The first whole-genome analysis of ancient human DNA from Southeast Asia, defined as the area east of India and south of China, identifies at least three major waves of human migration into the region over the last 50,000 years, each shaping the genetics of Southeast Asia ‘to a remarkable extent.’ The findings appear in the journal Science.

Southeast Asia has a complex history of human occupation, yet studying this history through genetics has remained a challenge because, for one, its humid and tropical environment presents unfavorable conditions for DNA preservation.

As such, hypotheses based on archaeological findings — predicting the human origins of cultural shifts brought on by the introduction of farming, for example — remain unresolved by genetic studies.

“A very important part of the world is now accessible for ancient DNA analysis. It opens a window into the genetic origins of the people who lived there in the past and those who live there now,” said study first author Dr. Mark Lipson, of Harvard Medical School.

Dr. Lipson and co-authors extracted and analyzed DNA from the remains of 18 people who lived between about 4,100 and 1,700 years ago (from the Neolithic period to the Iron Age) in what are now Vietnam, Thailand, Myanmar and Cambodia.

With additional support from archaeological and linguistic data, the scientists identified several major waves of genetic mixture indicative of specific migration events.

They found that the first migration took place about 45,000 years ago, bringing in people who became hunter-gatherers.

Then, during the Neolithic period, around 4,500 years ago, there was a large-scale influx of people from China who introduced farming practices to Southeast Asia and mixed with the local hunter-gatherers. People today with this ancestry mix tend to speak Austroasiatic languages, leading the team to propose that the farmers who came from the north were early Austroasiatic speakers.

The study authors also found that subsequent waves of migration during the Bronze Age, again from China, arrived in Myanmar by about 3,000 years ago, in Vietnam by 2,000 years ago and in Thailand within the last 1,000 years. These movements introduced ancestry types that are today associated with speakers of different languages.

The identification of three ancestral populations echoes a pattern first uncovered in ancient DNA studies of Europeans, but with at least one major difference: much of the ancestral diversity in Europe has faded over time as populations mingled, while Southeast Asian populations have retained far more variation.

“People who are nearly direct descendants of each of the three source populations are still living in the region today, including people with significant hunter-gatherer ancestry who live in Thailand, Malaysia, the Philippines and the Andaman Islands,” said senior author Professor David Reich, of Harvard Medical School and the University of Vienna.

“Whereas in Europe, no one living today has more than a small fraction of ancestry from the European hunter-gatherers.”

“The high diversity of Southeast Asia today can be partly explained by the fact that farmers arrived much more recently than in Europe, leaving less time for populations to mix and genetic variation to even out,” he added.

Also unexpected were the linguistic implications raised by analyses of the ancestry of people in western Indonesia.

“The evidence suggests that the first farmers of western Indonesia spoke Austroasiatic languages rather than the Austronesian languages spoken there today. Thus, Austronesian languages were probably later arrivals,” Professor Reich said.

“Additional samples from western Indonesia before and after 4,000 years ago should settle the question.”

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Mark Lipson et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science, published online May 17, 2018; doi: 10.1126/science.aat3188