Indonesia’s long history of human interaction

Eastern Indonesia has been a region of contact between diverse human groups. Using ancient DNA, we investigate the region's demographic history and uncover multiple human migrations and admixture events.
Indonesia’s long history of human interaction

Since DNA is digested by the cell’s own enzymes after death, within only a short time, all that’s left of our genome’s long molecules are short fragments. In cold and dry climates, the processes leading to degradation are slower, but in the tropics, heat and humidity accelerate them and every step in the laboratory has to be carried out with great diligence. Most promising is the sampling of the petrous bone, the part of our cranium that contains the inner ear. It is one of the densest bones in the human body – lying protected in the inside of the skull. When opening this bone, you can identify a shiny spot around the inner ear – if you are lucky. Kathrin had shown Selina (who was just starting her PhD) how to find this “sweet spot”, and how to carefully remove layer by layer, collecting the fine powder produced, and ensuring no dirt would contaminate the precious sample. After sampling, it takes weeks – stabilising the fragmented DNA molecules, equipping them with unique barcodes so they can be recognized after the final sequencing step. The big sequencing machines buzzed and hummed for another two days, before the computers started to piece together the resulting puzzle. Tiny fragments of DNA, not belonging to the same puzzle, but the pieces of hundreds of puzzles mixed, had to be sorted and mapped, before we could finally stare at the statistics and share the good news: DNA was preserved!

Curiously, this was not a unique experience. The excitement was felt at the same time in the two sister institutes: the Max-Planck-Institute for the Science of Human History in Jena, and the Max-Planck-Institute for Evolutionary Anthropology in Leipzig, only a mundane one-hour train ride away. In an interdepartmental meeting, both groups shared their success, and found that the region of interest was not the only commonality: we set out to answer the same questions, in the same time period, and for some samples even on the same tiny island of Morotai in the North Moluccas. There was no question - from now on, we would combine our efforts to understand the complex population history of Eastern Indonesia. The ensuing meetings to get the consent for this collaboration were the start of an iterative, co-creative process, trying to integrate several lines of evidence to better understand human migration and interaction in the region.

Map of the study region and sample provenience.

The islands of Southeast Asia are one of the most multifaceted regions on our planet. Always isolated from both Sahul, the Pleistocene Australia-New Guinea landmass, and Sunda - comprising of Southeast Asia and Western Indonesia - even during the Last Glacial Maximum, the Wallacean islands have been crucial for the evolution and distribution of local fauna and flora as well as the expansion of early hominins. Despite the challenges of early sea crossing, multiple archaic human groups including Homo erectus and Homo floresiensis are found in Wallacea1, while cave paintings suggest that anatomically modern humans have inhabited the islands for at least 45.5 thousand years2. The next known large event affecting Wallacea was the “Austronesian expansion”, where groups with advanced sailing and farming techniques departed from Taiwan 4 to 5 thousand years ago to settle in Wallacea, New Guinea and the Oceanian islands3. These groups spoke Austronesian languages which are widespread in the region today, but the survival of some Papuan languages, presumably spoken by earlier hunter-gatherers, indicates that both groups co-existed or mixed and contributed to the linguistic and cultural diversity we see today. Previous genetic studies of modern-day inhabitants have identified Papuan-related and Austronesian-related ancestries, but have yielded conflicting dates for this intermixing, ranging from 1,100 to nearly 5,000 years ago. Archaeological finds from the early Metal Age also demonstrate that the people were highly mobile and engaged in long-distance trade with Mainland Southeast Asia (MSEA) and India long before the European arrival and exploitation of the region.

We were all expecting to find signs of Austronesian-Papuan admixture in the ancient Wallaceans (~2,600-250 years old); after all, present-day groups from the region have been shown to be admixed. However, it was only after jointly analyzing all of the ancient individuals, that some surprising differences became obvious: the ancient individuals from the southern islands (East Nusa Tenggara) carried ancestry related to MSEA, in addition to the Austronesian- and Papuan-related ancestries, which were sufficient to model admixture in the North Moluccas. The surprise was even greater when we realized how old the admixture with MSEA could be. Our inferences on the order of admixture pointed to a first event involving Papuans and MSEA groups, therefore opening up the possibility for an early dispersal into Wallacea that can predate the Austronesian arrival. The radiocarbon dating of the Liang Bua sample (~2600 years BP) was also extremely helpful to set a lower bound to the arrival of the MSEA ancestry. Where in MSEA this ancestry came from is still unknown; archaeologists have yet to find any trace of a pre-Austronesian material culture in Wallacea that can be linked to MSEA. Nevertheless, our results clearly indicate that the seas were no impediment to the movement of people during the Neolithic period in SEA. We inferred that admixture occurred in multiple pulses or continuously since at least 3000 years ago throughout Wallacea and this went on until recent times in the North Moluccas. Yet, our surprises did not end there. When we searched for affinities between the ancient Wallaceans from this study and a previously published pre-Neolithic individual from Sulawesi (another Wallacean island)4, we found none! Instead, the post-Neolithic Wallaceans were closer to New Guinean groups, suggesting that these two regions were likely more connected in ancient times than we previously imagined.

Topogaro site in Sulawesi island, Indonesia. Photo: Rintaro Ono

As commonly happens in research, despite the new insights we presented in our study, we finished this project with even more questions than before. Future efforts to squeeze more ancient DNA from Wallacea will surely provide new discoveries concerning the complex human history of this fascinating region, and complement the influential works undertaken by archaeologists and linguists over many years.

Authors: Sandra Oliveira, Kathrin Nägele, and Selina Carlhoff

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Banner photo: © 123RF | donnchans


  1. van den Bergh, G. D. et al. Earliest hominin occupation of Sulawesi, Indonesia. Nature 529, 208–211 (2016).
  2. Brumm, A. et al. Oldest cave art found in Sulawesi. Sci. Adv. 7, eabd4648 (2021).
  3. Bellwood, P. First islanders: prehistory and human migration in Island Southeast Asia. (John Wiley & Sons, 2017).
  4. Carlhoff, S. et al. Genome of a middle Holocene hunter-gatherer from Wallacea. Nature 596, 543-547 (2021).