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First ancient human DNA found from key Asian migration route

Fragmentary remains of the human skull.

The compressed skull and teeth of a young woman were found inside an Indonesian cave.Credit: University of Hasanuddin

The 7,000-year-old skeleton of a teenage hunter-gatherer from Sulawesi in Indonesia could be the first remains found from a mysterious, ancient culture known as the Toaleans, researchers report this week in Nature1.

The largely complete fossil of a roughly 18-year-old Stone Age woman was found in 2015 buried in a fetal position in a limestone cave on Sulawesi. The island is part of a region known as Wallacea, which forms the central islands of the Indonesian archipelago.

DNA extracted from the skull suggests the woman shared ancestry with New Guineans and Aboriginal Australians, as well with an extinct species of ancient human.

“This is the first time anyone’s found ancient human DNA in that region,” says Adam Brumm, an archaeologist at the Australian Research Centre for Human Evolution at Griffith University in Brisbane, who is part of a team that described the find.

The authors say she may be one of the Toalean people, whose existence is known from scant archaeological evidence, such as distinctively notched stone tools, and who were thought to have lived in Sulawesi at around the same time.

Gateway to Australasia

The remains were found alongside Toalean-type tools, providing strong evidence of the woman’s link to these little-known people, agrees Shimona Kealy, an archaeologist at the Australian National University in Canberra.

Wallacea is the gateway through which ancestors of modern Papuan and Aboriginal Australians travelled, but very few ancient human remains have been discovered there. One of the most famous is the diminutive ‘Hobbit’ skeleton of the early human species Homo floresiensis, which was found on the island of Flores, south of Sulawesi.

The hot, moist tropical environment means DNA degrades rapidly in fossils, making genetic material a rare prize for researchers working in the region. The authors suspect that the skeleton’s burial inside the Leang Panninge limestone cave might have helped to preserve enough DNA for analysis.

Adding genomic analysis to archaeological evidence “provides much more insight into the early population movements and genetic diversity of people in that region”, Brumm says.

Kealy says the simple fact that DNA has been extracted from a fossil in this challenging environment for DNA preservation is a key achievement of the project. “To see these guys get enough of a sequence that they can actually do analysis on it — and from something that’s 7,000 years old, which is quite impressive — that’s the real excitement,” she adds.

Leang Panninge cave.

Sulawesi's Leang Panninge cave has been a rich source of information about ancient people.Credit: Leang Panninge research team

Waves of migration

The woman’s genome suggests a similar level of relatedness to present-day Aboriginal Australians and New Guineans, implying that her lineage split off before either of those groups diverged from one another around 37,000 years ago, says co-author Selina Carlhoff, who researches population genetics at the Max Planck Institute for the Science of Human History in Jena, Germany.

Kealy says it’s possible that the woman’s ancestors were part of a movement of people migrating through Sulawesi to Australia and New Guinea around 50,000–60,000 years ago, but that her lineage formed an offshoot population that remained in Sulawesi. Another possibility is that her ancestors were part of a later return wave of migration back into Wallacea from Australia and New Guinea, Kealy says.

The woman’s genome also contained Denisovan DNA. The Denisovans are an extinct subspecies of ancient human who lived 500,000–30,000 years ago, and whose existence is known only through fossil discoveries in Siberia and on the Tibetan Plateau.

The presence of Denisovan genetic material — also found in people in Australia and New Guinea — suggests that Wallacea might have been a region in which Denisovans and modern humans intermingled and interbred.

There’s also the question of whether this individual might be linked to 44,000-year-old cave paintings discovered in 2019 in Sulawesi — regarded as some of the world’s oldest known figurative cave art. “It would be super-interesting to be able to figure out if there were any connections between the people who made the paintings and the [Toaleans],” says Carlhoff.

Genetic traces in modern inhabitants

The region around Leang Panninge is today inhabited by people of the Bugis and Makassar cultures of Indonesia. These people are descendants of Austronesians who settled there after making their way from Taiwan about 3,500 years ago.

The woman’s genome shows no trace of Austronesian DNA, because she lived long before that migration took place. But a key question for researchers is whether the Bugis and Makassar people have ties to the ancient group to which she belonged.

Indonesian scientists involved with the project have named the woman Bessé´, which is a Bugis word for ‘young woman’. “Although physically different from the current population of Sulawesi, the Bessé´ will still be considered part of human history on the island,” says study co-author Muhammad Nur, an archaeologist at the University of Hasanuddin in South Sulawesi.

Brumm says that no trace of the woman’s genetic lineage has so far been found in samples taken from modern-day inhabitants of Sulawesi. However, this could be because the diverse population has not been sampled thoroughly enough.

It’s possible “that descendants of these Toalean peoples survived and lived on in some parts of South Sulawesi until recently, and their genes could still be surviving today, even though their culture disappeared thousands of years ago”, Brumm says.



  1. Carlhoff, S. et al. Nature (2021).

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