The study generated genomic data of eight individuals ranging in time from the earliest known human settlements to the establishment of the Tibetan Empire.
The findings demonstrate that the genetic make-up of high-altitude Himalayan populations has remained remarkably stable despite cultural transitions and exposure to outside populations through trade.
"We demonstrate that the Himalayan mountain region was colonised by East Asians of high altitude origin, followed by millennia of genetic stability despite marked changes in material culture and mortuary behaviour," said Christina Warinner, professor at the University of Oklahoma.
Yet, despite the economic and cultural importance of Himalayan trade routes, little was known about the region's peopling and early population history.
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The high altitude transverse valleys of the Himalayan arc were among the last habitable places permanently colonised by prehistoric humans due to the challenges of resource scarcity, cold stress and hypoxia.
"Ancient DNA has the power to reveal aspects of population history that are very difficult to infer from modern populations or archaeological material culture alone," said Mark Aldenderfer, from the University of California.
However, previous research suggests these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation.
Researchers, including those from University of Chicago and Uppsala University in Sweden, sequenced the nuclear and mitochondrial genomes of eight high-altitude Himalayan individuals dating to three distinct cultural periods spanning 3,150 to 1,250 years before present.
They compared these ancient DNA sequences to genetic data from diverse modern humans, including four Sherpa and two Tibetans from Nepal.
This strengthens evidence that the diverse material culture of prehistoric Himalayan populations is the result of culture diffusion rather than large-scale gene flow or population replacement from outside highland East Asia.
Both prehistoric individuals and contemporary Tibetan populations shared beneficial mutations in two genes, EGLN1 and EPAS1, which are implicated in adaptation to low-oxygen conditions found at high altitudes, researchers said.
The study was published in the journal PNAS.