Ancient DNA decodes genetic origins of China

By WANG CHUANCHAO / 06-30-2022 / Chinese Social Sciences Today

A teacher and students at the Institute of Anthropology at Xiamen University conduct human bone measurements and paleopathological analysis. Photo: THE INSTITUTE 

For most of its history, domestic archaeological research has been mainly based on the physical materials excavated in archaeological sites, such as pottery, stone tools, and jade ware, with less attention to the people who created those regional cultures. The cultural exchange and integration brought about by the migration of people from different origins is one of the driving forces behind the emergence of civilization. Studies of human genealogy and cultural development must learn from, verify, and complement each other, so as to deepen the understanding of human civilization evolution.

As the most important approach to human genealogy, ancient DNA (hereafter aDNA) research integrates knowledge of archaeology, history, and paleontology, analyzing the genealogy of ancient creatures, human origins and migration, domestication of animals and plants, etc. Beginning in the 1980s, aDNA research has become a promising discipline.
Advances and achievements
Since 2008, the birth of high-throughput sequencing technology has brought revolutionary changes to aDNA research. The Max Planck Institute in Germany and Harvard University have completed the whole genome sequencing of the Neanderthals and Denisovans, who went extinct around 30,000 years ago, as well as ancient humans of the Neolithic Age and different historical periods. Their research reveals that modern humans arose in Africa, carrying a few DNA elements derived from extinct Neanderthals, Denisovans, and several unidentified hominins by interbreeding.
In recent years, researchers have sequenced thousands of ancient human genomes from Europe, the Americas, Oceania, and Africa, rewriting the evolutionary history of human populations in Europe and reconstructing the origin and migration history of American populations. In Europe and the US, aDNA research focuses not only on ancient humans, but also on pathogenic bacteria. Scientists have successfully decoded the ancient genomes of pathogens that have caused large-scale plagues in history, such as Yersinia pestis, tubercle bacillus, and Mycobacterium leprae. In China, the Chinese Academy of Sciences, Fudan University, Xiamen University, Jilin University, and other domestic institutions have established ultra-clean labs and big data analysis platforms for aDNA studies, and carried out considerable research projects on human bones unearthed from major archaeological sites in China and surrounding countries and regions.
Origins of populations in north China
As early as 40,000 years ago, modern humans represented by the samples known as the Tianyuan individual [a 40,000-year-old individual found in Tianyuan Cave in Beijing] and AR33K [a Pleistocene female who lived about 33,000 years ago in the Amur region] had split from the ancestry of modern Europeans, displaying Asian genetic features. Modern humans, represented by the Tianyuan individual and AR33K, were widely distributed in north China and Northeast Asia, forming a northern lineage in contrast with the southern lineage in Asia, which included the indigenous Andaman islanders and Papuans from the islands in the Indian Ocean, Southeast Asia, and far Pacific Ocean.
After the Last Glacial Period, there has been widespread genetic continuity at the genome-wide level from about 14,000 years ago to the present, with a distribution from the Amur River Basin to the Mongolian Plateau. The Y chromosomal haplogroup C2b-F1396 and mitochondrial haplogroups D4 and C5 of ancient humans, dated between 8,000 and 7,000 years ago, are predominant in present-day Tungusic, Mongolic, and some Turkic-speakers. It confirms the origin of the related populations from a genetic perspective. Approximately 5,000 years ago, in the early and middle Bronze Age, the Yamnaya and Afanasievo steppe pastoralists expanded eastward into the Mongolian Plateau, and were then replaced by the middle and late Bronze Age steppe pastoralists who arrived 4,000–3,500 years ago. The Han-Chinese DNA “entered” the Mongolian Plateau and Northeast Asia around 2,000 years ago, as it was found within Xiongnu, Xianbei, Mohe, and other populations dated to that period.
In the Yellow River basin, the aDNA analysis of human bone samples from more than ten sites between the Neolithic Age and the Iron Age confirmed the genetic continuity of the middle and late Neolithic farming groups in the upper and middle reaches of the Yellow River. Populations with such genetic continuity are consistent with the westward expansion of the Yangshao Culture (c. 5000–3000 BCE) and its population as observed by archaeologists. The Neolithic farming groups in the upper and middle reaches of the Yellow River genetically contributed large quantities to the speakers of modern Han Chinese and Tibeto-Burman languages, and they became the shared ancestors of the Han Chinese and Tibeto-Burman speakers. Modern Han Chinese have a high frequency of the Y chromosome haplogroup Oα-F5 and its subclades, which is shared with Tibeto-Burman speakers. It is thought to be related to the expansion of the Neolithic farming groups in the middle and upper reaches of the Yellow River. The date of the expansion is estimated to be 5,800 years ago, which was consistent with linguistic and archaeological speculations that the Neolithic farmers cultivating foxtail millet in the upper and middle reaches of the Yellow River expanded southwest toward the Tibetan Plateau and spread present-day Tibeto-Burman languages.
After that, populations of the Yangshao Culture spread northward. In northeast China, the DNA of Yangshao-related populations has been detected in the farming groups living at the West Liao River basin since the Hongshan Cultural period (c. 4000–3000 BCE). The West Liao River farmers appeared to be an excellent candidate for the primary source population for present-day Korean and Japanese people. 
While the Yangshao Culture was expanding, people from south China continued to migrate to the Yellow River basin and integrated with the local people there. Both the Yangshao and Longshan populations had a certain proportion of their ancestry from the lineage of south China. The southern DNA of the Longshan population was greater than those of the Yangshao population. Such a pattern of migration and integration coincided with the northward spread of rice farming from the Yangtze River basin 4,500–4,000 years ago.
Origins of populations in south China
As for populations in south China, studies of the whole genomes of ancient people dated from 8,000–2,000 years ago, unearthed in Qihe Cave, Tanshi Mountain, and Xitou Village in Fujian Province, as well as Liangdao, Suogang in the Taiwan region, and other archaeological sites, reveal that the ancient Taiwan residents between the late Neolithic Age and the Iron Age show strong genetic links to modern Austronesian speakers in the Taiwan region and Southeast Asia. Samples of ancient Taiwan residents and modern Austronesian speakers share significantly more alleles at the genome-wide level with the ancient groups on the southeastern coast of the Chinese mainland and modern Tai-Kadai speakers. The mitochondrial DNA sequence of the Liangdao individuals is closest to that of the Austronesian population in the Taiwan region. The mitochondrial DNA type of the Liangdao individuals belongs to one of the early branches of the oldest haplogroup E, which is exclusively Austronesian, as a continuation from haplogroup M9. The haplogroup M9 is mainly detected in the East Asian continent, which suggests a close relationship between the Liangdao individuals and the early population on the East Asian continent. The haplogroup R9, found from another Liangdao sample, mainly exists in the modern Thao ethnic group, which belongs to the people living in the mountainous areas in the Taiwan region, as well as in the Dai, Miao, and Yao ethnic groups in south China, indicating a close connection with the modern Tai-Kadai speakers in south China and Austronesian speakers. This further confirms the unit of the local ethnic groups in south China, including the people living in the mountainous areas in the Taiwan region, as well as their origins in the Chinese mainland. The Austronesian speakers and Tai-Kadai speakers in south China were derived from the same lineage, which is supported by the fact that the dominant haplogroups in the Iron Age samples found in the Taiwan region are Y lineage O3a2c2-N6 and maternal mtDNA lineages E1a, B4a1a, F3b1, and F4b, which are shared in modern Austronesian speakers. It suggests that Austronesian speakers originated directly from the coastal areas of the southern Chinese mainland.
Around 3,000 BCE, Neolithic pottery makers and rice-growing populations migrated to the Taiwan region from the southern Chinese mainland. Subsequently, agriculture and pottery spread to the Philippines, then southwestward to mainland Southeast Asia and Madagascar, eastward through Indonesia and the Pacific Ocean to the Polynesian Islands, and finally to New Zealand. The genomes of the ancient individuals who lived 3,100–2,300 years ago in Vanuatu and Tonga in Oceania shared the same genetic lineage with the ancient people in China’s Fujian Province and the Taiwan region. These early settlers in Vanuatu and Tonga had little or no ancestry originating in Papua in Southeast Asia. Further analysis revealed that the Papuan DNA arrived in Vanuatu and Tonga around 2,300 years ago. Despite the dramatic changes in the genetic structure of the Far Oceania populations, the Papuan languages as an imported language didn’t replace the Austronesian languages.
From the Sui (581–618) to the Southern Song (1127–1279) dynasties, Asian rice and mung beans appeared in Madagascar and Comoros Island in Africa, and the mtDNA lineage B4a1a1, exclusive to East Asian populations, was also present on the east coast of Africa. Some scholars linked the origin of the Austronesian languages with the domestication of rice, and believe that the Neolithic people in the rice-growing areas in the lower reaches of the Yangtze River were original Austronesian speakers.
From a genetic perspective, the Neolithic agricultural populations living in the Yellow River basin and the Yangtze River basin were not linked in ancestry to Western populations. The prehistoric agricultural population in China rose indigenously, consistent with the indigenous origins of Chinese agriculture. China’s modern ethnic groups descend from the mixture of the Neolithic agricultural groups in the north and south of the country, which is different from Europe, where prehistoric agriculture was brought in by the spread of farmers from the Middle East. Middle Eastern farmers likewise contributed a significant part of the ancestry to modern European populations.
Wang Chuanchao is the director of the Institute of Anthropology at Xiamen University.