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Ancient Human Migrations Unraveled Through Population Genomics Studies

NEW YORK (GenomeWeb) – A collection of genomic studies published today in Nature are providing a refined view of human population history — from out-of-Africa migrations to the peopling of Australia, Papua New Guinea, and other parts of Eurasia.

For one of the studies, an international team tapped high-coverage genome sequences for 483 individuals from 148 self-identified populations profiled for the Estonian Biocentre Human Genome Diversity Panel. The genomes, all sequenced with Complete Genomics technology, clustered into a dozen regions and 106 genetically defined populations.

When the researchers scrutinized these sequences alone or alongside sequences from an ancient genome diversity panel representing more than 100 Neanderthal, Denisovan, or ancient modern human samples, they saw evidence for an early out-of-Africa migration involving ancient humans who died off before making large contributions to global ancestry.

Though present-day human populations primarily share ancestry from anatomically modern humans who participated in an out-of-Africa migration around 75,000 years ago, for example, they found evidence that a small proportion of Papuan ancestry likely came from humans that migrated out of Africa an estimated 120,000 years ago.

"[O]ur results suggest that while the genomes of modern Papuans derive primarily from the main expansion of modern humans out of Africa," the authors wrote, "we estimate that at least [2 percent] of their genome sequence reflects an earlier, otherwise extinct, dispersal."

For a related study, some of the same team members focused on samples from Australia and Papua New Guinea to take a look back at peopling of the region, and Aboriginal Australian population history. The researchers generated genome sequences for 83 Pama-Nyungan language-speaking Aboriginal Australians and 25 individuals from Papua New Guinea, which once belonged to the same Sahul continent as Australia and Tasmania.

The team analyzed these genomes, covered to between 20-fold and 100-fold depth, alongside existing genome or genotyping data, as well as new genotype information for another 454 individuals from the Papua New Guinea highlands. From these data, the investigators found that early Australians and Papua New Guinea populations descended from a lineage that was part of the main out-of-Africa migration and diverged from Eurasian populations some 51,000 to 72,000 years ago.

"We find that, once we take into account admixture with archaic humans, the vast majority of the Aboriginal Australian genetic makeup comes from the same African exit as other non-Africans," co-author Laurent Excoffier, an ecology and evolution researcher affiliated with the University of Bern and the Swiss Institute of Bioinformatics, said in a statement.

On the Sahul continent, the researchers estimated that populations diversified and began to split from one another some 25,000 to 40,000 years ago, preceding Papua New Guinea's physical split from Australia by at least 15,000 years. Across Australia, meanwhile, they saw pronounced genetic diversity in Aboriginal Australian populations, reflecting diversification that stretches back 10,000 to 32,000 years.

Finally, investigators from the Simons Genome Diversity Project presented their own population genomic analysis, focusing on genome sequences of 300 individuals from 142 populations, sequenced to an average 43-fold depth with Illumina instruments.

Along with clues to genetic variation and archaic hominin ancestry patterns from populations around the world, that analysis suggested more mutations have been accumulating in human populations that left Africa than those that remained.

Consistent with findings from the other studies, the researchers also found that most modern human ancestry in present populations, including Aboriginal Australians, is related to the main and more recent migration out of Africa rather than the earlier exodus. 

"These results are not in conflict with skeletal and archaeological evidence of an early modern human presence outside of Africa, as early migrations could have occurred but not contributed substantially to present-day populations," the authors noted.