Ancient DNA reveals new clues on genetic history of Southeast Asia

Groundbreaking study using DNA from 8,000-year-old skeletons reveals modern Southeast Asians descend from FOUR different ancient populations

  • Researchers took DNA from 26 ancient samples, some dating back 8,000 years
  • Skeletons from Malaysia, Thailand, Philippines, Vietnam, Indonesia, Laos, Japan
  • Study found Hòabìnhian hunter-gatherers mingled with East Asian migrants
  • This included Austroasiatic, Kradai, and Austronesian language speakers

Scientists have disagreed on the true origins of modern Southeast Asian populations for more than a century.

Now, a new DNA analysis on genetic material from 8,000-year-old skeletons could finally put the debate to rest – and if the findings are correct, it means neither of the two leading theories were entirely accurate.

According to a new study, the genetic diversity of Southeast Asia can be traced back thousands of years to the intermingling of the original Hòabìnhian hunter-gatherers and waves of migrants from three distinct cultures.

The researchers collected DNA from a total of 26 ancient individuals, and compared these with groups living in Southeast Asia today. The skeletal remains included individuals from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos, and Japan. A Hòabìnhian skull is shown

The international study, published in the journal Science, suggests the modern population has ties to at least four ancient populations.

It’s previously been suggested that the Hòabìnhian hunter-gatherers, an indigenous group who populated Southeast Asia beginning about 44,000 years ago, did not miz with the early famers from East Asia.

Instead, they were thought to have developed their own agricultural traditions.

The second leading theory, the ‘two-layer model,’ proposed migrating rice farmers from what is now China moved in and replaced the indigenous group.

But according to the new study, the truth is far more complex.

‘The evidence described here favors a complex model including a demographic transition in which the original Hòabìnhians admixed with multiple incoming waves of East Asian migration associated with the Austroasiatic, Kradai, and Austronesian language speakers,’ the researchers wrote in the study.

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The researchers collected DNA from a total of 26 ancient individuals, and compared these with groups living in Southeast Asia today.

The skeletal remains included individuals from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos, and Japan.

Previously, scientists have only been able to successfully sequence the genomes from 4,000-year-old samples from the region; the heat and humidity of Southeast Asia stands as a difficult challenge for DNA preservation.

The new group dated as far back as 8,000 years.

The analysis revealed, for the first time, a link between the Hòabìnhian hunter-gatherers and the Jomon, from Japan.

‘We put a huge amount of effort into retrieving ancient DNA from tropical Southeast Asia that could shed new light on this area of rich human genetics,’ said Professor Eske Willerslev, of St John’s College, University of Cambridge, and the University of Copenhagen.

‘The fact that we were able to obtain 26 human genomes and shed light on the incredible genetic richness of the groups in the region today is astonishing.’

According to the researchers, the new findings paint a much more complex history of Southeast Asian population.


An analysis of 40,000-year-old fossils is helping scientists retrace the earliest steps of our species and reveal the diverse genetic history of East Asians.

The fossils belong to the Tianyuan Man, who was thought to be the offspring of a Neanderthal and an ancient human.

But the new analysis has revealed that he only has traces of Neanderthal DNA, and was in fact an ancient human and a distant relative of people who live in East Asia and South America today.  

The new study marks the earliest ancient DNA from east Asia, and the first ancient genome-wide data from China.

Shown here is a chart of what we know about human and Neanderthal migration

Until now, east Asia has remained somewhat of a mystery, with warmer climates in the making it more difficult to extract ancient genetic material from fossils. 

The results show a complicated history of intermingling between distinct east Asian groups of early modern humans. 

Researchers found that the Tianyuan Man is most closely related to modern inhabitants of the region, including China, Japan and Korea, as well as southeast Asia and Australasia. 

However, he was not an ancestor of those populations.

Instead, he is a distant cousin, related to modern Asians but not part of the same direct lineage.

This suggests ancient populations moved around a lot and intermixed, with some leaving offspring who would go on to populate far flung corners of Siberia, North America and its sister continent to the south.

Others, like Tianyuan Man, have since died out, the only mark of their presence found in their fossilised remains. 

The region is one of the most genetically diverse in the world, and can now be linked to at least four ancient populations.

‘By sequencing 26 ancient human genomes – 25 from South East Asia, one Japanese Jomon – we have shown that neither interpretation fits the complexity of Southeast Asian history,’ says Hugh McColl, PhD student at the Center for GeoGenetics in the Natural History Museum of Denmark of the University of Copenhagen.

‘Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting islands in South East Asia and Vietnam.

‘Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.’

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