The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE - 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to ~3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.
The findings of the original study that reported evidence that the Afanasievo spread was the source of Steppe ancestry in the Iron Age Shirenzigou have been questioned with the proposal of alternative models that use ancient Kazakh Steppe Herders from the site of Botai, Wusun, Saka and ancient Tibetans from the site of Mebrak 15 in present-day Nepal as major sources for Steppe and East Asian-related ancestry . However, when we fit these models with Russia_Afanasievo and Mongolian_East_N added to the outgroups, the proposed models are rejected (P-values between 10 -7 and 10 -2), except in a model involving a single low coverage Saka individual from Kazakhstan as a source (P=0.17, likely reflecting the limited power to reject models with this low coverage). Repeating the modeling using other ancient Nepalese with very similar genetic ancestry to that in Mebrak results in uniformly poor fits (Online Table 5). Thus, ancestry typical of the Afanasievo culture and Mongolian Neolithic contributed to the Shirenzigou individuals, supporting the theory that the Tocharian languages of the Tarim Basin—from the second-oldest-known branch of the Indo-European language family—spread eastward through the migration of Yamnaya steppe pastoralists to the Altai Mountains and Mongolia in the guise of the Afansievo culture, from where they spread further to Xinjiang [5,7,8,27,29,30]. These results are significant for theories of Indo-European language diversification, as they increase the evidence in favor of the hypothesis the branch time of the second-oldest branch in the Indo-European language tree occurred at the end of the fourth millennium BCE [27,29,30].I'd say the authors are putting too much faith in their qpAdm mixture models. They ought to know that qpAdm has some serious limitations, especially in regards to fine scale ancestry. I would urge them to become better acquainted with the uniparental markers of the Iron Age Shirenzigou samples instead of forcing the ideas that these individuals harbor Afanasievo-derived ancestry and lack Tibetan-related ancestry. See also... They mixed up Huns with Tocharians A surprising twist to the Shirenzigou nomads story Afanasievo people may well have been proto-Tocharian speakers (Ning et al. 2019)