Genome of a middle Holocene hunter-gatherer from Wallacea

Selina Carlhoff,Adam Powell,Kathrin Nägele,Laurits Skov,Kay Prüfer,Dwia Aries Tina Pulubuhu,- Hasanuddin ,Muhammad Nur,Yinika Perston ,Adhi Agus Oktaviana,Suryatman Suryatman ,Cosimo Posth,David Mcgahan ,David Bulbeck,Akin Duli,Supriadi Supriadi ,Choongwon Jeong,Marlon Nr Ririmasse ,Stephen Chia,Budianto Hakim,Fardi Ali Syahdar,Basran Burhan,Andi Muhammad Saiful,Kim Newman,Iwan Sumantri,Benjamin M Peter,Johannes Krause,Adam Brumm

doi:10.1038/s41586-021-03823-6

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 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.

Highlights

These ancient and present-day peoples lack substantial amounts of Denisovan-related ancestry, suggesting that the Hòabìnhian-associated and Onge-related lineage diverged before the main archaic human introgression events[1]
We confirmed these results with f4-statistics[33], suggesting similar affinity of Leang Panninge and Papuan individuals to present-day Asian individuals, despite Near Oceanian groups forming a clade to the exclusion of Leang Panninge (Extended Data Fig. 7a, b)
We confirmed that Indigenous Australian and Papuan individuals carry a similar amount of Denisovan ancestry[18,21,40], whereas the Leang Panninge individual has a lower value of approximately 2.2 ± 0.5% (Supplementary Tables 18–20)

Summary

Discussion

Genome-wide analyses of the Leang Panninge individual show that most genetic drift is shared with present-day groups from New Guinea and Aboriginal Australia (Fig. 2b, Extended Data Fig. 7a). The scarcity of pre-Neolithic genomes from across Asia prevents us from defining the exact source and admixture proportions of this gene flow event It is noteworthy, that despite the reconstructed population trees (TreeMix and qpGraph) suggesting a genetic influence on middle Holocene Sulawesi from mainland East Asia, our qpAdm modelling cannot rule out a southeast Asian contribution from a group related to present-day Andamanese peoples That despite the reconstructed population trees (TreeMix and qpGraph) suggesting a genetic influence on middle Holocene Sulawesi from mainland East Asia, our qpAdm modelling cannot rule out a southeast Asian contribution from a group related to present-day Andamanese peoples To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Methods

Findings

Code availability