Ancient genomes reveal deep roots of East Asian populations

Newly sequenced ancient genomes from Yunnan, China, have shed new light on human prehistory in East Asia. In a study published in Science, a research team led by Prof. FU Qiaomei at the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences analyzed data from 127 ancient humans, dating from 7,100 to 1,400 years ago. The results show that this region is pivotal to understanding the origin of both Tibetan and Austroasiatic (i.e., ethnic groups with a shared language group in South and Southeast Asia) population groups.

The team found that a 7,100-year-old individual from Yunnan was as genetically distinct from most present-day East Asians as a 40,000-year-old individual from the area of present-day Beijing, suggesting a previously unobserved Asian ancestry, denoted in the study as Xingyi ancestry. Collectively, these ancestries highlight the profound genetic divergence among human populations in East Asia.

Although the individual genetically differed significantly from modern East Asians, the researchers noted that the individual’s ancestry shared qualities similar to those of populations indigenous to the Qinghai-Tibet Plateau. This aligns with previous observations that these plateau populations have certain genetic characteristics that make them distinct from other present-day human groups.

This individual’s genome has filled in a large piece of the puzzle, making it easier to study Tibetan prehistory. The study revealed that an early Asian population that separated at least 40,000 years ago persisted in Southwestern China until the Holocene and interacted with humans migrating westward from northern East Asia to originate Tibetan populations.

This deeply diverged Xingyi ancestry was also found in an 11,000-year-old Longlin individual previously sampled in Guangxi, yet it gradually disappeared in later Guangxi populations.

Moreover, the researchers conducted a genome-wide analysis of DNA from humans living in central Yunnan from 5,100–1,400 years BP. Their study revealed a shared ancestry that was closely related-but genetically distinct-from East Asian ancestries observed in northern and southern China. According to the researchers, the Yunnan individuals genetically diverged from northern and southern East Asian groups at least 19,000 years ago.

Interestingly, the Yunnan samples also share a close genetic relationship to Austroasiatic speakers, who are widespread today across Southeast Asia, as well as some regions of South Asia and southern China. 

Some scientists have hypothesized that the spread of Austroasiatic speakers was linked to the expansion of farming in this region. However, the presence of these Austroasiatic-related populations in central Yunnan predates agricultural practices.

This study may provide insights into the origins of Austroasiatic populations. It presents the oldest evidence of ancestry associated with Austroasiatic speakers, with a continuous record from 5,100–1,400 years BP. Looking to central Yunnan and the nearby Red River Valley could be crucial for unveiling Austroasiatic prehistory.

The study also sheds light on the history of populations in western and southeastern Yunnan. Specifically, genetic analyses show that populations with northern East Asian ancestry influenced populations in western Yunnan, whereas populations carrying northern East Asian ancestry influenced populations in southeastern Yunnan.

Southwest China is a key region for prehistoric human migration and interaction. By accessing the genetic history preserved in these ancient genomes from Yunnan, the researchers have uncovered deep genetic diversity that accounts for the rich ethnic and linguistic diversity in Yunnan today. This research has also transformed our understanding of ancient human dynamics over a much wider geographic area, from the Qinghai-Tibet Plateau to Southeast Asia.

The study’s comprehensive analysis of ancient DNA from 7,100–to 1,400-year-old Yunnan populations offers new insights into long-debated questions regarding the origins and expansion of various East Asian populations.