Research ArticleANTHROPOLOGY

Ancient nuclear genomes enable repatriation of Indigenous human remains

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Science Advances  19 Dec 2018:
Vol. 4, no. 12, eaau5064
DOI: 10.1126/sciadv.aau5064
  • Fig. 1 Details of the locations and language groups of Aboriginal Australian samples.

    Light orange shading indicates the distribution and location of Pama-Nyungan language families. Orange shading indicates the distribution of non–Pama-Nyungan language families. Dashed lines show the approximate distribution of accepted major language subgroups as published in (20) with language names in italics. Red symbols indicate previously published mitochondrial or nuclear genomes; blue symbols indicate new unpublished data. Circles indicate contemporary Aboriginal Australian samples, and stars represent ancient individuals. Sample code abbreviations have been included in parentheses.

  • Fig. 2 Mitochondrial maximum likelihood phylogeny of ancient and contemporary Aboriginal Australian mitogenomes.

    Mitochondrial maximum likelihood phylogenetic relationships among ancient subgroups (bold) and contemporary Aboriginal Australians are shown. Colored segments indicate separate mitochondrial haplogroups.

  • Fig. 3 Genetic structure of ancient and contemporary Aboriginal Australians.

    (A) First two principal components of a PCA of individuals from non-African populations, with ancient individuals (black outlines) projected. (B) Supervised admixture of contemporary Australians using five putative ancestry sources. Many modern Australians show evidence for European (French; orange stars) or East Asian (Han; blue diamonds) admixture. All ancient individuals cluster tightly with previously described Australian Aboriginals without recent admixture (WCD).

  • Fig. 4 Genetic affinities between ancient and contemporary Aboriginal Australians.

    (A) Modern Australians projected onto a PCA inferred from the five higher-coverage ancient individuals covering all geographic regions samples. Inset shows full PCA including ancient individuals, and larger plot shows zoomed region of modern individuals only (dashed box in inset). Polygons and large symbols indicate the range and median of the principal components for each modern population, respectively. (B) Multidimensional scaling based on pairwise genetic drift sharing (outgroup f3 statistics) between ancient individuals and modern populations (using masked data). The results highlight the considerable genetic structure among ancient Aboriginal Australians. In both analyses, modern individuals show closest affinities with ancient individuals from the same geographic region.

  • Fig. 5 Admixture graph models for the population history of ancient Aboriginal Australian genomes.

    Three admixture graph models for Aboriginal Australians including each major regional group (represented by the respective highest-coverage ancient individual) are shown. While all three models fit the data with |Z| < 3 (worst f statistic indicated below each graph), only the topology where individuals from north-western Queensland (WPAH4 and MH8) form an outgroup to north-eastern Queensland (PA86) and New South Wales (KP1 and WLH4) (left panel) results in no trifurcation (branches with length zero highlighted in red in the other two topologies). Individual PA86 is fit as a mixture with 13 to 15% of Papuan-related ancestry in all three models.

  • Fig. 6 Allele sharing between ancient and contemporary Aboriginal Australians.

    Each panel shows f4 statistics of the form f4 (Mbuti,Ancient;Modern,Papuan). Negative values indicate the amount of excess allele sharing of the respective ancient individual with a contemporary Australian group (y axis) compared to Papuans (masked dataset). Error bars show three SEs obtained from a block jackknife. Contemporary groups are sorted according to the amount of excess allele sharing in each panel. Notably, ancient individuals show the highest amount of sharing with their respective local contemporary group.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/12/eaau5064/DC1

    Supplementary Text

    Fig. S1. Novel mitochondrial clades M42c1b and M42c1b1.

    Fig. S2. Novel mitochondrial clades R12a, R12a1, and R12b.

    Fig. S3. Novel mitochondrial haplotype M42a3.

    Fig. S4. Novel mitochondrial haplotype P5b1.

    Fig. S5. Novel mitochondrial haplotypes P5a1a and P5a1a1.

    Fig. S6. Novel mitochondrial haplotypes P12a and P12a1.

    Fig. S7. Novel mitochondrial haplotype P12b.

    Fig. S8. Local continuity between ancient and contemporary groups.

    Fig. S9. Supervised admixture of ancient Aboriginal Australians using five putative ancestry sources.

    Table S1. Weipa and Mapoon Hair samples background.

    Table S2. Summary statistics for ancient Aboriginal Australian samples.

    Table S3. Contemporary mitochondrial dataset.

    Table S4. Contemporary nuclear dataset.

    Table S5. Masked outgroup f3 statistics.

    Table S6. Masked outgroup f4 statistics.

    References (5890)

  • Supplementary Materials

    The PDF file includes:

    • Supplementary Text
    • Fig. S1. Novel mitochondrial clades M42c1b and M42c1b1.
    • Fig. S2. Novel mitochondrial clades R12a, R12a1, and R12b.
    • Fig. S3. Novel mitochondrial haplotype M42a3.
    • Fig. S4. Novel mitochondrial haplotype P5b1.
    • Fig. S5. Novel mitochondrial haplotypes P5a1a and P5a1a1.
    • Fig. S6. Novel mitochondrial haplotypes P12a and P12a1.
    • Fig. S7. Novel mitochondrial haplotype P12b.
    • Fig. S8. Local continuity between ancient and contemporary groups.
    • Fig. S9. Supervised admixture of ancient Aboriginal Australians using five putative ancestry sources.
    • References (5890)

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • Table S1 (Microsoft Excel format). Weipa and Mapoon Hair samples background.
    • Table S2 (Microsoft Excel format). Summary statistics for ancient Aboriginal Australian samples.
    • Table S3 (Microsoft Excel format). Contemporary mitochondrial dataset.
    • Table S4 (Microsoft Excel format). Contemporary nuclear dataset.
    • Table S5 (Microsoft Excel format). Masked outgroup f3 statistics.
    • Table S6 (Microsoft Excel format). Masked outgroup f4 statistics.

    Files in this Data Supplement:

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