North European admixture in the Han Chinese (Charleston et al. 2017 preprint)

Over at bioRxiv at this LINK. Emphasis is mine. The estimated date of the North European-related admixture signal is probably much too late. These sorts of estimates always look way off. And I doubt that it's largely the result of the Silk Road, which linked China to the Near East and Mediterranean rather than to Northern Europe. More likely it reflects gene flow from the Pontic-Caspian steppe in Eastern Europe during the Bronze and Iron ages, via the Afanasievo, Andronovo, and other closely related steppe peoples (see here).

Abstract: As are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world's largest ethnic group.

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One finding from our analysis of admixture signals that most likely fit a one-pulse admixture model is our observation of admixture from Northern European populations to the Northwestern provinces of China (Gansu, Shaanxi, Shanxi), but not other parts of China. Previous analysis of the HGDP data, based on patterns of haplotype sharing among 10 Han Chinese from Northern China, estimated a single pulse of ~6% West Eurasian ancestry among the Northern Han Chinese. The estimated date of admixture was around 1200 CE. This signal is also observed among the Tu people, an ethnic minority also from Northwestern China; the authors attributed this signal to contact through the Silk Road (Hellenthal et al. 2014). We estimate a lower bound of admixture proportion due to Northern Europeans at approximately 2%-5%, with an admixture date of about 26 +/-3 generations for Gansu, and 47 +/-3 generations for Shaanxi [Table S8]. Using a generation time of about 26-30 years (Moorjani et al. 2016), these estimates correspond to admixture events occurring at around 700 CE and 1300 CE, respectively, corresponding roughly to the Tang and Yuan dynasty in China. However, these estimated dates should be interpreted with caution, as both the violation of a single pulse admixture model and the additional noise in inter-­marker LD estimates due to low coverage data could bias the estimates.

Charleston et al.,A comprehensive map of genetic variation in the world's largest ethnic group - Han Chinese, bioRxiv, Posted July 13, 2017, doi: https://doi.org/10.1101/162982

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...