Genomic study of ancient humans sheds light on human evolution on the Tibetan Plateau

The Tibetan Plateau, the highest and largest plateau above sea level, is one of the harshest environments inhabited by humans. It has a cold and dry environment and its altitude often exceeds 4000 meters above sea level (masl). The plateau covers much of Asia – about 2.5 million square kilometers – and is home to more than 7 million people, mainly belonging to the Tibetan and Sherpa ethnic groups.

However, our understanding of their origins and history on the plateau is fragmentary. Despite a rich archaeological context that spans the plateau, DNA sampling from ancient humans has been confined to a thin slice of the southwestern plateau in the Himalayas.

Now, a study published in Scientific progress led by Prof. Fu Qiaomei of the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences has filled this gap by sequencing the genomes of 89 ancient humans dating back to 5100 BP from 29 archaeological sites scattered across the Tibetan Plateau .

The researchers found that ancient people who lived on the plateau share a single origin, coming from a Northeast Asian population that mixed with a widely divergent, but unsampled, human population.

“This pattern is found in populations since 5,100 years ago, before the arrival of domesticated crops on the plateau,” said Prof. Fu. She noted that the introduction of Northeast Asian ancestry into plateau populations occurred before barley and wheat were introduced and was not associated with migrating wheat/barley farmers.

A deeper comparison across the plateau reveals different genetic patterns before 2500 BP, indicating that three very distinct Tibetan populations occupied the northeast, southern/central, and southern/southwestern regions of the plateau, with previously sampled plateau populations belonging only to the latter group. .

Different population dynamics can be observed in these three regions. Northeastern populations younger than 4700 BP show an influx of additional North East Asian ancestry into lower elevations (~3000m above sea level), such as the Gonghe Basin. However, this influx is not observed in higher altitude (~4000 m above sea level) populations dating to 2800 BP only 500 km away.

An extensive network of people also lived along the Yarlung Tsangpo River, with shared ancestry found in southern/southwestern populations dating to 3400 BP, western populations from Ngari Prefecture dating to 2300 BP, and southeastern populations from Nyingchi Prefecture dating to 2000 BP . The extensive impact of these populations shows the important role this river valley played in Tibetan history.

“Between these two groups, central populations before 2500 BP share an ancestor that differed from those further north and south. However, samples from central populations after 1600 BP show that they share a closer genetic relationship with southern/southwestern populations. These patterns capture a dynamic in human populations on the plateau,” said Melinda Yang, an assistant professor at the University of Richmond and a previous postdoctoral fellow at IVPP.

“While ancient plateau populations show mostly East Asian ancestry, Central Asian influences can be found in some ancient plateau populations,” said Wang Hongru, a professor at the Agricultural Genomics Institute in Shenzhen and a previous postdoctoral fellow at IVPP. “Western populations show partial Central Asian ancestry as early as 2300 BP, and an individual dating to 1500 BP from the Southwestern Plateau additionally shows ancestry associated with Central Asian populations.”

Contemporary Tibetans and Sherpas show strong influence from lowland East Asian populations, with varying levels of gene flow correlating with longitude. This pattern is not observed in older transect populations, including those from 1200-800 BP, indicating that lowland East Asian gene flow was largely a product of very recent human migration.

Previous research has shown that current plateau populations possess high frequencies of an endothelial Pas domain protein 1 (EPAS1) variant that adapts to life at high altitudes and probably arose from past admixture with the archaic humans known ​​​​as Denisovans.

“People from this study show an archaic ancestry typical of lowland East Asians, but the oldest individual dating to 5100 BP is homozygous for the adaptive variety,” said Prof. Fu. “Thus, the arrival of this variant occurred before 5100 BP in the ancestral population that contributed to all plateau populations.”

Through their broad spatiotemporal examination of ancient human DNA from the Tibetan Plateau, Prof. Fu and her team have revealed a Tibetan lineage dating back to at least 5,100 years ago on the Tibetan Plateau. The ancestral population diversified rapidly so that three regional groups showed unique historical patterns that began to merge after 2500 BP.

“This is the largest study of ancient genetics on the Tibetan Plateau to date,” said Lu Hongliang, a professor at Sichuan University. The new evidence in this study on the formation of unique components in the ancient populations of the Qinghai-Tibet Plateau relies heavily on collaboration between multiple archaeological teams and geneticists. prof. Lu notes that “analyzing ancient DNA allows us to go beyond the study of cultural interaction by using archaeological evidence alone, and to bring forward new ideas for archaeological research on the plateau.”

Future sampling is still needed as the origin of the unsampled, widely divergent ancestry found in all plateau populations remains unexplained. In addition, it is still unknown when and where the adaptive EPAS1 allele first entered the ancestral Tibetan population.

But this research is a step in the right direction. “These genomes reveal a deep and varied history of people on the plateau,” said Prof. Fu. “With these findings, we have a much better understanding of an important part of human history in Asia.”