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Ancient DNA Provides Glimpse into Waves of Settlement of Wallacea

NEW YORK — A new ancient DNA-based study has uncovered regional variation in genetic ancestry among Wallaceans.

Modern humans first settled the Wallacean islands, which are part of present-day eastern Indonesia and Timor Leste, about 47,000 years ago. The region's genetic ancestry is thought to be largely shaped by the settlement of the Sahul — Australia, New Guinea, and the Aru Islands — and by the Austronesian expansion. A cultural transition occurred in Wallacea about 3,500 years ago that coincides with the expansion of Austronesian-speaking farmers, though estimates of when intermixing of local hunter-gatherers and farmers took place range by thousands of years.

To dive deeper into the genetic ancestry of Wallacea, a Max Planck Institute for Evolutionary Anthropology-led team generated genome-wide data for 16 individuals who lived in different regions of Wallacea between 250 and 2,600 years ago. As they reported in Nature Ecology & Evolution on Thursday, they uncovered that while individuals from northern Wallacea harbored more ancestry related to Austronesian and Papuan groups, individuals from southern Wallacea also had genetic ancestry related to groups from mainland Southeast Asia.

"We found striking differences between regions in Wallacea and surprisingly, the ancestry of ancient individuals from the southern islands cannot be simply explained by admixture between Austronesian- and Papuan-related groups," co-first author Sandra Oliveira from Max Planck said in a statement.

The researchers obtained DNA from skeletal remains from 16 individuals from eight archaeological sites across the region.

All of the ancient Wallaceans, they found, were genetically more closely related to present-day Papuans than to a pre-Neolithic individual living in Sulawesi, one of the more western and northern Wallacean islands, indicating a lack of direct genetic continuity in the region and suggesting that the local hunter-gatherers were largely replaced.

Within the ancient individuals from East Nusa Tenggara, in present-day southern Indonesia, the researchers noted genetic influence from mainland Southeast Asian groups. They speculated that human groups from mainland Southeast Asia crossed into southern Wallacea before the Austronesian-related groups did, a supposition they noted is supported by studies of black rats that spread with humans. But from where these mainland Southeast Asian groups hailed is unclear, though the researchers said the best present-day proxies include the Mlabri from Thailand and Laos and the Nicobarese from the Nicobar islands.

Ancient Wallaceans in the North Moluccas, meanwhile, exhibited greater affinity with Mariana Islanders. However, the researchers noted that other studies have found that the Mariana Islands were likely settled via the Philippines, instead suggesting that this affinity could be due to shared ancestry from a common Austronesian source.

These findings further home in on when that contact between Austronesians and Papuans may have occurred, placing it at least 2,150 years ago in the North Moluccas and 2,600 years ago in East Nusa Tenggara.

"Previous studies based on present-day populations have reported widely different estimates, some of which preceded the archaeological evidence for the Austronesian expansion, while others were much more recent. Since we now have ancient individuals from different time periods we can directly show that admixture occurred in multiple pulses or continuously since at least 3,000 years ago throughout Wallacea," senior author Mark Stoneking from Max Planck said in a statement. "Future studies on older genomes might extend this date even further."