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Aboriginal Australian Genome Provides Peek at Historical Human Migrations

By Andrea Anderson

NEW YORK (GenomeWeb News) – An international research team reported in Science online today that it has sequenced the first Aboriginal Australian genome, using information in the genome to find clues about human population and migration history.

Researchers sequenced the genome from a hair sample donated by an Aboriginal man from Western Australia in the early 1920s. By analyzing and comparing patterns in his genome with those in sequences from other populations, the team discerned new details about the history of human migration into Asia and relationships between human populations.

The findings suggest that the ancestors of Australian Aboriginals arrived in eastern Asia as far back as 62,000 to 75,000 years ago — thousands of years before the ancestors of most modern-day Asian populations.

"Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia," the study authors wrote, "likely representing one of the oldest continuous populations outside Africa."

Data from archeological and genetic studies indicate that modern humans migrated out of Africa in one main wave, followed by a series of dispersals into other parts of the world. In some cases, though, questions remain about the details of these subsequent migrations.

For example, co-senior author Rasmus Nielsen, an integrative biology and statistics researcher at the University of California at Berkeley, told GenomeWeb Daily News, there has been much debate over the history of human migration to Australia.

Some researchers have proposed that present day Aboriginal Australian populations are descended from a population that split off from modern Asian ancestors following a single migration into Asia. Others suspect that there were two waves of human migration to that part of the world, one following a southern route into Asia and Australia and another more recent migration into Europe and Asia.

"It's one of the major controversial issues in anthropology," Nielsen said, "whether there was one dispersal wave or two dispersal waves by which Europe, Asia, and Australia were populated."

In an effort to learn more about human migration patterns, in general, as well as Aboriginal population history, the researchers did genome sequencing on DNA from a hair sample obtained from an Aboriginal Australian man in 1923.

Nielsen noted that study authors consulted with members of an Aboriginal tribal counsel based in the same region that the man was from prior to undertaking the study.

"What we found was that they were quite interested in learning about their genetic history and having genetic studies done," he said. "We did not find that there were any signs that they were reluctant to have those kinds of studies done or to participate in those kinds of studies."

Although DNA in the sample was fairly fragmented, collaborators at BGI-Shenzhen generated sequence covering the nuclear genome at an average depth of 6.4 times using the Illumina HiSeq2000 platform. Sequence coverage was deeper over 60 percent of the genome, averaging a depth of 11 times. The mitochondrial genome, meanwhile, was sequenced to an average depth of 338 times.

The researchers identified more than 2.7 million SNPs in the nuclear genome, including 449,115 SNPs that they classified as high confidence and 28,395 variants not found in other human genomes so far.

The genome did not contain sequences indicating recent European ancestry, researchers reported, and the sample tested had low levels of contamination with European DNA.

Consistent with findings in other human populations, the team found evidence of admixture between the individual's ancestors and archaic human forms. The proportion of Neandertal DNA resembled that found in European and Asian genomes, consistent with the theory that modern humans mixed with Neandertals shortly after moving out of Africa.

"You see Neandertal admixture in all of the out-of-Africa populations," Nielsen explained. "The only way, really, to explain that is if the admixture happened between modern humans as they first dispersed out of Africa and then met Neandertals."

On the other hand, the proportion of Denisovan alleles in the genome was higher than that found in Eurasian populations and was more comparable to that found in populations from Papua New Guinea.

When they compared genetic variants in the Aboriginal Australian genome with SNP data on more than 1,200 individuals from 79 modern human populations, the researchers found that the sequences clustered most closely with those from Papua New Guinea and the Aeta population in the Philippines.

In general, the derived allele patterns in the genome were more similar to those in Asian populations than French Europeans, the team reported. But Asian and French populations shared more derived alleles than did the Aboriginal Australian and the French, suggesting a more recent split between Europeans and Asians.

"[O]ur results favor the multiple-dispersal model in which the ancestors of Aboriginal Australian and related populations split from the Eurasian population before Asian and European populations split from each other," they wrote.

Based on more detailed analyses on a few Han Chinese, African, and European genomes, the researchers estimate that Aboriginal Australians ancestors split from ancestral Europeans and moved into eastern Asia some 62,000 to 75,000 years ago. In contrast, modern Asian populations appear to have migrated to the area more recently, diverging from ancestral Europeans around 25,000 to 38,000 years ago.

Nevertheless, the study authors noted, there is evidence of gene flow between the earlier- and later-arriving populations before ancestors of Native American split off from the Asian population between 15,000 and 20,000 years ago.

While they were somewhat hesitant to draw conclusions about Aboriginal Australian population history as a whole based on genetic information for just one individual, those involved in the study argued that the at least some Aboriginal Australians likely have similar ancestry patterns as the individual who was sequenced.

"We cannot, of course, know whether there are different sub-populations in Australia that have different histories," Nielsen said. "If that's the case, this individual is not representative [of the Aboriginal Australian population as a whole]."

But, he said, the genetic data, combined with other evidence, hints that other members of this population likely share some of the genetic patterns found in the newly sequenced genome, suggesting the Aboriginal Australian population may be the oldest surviving population outside of sub-Saharan Africa.

"It's highly likely that modern-day Australians, at least in part, are descendants of individuals coming very early from the southern [migration] route about 50,000 years ago or perhaps further back," Nielsen said.

In the future, he said, the team hopes to do more sequencing studies of indigenous populations around the world to learn more about the history of human populations. Such studies may also prove beneficial for these populations, Nielsen added, as researchers continue to try to uncover and apply medically relev

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