First ancient human DNA from the islands between Asia and Australia

Credit: University of Hasanuddin

A research team co-led by Griffith University archaeologists has discovered DNA in the remains of a hunter-gatherer woman who died 7200 years ago on the Indonesian island of Sulawesi. Nicknamed Bessé’, she is the first known skeleton from an early foraging culture called the Toaleans.  

Genomic analysis shows that this ancient individual was a distant relative of Aboriginal Australians and Papuans. But it also revealed that Bessé’ is a rare ‘genetic fossil’, in the sense that she belonged to a group with an ancestral history that was unlike that of any previously known human population.  

Excavations at Leang Panninge cave. Credit: Leang Panninge Research Project.

This surprising find, published in the journal Nature, is the first time ancient human DNA has been reported from ‘Wallacea’, the vast group of islands between Borneo and New Guinea and the gateway to the continent of Australia.   

The Sulawesi remains were excavated in 2015 from a cave called Leang Panninge (‘Bat Cave’). They belong to a young female hunter-gatherer who was about 17-18 years old at time of death. She was buried in a foetal position and partially covered by rocks. Stone tools and red ochre (iron-rich rock used to make pigment) were found in her grave, along with bones of hunted wild animals.  

The University of Hasanuddin archaeologists who discovered the woman affectionately dubbed her Bessé’, following a custom among Bugis royal families of bestowing this nickname on newly born princesses before they were formally named.  

This is the first relatively complete skeleton to be found alongside securely dated artefacts of the Toalean culture, according to study co-leader Professor Adam Brumm from Griffith’s Australian Research Centre for Human Evolution 

“The Toaleans were early hunter-gatherers 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,” Professor Brumm said.   

Professor Brumm’s team re-excavated Leang Panninge in 2019 to clarify the context of the burial and collect more samples for dating. Through radiocarbon dating the team was able to constrain the age of Bessé’ to between about 7300 to 7200 years old. 

Toalean artefacts have only been found in one small part of Sulawesi, encompassing about 6% of the total land area of the island, the world’s eleventh largest.  

“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,” said study co-author Adhi Agus Oktaviana, a researcher in Indonesia’s national archaeological research institute (Pusat Penelitian Arkeologi Nasional) and a doctoral candidate in the Griffith Centre for Social and Cultural Research. 

Archaeologists have long debated the origins of the Toaleans. But now analyses of ancient DNA from the inner ear bone of Bessé’ partly confirm existing assertions 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,” Professor Brumm said. 

Professor Adam Brumm.

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

The genomic analyses were led by Selina Carlhoff from the Max Planck Institute for the Science of Human History at Jena, Germany, under the supervision of Professor Cosimo Posth (University of Tübingen) and Professor Johannes Krause (Max Planck Institute for Evolutionary Anthropology, Leipzig). 

The results show that Bessé’ shares about half of her genetic makeup with present-day Indigenous Australians and people in New Guinea and the Western Pacific islands. This includes DNA inherited from the now-extinct Denisovans, distant cousins of 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,” Professor Posth said. 

The research could suggest that ancestors ofBessé’ were among the first modern humans to reach Wallacea, but instead of island hopping eastward to Sahul they remained in Sulawesi.  

If so, it may have been the forebears of Bessé’ who created the very old cave paintings found in South Sulawesi. As recently shown by Griffith University researchers, this rock art dates to at least 45,500 years ago and includes what may be the earliest known human representations of animals.   

But analyses also revealed something unexpected in the genome of Bessé’: a deep ancestral signature from an early modern human population of Asian origin. This group did not intermix with the predecessors of Aboriginal Australians and Papuans, suggesting it may have entered the region after the initial 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,” said Indonesian senior author Professor 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.” 

The researchers could detect no ancestry resembling that of Bessé’ in the DNA of people who live in Sulawesi today, who seem to largely descend from Neolithic farmers (‘Austronesians’) who arrived in the region from Taiwan some 3,500 years ago.  

This is not unexpected, given that the last traces of Toalean culture vanished from the archaeological record by the fifth century AD. The scientists do note, however, that more extensive genomic sampling of Sulawesi’s diverse population could reveal evidence for the genetic legacy of Toaleans.  

“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,” Professor Brumm said. 

Archaeological research conducted at Leang Panninge involved a formal collaboration between Griffith University and Indonesia’s national archaeological research institute, the Pusat Penelitian Arkeologi Nasional (ARKENAS). Also involved in the archaeological research were Griffith University PhD students Basran Burhan, Adhi Agus Oktaviana, David McGahan, Yinika Perston, and Kim Newman.