Genomic Study Of The Ancient Populations From The Period Of YangShao To LongShan Culture In Central Plain

The Central Plain area（Henan）located in the middle reaches of the Yellow River Valley is rich in archaeological cultures.Due to climate conditions and abundant nature resources,the region has been cradle of the Chinese civilization.With compare to Jianghuai Basin,the material cultures in the Yellow River Valley showed a strong and a long-term continuity,but with cultural influences from nearby regions or vice versa.Many archaeological studies have been published on the interactions between Yangshao and Longshan cultures,which the transmission and influences of between them have been well studied.However,it is still unclear whether the dispersal of different cultures is due to population migrations or by cultural influences.Ancient DNA would be a key to answer these questions.However,due to the poor preservation of ancient DNA in Central Plain area,the existing studies are only limited to short fragments of mitochondrial DNA,which the resolution is not enough to explicit the above questions.In this study,we present the first whole genome sequences of 17 individuals from four archaeological sites that are belonged to Yangshao and Longshan cultures,namely Xiaowu,Wanggou,Haojiatai and Pingliangtai cemeteries.By analyzing those data,we detected 7 males and 10 females,which belong to 10 haplogroups,such as B4d1,D4,D4g2a1,D4b2,D4j1b2,D4e1a,D4b1a,F4a2,F1a1 and F2h.All those haplogroups are characteristic in East Asian populations,which haplotype D and F are the most prevalent.The result suggests that haplogroup D and F dominated the maternal genetic components of the Yangshao and Longshan populations in the Central Plains.Among the 17 individuals,3 individuals from Pingliangtai site showed the first or secondary relatedness with each other.By further combining the ages and the ¹⁴C dating of those individuals,the family tree of those three individuals was constructed,which provides the key evidence for understanding the social structure of Longshan population.Principal component analysis（PCA）suggests that the Yangshao and Longshan populations are close to each other.We further assess the genome-wide affinities of the ancient individuals in the Central Plains,by computing outgroup f3-statistics of the form f3（Mbuti;YS_MN/LS_LN,X）.We find that either YS_MN individuals or LS_MN individuals is most closely related to Han,She,Miao and Tujia.However,we also observe small but significant differences between Yangshao and Longshan populations.LongShan individuals（“LS_LN”）show slightly higher genetic affinity with populations from southern China and Southeast Asians compared to earlier Middle Neolithic YangShao individuals（“YS_MN”）,measured by positive f₄（LS_LN,YS_MN;X,Mbuti）.The Admixture results also support this point.The material culture of the Longshan period in the Central Plain contrasts qualitatively with that of earlier period in the same region.Evidence from isotopes indicates that cultural communications between Yangtze River Basin and Yangtze River Basin occurred during Longshan period in Henan.This is in line with our genetic observation that the Longshan population shares more southern genetic components than the Yangshao population.In sum,the ancient individuals of Yangshao and Longshan period show strong genetic affinity with each other.However,Longshan individuals show slightly higher genetic affinity with populations from southern China and Southeast Asia than Yangshao individuals.These results provide an example of how population movements propelled cultural changes in the deep past.Moreover,it filled the gap of the ancient genome data in Central Plain and provided reference data for future studies.