The 37,000-year-old skull was not related to Aboriginal Australians, researchers found.
The ancient cranium fragments nicknamed "Deep Skull" by anthropologists were discovered 50 years ago on the island of Borneo and were believed to belong to the first human species who arrived on the island, the Aboriginal Australians.
However, a recent study of the bones revealed that they belonged to another group of modern humans.
"Our analysis overturns long-held views about the early history of this region," Darren Curnoe, lead researcher and associate professor and director of the University of New South Wales Palaeontology, Geobiology and Earth Archives Research Centre (PANGEA), said in a press release.
"We've found that these very ancient remains most closely resemble some of the Indigenous people of Borneo today, with their delicately built features and small body size, rather than Indigenous people from Australia," Curnoe added.
Anthropologists had thought the ancient bone specimen first discovered in the Niah Cave in Sarawak in Borneo belonged to a teenage boy related to the early ancestors of Australian Aborigines, particularly Tasmanians. They were believed to have spread from south Asia through the Pacific and into Australia about 45,000 to 60,000 years ago.
However, recent discoveries revealed that the early settlers of Borneo were not the relatives of the Australian Aborigines.
It turned out that the Deep Skull belonged to a middle-aged female, not a teenage boy, and resembled people in the northern parts of South-East Asia.
"Our discovery that the remains might well be the ancestors of Indigenous Bornean people is a game changer for the prehistory of South-East Asia," Ipoi Datan, director of the Sarawak Museum Department, said in a statement.
According to the researchers, the Deep Skull discovery also concluded the "two layer" hypothesis in which South-East Asia is thought to have been initially settled by people related to Indigenous Australians and New Guineans, who were then replaced by farmers from southern China thousands of years ago.
The study, which was published in Frontiers in Ecology and Evolution, showed that the earliest people in Borneo were much more like the indigenous people living there today, and that the indigenous group was not replaced by migrating farmers but have instead learned to adopt the new farming culture 3,000 years ago.