884–6757C1cXYSMP3.1536556323.920.08
    • *Calibrated 95% range, SHcal13 (65, 66).

    • †Sex was determined from sequence reads.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/11/eaau4921/DC1

    Supplementary Materials and Methods

    Fig. S1. Location of ancient and modern samples.

    Fig. S2. DNA damage patterns for the ancient individuals.

    Fig. S3. Heterozygosity rate calculated with overlapping ascertained SNPs from the SAN panel of the Affymetrix Human Origin Array.

    Fig. S4. Maximum likelihood trees with m = 1 migration events.

    Fig. S5. Cluster analysis generated by ADMIXTURE.

    Table S1. Radiocarbon determinations on five individuals from the Ilave region.

    Table S2. Contamination estimates.

    Table S3. Modern Aymara sequencing results.

    Table S4. Positive selection candidates associated with the Andean highlands and pathogen response.

    Table S5. Selection scan top signals.

    Table S6. Demographical model parameters.

    References (6988)

  • Supplementary Materials

    This PDF file includes:

    • Supplementary Materials and Methods
    • Fig. S1. Location of ancient and modern samples.
    • Fig. S2. DNA damage patterns for the ancient individuals.
    • Fig. S3. Heterozygosity rate calculated with overlapping ascertained SNPs from the SAN panel of the Affymetrix Human Origin Array.
    • Fig. S4. Maximum likelihood trees with m = 1 migration events.
    • Fig. S5. Cluster analysis generated by ADMIXTURE.
    • Table S1. Radiocarbon determinations on five individuals from the Ilave region.
    • Table S2. Contamination estimates.
    • Table S3. Modern Aymara sequencing results.
    • Table S4. Positive selection candidates associated with the Andean highlands and pathogen response.
    • Table S5. Selection scan top signals.
    • Table S6. Demographical model parameters.
    • References (6988)

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