The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000–2800 bc from the Dzungarian Basin and 13 individuals dating to around 2100–1700 bc from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early–Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria–Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

Objectives: The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. Materials and Methods: Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. Results: A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sublineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sublineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics.

Objectives Haplogroup C2a‐M48 is the predominant paternal lineage of Tungusic‐speaking populations, one of the largest population groups in Siberia. Up until now, the origins and dispersal of Tungusic‐speaking populations have remained unclear. In this study, the demographic history of Tungusic‐speaking populations was explored using the phylogenetic analysis of haplogroup C2a‐M86, the major subbranch of C2a‐M48. Materials and methods In total, 18 newly generated Y chromosome sequences from C2a‐M48 males and 20 previously available Y‐chromosome sequences from this haplogroup were analyzed. A highly revised phylogenetic tree of haplogroup C2a‐M86 with age estimates was reconstructed. Frequencies of this lineage in the literature were collected and a comprehensive analysis of this lineage in 13 022 individuals from 245 populations in Eurasia was performed. Results The distribution map of C2a‐M48 indicated the most probable area of origin and diffusion route of this paternal lineage in North Eurasia. Most C2a‐M86 samples from Tungusic‐speaking populations belonged to the sublineage C2a‐F5484, which emerged about 3300 years ago. We identified six unique sublineages corresponding to the Manchu, Evenks, Evens, Oroqen, and Daurpopulations; these sublineages diverged gradually over the past 1900 years. Notably, we observed a clear north‐south dichotomous structure for sublineages derived from C2a‐F5484, consistent with the internal north‐south divergence of Tungusic languages and ethnic groups. Conclusions We identified the important founding paternal haplogroup, C2a‐F5484, for Tungusic‐speaking populations as well as numerous unique subgroups of this haplogroup. We propose that the timeframe for the divergence of C2a‐F5484 corresponds with the early differentiation of ancestral Tungusic‐speaking populations.

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