A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea

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Science  15 Sep 2017:
Vol. 357, Issue 6356, pp. 1160-1163
DOI: 10.1126/science.aan3842
  • Fig. 1 PNG samples.

    (A) Each language group is represented by a circle; the area indicates the number of genotyped individuals, and the color indicates the top-level language phylum. 39 individuals are not included because either the specific language is unknown or the two parents are from different language groups. Also see fig. S1. (B) Papuan (blue) and Southeast Asian (red) ancestry proportions as estimated by ADMIXTURE [number of ancestry components (K) = 2, with 504 East Asian individuals from the 1000 Genomes Project; also see fig. S3]. Individuals are grouped by province and then language group (separated by black bars). Ancestry proportions correlate strongly [correlation coefficient (r) = 0.988] with those estimated using f4-ratios (11).

  • Fig. 2 PNG population structure.

    (A) When projected onto principal components (PCs) constructed with only highlander genotypes, all lowlanders (excepting a few outliers) group uniformly. Also see fig. S10. (B) When projected onto PCs constructed with only lowlander genotypes, all highlanders (excepting a few outliers) group uniformly. Also see fig. S11. (C to F) Quantile-quantile plots comparing z scores from D-statistics relating highlanders and lowlanders to those expected under a normal distribution (11). The African Yoruba population is used as an outgroup. (C) Lowlanders are equally similar to different highlander groups. (D) Highlanders have stronger affinity to some lowlander groups than to others. (E) Highlanders are more similar to each other than to lowlanders. (F) Lowlanders are not always more similar to each other than to highlanders. (G) The z scores (capped at 6) of two different D-statistics measuring (i) if the highland Gende speakers are more similar to the lowland Sop speakers, living just 40 km away, or to other highlanders (blue indicating more highlander similarity) and (ii) if Sop speakers are more similar to Gende speakers or to other lowlanders (red indicating more lowlander similarity). (H) Genetic affinity of highlanders (treated as a single group, in gray) to different lowland groups measured by the outgroup f3-statistic f3(Highlanders, X; Aboriginal Australian) (red indicating higher affinity). (C) to (H) were calculated after masking lowlander genomes for Southeast Asian ancestry.

  • Fig. 3 Time depth of population separation and growth in PNG.

    (A) Cross-coalescence curves between highlanders and a northern lowlands Middle Sepik group suggests a split time between 10 and 20 ka. (B) Cross-coalescence curves between highland groups suggest split times within the last ~10 ky (Huli representing the western cluster, Gende and HGDP_H the eastern, figs. S8 and S10). These were inferred using MSMC on genomes physically phased by performing linked-read sequencing. Also see fig. S12. (C) Effective population-size histories inferred using SMC++ on five genomes per group. Also see fig. S14.

  • Fig. 4 Genetic differentiation in PNG.

    Geographical distance between groups plotted against FST, after masking lowlander genomes for Southeast Asian ancestry. Gray lines indicate FST between selected 1000 Genomes Project populations.

Supplementary Materials

  • A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea

    Anders Bergström, Stephen J. Oppenheimer, Alexander J. Mentzer, Kathryn Auckland, Kathryn Robson, Robert Attenborough, Michael P. Alpers, George Koki, William Pomat, Peter Siba, Yali Xue, Manjinder S. Sandhu, Chris Tyler-Smith

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S15
    • Tables S1 to S4
    • References

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