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Link to original content: https://pubmed.ncbi.nlm.nih.gov/22042846/
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. 2011 Nov 8;108(45):18301-6.
doi: 10.1073/pnas.1108181108. Epub 2011 Oct 31.

Archaic human ancestry in East Asia

Pontus Skoglund  1 , Mattias Jakobsson
Affiliations

Archaic human ancestry in East Asia

Pontus Skoglund et al. Proc Natl Acad Sci U S A. .

Abstract

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome--a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Modern human genetic variation projected on axes of variation defined by chimpanzee, Denisova, and Neandertal. (A) A model of hominin evolutionary history suggested in the work in ref. with putative admixture events indicated by arrows. (B) Population means for each of 62 populations. (C) PC1 in individuals from Eurasia and America as a function of distance from East Africa (kilometers). (D) Interpolated spatial distribution of PC2 [transformed for visualization as (−1) × log10 (x + C), where x is the PC loading and C = 0.04231] in individuals from Eurasia, Oceania, and America. (E) Interpolated spatial distribution of the frequency of Denisova alleles at SNPs where Denisova is different from chimpanzee and Neandertal. Sample localities are indicated with rectangles.
Fig. 2.
Fig. 2.
PCA of archaic ancestry under a serial founder model with (or without) archaic admixture. PCA was performed by projecting hypothetical extant humans onto the variation of a hypothetical chimpanzee and two hypothetical archaic hominins that shared a recent history with modern humans ∼400 kya. (A) A model with no admixture between colonizing and archaic populations. (B) A model with two separate admixture events: from archaic population A into colony 25 (forward in time, 2.5% of colony 25 is replaced) and from archaic population B into colony 97 (forward in time, 5% of colony 97 is replaced). This model is similar to the model suggested in ref. (Fig. 1A). (C) A model with the two admixture events in B and an additional admixture event from archaic population B into colony 75 (forward in time, 1% of colony 75 is replaced). D–F show PCA results from models A, B, and C, respectively. G–I show PCA results for models A, B and C, respectively, but with SNPs with minor allele frequency (MAF) < 5% excluded. In D–I, we display the mean PC loading of 10 samples from each colony numbered and colored according to distance from the founding population. The model in C produced the qualitatively most similar result compared with the empirical data in Fig. 1B.
Fig. 3.
Fig. 3.
Results of 4-population tests suggest Denisova-related ancestry in Southeast (SE) Asia. Z scores for the D statistic in all pairwise comparisons between Africa, Middle East, Central/South Asia, Southeast Asia, Northeast (NE) Asia, Oceania, and America are displayed. The configuration of each pairwise comparison that gives a positive value of D in the test (Pop1, Pop2, Denisova, chimpanzee) was chosen to ease visualization. Except for Oceanians and the comparison between SE Asia and NE Asia, populations that show high affinity to Denisova compared with chimpanzee tend to also show a higher affinity to Neandertal compared with Denisova (negative values on the y axis). Comparisons with Africans are shown by triangles. The area corresponding to significant deviations from 0 (|Z| > 2) is shaded, with the overlap representing significant deviations for both tests (Table S4).
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References

    1. Cann RL, Stoneking M, Wilson AC. Mitochondrial DNA and human evolution. Nature. 1987;325:31–36. - PubMed
    1. Stringer C. Modern human origins: Progress and prospects. Philos Trans R Soc Lond B Biol Sci. 2002;357:563–579. - PMC - PubMed
    1. Ramachandran S, et al. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci USA. 2005;102:15942–15947. - PMC - PubMed
    1. Trinkaus E. Early modern humans. Annu Rev Anthropol. 2005;34:207–230.
    1. Mellars P. Going east: New genetic and archaeological perspectives on the modern human colonization of Eurasia. Science. 2006;313:796–800. - PubMed

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