First Recovery Of Ancient Human DNA From Evolutionary Hotspot In Indonesia


Stephen Luntz


Stephen Luntz

Freelance Writer

Stephen has a science degree with a major in physics, an arts degree with majors in English Literature and History and Philosophy of Science and a Graduate Diploma in Science Communication.

Freelance Writer

Besse's cave

Leang Panninge cave in the southern Sulawesi highlands, Indonesia, has provided the first ancient human DNA from this part of the world where many human species met. Image Credit: Leang Panninge Research Project

Human DNA more than 7,000 years old has been recovered from Sulawesi, marking the first time this has been achieved from the island South-East Asia. Besides the remarkable technical achievement, this could help unravel the complex history of human evolution in the area, where many populations met and interbred. It could also improve our understanding of an exceptional and puzzling culture present in the area around this time.

Although humans first evolved in Africa, some of the most interesting aspects of our subsequent development took place on the islands of South-East Asia. That fact has been revealed both from the DNA of people living there today and in fossils that indicate the presence of at least three species of early humans. However, a lack of ancient DNA has left scientists puzzling over what occurred between these people, and how it affects us today.


Besides extinct species such as Homo floresiensis and Homo luzonensis, island South-East Asia was colonized by several waves of modern humans, and a paper in Nature reports a discovery that provides unprecedented insight into these events. DNA has been extracted from a skeleton buried around 7,200 years ago in the Leang Panninge Cave, South Sulawesi, not far from where the world’s oldest depiction of hunting was found two years ago.

Hot, humid climates degrade DNA quickly, so it has been considered almost impossible to learn anything about the peoples who inhabited this area through fossil DNA. However, recently ancient DNA has been sequenced from human fossils in places with similar climates, so Professor Adam Brumm of Griffith University and colleagues decided to try to do the same with the Lean Panninge skeleton, known as Bessé.

Bessé’s skeleton as it was found. Hasanuddin University, Indonesia

Although 2 percent of Bessé’s DNA survived well enough to be sequenced, this was still sufficient to reveal 2.2 percent Denisovan inheritance. This suggests Bessé was descended from the same people who went on to colonize New Guinea and Australia. However, she also carried genes from an unknown Asian population, indicating there were at least two waves of colonization of Indonesia prior to the Austronesia arrival 4,000 years ago, with Bessé descended from both.

From 8,000 to 1,500 years ago a people known as the Toaleans left small tools across southern Sulawesi that are unlike anything seen elsewhere in the world. These included serrated stones known as Maros points that may have been used as arrowheads. Astonishingly, there is no evidence of trade between the Toaleans and their neighbors elsewhere on Sulewesi  or nearby islands, although some archaeologists speculate they had contact with Australia’s Kimberly region, where somewhat similar tools appeared at the time.

Typical Maros points, made by the Toalean culture. Inexplicably, there is no evidence of trade between Toaleans and their neighbors, or the interchange of ideas. Image Credit: Yinika L Perston

“We were able to assign the burial at Leang Panninge to that culture,” Brumm said in a statement. “This is remarkable since it is the first largely complete and well preserved skeleton associated with the Toalean culture.” Bessé’s DNA is the first indication we have of where the Toaleans fit in the human family tree.

Brumm told IFLScience Bessé’s DNA does not match any known surviving population, but; “There is a lot of ethnic diversity on Sulewesi and it has been very poorly sampled. The Toalean culture is gone, but it is entirely possible their genes persisted [mixed with those of later arrivals].”

Bessé was 17-18 when she died, with no severe injuries or other obvious causes of death.

Fragmentary remains of the human skull, whose preservation allowed the extraction of sequencing Ancient DNA from island South East Asia's tropical climate. Credit: Hasanuddin University, Indonesia

Several factors made the sequencing of Bessé’s genome possible. The DNA was extracted from the petrous bone at the base of the skull. Named for its extreme hardness, this part of the skeleton is precious to archaeologists for how well it preserves material inside. Moreover, Bessé was buried in the Sulawesi highlands, where the climate is cooler than near the coast.


“We’re keen to find out if this was an absolute fluke of preservation, or if we can find even older DNA in the highlands,” Brumm told IFLScience. “The past is an exciting place.”



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