Haowen Tong
DNA was analyzed from a partial skeleton of a 40,000-year-old human found at Tianyuan Cave.
Was this ancient person from China the offspring of modern humans and Neandertals?
By
Ann Gibbons
Oct. 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.
doi:10.1126/science.aar1993
Was this ancient person from China the offspring of modern humans and Neandertals? | Science | AAAS
Melinda A. Yang, Xing Gao, Christoph Theunert, Haowen Tong, Ayinuer Aximu-Petri, Birgit Nickel, Montgomery Slatkin, Matthias Meyer, Svante Pääbo, Janet Kelso, Qiaomei Fu.
40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia.
Current Biology (2017). DOI:
http://dx.doi.org/10.1016/j.cub.2017.09.030
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In Mandarin,
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Genome-wide Data from a 40,000-year-old Man in China Reveals Complicated Genetic History of Asia
Oct 13, 2017
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 Biology analyzing 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.
The Tianyuan man is only one individual, but the deeper sequencing of his genome by Professor FU and her team reveals a complicated separation for ancient Europeans and Asians and hints at a diverse genetic landscape for humans in East Asia. Their study also showed that he derives from a population that is related to present-day East Asians, but is not directly ancestral to these populations, further suggesting that multiple genetically distinct populations were located in Asia from 40,000 years ago until the present.
The Tianyuan man shows us that between 40,000 years ago and the present, there are many unanswered questions about the past populations of Asia, and ancient DNA will be the key solving those questions.
This research was supported in part by grants from the National Natural Science Foundation of China, the Chinese Academy of Sciences, and the Howard Hughes Medical Institute.
Fig. 2 Graphical Abstract highlighting major relationships for the Tianyuan man and other individuals and populations (Image by FU Qiaomei)
Genome-wide Data from a 40,000-year-old Man in China Reveals Complicated Genetic History of Asia---Chinese Academy of Sciences
