The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30x-60x) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modem humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modem human sequences compose-6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal -like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to similar to 62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese similar to 15,000 to similar to 9,000 years ago, which can be largely attributed to post-LGM arrivals. Analysis of similar to 200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (-82%), Central Asia and Siberia (similar to 11%), South Asia (similar to 6%), and western Eurasia and Oceania (similar to 1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools but that their origins are much more complicated and ancient than previously suspected. We provide compelling evidence of the co-existence of Paleolithic and Neolithic ancestries in the Tibetan gene pool, indicating a genetic continuity between pre-historical highland-foragers and presentday Tibetans. In particular, highly differentiated sequences harbored in highlanders' genomes were most likely inherited from pre-LGM settlers of multiple ancestral origins (SUNDer) and maintained in high frequency by natural selection.
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