Ancient DNA testing solves 100-year-old controversy in Southeast Asian prehistory

July 6, 2018, University of Cambridge
Skull from a Hòabìnhian person from Gua Cha archaeological site, Malaysian Peninsula. Credit: Fabio Lahr

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 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.

Academics from around the world collaborated on new research just published in Science which found that neither theory is completely accurate. Their study discovered that present-day Southeast Asian populations derive ancestry from at least four ancient populations.

DNA from human skeletal remains from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos and Japan dating back as far as 8,000 years ago was 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, revealing a long suspected genetic link between the two populations.

In total, 26 ancient human genome sequences were studied by the group and they were compared with modern DNA samples from people living in Southeast Asia today.

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.

Professor Eske Willerslev, who holds positions both at St John's College, University of Cambridge, and the University of Copenhagen, led the international study.

He 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."

Hugh McColl, Ph.D. 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 J?mon—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 is 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."

Explore further: Scientists analyze first ancient human DNA from Southeast Asia

More information: Hugh McColl et al, The prehistoric peopling of Southeast Asia, Science (2018). DOI: 10.1126/science.aat3628

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Zzzzzzzz
not rated yet Jul 06, 2018
Reality is ALWAYS more complex than we imagined.....
Surveillance_Egg_Unit
3.4 / 5 (5) Jul 07, 2018
...said: "By sequencing 26 ancient human genomes—25 from South East Asia, one Japanese J?mon—...

How strange that the authors of the paper, with all their gray matter in gear, weren't able to do a simple spell check for "Jomon". It is, after all, coming from the University of Cambridge. So why the question mark?

Jomon may be connected with the indigenous people of Hokkaido, the Ainu. Although the Ainu have been described by some past researchers as having a few similarities to Caucasoids, the majority say that they have no ethnic relationship to the White race.
Thorium Boy
1.7 / 5 (6) Jul 07, 2018
More and more proof Africa was not the only place humans arose.
zz5555
4.8 / 5 (4) Jul 07, 2018
How strange that the authors of the paper, with all their gray matter in gear, weren't able to do a simple spell check for "Jomon". It is, after all, coming from the University of Cambridge. So why the question mark?

The authors of the paper didn't write this article, it would have been written by some PR person from Cambridge. The authors may not have seen this article, or the copy they saw may not have had this typo. The typo may not have existed when the paper was still at Cambridge - it may have been introduced after leaving Cambridge. Elsewhere, it's apparent the '?' Should be an 'ō'. Some software probably choked on this 'ō' and replaced it with a ?. I'm not sure why, though, you would expect a spell checker to pick up Jōmon.
jonesdave
3.5 / 5 (11) Jul 07, 2018
More and more proof Africa was not the only place humans arose.


Errrr, no, it isn't.
wailuku1943
5 / 5 (3) Jul 07, 2018
Speaking as a person who designs books, the ? problem most likely is a font problem (sure, that's "software" in the largest sense). Some fonts will not display the macron -- they just won't. The original must have been OK, but down the line there was a font substitution and no one noticed -- or if they did, they were powerless to do anything about it (meaning to change the font).
rrwillsj
1 / 5 (2) Jul 07, 2018
There are a multitude of error-tainted books & publications. Working backwards through the cascade of printed mistakes.

The writers are concentrating on getting their ideas down before they forget the intended plotline.

Editors can be roughly divided into three groups. The smallest number are those with a Classical Liberal Arts education. They work for exclusive academic-oriented publishing houses and literary societies.

The next group are professional editors. They are very expensive too hire to edit your book. You might try begging. Good luck with that.

The great majority of editors bring to mind the old joke: "What do you call the lowest-ranking medical school graduate? Doctor!"

They generally wind up as contracted labor for some mass-publishing conglomerate.

Inundated with manuscripts dumped on them to process. With all the finesse of an industrial assembly line. They do not get paid to read. They get paid to get the product assembled & out the door.
granville583762
3 / 5 (6) Jul 08, 2018
Out of China, the Chinese monkey and Chinese humans
You can tell where a particular tribe of humans come from by looking at their closest relatives monkeys that live on the Chinese country side in close knit groups grazing where the Chinese natives have retained their distinctive facial and physical traits from their Chinese monkey relatives
China is a very large place and we live in small groups as we have throughout our animal evolution,
It is total arrogance to suggest monkeys and humans evolved from one planet in the entire universe and not only that, but on one small place on planet Earth and nowhere else.
yep
5 / 5 (2) Jul 08, 2018
Aaaaa Yeah, Granville pass whatever your smoking over here, must be good.
Surveillance_Egg_Unit
4.2 / 5 (5) Jul 09, 2018
Out of China, the Chinese monkey and Chinese humans
You can tell where a particular tribe of humans come from by looking at their closest relatives monkeys that live on the Chinese country side in close knit groups grazing where the Chinese natives have retained their distinctive facial and physical traits from their Chinese monkey relatives
China is a very large place and we live in small groups as we have throughout our animal evolution,
It is total arrogance to suggest monkeys and humans evolved from one planet in the entire universe and not only that, but on one small place on planet Earth and nowhere else.

says granville

Perhaps you are either not aware, of have forgotten that the comments in these threads remain available on the 'net for anyone to read, so it is a mystery to me (and I'm sure others) as to your reason(s) for comparing Chinese people to monkeys.
-CONTINUED-
Surveillance_Egg_Unit
3.8 / 5 (4) Jul 09, 2018
-CONTINUED-
The rest of my comment has disappeared.
But what you said about Chinese and comparing them to monkeys is very racist. You should rethink your opinions on this matter as wherever you have gotten such an idea is totally wrong. Not even amusing in the least.
granville583762
5 / 5 (3) Jul 10, 2018
Being referred to one descendants
Surveillance_Egg_Unit> But what you said about Chinese and comparing them to monkeys is very racist

I might agree with you on that one Surveillance_Egg_Unit, If I was a Monkey and referred to being from your ancestry Surveillance_Egg_Unit, I would be mortally offended and I would request an audience from your grand creator for my money back!
Surveillance_Egg_Unit
3.7 / 5 (3) Jul 10, 2018
I might agree with you on that one Surveillance_Egg_Unit, If I was a Monkey and referred to being from your ancestry Surveillance_Egg_Unit, I would be mortally offended and I would request an audience from your grand creator for my money back!


WRT my beliefs, there is no such monkey/ape ancestry due to the creation of the first man (and woman) having been created separately from the animals that were in the region at the time. The animals evolved from the first single-celled life forms in the seas. Humans did not. And humans also did not evolve from the Homo erectus, etc. life forms that preceded them. Those Homo life forms were only experimental models who eventually failed. Thus, the Creator chose to create a different kind of life form - a human that was far less animal and was capable of speech, comprehension, innovation, and had other traits which animals did not have...and could never have.
Surveillance_Egg_Unit
3 / 5 (4) Jul 10, 2018
-CONTINUED-
The Creator endowed the first couple of Homo Sapiens with a Spiritual Soul, something that animals lack. The Soul is what sets humans apart from the animals, even though percentages of DNA/RNA is shared between animals and man. There is much more, but it is too lengthy to include in 1000 characters.
I know that the British once were notorious racists wrt India, China and other nonWhite peoples. But racism is a form of low character and a false sense of superiority in those who practice it.
antialias_physorg
3 / 5 (4) Jul 10, 2018
How strange that the authors of the paper, with all their gray matter in gear, weren't able to do a simple spell check for "Jomon". It is, after all, coming from the University of Cambridge. So why the question mark?

If you go to the original (which is linked at the bottom of the article) you will notice that it is spelled correctly. Strange text formats /also exponents) often does not survive the copy&paste approach employed by physorg.

So before you accuse people of not using their gray matter - maybe you should start using yours?
Surveillance_Egg_Unit
4 / 5 (4) Jul 11, 2018
So before you accuse people of not using their gray matter - maybe you should start using yours?

says anti_p

You seem perturbed over my observation of the author(s) failing to do a spell check. If you had bothered to read my comment more carefully, you might have noticed that I did NOT accuse "people" of not using their gray matter. I said that they weren't able to do a spell check.

Well, of course the Abstract is going to contain the proper spelling of Jomon. There was never any doubt about a publication missing such an error and not correcting it before publishing.

In case you were not aware, I was referring to the Physorg article and the error contained therein since that is where the error occurred.
Two commenters, zz5555 and wailuku1943 have already provided their explanations for the error and the probable cause, and I thank them both
rrwillsj
1 / 5 (1) Jul 11, 2018
Great! Now we got the incredibly uncredible of credulous irrational fantasists arguing over which of them has the more ridiculous plagiarized mythical religious belief to belabor us all with in their evangelizing zeal.

Monotonous stupidity resulting from tedious ignorance. Finally achieving mindless ennui.
TheGhostofOtto1923
1 / 5 (1) Jul 12, 2018
the incredibly uncredible of credulous irrational fantasists arguing over which of them has the more ridiculous plagiarized mythical religious belief to belabor us all with in their evangelizing zeal
"if their speech is so odd, how come smart people get taken in by them? Why do we fail to pick up the inconsistencies?

"Part of the answer is that the oddities are subtle so that our general listening mode will not normally pick them up. But my own experience is that some of the "skipped" or oddly arranged words, or misused words are automatically reinterpreted by OUR brains in the same way we automatically "fill in the blank" space on a neon sign when one of the letters has gone out. We can be driving down the road at night, and ahead we see M_tel, and we mentally put the "o" in place and read "Motel." Something like this happens between the psychopath and the victim..."

Your posts are mostly blank spots you freeking psychopath.

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