Ancient DNA Offers Insight on Origins of Southeast Asia’s Present-Day Population

Researchers sequenced 26 genomes using DNA samples dating as far back as 8,000 years

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An 8,000-year-old skull found in Gua Cha, Malaysia, provided DNA used in the study Fabio Lahr

When it comes to the ancient origins of Southeast Asia’s present-day population, two dominant theories have divided scientists for more than a century. One posits that the indigenous Hòabìnhian hunter-gatherers, who populated the region from 44,000 years ago, independently developed agricultural practices. The other, known as the “two-layer model,” argues that migrating rice farmers from the area constituting present-day China replaced the Hòabìnhian.

Neither theory is wholly correct, according to new research recently published in Science. Instead, an international team of scientists found that the genetic diversity of the region is more complex than initially suspected, with Hòabìnhian, East Asian, Southeast Asian and Vietnamese populations all contributing to the mix.

A press release states that the scientists spent two and a half years tracking down samples of ancient DNA, which came from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos and Japan. In total, the researchers examined 43 ancient skeletons to sequence 26 ancient human genomes, which were then compared with DNA from modern-day Southeast Asians.

The complete skull of a Hòabìnhian individual found in Gua Cha, Malaysia, and an 8,000-year-old Hòabìnhian skeleton discovered in a cave in Pha Faen, Laos were among the samples; they represent the region’s oldest successfully sequenced DNA, as the heat and humidity of Southeast Asia tend to prevent DNA preservation. Previously, scientists had only been able to sequence 4,000-year-old samples from the region.

The team’s findings have enabled them to assemble a DNA portrait of Southeast Asia's ancient humans, suggesting that contemporary Southeast Asians can trace their ancestry to at least four ancient populations.

In the statement, Hugh McColl, PhD student at the University of Copenhagen and one of the lead authors of the paper, notes that “both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity,” with migration from other regions further diversifying the gene pool.

Science’s Peter Bellwood adds that the original Pleistocene hunter-gatherers, as emphasized by the Hòabìnhian theory, were the main occupants of Southeast Asia until roughly 5,000 to 4,000 years ago, when mid-Holocene Neolithic farmers, as emphasized by the two-layer model, migrated from southern China to the mainland and islands of Southeast Asia.

According to the study, “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 new findings, therefore, don’t so much debunk the two dominant theories as refine and combine them. Although the Hòabìnhians did not remain wholly distinct from incoming migrant populations, they were not wiped out by the new settlers. Instead, the original inhabitants mixed with the new, paving the way for today's richly diverse Southeast Asian population.

Correction, July 16, 2019: This piece has been updated to clarify when indigenous Hòabìnhian hunter-gatherers first populated the region.

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