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Using genome-wide data of 89 ancient individuals dated to 5100 to 100 years before the present (B.P.) from 29 sites across the Tibetan Plateau, we found plateau-specific ancestry across plateau populations, with substantial genetic structure indicating high differentiation before 2500 B.P. Northeastern plateau populations rapidly showed admixture associated with millet farmers by 4700 B.P. in the Gonghe Basin. High genetic similarity on the southern and southwestern plateau showed population expansion along the Yarlung Tsangpo River since 3400 years ago. Central and southeastern plateau populations revealed extensive genetic admixture within the plateau historically, with substantial ancestry related to that found in southern and southwestern plateau populations. Over the past ~700 years, substantial gene flow from lowland East Asia further shaped the genetic landscape of present-day plateau populations. The high-altitude adaptive EPAS1 allele was found in plateau populations as early as in a 5100-year-old individual and showed a sharp increase over the past 2800 years.

The lack of archaeological work has long impeded our understanding of prehistoric and historical human inhabitation and East-West interactions on the southeastern Tibetan Plateau (TP). In this study, we conducted a series of systematic archaeological investigations in the Nyingchi region, on the southeastern TP. We examined archaeological stratigraphies from 10 sites and collected charred seeds and charcoals for accelerator mass spectrometry (AMS) dating. The 26 radiocarbon dates show that the earliest inhabitation in the Nyingchi region can be traced back to as early as the fifth millennium BP. In addition, results of summed probability distribution (SPD) of radiocarbon dates suggest that intensive human activities occurred between c. 2700 and 2000 cal. yr BP. Together with the pottery net sinkers found in previous investigation, the newly identified archaeobotanical assemblages, including crops such as barley ( Hordeum vulgare), naked barley ( Hordeum vulgare var. nudum), wheat ( Triticum aestivum) and pea ( Pisum sativum), also confirm that cultivation and fishing were important subsistence strategies for people living in the prehistoric Nyingchi. The discoveries of domesticated crops from Southwest Asia also suggest that the southeastern TP, represented by the Nyingchi region, was part of the early communication network between the East and the West, predating historical Highland Silk Road.