Hereditary constitution analysis of Shaolingyuan ancient human in Xi’an, northwestern China — Oak Academic Publishing
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Hereditary constitution analysis of Shaolingyuan ancient human in Xi’an, northwestern China
Department of Oral Biology, Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, Xi’an, China;Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
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Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
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Shaanxi Provincial Institute of Archaeology, Xi’an, China
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Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
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Department of Oral Biology, Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medi- cal University, Xi’an, China
1 Department of Oral Biology, Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, Xi’an, China;Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
2 Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
3 Shaanxi Provincial Institute of Archaeology, Xi’an, China
4 Department of Orthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, China
5 Department of Oral Biology, Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medi- cal University, Xi’an, China
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.
KeywordsHVR-IChineseAncient3000 Years Ago
Kirsanow, K. and Burger, J. (2012) Ancient human DNA. Annals of Anatomy, 194, 121-132. doi:10.1016/j.aanat.2011.11.002
Rasmussen, M., Ying-rui, L., Lindgreen, S., Pedersen, J.S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gil bert, M.T.P., Yong, W., Raghavan, M., Campos, P.F., Kamp, H.M., Wilson, A.S., Gledhill, A., Tridico, S., Bun ce, M., Lorenzen, E.D., Binladen, J., Xiao-sen, G., Jing, Z., Xiuqing, Z., Hao, Z., Zhuo, L., Minfeng, C., Orlando, L., Kristiansen, K., Bak, M., Tommerup, N., Bendixen, C., Pierre, T.L., Gronnow, B., Meldgaard, M., Andreasen, C., Fedorova, S.A., Osipova, L.P., Thomas, F., Higham, G., Ramsey, C.B., Hansen, T.O., Nielsen, F.C., Crawford, M.H., Brunak, S., Sicheritz-Ponten, T., Villems, R., Niel sen, R., Krogh, A., Jun, W. and Willerslev, E. (2010) An cient human genome sequence of an extinct Palaeo-Es kimo. Nature, 463, 757-762. doi:10.1038/nature08835
Rohland, N. and Hofreiter, M. (2007) Ancient DNA ex traction from bones and teeth. Nature Protocols, 2, 1756-1762. doi:10.1038/nprot.2007.247
Umetsua, K. and Yuasa, I., 2005Recent progress in mito chondrial DNA analysis. Legal Medicine, 7, 259-262. doi:10.1016/j.legalmed.2005.01.005
Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J., Staden, R. and Young, I.G. (1981) Sequence and orga nization of the human mitochondrial genome. Nature, 290, 457-465. doi:10.1038/290457a0
Brown, T.A. and Brown, K.A. (1993) Ancient DNA: using molecular biology to explore the past. Bioessays, 16, 719-726. doi:10.1002/bies.950161006
Shaanxi Provincial Institute of Archaeology, The archaeology report of the Shaolingyuan tombs. Science Press, 2009.
Adachi, N., Umetsub, K., Takigawa, W. and Sakaue, K. (2004) Phylogenic analysis of the human ancient mito chondrial DNA. Journal of Archaeological Science, 31, 1339-1348. doi:10.1016/j.jas.2004.02.011
Oota, H., Saitou, N., Matsushita, T. and Ueda, S. (1995) A genetic study of 2000-year-old human remains from Ja pan using mitochondrial DNA sequences. American Jour nal of Physical Anthropology, 98, 133-145. doi:10.1002/ajpa.1330980204
Oota, H., Saitou, N., Matsushita, T. and Ueda, S. (1999) Molecular genetic analysis of remains of a 2000-year-old human population in China and its relevance for the ori gin of the modern Japanese population. The American Journal of Human Genetics, 64, 250-258. doi:10.1086/302197
Metress, J.F. and Conway, T. (1975) Standardized system for recording dental caries in prehistoric skeletons. Jour nal of Dental Research, 54, 908. doi:10.1177/00220345750540043901
Dongya, Y. and Kathy, W. (2005) Contamination controls when preparing archaeological remains for ancient DNA analysis. Journal of Archaeological Science, 32, 331-336. doi:10.1016/j.jas.2004.09.008
Alakoc, Y.D. and Aka, P.S. (2009) “Orthograde entrance technique” to recover DNA from ancient teeth preserving the physical structure. Forensic Science International, 188, 96-98. doi:10.1016/j.forsciint.2009.03.020
Cobb, J.C. (2002) Ancient DNA recovered by a non destructive method. Ancient Biomolecules, 4, 169-172. doi:10.1080/1358612021000028461
Archie, J.W. and Felsenstein, J. (1993) The number of evolutionary steps on random and minimum length trees for random evolutionary data. Theoretical Population Bi ology, 43, 52-79. doi:10.1006/tpbi.1993.1003
Kong, Q.P., Yao, Y.G., Sun, C., Bandelt, H.J., Zhu, C.L. and Zhang, Y.P. (2003) Phylogeny of East Asian mito chondrial DNA lineages inferred from complete se quences. The American Journal of Human Genetics, 73, 671-676. doi:10.1086/377718
Barros, M.C., Sampaio, I. and Schneider, H. (2003) Phy logenetic analysis of 16S mitochondrial DNA data in sloths and anteaters. Genetics and Molecular Biology, 26, 5-11. doi:10.1590/S1415-47572003000100002
Saitou, N. and Imanishi, T. (1989) Relative efficiencies of the Fitch Margoliash, maximum-parsimony, maximum likelihood, minimum-evolution, and neighbor-joining me thods of phylogenetic tree construction in obtaining the correct tree. Molecular Biology and Evolution, 6, 514 525.
Starikovskaya, Y.B., Sukernik, R.I., Theodore, Schurr, G., Kogelnik, A.M. and Wallace, D.C. (1998) MtDNA diver sity in Chukchi and Siberian Eskimos: implications for the genetic history of ancient beringia and the peopling of the New World. The American Journal of Human Genet ics, 63, 1473-1491. doi:10.1086/302087
Fan, L. and Yao, Y.G. (2011) Mitotool: A web server for the analysis and retrieval of human mitochondrial DNA sequence variations. Mitochondrion, 11, 351-356. doi:10.1016/j.mito.2010.09.013
Wallace, D.C. (2007) Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine. Annual Review of Biochemistry, 76, 781-821. doi:10.1146/annurev.biochem.76.081205.150955
Smith, A.B. and Peterson, K.J. (2002) Dating the time of origin of major clades: Molecular clocks and the fossil record. Annual Review of Earth and Planetary Sciences, 30, 65-88. doi:10.1146/annurev.earth.30.091201.140057
Soares, P., Rito, T., Trejaut, J., Mormina, M., Hill, C., Hundal, E.T., Braid, M., Clarke, D.J., Loo, J.H., Thomson, N., Denham, T., Donohue, M., Macaulay, V., Lin, M., Op penheimer, S. and Richards, M.B. (2011) Ancient voyag ing and Polynesian origins. The American Journal of Human Genetics, 88, 239-247. doi:10.1016/j.ajhg.2011.01.009
Feng, J., Zhang, J.Y. and Liu, M. (2011) Association of mtDNA haplogroup F with healthy longevity in the fe male Chuang population, China. Experimental Gerontol ogy, 9, 1-7.
Zheng, X.Y. (1994) Ethnic ingredient research of the ancient residents northwestern China. China Academic Journal Electronic Publishing House, 2008, 85-89.
Cui, Y.Q., Duan, R.H., Ji, C.N., Zhu, H., Li, W., Min, M.Y. and Zhou, H. (2002) Analys is of mitochondrial DNA from the ancient ruins of Jiao-he, China. Chemical Journal of Chinese Universities, 23, 1510-1514.
Zhu, H. (2006) Ancient race of Northwest China. Archive of Cult Relics, 5, 60-65.
Ballinger, S.W., Schurr, T.G., Torroni, A., Gan, Y.Y., Hodge, J.H., Hassan, K., Chen, K.H. and Wallace, D.C. (1992) Southeast Asian mitochondrial DNA analysis re veals genetic continuity of ancient mongoloid migrations. Genetics, 130, 139-152.
Simon, Y.W., Ho, M., Thomas, P. and Gilbert (2010) An cient mitogenomics. Mitochondrion, 10, 1-11.
Izagirre, N., Dela, C. and Ru, A. (1999) An mtDNA analysis in ancient Basque populations: Implications for haplogroup V as a marker for a major Paleolithic expan sion from Southwestern Europe. The American Journal of Human Genetics, 65, 199-207. doi:10.1086/302442
Ricaut, F.X., Thomas, T., Mormina, M., Cox, M.P., Bel latti, M., Foley, R.A. and Marta, M.L. (2010) Ancient Solomon islands mtDNA: Assessing holocene settlement and the impact of European contact. Journal of Archaeo logical Science, 37, 1161-1170. doi:10.1016/j.jas.2009.12.014