First ancient human DNA from the gateway between Asia and Australia

When Griffith University archaeologist Adam Brumm heard from local villagers on the Indonesian island of Sulawesi about a vast cave used to house local games of badminton, his scientific spidey-senses started to tingle.

Brumm, from Griffith’s Australian Research Centre for Human Evolution, specialises in the archaeology of the region known as Wallacea, the cluster of islands between Borneo and New Guinea which are the seafaring gateway between Asia and Australia. He intuited that a cave of that size would have been attractive to ancient humans living on the island, and could potentially unravel the secrets of one of the region’s most mysterious peoples.

He visited the cave, known as Leang Panninge (“bat cave”) in 2013, but was unable to carry out extensive investigations. Then, in 2015, his colleagues from Indonesia’s University of Hasanuddin went back and made a startling discovery.

An unprecedented find

“Bessé” was a roughly 17-year-old hunter-gatherer woman when she died some 7,200 years ago. She was buried carefully in a grave under the overhang of Leang Panninge, her body curled into the foetal position. Someone placed stone tools and red ochre in the ground with her and then, perhaps gently, covered her body with rocks.

After her discovery and painstaking excavation, the international team of researchers decided to send a piece of her petrous bone – the bone of the inner ear – to the Max Planck Institute in Germany, in the hopes of extracting genetic material for genomic analysis. “By some miracle, there’s ancient DNA preserved in the dense inner ear bone of this woman,” Brumm says.

This was particularly amazing because ancient DNA is so difficult to find in the hot, humid tropics, where genetic material breaks down quickly. “It’s the first time we’ve really had the story told to us by the ancient DNA in this part of the world,” Brumm says.

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Genomic analysis identified Bessé, named by archaeologists from Indonesia’s University of Hasanuddin after the customary Bugis nickname for a newborn princess, as a distant relative of Aboriginal Australians and Papuans, as well as belonging to a newly discovered ancient population with no genetic links to any previously known human groups.

The exciting discovery, published today in the journal Nature, marks the first time ancient human DNA has been found in Wallacea. Moreover, Brumm says the find is the first relatively complete skeleton from the Toalean culture, a people who lived and foraged in the region for thousands of years.

Who were the mysterious Toaleans?

The Toaleans are a “rather mysterious culture”, says Brumm, “who lived a secluded existence in the forests of South Sulawesi from around 8,000 years ago until 1,500 years ago, hunting wild pigs and collecting edible shellfish from rivers.”

The Toaleans appear to have lived a private life: artefacts are only found in a tiny corner – just 6% – of Sulawesi’s vast expanse (the island is the 11^th largest on Earth). “This suggests that this past culture had limited contact with other early Sulawesi communities or people in nearby islands, existing for thousands of years in isolation,” says study co-author Adhi Agus Oktaviana, a researcher in Indonesia’s National Research Centre for Archaeology (Pusat Penelitian Arkeologi Nasional) and a doctoral candidate in the Griffith Centre for Social and Cultural Research. 

“We can call them a culture because they made very distinctive, very complex types of stone tools, including these beautiful, exquisitely shaped stone arrowheads,” Brumm says. But until now, no human Toalean remains had been found.

Brumm says that understanding who the Toaleans were has been a “century-old archaeological mystery”, and all archaeological traces of them vanish around the 5th century AD, suggesting they were supplanted by the Neolithic farmers from Taiwan – the Austronesians – that populated Sulawesi some 3,500 years ago.

Some archaeologists suspect the Toaleans may have been responsible for providing Australia with one of its most iconic species, the dingo.

“[The dingo] is embedded in Aboriginal society and culture, and it’s become an important part of the Australian ecosystem. But it’s an Asian dog and somehow it got to Australia three or four thousand years ago,” Brumm says. “It must have been brought here by prehistoric Asian voyagers, but no one has ever had any idea who the hell these people were.”

The ancient DNA they’ve extracted doesn’t tell us whether the Toaleans brought the dingo to our shores, but Brumm says it does tell us important information about who they were from a genetic perspective.

Ancient DNA in Wallacea: Tracing the ancestry of Australasia

The genomic analysis of ancient DNA from Bessé’s inner ear bone confirmed existing suspicions that Toalean foragers were related to the first modern humans to enter Wallacea some 65,000 years ago, the ancestors of Aboriginal Australians and Papuans. 

“These seafaring hunter-gatherers were the earliest inhabitants of Sahul, the supercontinent that emerged during the Pleistocene [Ice Age] when global sea levels fell, exposing a land bridge between Australia and New Guinea,” Brumm says.

“To reach Sahul, these pioneering humans made ocean crossings through Wallacea, but little about their journeys is known.”

So, Brumm says, “this region has been host to a very ancient human story about which we know relatively little.”

Bessé shares about half her genetic makeup with present-day Indigenous Australians and people in New Guinea and the Western Pacific Islands. This includes DNA inherited from now-extinct Denisovans, an archaic hominin related to Neanderthals whose fossils have only been found in Siberia and Tibet.

“In fact, the proportion of Denisovan DNA in Bessé, relative to other ancient as well as present-day groups in the region, may indicate that the crucial meeting point between our species and Denisovans was in Sulawesi or another Wallacean island,” says Cosimo Posth of the University of Tübingen, Germany, who contributed to the genomic analysis alongside Selina Carlhoff from the Max Planck Institute for the Science of Human History and Johannes Krause from the Max Planck Institute for Evolutionary Anthropology.

This suggests that Bessé’s ancestors may have been among the first humans to migrate to Wallacea, but instead of following their island-hopping relatives onwards to Sahul, they settled in Sulawesi. This may also mean that it was Bessé’s forebears who created the 45,000-year-old cave paintings found in South Sulawesi depicting a vibrant cosmology of animal-human hybrids.

An undiscovered human population

Surprisingly, the analysis also revealed an unexpected signature in Bessé’s genome: the genetic fingerprints of an ancient early-modern human population of Asian origin previously unknown to science. This group did not share genetic material with the predecessors of Aboriginal Australians and Papuans, suggesting they may have entered the region after the peopling of Sahul.

“It is unlikely we will know much about the identity of these early ancestors of the Toaleans until more ancient human DNA samples are available from Wallacea,” says senior author Akin Duli from the University of Hasanuddin. “But it would now appear that the population history and genetic diversity of early humans in the region were more complex than previously supposed.”

What’s more, the researchers found that the modern people of Sulawesi share no DNA with Bessé, though Brumm notes that more extensive sampling of Sulawesi’s population may reveal closer genetic links to this vanished culture.

“The discovery of Bessé and the implications of her genetic ancestry show just how little we understand about the early human story in our region, and how much more there is left to uncover,” Brumm says.