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Author Topic: Data from a 40,000-year-old man in China reveals complicated genetic history of Asia
Doug M
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CHINESE ACADEMY OF SCIENCES HEADQUARTERS—The biological makeup of humans in East Asia is shaping up to be a very complex story, with greater diversity and more distant contacts than previously known, according to a new study in Current Biologyanalyzing the genome of a man that died in the Tianyuan Cave near Beijing, China 40,000 years ago. His bones had enough DNA molecules left that a team led by Professor FU Qiaomei, at the Molecular Paleontology Lab at the Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), could use advanced ancient DNA sequencing techniques to retrieve DNA from him that spans the human genome.

Though several ancient humans have been sequenced in Europe and Siberia, few have been sequenced from East Asia, particularly China, where the archaeological record shows a rich history for early modern humans. This new study on the Tianyuan man marks the earliest ancient DNA from East Asia, and the first ancient genome-wide data from China.

The Tianyuan man was studied in 2013 by the same lab. Then, they found that he showed a closer relationship to present-day Asians than present-day Europeans, suggesting present-day Asian history in the region extends as far back as 40,000 years ago. With new molecular techniques only published in the last two years, Professor FU and her team, in a joint collaboration with experts at the Max Planck Institute of Evolutionary Anthropology and UC Berkeley, sequenced and analyzed more regions of the genome, particularly at positions also sequenced in other ancient humans.

Since 2013, DNA generated from ancient Europeans has shown that all present-day Europeans derive some of their population history from a prehistoric population that separated from other early non-African populations soon after the migration out of Africa. The mixed ancestry of present-day Europeans could bias tests of genetic similarity, including the results found for the Tianyuan man. With the newly published data, however, the Fu lab showed that his genetic similarity to Asians remained in comparisons including ancient Europeans without mixed ancestry. They confirmed that the closest relationship he shares is with present-day Asians. That was not, however, the most exciting result they found.

With a close relationship to present-day Asians, they expected him to act similarly to present-day Asian populations with respect to Europeans. It was a surprise when they found that a 35,000-year-old individual from Belgium, GoyetQ116-1, who in other ways behaved as an ancient European, shared some genetic similarity to the Tianyuan individual that no other ancient Europeans shared. It is unlikely that this is due to direct interactions between populations near the east and west coasts of Eurasia, since other ancient Europeans do not show a similar result. Instead, the researchers suggested that the two populations represented by the Tianyuan and GoyetQ116-1 individuals derived some of their ancestry from the same sub-population prior to the European-Asian separation. The genetic relationship observed between these two ancient individuals is direct evidence that European and Asian populations have a complex history.

A second unexpected result shed some light on human genetic diversity in prehistoric East Asia. In 2015, a study comparing present-day populations in Asia, the Pacific and the Americas showed that some Native American populations from South America had an unusual connection to some populations south of mainland Asia, most notably the Melanesian Papuan and the Andamanese Onge. That study proposed that the population that crossed into the Americas around 20,000 years ago could not be thought of as a single unit. Instead, one or more related but distinct populations crossed at around the same time period, and at least one of these groups had additional ties to an Asian population that also contributed to the present-day Papuan and Onge.

No trace of this connection is observed in present-day East Asians and Siberians, but unlike them, the Tianyuan man also possesses genetic similarities to the same South Americans, in a pattern similar to that found for the Papuan and Onge. The new study directly confirms that the multiple ancestries represented in Native Americans were all from populations in mainland Asia. What is intriguing, however, is that the migration to the Americas occurred approximately 20,000 years ago, but the Tianyuan individual is twice that age. Thus, the population diversity represented in the Americas must have persisted in mainland Asia in two or more distinct populations since 40,000 years ago.

http://popular-archaeology.com/issue/fall-2017/article/genome-wide-data-from-a-40-000-year-old-man-in-china-reveals-complicated-genetic-history-of-asia
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Thereal
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What's with this broad generalization when reporting certain regions of the world? I want to know specifics though this paper had some interesting tibits.
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Elite Diasporan
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An East Asian possessing affinity with Indigenous Americans. Interesting.
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beyoku
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quote:
Originally posted by Elite Diasporan:
An East Asian possessing affinity with Indigenous Americans. Interesting.

The idea is not surprising at all. Autosomal results prior to Ancient DNA always hinted at this. The AGE of the remains is whats interesting.

Its implications for other regions around the world is what I look forward to.

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Thereal
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Northern native look far more Chinese than southern and central natives so it isn't all that surprising.
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Swenet
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Always had a lingering suspicion that GoyetQ-116's mtDNA M represents an affinity not shared with most other UP Europeans. They were trying to pass GoyetQ-116's mtDNA off as a European heritage that died off. It may have died off, but it's definitely not a European heritage.

Just superimpose a map of mtDNA M on Tianyuang's global affinities. Tianyuang's affinities seem mtDNA M mediated, and entirely distinct from the mtDNA N-dominated OOA wave that today survives mostly in western Eurasia and the Sahul. Looks like Mellars was right all along about a distinctive OOA presence in Asia, albeit not in the way he envisioned it.

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capra
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This is not about the general East Asian ancestry of Native Americans. The majority of all Amerindians' ancestry is North East Asian, related to Chinese, Mongols, Samoyeds, Tungus, etc. It's also not about more recent gene flow from Arctic bringing additional East Asian ancestry - which is probably what you are thinking of with northern Natives, Thereal. This is about something else entirely.

So certain indigenous people of the Amazon turn out to be slightly more closely related to Papuans, Melanesians, Australian Aborigines, etc, and Onge (from the Andamanese islands) than other Amerindians are. Amerindians are thought to pretty much all descend from the same relatively small founding population and hence any one Amerindian group normally will have almost exactly the same degree of relationship to any population outside of the Americas as any other Amerindian group (barring obviously Post-Columbian ancestry, and also that Arctic gene flow mentioned earlier).

So Amazonians have a few percent of some kind of ancestry that is closer to these indigenous Indo-Pacific populations than to North East Asians (we can call this 'Paleo-Asian'). The mystery population that contributed it is called 'Population Y'. We don't know how the heck they ended up in the middle of the Amazon specifically.

Tianyuan Man, 40 000 years old, comes from a cave in the Beijing area. A small part of his genome were actually sequenced several years ago, but now his whole genome has been done. He isn't directly ancestral to modern East Asians to any significant degree, but he does turn out to be a kind of Paleo-Asian; the Amazonians are related to him as well.

Also GoyetQ116-1, who is from Belgium and 35 000 years old, has some of this Tianyuan-related ancestry too (mostly he is like other Ice Age Europeans). So it seems this kind of Paleo-Asian got around back in the day. (I suspect that we will find small amounts of it are all over the place, but I could be wrong, and that isn't in the actual study.)

Anyway, finding the potential source of ancestry found in Amerindians in northern China should not come as a surprise to anyone, because they come from Northeast Asia! But the Population Y mystery remains.

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capra
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quote:
Originally posted by Swenet:
Just superimpose a map of mtDNA M on Tianyuang's global affinities. Tianyuang's affinities seem mtDNA M mediated, and entirely distinct from the mtDNA N-dominated OOA wave that today survives mostly in western Eurasia and the Sahul.

Tianyuan was haplogroup R (specifically B) and Sahul has more of the Paleo-Asian element than places with more M. So I don't think that makes sense. Not to say that the Paleo-Asian in GoyetQ116-1 isn't linked to his M, that's surely plausible.
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Elite Diasporan
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quote:
Originally posted by beyoku:
quote:
Originally posted by Elite Diasporan:
An East Asian possessing affinity with Indigenous Americans. Interesting.

The idea is not surprising at all. Autosomal results prior to Ancient DNA always hinted at this. The AGE of the remains is whats interesting.

Its implications for other regions around the world is what I look forward to.

Now that you mentioned it really isn't surprising. But I do hope to see more.
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Swenet
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quote:
Originally posted by capra:
quote:
Originally posted by Swenet:
Just superimpose a map of mtDNA M on Tianyuang's global affinities. Tianyuang's affinities seem mtDNA M mediated, and entirely distinct from the mtDNA N-dominated OOA wave that today survives mostly in western Eurasia and the Sahul

Tianyuan was haplogroup R (specifically B) and Sahul has more of the Paleo-Asian element than places with more M. So I don't think that makes sense. Not to say that the Paleo-Asian in GoyetQ116-1 isn't linked to his M, that's surely plausible.
True. Just remember that Tianyuan just has this affinity. Tianyuan is not necessarily the source of this affinity, and so he doesn't necessarily have to have mtDNA M in the scenario I just painted. MtDNA M could easily be in his pedigree (e.g. if his father had mtDNA M he wouldn't have inherited it) even if he doesn't carry it. And, quite possibly, since mtDNA N is older according to some sources (e.g. Behar et al 2012), the mtDNA M people could also have carried some mtDNA N.

It might look like a hasty conclusion drawn from a couple of aDNA samples, but there is a lot of evidence to support it. Start with Mellars' research if you're interested.

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DD'eDeN
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But, most interestingly it was surprising that when they compared Tianyuan to the 35,000-year-old individual from Belgium, GoyetQ116-1, who in other ways reflected an ancient European, he shared some genetic similarity to the Tianyuan individual that no other ancient Europeans shared.

Why? Because they had domestic dogs from Phu Quoc Island.


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http://www.nbcnews.com/id/27240370/ns/technology_and_science-science/t/worlds-first-dog-lived-years-ago-ate-big/#.WeI7H7pFzDd
An international team of scientists has just identified what they believe is the world's first known dog, which was a large and toothy canine that lived 31,700 years ago and subsisted on a diet of horse, musk ox and reindeer, according to a new study.

Remains for the older prehistoric dog, which were excavated at Goyet Cave in Belgium

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xyambuatlaya

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Doug M
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My personal opinion on this is that across Eurasia there were many aboriginal types with a wide diversity in features and hair textures, including straight hair which we see remnants of in India, Australia and the Pacific. Those populations in the north becoming the later East Asian populations we see today. There are still some pockets of these northern Aboriginals in the Eskimo and parts of Tibet and Northern India. And it is that kind of aboriginal type of mainland Asian that settled the Americas.

Unfortunately many people have the opinion that the only aboriginal "type" of mainland Asia is the short Negrito which is absolutely not correct.

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DD'eDeN
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Doug M: "Unfortunately many people have the opinion that the only aboriginal "type" of mainland Asia is the short Negrito which is absolutely not correct."

Pygmies, actually, first along the tropical belt, now mostly admixed with later arrivals including AMHs OOA2; Denisovans in Papuans & Australians and some Philippinos.

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xyambuatlaya

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Linda Fahr
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Doug M, your academic link from China is a little bit incomplete, and not on the point! Therefore, I decide to post a link about Tianyuan Man written by Ann Gibbons, which has more details in all aspects, including his European inherited Neanderthal DNA, and the Tribe names of Amerindians living in South America, which share DNA with Tianyuan Man. I am also posting 2 videos from Brazil about an isolated tribe from Peru, which crossed the border to ask for help, because they were attacked by WHITE MEN. As you will see in those videos, there is no doubt those nude isolated Amerindians living in the Amazonas Forest, are in fact Mongoloids, possible from East China, because they still have mongoloid eyes with tight epicanthic folds.


Was this ancient person from China the offspring of modern humans and Neandertals?

By Ann GibbonsOct. 12, 2017 , 12:00 PM

When scientists excavated a 40,000-year-old skeleton in China in 2003, they thought they had discovered the offspring of a Neandertal and a modern human. But ancient DNA now reveals that the “Tianyuan Man” has only traces of Neandertal DNA and none detectable from another type of extinct human known as a Denisovan. Instead, he was a full-fledged member of our species, Homo sapiens, and a distant relative of people who today live in East Asia and South America. The work could help scientists retrace some of the earliest steps of human migration.

“The paper is very exciting because it is the first genome to fill a really big gap, both geographically and temporally, in East Asia,” says paleogeneticist Pontus Skoglund of Harvard Medical School in Boston, who was not involved in the work.

The first modern humans arose in Africa about 300,000 years ago. By 60,000 years ago, a subset swept out of Africa and mated with Neandertals, perhaps in the Middle East. After that, they spread around the world—DNA from ancient humans in Europe, western Asia, and the Americas has revealed the identity of those early migrants and whether they were related to people living today, especially in Europe. But the trail grows cold in eastern Asia, where warmer climates have made it hard to get ancient DNA from fossils.

The new genome sheds some light on those missing years. In the first genome-wide study of an ancient East Asian, researchers led by Qiaomei Fu, a paleogeneticist at the Chinese Academy of Sciences in Beijing, extracted DNA from the thighbone of the Tianyuan Man—so named because he was found in Tianyuan Cave, 56 kilometers southwest of Beijing.

The team calculated that the Tianyuan Man inherited about as much Neandertal DNA—4% to 5%—as ancient Europeans and Asians of similar age. That’s a bit higher than the 1.8% to 2.6% of Neandertal DNA in living Europeans and Asians. The Tianyuan Man did not have any detectable DNA from Denisovans, an elusive cousin of Neandertals known only from their DNA extracted from a few teeth and small bones from a Siberian cave and from traces of their DNA that can still be found in people in Melanesia—where they got it is a major mystery.

A big surprise is that the Tianyuan Man shares DNA with one ancient European—a 35,000-year-old modern human from Goyet Caves in Belgium. But he doesn’t share it with other ancient humans who lived at roughly the same time in Romania and Siberia—or with living Europeans. But the Tianyuan Man is most closely related to living people in east Asia—including in China, Japan, and the Koreas—and in Southeast Asia, including Papua New Guinea and Australia.

All of this suggests that the Tianyuan Man was not a direct ancestor, but rather a distant cousin, of a founding population in Asia that gave rise to present-day Asians, Fu’s team reports today in Current Biology. It also shows that these ancient “populations moved around a lot and intermixed,” says paleoanthropologist Erik Trinkaus of Washington University in St. Louis in Missouri, who is not a co-author.

And some left offspring whereas others did not. “I find it interesting that … some of the early modern colonizers of Eurasia were successful while others were not,” says co-author Svante Pääbo, a paleogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The Tianyuan Man also was a distant relative of Native Americans living today in the Amazon of South America, such as the Karitiana and Surui peoples of Brazil and the Chane people of northern Argentina and southern Bolivia. They inherited about 9% to 15% of their DNA from an ancestral population in Asia that also gave rise to the Tianyuan Man. But he is not an ancestor to ancient or living Native Americans in North America, which suggests there were two different source populations in Asia for Native Americans.

This is welcome news to Skoglund, who found in a separate study in 2015 that the Karitiana and Surui peoples are closely related to indigenous Australians, New Guineans, and Andaman Islanders. At the time, he predicted that they came from the same “ghost” source population in Asia, which was separate from another Asian population that gave rise to Native Americans in North America. “It’s fascinating that a prediction of a ‘ghost population’ based on modern-day populations alone can be confirmed in this way,” he says.

Posted in: Asia/PacificEvolutionPaleontology
http://www.sciencemag.org/news/2017/10/was-ancient-person-china-offspring-modern-humans-and-neandertals

Primitive Chinese isolated tribe living in in the Amazonas Forest in Peru, South America.

https://www.youtube.com/watch?v=Sb7alahD-BE

https://www.youtube.com/watch?v=1e5GPuEJJzs

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---lnnnnn*

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Clyde Winters
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The sample used in the study were the archaic humanoids: Altai Neanderthals, and the Denisova; the western Eurasian clade was represented by Mal’ta 1 and , Ust’-Ishim individuals; indigenous populations from , New Guinea, Australia, Onge ( from the Andaman Islands), and the Ami (aboriginal Taiwanese) represented the eastern clade.

The basic error in this method is that the authors are comparing ancient and modern DNA, with the full knowledge that the ancient DNA, rarely corresponds to contemporary populations. In addition the authors use the date of the Ust’-Ishim individual as the terminal date for the separation of the eastern and western clades.

Granted, the authors acknowledge that the Ust’-Ishim individual shows no admixture in Australasians . But this is not surprising , there are no living descendants of Ust’-Ishim. As a result, s/ he can not represent the point when the eastern and western clades separated .

Interestingly, the Tianyuan DNA, belongs to the mtDNA R macrohaplogroup, namely haplogroup B, in addition a deletion of a 9-bp motif (5′-CCCCCTCTA-3′, revised Cambridge reference sequence positions 8,281–8,289). This haplogroup is not carried by the indigenous populations from , New Guinea, Australia, Onge ( from the Andaman Islands), and the Ami (aboriginal Taiwanese) that represented the eastern clade in this study.

The failure to adequately discuss the Tianyuan DNA, makes the conclusion of the paper suspect, since the authors are claiming that the Australasians, represent the eastern clade, eventhough the Tianyuan individual is 45ky old. Moreover, the presence of the 9-bp motif clearly indicates an African influence among the Tianyuan.

The argument implying that Tianyuan man relates to Native Americans is pure bs. It is bs because Asians could not cross the Bearing Straits until 25,000 years after this man had died. Given the separation in time between the Native Americans and Tianyuan man make this proposition ludicrous.


Reference:
Qiaomei Fu et al. DNA analysis of an early modern human from Tianyuan Cave, China. PNAS, published online before print January 22, 2013. http://www.pnas.org/content/110/6/2223.full

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C. A. Winters

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