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, 110 (5), 1803-8

Genome-wide Data Substantiate Holocene Gene Flow From India to Australia

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Genome-wide Data Substantiate Holocene Gene Flow From India to Australia

Irina Pugach et al. Proc Natl Acad Sci U S A.

Abstract

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Geographic distribution of samples used in this study.
Fig. 2.
Fig. 2.
LD measured for each population and each pair of SNPs within the 50 evenly spaced recombination distance categories. Shortest genetic distances between the SNPs are represented on the left and progress toward the largest genetic distances on the right.
Fig. 3.
Fig. 3.
Results of the PCA and ADMIXTURE analyses. (A) PCA of AUA, NGH, CEU, and 26 Indian populations. PC1 is driven by differences between the populations of Sahul and Eurasia. PC2 reflects a north-to-south gradient of European ancestry observed in Indian groups, with the southernmost group being the Onge, a Negrito population from the Andaman islands. (B) Population structure estimated using ADMIXTURE for K = 4. Each vertical bar represents an individual and each color describes the proportion of each individual’s genome that comes from one of the four hypothetical ancestral populations (K). The asterisk indicates the two individuals from the Srivastava group.
Fig. 4.
Fig. 4.
Results of the TreeMix analysis. (A) The maximum-likelihood tree of nine populations included in the analysis. (B) Residual fit from the tree. Residuals above zero indicate pairs of populations that are candidates for admixture events. (C) Population graph that best fits the data, based on the smallest residuals (D).

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