Jan 142013

Genome-wide data substantiate Holocene gene flow from India to Australia

PNAS online publication January 14, 2013; doi: 10.1073/pnas.1211927110
Irina Pugach, Frederick Delfin, Ellen Gunnarsdóttir, Manfred Kayserd, and Mark Stoneking

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.


At K = 5, the proportion of Australian ancestry not shared with the New Guineans most closely resembles the ancestry profile of the three Indian populations [Chenchu and Kurumba (tribal Dravidian speakers) plus nontribal Dravidian speakers from south India] at this value of K.

Additionally, at K = 7, six runs with the highest log-likelihood scores ascribe 11% of Australian ancestry to India, whereas an additional 9% is shared with the Mamanwa

Pugacha et al. (2013) Fig. S5B&C
Figs. S5B and S5C

The graph that best fits the data has four inferred migration edges: Chenchu to CHB (weight, 4%), Onge to India (17) (weight, 6%); one of the edges captures shared ancestry between NGH, AUA, and MWA (5, 23) (weight, 15%); and one of the edges provides evidence for the gene flow from India to Australia. The weight for this migration edge is estimated to be 11%, in agreement with the admixture proportion obtained in the ADMIXTURE analysis.

Pugacha et al. (2013) Fig. 4C
Fig. 4C

… our study includes 11 populations from island SE Asia [Borneo: Land Dayak; Sumatra: Besemah and Semende; Philippines: Manobo and (negrito) Mamanwa; Nusa Tenggara: Alor, Flores, Roti, Timor; Moluccas: Hiri and Ternate], but there is no signal whatsoever of recent gene flow from India into these populations or from these populations into Australia (Fig. S8), which renders this scenario of Indian ancestry via SE Asia unlikely.

Pugacha et al. (2013) Fig. S8B
Fig. S8B

Quick thoughts

The aboriginal Australian samples in this study were obtained from individuals in “a broad geographical area of the Northern Territory” — as the authors acknowledge, it can’t be presumed that this 11% “Indian” contribution is uniform across all aboriginal Australian populations, and broader sampling would be desirable. (Now, what would really be interesting would be genomic data from historic Tasmanian aborigines.)

This “Indian” element is evident neither in contemporary insular SE Asia (granted, the present-day non-Negrito inhabitants of the region seem to be, to a large extent, replacement populations) nor in (highland) New Guinea. (How about lower elevations?)

Chenchu to Beijing Han: Indian subcontinental admixture in China (but not Bornean Dayaks)?

That “Mamanwa”-modal component showing up in Australian aborigines — but not NGH — at K = 7: again something that made it into Australia while skirting (highland) New Guinea? Shades of Birdsell’s first-wave “negritos”?  Let’s remember that the Mamanwa were found previously to derive almost three-quarters of their ancestry from an East Asian-like source…

In closing … some remarks by Jonathan Morris, writing of Alfredo Trombetti and his early-20th-century precursor to Greenberg’s “Indo-Pacific”:

While my primary aim is an accurate portrayal of Trombetti’s ideas and data rather than an assessment of their merits, we may note in passing that the revision of his hypothesis to include Dravidian has the anomaly of showing better matches with Australian than with Andamanese or Papuan.

[...] Viewed from a modern perspective, I wonder whether Trombetti’s link to Dravidian is not demonstrating something else, i.e. evidence of a much later migration from India to Australia during the Mesolithic/Neolithic… [...] If so, then the implications of Trombetti’s work are that the South Indian populations which migrated to Australia were Dravidian speakers, even if he was probably wrong to include this family in his Andamanese-Papuan-Australian phylum.

  One Response to “Indian subcontinental gene flow into aboriginal Australia c. 4200 years ago?”

  1. More on this subject:

    Letter: Interpreting the evidence for middle Holocene gene flow from India to Australia

    Michael Holton Price and Douglas W. Bird

    PNAS 2013 ; published ahead of print June 10, 2013, doi:10.1073/pnas.1306505110

    Full Text (PDF)

    Letter: Reply to Price and Bird: No inconsistency between the date of gene flow from India and the Australian archaeological record

    Irina Pugach and Mark Stoneking

    PNAS 2013 ; published ahead of print June 10, 2013, doi:10.1073/pnas.1307961110

    Full Text (PDF)

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