Genome of a middle Holocene hunter-gatherer from Wallacea.

Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)1. Here we 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). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

Validating earliest rice farming in the Indonesian Archipelago.

Preserved ancient botanical evidence in the form of rice phytoliths has confirmed that people farmed domesticated rice (Oryza sativa) in the interior of Sulawesi Island, Indonesia, by at least 3,500 years ago. This discovery helps to resolve a mystery about one of the region's major events in natural and cultural history, by documenting when rice farming spread into Indonesia, ultimately from a source in mainland China. At the Minanga Sipakko site in Sulawesi, preserved leaf and husk phytoliths of rice show the diagnostic morphology of domesticated varieties, and the discarded husks indicate on-site processing of the crops. The phytoliths were contained within an undisturbed, subsurface archaeological layer of red-slipped pottery, a marker for an evidently sudden cultural change in the region that multiple radiocarbon results extend back to 3,500 years ago. The results from Minanga Sipakko allow factual evaluation of previously untested hypotheses about the timing, geographic pattern, and cultural context of the spread of rice farming into Indonesia, as well as the contribution of external immigrants in this process.