100-year-old controversy solved

Complete skull from a Hoabinhian person from Gua Cha, Malaysian Peninsula. Photo credit: Fabio LahrTwo competing theories about the human occupation of Southeast Asia have been debunked by ground-breaking analysis of ancient DNA extracted from 8,000 year-old skeletons. Southeast Asia is one of the most genetically diverse regions in the world, but for more than 100 years scientists have disagreed about which theory of the origins of the population of the area was correct.

One theory believed the indigenous Hòabìnhian hunter-gatherers who populated Southeast Asia from 44,000 years ago who later adopted agricultural practices independently, without the input from early farmers from East Asia. Another theory, referred to as the ‘two-layer model’ favours the view that migrating rice farmers from what is now China replaced the indigenous Hòabìnhian hunter-gatherers

Professor Dr Maude E Phipps and Dr Farhang Aghakhanian, human geneticists from the Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia were part of an international group of academics from around the world who collaborated on this new research, recently published in Science, one of the world’s top academic journal.

“Our ability to shed light on the peopling of South East Asia would not have been possible without a transdisciplinary research approach. Archaeology, Genomics and Bioinformatics are a very powerful combination and I am glad that we the researchers in Malaysia and our indigenous communities, have played major roles,” shared Prof Phipps.

Led by Professor Eske Willerslev, who holds positions both at St John’s College, University of Cambridge, and the University of Copenhagen, the study found that neither theory is completely accurate. It discovered that present-day Southeast Asian populations derive ancestry from at least four ancient populations.

DNA samples from human skeletal remains from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos and Japan dating back as far as 8,000 years ago were extracted for the study – scientists had previously only been successful in sequencing 4,000-year-old samples from the region.

The samples also included DNA from Hòabìnhian hunter-gatherers and a Jomon from Japan – a scientific first which revealed a long suspected genetic link between the two populations. In total, 26 ancient human genome sequences were studied by the group and compared with modern DNA samples from people living in Southeast Asia today including Jehai, the last of hunter gatherer indigenous group in Malaysia. The pioneering research is particularly impressive because the heat and humidity of Southeast Asia means it is one of the most difficult environments for DNA preservation, posing huge challenges for scientists.

Prof Willersley explained: “We put a huge amount of effort into retrieving ancient DNA from tropical Southeast Asia that could shed new light on this area of rich human genetics. The fact that we were able to obtain 26 human genomes, and shed light on the incredible genetic richness of the groups in the region today is astonishing.”

Prof Maude Phipps

Hugh McColl, PhD student at the Centre for GeoGenetics in the Natural History Museum of Denmark of the University of Copenhagen, and one of the lead authors on the paper, said: “By sequencing 26 ancient human genomes - 25 from South East Asia, one Japanese Jōmon - we have shown that neither interpretation fits the complexity of Southeast Asian history. Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting islands in South East Asia and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.”

Dr Fernando Racimo, Assistant Professor at the Centre for GeoGenetics in the Natural History Museum of the University of Copenhagen, the other lead author, said: “The human occupation history of Southeast Asia remains heavily debated. Our research spanned from the Hòabìnhian 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.”

Some of the samples used in the two and a half year study were from The Duckworth Collection, University of Cambridge, which one of the world's largest repositories of human remains. Professor Marta Mirazón Lahr, Director of the Duckworth Laboratory and one of the authors on the paper, said: “This study tackles a major question in the origins of the diversity of Southeast Asian people, as well as on the ancient relationships between distant populations, such as Jomon and Hòabìnhian foragers, before farming. The fact that we are learning so much from ancient genomes, such as the one from Gua Cha, highlights the importance of amazing collections such as the Duckworth.”

Dr Fabrice Demeter, one of the lead authors, from the Centre for GeoGenetics in the Natural History Museum of the University of Copenhagen and the National Museum of Natural History, Ecoanthropology and Ethnobiology, Musee de l'Homme, Paris, said: “Of particular importance to the study was Pha Faen, an 8,000 year old Hòabinhian skeleton found in a cave in Laos, sampled in collaboration with Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Laos. This sample, along with the Gua Cha from Malaysia anchors the study deeper in the past than has previously been possible.”

Other Malaysian researchers were Professor Dato Dr Mohd Mokhtar Saidin and Shaiful Shahidan, archaeologists from Universiti Sains Malaysia.

For full journal article, please click here.