The genetic history of Aboriginal Australians and Papuans

Evidence found for a single major 'Out of Africa' migration event

The first major genomic study of Aboriginal Australians has provided several new pieces in the puzzle of how modern humans spread across the world. Published in Nature along with two other related papers on worldwide genetic diversity, this research addressed a fundamental question in human population history by finding evidence for a single major “Out of Africa” migration event.

As part of an international team of scientists and Aboriginal Australians, researchers from the Wellcome Trust Sanger Institute also showed that Aboriginal Australian and Papuan people have remained genetically independent from the rest of the world until very recent times.

How Australia was initially populated, and how changes in language and culture in the continent happened, has been debated for many years. Australia contains some of the oldest archaeological evidence of modern humans outside Africa, dating back to about 50,000 years. Yet, 90 per cent of Aboriginal Australians speak languages belonging to a single linguistic family that dates back no more than a few thousand years.

Working closely with Aboriginal community elders and representative organisations, the international team of scientists developed consent to sequence the Aboriginal Australian genomes. Using DNA extracted from saliva, the team sequenced the genomes of 83 Aboriginal Australians and 25 Papuans from the highlands of New Guinea, just north of Australia. They then compared them to each other and to existing data from other parts of the world to infer the history of these populations.

“It is a really wide-ranging study and important on a number of levels. Firstly, it deals with the question of how humans left Africa, which is still very much contested. But it also tells us about how Australia was populated, and about how its population developed.

“Aboriginal Australians have been the subject of scientific mystery – how did they get there, what was their relationship to other groups, and how does their arrival change our understanding of how populations spread? Technologically and politically, it has not really been possible to answer those questions until now.”

Professor Eske Willerslev From St John’s College, University of Cambridge, the Sanger Institute and the University of Copenhagen, who initiated and led the research

With this first large-scale study of genomes of Aboriginal Australians the researchers found, in contrast to many earlier theories, that this population derived the vast majority of its genetic ancestry from the same wave of migrants as all other present-day non-African populations, who left Africa approximately 60-70,000 years ago.

The DNA sequences showed that the ancestors of Aboriginal Australians and Papuans had then split from Europeans and Asians by at least 51,000 years ago. By comparison, the ancestors of Europeans and Asians only became genetically distinct from each other roughly 10,000 years later. The researchers charted several further divergence events in which various parts of the population became separated.

”We compared the genomes of Papuan people to those of Aboriginal Australians, and discovered that these two populations are actually strikingly distinct from each other. Surprisingly, Papuans and Aboriginal Australians appear to have diverged from each other at least 25,000 years ago, even though the landmasses of Australia and New Guinea were only separated by rising sea levels less than 10,000 years ago.”

Anders Bergström A first author on the paper from the Sanger Institute

A subsequent expansion within Australia may explain the single widespread language family.

Researchers at the Sanger Institute also contributed to two further large-scale sequencing papers on human genetic diversity and population history, which are published in the same issue of Nature. One of these, by Mallick et al., reports genome sequences from 142 diverse worldwide populations. They found that the population that gave rise to all present-day humans began to diversify at least 200,000 years ago within Africa, and also reached the conclusion of a single major exit from Africa.

The other paper, from Luca Pagani and colleagues, similarly examined sequences from 148 worldwide populations and suggested that a small fraction (at least 2 per cent) of the genomes of Papuans reflects ancestry from a distinct population that migrated out of Africa before 75,000 years ago. However, all three papers conclude that the vast majority of the genomes of non-Africans alive today stems from one ancestral group of migrants who left Africa together.

“Our results suggest that, rather than having left in a separate wave, most of the genomes of Papuans and Aboriginal Australians can be traced back to a single ‘Out of Africa’ event which led to all modern populations outside Africa. There may have been other migrations, but the evidence so far points to one major exit event. However, there is a clear need to extend such studies to fully understand the patterns of early human dispersal out of Africa.”

Dr Manjinder Sandhu A senior author on the Aboriginal Australian paper from the Sanger Institute and University of Cambridge

These large-scale population genomics studies allow scientists to better understand the historical events that underlie patterns of present-day human genetic variation, and trace the routes of our early ancestors as they spread across and colonized the world.