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Genome of Ancient Hunter-Gatherer Offers Look at Modern Human, Denisovan Population Dynamics

NEW YORK – By sequencing the genome of an ancient female hunter-gatherer from a region in the present-day Wallacea island zone near Indonesia, a team led by investigators at two Max Planck institutes, the University of Tübingen, and Griffith University in Australia has untangled dynamics of the modern human and archaic hominin populations migrating through and settling in the area.

"This new piece of the genetic puzzle … illustrates above all just how little we know about the genetic history of modern humans in southeast Asia," co-senior and co-corresponding author Cosimo Posth, a researcher at the University of Tübingen's Senckenberg Centre for Human Evolution and Palaeoenvironment, said in a statement.

As reported in Nature on Wednesday, the team used shotgun sequencing, targeted sequencing of enriched DNA, and mitochondrial DNA sequencing to assess ancient DNA extracted from a petrous bone sample roughly 7,200 to 7,300 years old from Wallacea, an island region set between western Indonesia and New Guinea.

"[W]e report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea)," the authors wrote.

The ancient female hunter-gather individual — dubbed Leang Panninge for the South Sulawesi cave in Indonesia where she was found — appeared to be part of a population present in the area some 1,500 to 8,000 years ago that has been linked to the Toalean culture based on the burial features and other artifacts detected at the site.

From their analyses, the investigators concluded that the woman was primarily descended from an ancient modern human population that migrated into Wallacea and through the region roughly 50,000 years or more ago. Part of this population appeared to move on to what is now Papua and Australia, they explained, while some individuals remained in Wallacea, leaving their mark on the pre-Neolithic forager population present there.

"Our analyses suggest that the Leang Panninge individual descends from the first wave of early modern humans to cross through the Wallacean archipelago to Sahul (the combined ice age landmass of Australia and New Guinea) at least 50,000 years ago, but that her lineage essentially remained in Sulawesi and thus split off at an early point in time from the Australian-Papuan populations," co-senior and co-corresponding author Adam Brumm, a human evolution researcher at Griffith University, explained in an email.

Along with additional ancestry from an Asian population that was not previously documented in the region's archeological record and that appears to have occurred after the Australian-Papuan population divergence, he noted, the hunter-gatherer woman carried Denisovan DNA at levels comparable to those found in other populations in the area.

"[T]he amount of Denisovan DNA in this woman relative to other modern-day groups and ancient populations in the region could suggest that the main meeting point between our species and the Denisovans was in Sulawesi itself (or perhaps elsewhere in Wallacea)," Brumm said.

So far, ancestry stemming from the Leang Panninge population has not been detected in populations found in the region today, the team noted, perhaps due to limited sampling in the area or to subsequent modern human migrations into the region that may have replaced the hunter-gatherer group.

"Higher coverage genetic data from present-day populations in Sulawesi, and additional Toalean ancient genomes, are needed to further investigate this unique ancestry profile and the genetic diversity of hunter-gatherers from Wallacea more generally," the authors concluded.