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The theories of the human habitation of Southeast Asia, a critical crossroads of multiple continents, have always competed. Whether the ancient hunter-gatherers adopted and developed their own agriculture, or rice farmers moved in and essentially took over the region, has been a major anthropological debate for decades.

Skeletal DNA has continued to make things more complicated.

A paper in Science in May by David Reich of Harvard and dozens of other scientists found that three waves of settlement have progressively changed the makeup of Southeast Asian societies.

Now, a new paper also in Science, by a team from Cambridge and dozens of other institutions from around the world finds that four ancient populations went into the “melting pot” of the region, from the Hoabinhian hunter-gatherers who appeared around 44,000 years ago, to the early farmers from parts north like modern-day China.

“The human occupation history of Southeast Asia remains heavily debated,” Fernando Racimo, of the Natural History Museum of the University of Copenhagen, added. “Our research spanned from the Hoabinhian to the Iron Age and found that present-day Southeast Asian populations derive ancestry from at least four ancient populations. This is a far more complex model than previously thought.”

The skeletons were recovered from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos and Japan.

They were able to shotgun-sequence the genomes from 8,000-year-old samples, despite the difficulties posed by the heat and humidity on recovering biological specimens, the researchers said.

Eske Willerslev, lead author of the University of Cambridge and the University of Copenhagen, called the feat “astonishing” in a statement released about the work.

Overall, the researchers produced 26 genomes, including one from the ancient Jomon populace of modern-day Japan.

The branches of the tree of humanity in the region showed overlap, and significant complexity, according to Hugh McColl of the University of Copenhagen. The two dominating theories have thus not captured the essence of the “melting pot,” McColl said.

One group included Hoabinhians from Laos that were clustered clesest with Onge peoples from the Andaman Islands. Another group contained late Stone Age and early Bronze Age from Vietnam—Laos and Malaysia—that was related to modern Austroasiatic populations like the Mlabri and Htin. Another ground from Malaysia and the Philippines showed most similarities to modern-day Austronesians. Another grouping centered around Indonesians, ancient and modern, and yet another was from northern Vietnam, with DNA most similar to modern Dai, Amis and Kradai speakers from around Thailand.

“The evidence described here favors a complex model including a demographic transition in which the original Hoabinhians admixed with multiple incoming waves of East Asian migration associated with the Austroasiatic, Kradai and Austronesian language speakers,” according to the paper.

The previous study by Harvard and others analyzed 146 individuals from five ancient sites in Vietnam and Thailand, spanning millennia.

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