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. 2017 Apr 1;34(4):889-902.
doi: 10.1093/molbev/msw293.

A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa

Mark Lipson  1 , David Reich  1   2   3
Affiliations

A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa

Mark Lipson et al. Mol Biol Evol. .

Abstract

A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.

Keywords: admixture graph; human history; population genetics.

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Figures

F<sc>ig</sc>. 1
Fig. 1
Final best-fitting graph model. Colors of filled nodes (sampled populations and selected internal split points) and edge arrows correspond to subsets of the graph: green, Chimp and archaic; yellow, African and basal non-African; dark blue, eastern clade; light blue, Australasian sub-clade; red, western clade; purple, northern sub-clade. Tree edges (solid lines) are labeled with branch lengths in 1000 times drift units (rounded to the nearest integer value), while admixtures (dotted lines) are shown with their inferred proportions. The three drift lengths surrounding an admixture event (immediately preceding each mixing population and immediately following the admixed population) cannot be solved for individually in our framework and instead form a single compound parameter (Lipson et al. 2013); we omit the first two and report the total drift on the edge following the admixture. The terminal drifts leading to ancient individuals are inflated as a result of a combination of single-individual populations, lower coverage, and/or haploid genotype calls.
F<sc>ig</sc>. 2
Fig. 2
Pairwise f2 residuals in the final model, in units of Z-score (fitted minus observed divided by standard error).
F<sc>ig</sc>. 3
Fig. 3
Plot of f4-statistics f4(New Guinea, Ami; Oi, Oj) against f4(New Guinea, Denisova; Oi, Oj) for all pairs of outgroup populations O from the set consisting of Chimp, Altai, Dinka, Ust’-Ishim, and K14. The R2 value for the best-fitting line through the origin is shown. The negative correlation implies that New Guinea can be modeled as a mixture of populations related to Ami and Denisova, with the slope informative about the relative proportions (as shown). Standard errors are approximately 0.0005 along the x-axis and 0.001 along the y-axis.
F<sc>ig</sc>. 4
Fig. 4
Admixture graph schematics representing alternative historical scenarios to explain shared drift between MA1 and East Asians. (A) MA1 is admixed, with East Asian-related ancestry. (B) Ami is admixed, with MA1-related ancestry. Other relationships are assumed as shown (the position of the root is arbitrary). The expected values of the statistics (1) f4(MA1, K14; Ami, Ust’-Ishim) and (2) f4(Ust’-Ishim, MA1; Onge, Ami) are equal to a branch length times a mixture proportion: red for (1) and black for (2) [times α1 in (A) and α2 in (B)].
F<sc>ig</sc>. 5
Fig. 5
Model fit with SGDP data. Notation is the same as in figure 1.
See this image and copyright information in PMC

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References

    1. Armitage SJ, Jasim SA, Marks AE, Parker AG, Usik VI, Uerpmann HP.. 2011. The southern route “out of Africa”: Evidence for an early expansion of modern humans into Arabia. Science 331(6016): 453–456. - PubMed
    1. Blinkhorn J, Achyuthan H, Petraglia M, Ditchfield P.. 2013. Middle Palaeolithic occupation in the Thar Desert during the Upper Pleistocene: The signature of a modern human exit out of Africa? Quaternary Sci Rev. 77:233–238.
    1. Clarkson C, Smith M, Marwick B, Fullagar R, Wallis LA, Faulkner P, Manne T, Hayes E, Roberts RG, Jacobs Z, et al. 2015. The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation. J Hum Evol. 83:46–64. - PubMed
    1. Demeter F, Shackelford L, Westaway K, Duringer P, Bacon AM, Ponche JL, Wu X, Sayavongkhamdy T, Zhao JX, Barnes L, et al. 2015. Early modern humans and morphological variation in Southeast Asia: Fossil evidence from Tam Pa Ling, Laos. PLoS ONE 10(4): e0121193. - PMC - PubMed
    1. Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Pääbo S.. 2013. DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci U S A. 110(6): 2223–2227. - PMC - PubMed

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