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First Aboriginal genome sequenced

September 22, 2011 By Ewen Callaway This article courtesy of Nature News.

1920s hair sample reveals Aboriginal Australians' explorer origins.

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A 90-year-old tuft of hair has yielded the first complete genome of an Aboriginal Australian, a young man who lived in southwest Australia.

He, and perhaps all Aboriginal Australians, the genome indicates, descend from the first humans to venture far beyond Africa more than 60,000 years ago, and thousands of years before the ancestors of most modern Asians trekked east in a second migration out of Africa.

"Aboriginal Australians are descendents of the first human explorers. These are the guys who expanded to unknown territory into an unknown world, eventually reaching Australia," says Eske Willerslev, a palaeogeneticist at the University of Copenhagen, Denmark, who led the study. It appears online today in Science1.

Hanging on a hair

The oldest human remains in Australia date to around 50,000 years ago2, and yet older stone tools found in India and elsewhere hint at an early southern migration of anatomically modern humans out of Africa and through India and Southeast Asia.

However, genetic studies of contemporary Asians and Oceanians haven't always told the same story. The most comprehensive genetic analysis carried out so far pointed to a single migration that spawned all Asian populations, including Aboriginal Australians3. But estimated times of the separation of European and Asian ancestors in this population does not chime well with the archaeological evidence for the continuous settlement of Australia from much earlier times.

These papers make an overwhelming case for multiple waves of migration.
David Reich
Harvard Medical School

A complete genome from an Aboriginal Australian would settle this debate, Willerslev says. Many contemporary Aboriginal Australians also descend from Europeans because of recent interbreeding between Aboriginals and Australian colonists. To get a better picture of the ancient history of Aboriginals, Willerslev wanted to sequence the genome of someone who did not descend from Europeans.

About a year ago, his team obtained a hair sample originally collected by the British ethnologist Alfred Cort Haddon. Historical records suggest that Haddon got the hair from a young Aboriginal man in the early 1920s while on a train journey from Sydney to Perth.

Willerslev believes that the man offered his hair to Haddon willingly, and a Danish bioethics review board saw no problem with sequencing his genome. Willerslev later received the blessing of a committee that represents Aboriginal people in the region where the man probably lived.

An analysis of his genome indicates that his ancestors started their journey more than 60,000 years ago, branching off from humans who left Africa. The ancestors of contemporary Europeans and most other Asians probably went their separate ways less than 40,000 years ago, according to Willerslev's team.

Ancient relations

Like other populations outside Africa, the Australian Aboriginal man owes small chunks of his genome to Neanderthals4. More surprisingly, though, his ancestors also interbred with another archaic human population known as the Denisovans. This group was identified from 30,000–50,000-year-old DNA recovered from a finger bone found in a Siberian cave5. Until now, Papua New Guineans were the only modern human population whose ancestors were known to have interbred with Denisovans.

A second study incorporating genomic surveys from different Aboriginal Australians paints an even clearer picture of their ancestors' exploits with the Denisovans. Researchers led by Mark Stoneking at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, calculated the portion of Denisovan ancestry found in the genomes of 243 people representing 33 Asian and Oceanian populations. Patterns of Denisovan interbreeding in human populations could reveal human migration routes through Asia, reasoned the team. The paper is published today in the American Journal of Human Genetics6.

This comparison revealed a patchwork in which some populations, including Australian Aboriginals, bore varying levels of Denisovan DNA, while many of their neighbours, like the residents of mainland Southeast Asia, contained none.

Stoneking says that this pattern hints at at least two waves of human migration into Asia: an early trek that included the ancestors of contemporary Aboriginal Australians, New Guineans and some other Oceanians, followed by a second wave that gave rise to the present residents of mainland Asia. Some members of the first wave (though not all of them) interbred with Denisovans. However, the Denisovans may have vanished by the time the second Asian migrants arrived. This also suggests that the Denisovan's range, so far linked only to a cave in southern Siberia, once extended to Southeast Asia and perhaps Oceania.

"Put together, these two papers make an overwhelming case for multiple waves of migration," says David Reich, a population geneticist at Harvard Medical School in Boston, an author on the second study.

Alan Redd, a biological anthropologist at the University of Kansas in Lawrence, says that the peopling of Australia may have been more complicated than either paper suggests. Dingoes, for instance, were brought to the island continent by humans who arrived in the last 5,000 years. "It's certainly possible that people were trickling in at different times," he says.

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