The Tianyuan Cave man; the earliest (40,000 yBP) ancient DNA from East Asia and what we have learned from it

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  study analyzing the genome of a man that died in the Tianyuan Cave near Beijing, China 40,000 years ago.

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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.

*(NovoScriptorium: This seems very absolute to say, even wrong, as there are other researchers suggesting other ancestries as well. The closest to the truth is that ‘most of the multiple ancestries in Native Americans were from populations in mainland Asia’)

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.

(Source: https://www.archaeology.wiki/blog/2017/10/19/genome-wide-data-40000-year-old-man-china-reveals-complicated-genetic-history-asia/)

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Abstract The Tianyuan Cave is the only human fossil-bearing site containing rich mammalian fossils found in the last decades near Zhoukoudian. Up to now more than 34 specimens of the human body have been recovered, and the mammalian fossils can be put into 29 species. Cervids dominate the fauna, and carnivores are very rare. Based on the primary examination, the human fossils can be attributed to the species Homo sapiens. All the mammalian fossils, except one between tooth of Crocuta belong to the species that still exist today. But some of them are the first records in fossil form north of the Yellow River, such as Arctonyx andCapricornis. Based on the mammalian fauna study, it seems that the Tianyuan Cave can be correlated with the Upper Cave. Sixty-three percent of the species of the mammalian fauna from the Tianyuan Cave are also present in the Upper Cave. The characters of the deposits also share some similarities between the Tianyuan Cave and the Upper Cave; both of them are mainly composed of breccia without cement. The dating using the U-series method on deer tooth samples indicates that the geological age of the new site is around 25 thousand years B.P. This is the first discovery of human sites outside the core area of the Peking Man Site at Zhoukoudian, which throws new light onto this world famous site complex.

(Source: “A preliminary report on the newly found Tianyuan Cave, a Late Pleistocene human fossil site near Zhoukoudian”, by Haowen Tong et al.)

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Abstract For more than a century, scientists have returned time and again to the issue of modern human emergence-the when and where of the evolutionary process and the human behavioral and biological dynamics involved. The 2003 discovery of a human partial skeleton at Tianyuandong (Tianyuan Cave) excited worldwide interest. The first human skeleton from the region to be directly radiocarbon-dated (to 40,000 years before present), its geological age places it close to the time period during which modern humans became permanently established across the Old World (between 50,000 and 35,000 years ago). Through detailed description and interpretation of the most complete early modern human skeleton from eastern Asia, The Early Modern Human from Tianyan Cave, China, addresses long-term questions about the ancestry of modern humans in eastern Asia and the nature of the changes in human behavior with the emergence of modern human biology. This book is a detailed, paleontological and paleobiological presentation of this skeleton, its context, and its implications. By providing basic information for this important human fossil, offering inferences concerning the population processes involved in modern human emergence in eastern Eurasia, and by raising questions concerning the adaptations of these early modern human hunter-gatherers, The Early Modern Human from Tianyuan Cave, China will take its place as a core contribution to the study of modern human emergence.

(Source: “Early modern human from Tianyuan Cave, China”, by H. Shang and Erik Trinkaus)

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Abstract Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

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The term “early modern humans” generally refers to humans who fall within the morphological variation of present-day humans and date to the Middle or Early Upper Paleolithic. The earliest modern humans appear in the Eurasian fossil record about 45,000 y ago, whereas the last remains that tend to be classified as early modern humans are about 25,000 y old. Early modern humans may exhibit some archaic features shared with other earlier forms of humans such as Neandertals. Although early modern humans are thus only vaguely defined as a group, their genetic relationship to present-day humans is unclear. Similarly, their relationship to archaic humans is of interest, given that they may have interacted directly with them.

To begin to explore the genetic relationships of early modern humans with present-day humans, we have analyzed a partial human skeleton that was unearthed in 2003, along with abundant late Pleistocene faunal remains, in the Tianyuan Cave near the Zhoukoudian site in northern China, about 50 km southwest of Beijing. The skeleton was radiocarbon-dated to 34,430 ± 510 y before present (BP) (uncalibrated), which corresponds to ∼40,000 calendar years BP. A morphological analysis of the skeleton confirms initial assessments that this individual is a modern human, but suggests that it carries some archaic traits that could indicate gene flow from earlier hominin forms. The Tianyuan skeleton is thus one of a small number of early modern humans more than 30,000 y old discovered across Eurasia and an even smaller number known from East Asia.

Conclusion The DNA hybridization capture strategy described here allows sequencing of large sections (>>1 Mbp) of the nuclear genome from mammalian samples even in the presence of a large excess of microbial DNA, a situation typical of almost all ancient samples outside permafrost regions. This opens the possibility of generating DNA sequences from previously inaccessible ancient samples. We use this capture strategy to analyze an early modern human, the Tianyuan individual, who contains less than 0.03% endogenous DNA.

The results show that early modern humans present in the Beijing area 40,000 y ago were related to the ancestors of many present-day Asians as well as Native Americans. However, they had already diverged from the ancestors of present-day Europeans.

That Europeans and East Asians had diverged by 40,000 y ago is consistent with dates for the first archaeological appearance of modern humans in Europe and also with the upper end of an estimate [23 ka BP (95% CI: 17–43 ka BP)] for the divergence of East Asian and European populations from nuclear DNA variation in present-day populations. The results also show that the Tianyuan individual did not carry any larger proportion of Neandertal or Denisovan DNA sequences in its genome than present-day people in the region. More analyses of additional early modern humans across Eurasia will further refine our understanding of when and how modern humans spread across Eurasia.

(Source: “DNA analysis of an early modern human from Tianyuan Cave, China”, by Fu Qiaomei et al.)

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Research-Selection-Comments for NovoScriptorium: Maximus E. Niles

 

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