Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors

Chi-Chun Liu,John Novembre,Choongwon Jeong,Ju Hyeon Lee,Raphaela Stahl,Mark Aldenderfer,Christina Warinner,Nisha Patel,Anna Gosling,David Witonsky,Harald Ringbauer,Anna Di Rienzo,Richard Hagan

doi:10.1038/s41467-022-28827-2

Abstract

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.

Highlights

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered
We obtain aDNA data from additional individuals from these and four additional Himalayan sites in the Mustang and Manang districts (MMD), increasing the temporal coverage by more than 600 years, from ca. 1420 BCE–650 CE, and providing the earliest genetic evidence to date for Plateau populations. We show that these ancient Himalayan populations genetically cluster with present-day Tibetans and that they represent an early branch within the Tibetan lineage, making them informative for inferring the history of the Tibetan gene pool, its origins, and its current distribution among the present-day Tibetans and their neighbors
Whereas we focused most of our analyses on the Human Origins (HO) set for its higher single nucleotide polymorphisms (SNPs) density, we used the Illumina set for in-depth analysis of diverse Himalayan populations across Nepal, Bhutan, India, and Tibet Autonomous Region[24]

Summary

Introduction

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. We obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau and harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. Chen et al.[8] and others have argued that a permanent population on the central Plateau was not possible until the advent of barley-based agriculture around 3.6 kya The latter model generally presumes that agriculture was introduced onto the Plateau by migrants from lower elevation sites (

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Conclusion