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Tibetan Plateau Population Relationships, Adaptations Assessed With Ancient Genomes

NEW YORK – A research team from China and the US has used ancient genomic data to retrace population interactions going back thousands of years in the cold, high-altitude environment on the Tibetan Plateau, identifying plateau-specific ancestry corresponding to northern East Asia and an early-diverging, yet-to-be-discovered human group.

For a paper appearing in Science Advances on Friday, researchers at the Chinese Academy of Sciences and other centers in China and the US used targeted enrichment sequencing to assess roughly 1.2 million SNPs in 100- to 5,100-year-old remains from 97 ancient individuals at dozens of archaeological sites in what is now the Tibet Autonomous Region and China's Qinghai province.

From there, they analyzed sequences from 89 ancient samples with sufficient sequence quality and depth alongside published genetic data on ancient and modern-day representatives from the Tibetan Plateau, East Asia, Central Asia, Siberia, and elsewhere.

"These genomes reveal a deep and diversified history of humans on the plateau," senior and corresponding author Qiaomei Fu, a researcher with the Chinese Academy of Sciences and the Shanghai Qi Zhi Institute, said in a statement. "With these findings, we have a much better understanding of an important part of human history in Asia."

Along with admixture linked to groups moving into or out of the region more recently, the team's analyses pointed to shared genetic features that appeared to be present across the Tibetan Plateau for at least 5,100 years, Fu explained, including northern East Asia ancestry that arrived before the introduction of domesticated barley or wheat crops.

Likewise, an EPAS1 variant previously implicated in high-altitude adaptations in the region turned up in the oldest samples considered, though the frequency of the adaptive EPAS1 haplotype has increased dramatically in the last 3,000 years, becoming especially common in Tibetan individuals in the most recent 700 years.

The researchers also documented more subtle population delineations in different parts of the region, particularly in samples from more than 2,500 years ago.

Their results suggested populations at relatively low elevations in the northeastern plateau were influenced by another wave of northern East Asian migration within the last 4,700 years, for example, while populations in parts of the southern and southwestern plateau showed geographic expansions, along with waves of mixing with groups from Central Asia.

"While ancient plateau populations show primarily East Asian ancestry, Central Asian influences can be found in some ancient plateau populations," co-first author Hongru Wang said in a statement. "Western populations show partial Central Asian ancestry as early as 2300 [before present (BP)], and an individual dating to 1500 BP from the southwestern plateau additionally shows ancestry associated with Central Asian populations."

Wang was based at the Chinese Academy of Sciences when the study was performed and is currently affiliated with the Agricultural Genomics Institute in Shenzhen.

The team detected still other population dynamics in the south-central region of the Tibetan Plateau, although groups in that region appeared to have become more similar to populations in the southern and southwestern plateau over the last 1,600 years.

"Interactions with diverse ancestries from neighboring regions affected plateau populations, but the largest genetic shifts are caused by the mixture of populations from different regions of the plateau, potentially associated with large-scale political shifts related to the expansion and collapse of major state-level societies in historical times," the authors explained.

The researchers also flagged relatively high levels of lowland East Asian ancestry in current Tibetan and Sherpa populations, contrasting with older samples dated to around 1,000 years ago.

"These patterns are not found in 1,100- to 700-year-old individuals, suggesting extensive gene flow from lowland East Asians occurred over the past 700 years," the authors reported, noting that "[p]resent-day populations on the Tibetan Plateau are characterized by a longitudinal cline with eastern populations showing higher genetic affinity with lowland East Asians."