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In order to identify the kinship of Shaolingyuan ancient human excavated from Shaolingyuan archaeological site with high level of certainty, and infer racial origins more clearly and reliably, this paper analyzed the hereditary constitution of this population. We used the “Reverse root canal technique” to extract ancient DNA from 28 teeth in 28 skeletal remains (3057-2784 BP) of Shaolingyuan archaeological site, obtained the sequences of mtDNA Hypervariable region I (HVR-I) by PCR amplifications; then used MEGA 5.5 software to construct phylogenetic trees and compared the sequences among the sequences of interraces, intraraces. The phylogenetic tree showed that there were two major clusters, Cluster 1 with 16 individuals, and Cluster 2 with 5 individuals. Either the genetic gap or the geographic position of the individuals was small. The frequency of SNP site 16223 T > C was 71.4%, significantly higher than other sites. The comparisons of different population demonstrated that there is no significant difference among them. All of them shared the same haplogroup L1’2’3’4’5’6, close to African. Finally, we confirm that there is a very close genetic relationship between some individuals in this cemetery. We regarded Shao-lingyuan Western Zhou cemetery as a family cemetery, and these people belong to East Asia lineage.