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Ancient Genomes Point to Three Waves of Human Migration Into Southeast Asia

NEW YORK (GenomeWeb) – According to a new analysis of ancient genomes from Southeast Asia, three waves of human migration produced the genetic landscape of the region.

While the humid environment there has made it difficult to analyze ancient DNA, an international team of researchers was able to isolate and analyze the genomes of 18 individuals dating back between 1,700 years and 4,100 years ago from what is now Vietnam, Myanmar, Thailand, and Cambodia.

As they reported today in Science, the researchers found that hunter-gatherers first arrived in Southeast Asia about 45,000 years ago, and farmers from China arrived during the Neolithic Period about 4,500 years ago, followed by Bronze Age migrations from China about 3,000 years ago. This, the researchers noted, mirrors migrations in Europe.

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

He and his colleagues analyzed samples obtained from five sites in Southeast Asia: a Neolithic sample from Man Bac in Vietnam, a Bronze Age sample from Nui Nap in Vietnam, a Late Neolithic/Bronze Age sample from Oakaie in Myanmar, a Late Neolithic sample from Ban Chiang in Thailand, and an Iron Age sample from Vat Komnou in Cambodia. In all, they screened 350 next-generation sequencing libraries generated from bone samples from 146 different individuals.

In an initial principal components analysis, the researches compared their samples to set of diverse modern-day non-Africans and found that most of the ancient samples clustered with present-day Chinese and Vietnamese individuals. A few of the samples, the researchers noted, skewed slightly more toward Papuans and to the Onge people of the Andaman Islands in the Bay of Bengal.

When they then compared the ancient individuals to only modern Southeast Asian individuals, they found that the Man Bac, Ban Chiang, and Vat Komnou samples clustered most closely with modern-day Austroasiatic speakers, while the Nui Nap samples fell closer to modern Vietnamese and Dai individuals, and the Oakaie samples grouped near modern Myanmar and Sino-Tibetan speakers' samples.

Similarly, outgroup f3-statistic analyses found the Man Bac, Ban Chiang, and Vat Komnou shared the most alleles with modern Austroasiatic speakers, while the Nui Nap shared the most alleles with Austronesian speakers like the Dai and Kinh and the Oakaie with Sino-Tibetan speakers.

Lipson and his colleagues then constructed admixture graph models to test the relationships between their ancient samples and modern-day groups. Through this, they found the ancient Man Bac and present-day Nicobarese and Mlabri have ancestry stemming from a Southeast Asian farmer-related source as well as from a deeply diverging eastern Eurasian source. A model of these ancestry events suggested it involved a shared ancestral admixture event, followed by the divergence of the Man Bac from present-day Austroasiatic speakers, and a wave of deep ancestry into the Nicobarese.

Similarly, they found western Indonesians had ancestry stemming from Austronesian-, Austroasiatic-, and Papuan-related sources, while the Juang of eastern India had ancestry from a western Eurasian, deep eastern Eurasian, and Austroasiatic clades.

From this, the researchers pieced together a scenario in which early Austroasiatic-speaking migrants from southern China brought farming to mainland Southeast Asia during the Neolithic where they mixed with local hunter-gatherers. Then, during the Bronze Age, another wave of migrants arrived in Myanmar from China about 3,000 years ago, reaching Vietnam about 2,000 years ago and Thailand about 1,000 years ago.

This pattern of genetic changes accompanying cultural shifts resembles what has reported to have occurred in Europe, the researchers noted, with one exception: Ancestral diversity in Europe has been lost over time, while it remains in Southeast Asia.

"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," Harvard's David Reich, a co­-senior author of the paper, added. "Whereas in Europe, no one living today has more than a small fraction of ancestry from the European hunter­-gatherers."