Genome of a middle Holocene hunter-gatherer from Wallacea
Selina Carlhoff, Akin Duli, Kathrin Nägele, Muhammad Nur, Laurits Skov, Iwan Sumantri, Adhi Agus Oktaviana, Budianto Hakim, Basran Burhan, Fardi Ali Syahdar, David McGahan, David Bulbeck, Yinika Perston, Kim Newman, Andi Muhammad Saiful, Marlon Ririmasse, Stephen Chia, Hasanuddin Hasanuddin, Dwia Aries Tina Pulubuhu, Nfn Suryatman, Supriadi Supriadi, Choongwon Jeong, Benjamin M. Peter, Kay Prüfer, Adam Powell, Johannes Krause, Cosimo Posth, Adam Brumm
Abstract
Abstract 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 DNA 1 . 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 Panninge 2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the ‘Toalean’ technocomplex 3,4 , 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 ago 5 . We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.