DNA testing

Where do Southeast Asians come from?

A fascinating study has potentially unlocked the secret of the origins of Southeast Asians, resolving a long-standing debate on the prehistory of the region

Uffe Wilken
July 12, 2018
Where do Southeast Asians come from?
Skull from a Hòabìnhian person from Gua Cha archaeological site, Malaysian Peninsula Photo: Fabio Lahr

Southeast Asia is a melting pot of genetic diversity. One of the big questions about the origins of this diversity has until now been unresolved. In the groundbreaking study The Prehistoric Peopling of Southeast Asia, published in the scientific journal Science, 43 researchers from Thailand, Japan, Laos, Malaysia, Indonesia, France, Germany, the UK and Denmark shed light on this question.

Two main competing theories about the peopling of Southeast Asia have dominated academic discussions for a long time. Both are based on the fact that the first migration into the region consisted of descendants from the first people who left Africa 60,000 to 70,000 years ago. But from there, the theories take their own course.

One theory says that people from the Hòabìnhian culture – the original hunter-gatherers that peopled Southeast Asia about 44,000 years ago – gradually developed a farming society. Another theory says farmers coming from present-day China about 4,000 years ago pushed out the Hòabìnhians.

Decedents of the Hòabìnhians were thought to have remained in isolated pockets in Southeast Asia where today there are indigenous people with physical characteristics similar to those of African pygmies and Australian Aboriginals in places like the Andaman Archipelago and the Philippines.

However, according to the study’s leader, Professor Eske Willerslev from the University of Cambridge and the University of Copenhagen, neither of the two theories can fully explain the big genetic diversity found in Southeast Asia today.

The four migrations

Extracting ancient DNA from human teeth and bones buried for thousands of years in humid tropical environments is no easy task, as DNA degrades fast under these conditions. However, the researchers managed to extract samples from 8,000 year old ancient human remains from Thailand, Indonesia, the Philippines, Malaysia, Laos, Japan and Vietnam, and compared it to DNA from present-day Southeast Asians. The results showed a more complex picture of the origin of the genetic diversity. According to the researchers, the genetic pattern found in Southeast Asia today has been formed by four migrations.

The first was by descendants of the first people who migrated out of Africa and settled in Southeast Asia about 40,000 years ago. These Hòabìnhians were widespread across Southeast Asia until 4,000 years ago, when the second migration – farmers from present-day China – migrated into the area, bringing rice with them.

The cave at Ujong Karong near Takengon, northern Sumatra, Indonesia, where ancient DNA was extracted from skeletal remains. The cave is situated at the foot of the hills Photo: Uffe Wilken

A third migration, originating in Taiwan and spreading Austronesian languages throughout Southeast Asia, is said to have occurred around 4,000 years ago, supported by the distinctly Austronesian ancient individuals present in the northern Philippines some 2,000 years ago. Finally, the arrival of a new East Asian genetic component centered in northern Vietnam historically accords with the imperial expansion of the Han Chinese.

“The populations that merged to form present-day Southeast Asians were from two genetic lineages that diverged a long way back in time,” said PhD student Hugh McColl of the University of Copenhagen, one of the leading authors of the study.

“The first are the Hòabìnhians, who we find are genetically most similar to the Onge from the Andaman Islands, and the second were the incoming farmers from the north, more closely related to the 40,000-year-old East Asian Tianyuan,” he added.

The researchers also found archaeological evidence connecting these populations.

“The diversity we refer to is genetic, although we do detect parallels with theories based on language and pottery,” said McColl. “Of the ancient individuals, the most genetically divergent populations were the Hòabìnhian hunter-gatherers and the East Asian farmers. However, within the multiple waves of migration from the north, there was also considerable genetic diversity.”

So what happened with the Hòabìnhians when the East Asian farmers arrived 4,000 years ago? Were they squeezed out of the region? Not quite. The DNA analyses show that the Hòabìnhians and migrating farmers interbred, both contributing to the diverse Southeast Asian gene pool.

This new study could just be the beginning of a much more complex scholarship to come, according to McColl.

“Previously, theories have been based on phenotypic differences (i.e., your physical appearance) and language within Southeast Asia, and more recently with present-day genetic data,” he said.

“Here, the ancient DNA method provides snapshots back in time, allowing us to directly investigate the complexities of Southeast Asia’s genetic history. Our work stands as a valuable starting dataset for future studies investigating Southeast Asia’s history.”





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