Acta Anthropologica Sinica ›› 2020, Vol. 39 ›› Issue (04): 706-716.doi: 10.16359/j.cnki.cn11-1963/q.2020.0062
Previous Articles Next Articles
ZHAO Jing1,2(), WANG Chuanchao1()
Received:
2020-07-30
Revised:
2020-09-27
Online:
2020-11-15
Published:
2020-11-23
Contact:
WANG Chuanchao
E-mail:465582984@qq.com;wang@xmu.edu.cn
CLC Number:
ZHAO Jing, WANG Chuanchao. Comparison and summary of ancient DNA extraction technology[J]. Acta Anthropologica Sinica, 2020, 39(04): 706-716.
Add to citation manager EndNote|Ris|BibTeX
URL: https://www.anthropol.ac.cn/EN/10.16359/j.cnki.cn11-1963/q.2020.0062
[1] |
Campos PF, Willerslev E, Sher A, et al. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010,107(12):5675-5680
doi: 10.1073/pnas.0907189107 URL pmid: 20212118 |
[2] |
Leonard JA, Wayne RK, Cooper A. Population genetics of ice age brown bears[J]. Proceedings of the National Academy of Sciences of the United States of America, 2000,97(4):1651-1654
doi: 10.1073/pnas.040453097 URL pmid: 10677513 |
[3] |
Pinsky ML, Newsome SD, Dickerson BR, et al. Dispersal provided resilience to range collapse in a marine mammal: insights from the past to inform conservation biology[J]. Mol Ecol, 2010,19(12):2418-2429
doi: 10.1111/j.1365-294X.2010.04671.x URL pmid: 20497323 |
[4] | Shapiro B, Drummond AJ, Rambaut A, et al. Rise and fall of the Beringian steppe bison[J]. Science, 2004,306(5701):1561-1565 |
[5] |
Stiller M, Baryshnikov G, Bocherens H, et al. Withering away--25,000 years of genetic decline preceded cave bear extinction[J]. Mol Biol Evol, 2010,27(5):975-978
doi: 10.1093/molbev/msq083 URL pmid: 20335279 |
[6] |
Ning C, Li TJ, Wang K, et al. Ancient genomes from northern China suggest links between subsistence changes and human migration[J]. Nature communications, 2020,11(1):2700
doi: 10.1038/s41467-020-16557-2 URL pmid: 32483115 |
[7] | Wang K, Goldstein S, Bleasdale M, et al. Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa[J]. Science Advance, 2020, 6 eaaz0183 |
[8] |
Narasimhan VM, Patterson N, Moorjani P, et al. The Genomic Formation of South and Central Asia[J]. bioRxiv, 2018
doi: 10.1101/2020.11.06.371971 URL pmid: 33173866 |
[9] |
Green RE, Krause J, Briggs AW, et al. A draft sequence of the Neandertal genome[J]. Science, 2010,328(5979):710-722
doi: 10.1126/science.1188021 URL pmid: 20448178 |
[10] | Shapiro B, Sibthorpe D, Rambaut A, et al. Flight of the Dodo[J]. Science, 2002,2951683 |
[11] | Krause J, Unger T, Nocon A, et al. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary[J]. BMC Evol Biol, 2008,8220 |
[12] | Orlando L, Metcalf J, Alberdi M, et al. Revising the recent evolutionary history of equids using ancient DNA[J]. Proc Natl Acad Sci USA, 2009, 10621754-21759 |
[13] | Barquera R, Krause J. An ancient view on host-pathogen interaction across time and space[J]. Current opinion in immunology, 2020, 6565-69. |
[14] | 吴苡婷. 古DNA检测技术在抗击新冠中的特殊作用[N]. 上海科技报, 2020. |
[15] | Collins MJ, Nielsen-Marsh CM, Hiller J, et al. The survival of organic matter in bone: a review[J]. Archaeometry, 2002,44(3):383-394 |
[16] |
Hofreiter M, Paijmans JL, Goodchild H, et al. The future of ancient DNA: Technical advances and conceptual shifts[J]. Bioessays, 2015,37(3):284-293
doi: 10.1002/bies.201400160 URL pmid: 25413709 |
[17] |
Campos PF, Craig OE, Turner-Walker G, et al. DNA in ancient bone - where is it located and how should we extract it?[J]. Ann Anat, 2012,194(1):7-16
doi: 10.1016/j.aanat.2011.07.003 URL pmid: 21855309 |
[18] | Korlevic P, Gerber T, Gansauge MT, et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth[J]. BioTechniques, 2015,59(2):87-93 |
[19] | Lindahl T. Instability and decay of the primary structure of DNA[J]. Nature, 1993, 362709-715 |
[20] |
Brundin M, Figdor D, Sundqvist G, et al. DNA binding to hydroxyapatite: a potential mechanism for preservation of microbial DNA[J]. J Endod, 2013,39(2):211-216
URL pmid: 23321233 |
[21] |
Svintradze DV, Mrevlishvili GM, Metreveli N, et al. Collagen-DNA Complex[J]. Biomacromolecules, 2008, 921-28
URL pmid: 11710050 |
[22] |
Reich D, Green RE, Kircher M, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia[J]. Nature, 2010,468(7327):1053-1060
doi: 10.1038/nature09710 URL pmid: 21179161 |
[23] |
Prufer K, Racimo F, Patterson N, et al. The complete genome sequence of a Neanderthal from the Altai Mountains[J]. Nature, 2014,505(7481):43-49
doi: 10.1038/nature12886 URL pmid: 24352235 |
[24] | Gamba C, Jones ER, Teasdale MD, et al. Genome flux and stasis in a five-millennium transect of European prehistory[J]. Nature, communications, 2014,55257 |
[25] | Burbano HA, Hodges E, Green RE, et al. Targeted Investigation of the Neandertal Genome by Array-Based Sequence[J]. Science, 2010, 328723-725 |
[26] | Avila-Arcos MC, Cappellini E, Romero-Navarro JA, et al. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA[J]. Sci Rep, 2011,174 |
[27] |
Fu QM, Meyer M, Gao X, et al. DNA analysis of an early modern human from Tianyuan Cave, China[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013,110(6):2223-2227
URL pmid: 23341637 |
[28] |
Carpenter ML, Buenrostro JD, Valdiosera C, et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries[J]. Am J Hum Genet, 2013,93(5):852-864
URL pmid: 24568772 |
[29] |
Castellano S, Parra G, Sanchez-Quinto FA, et al. Patterns of coding variation in the complete exomes of three Neandertals[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014,111(18):6666-6671
doi: 10.1073/pnas.1405138111 URL pmid: 24753607 |
[30] | Meynert AM, Ansari M, FitzPatrick DR, et al. Variant detection sensitivity and biases in whole genome and exome sequencing[J]. BMC Bioinformatics, 2014,15247 |
[31] | Briggs AW, Stenzel U, Johnson PLF, et al. Patterns of damage in genomic DNA sequences from a Neandertal[J]. Proc. Natl. Acad. Sci, 2007, 10414616-14621 |
[32] |
Gansauge MT, Meyer M. Selective enrichment of damaged DNA molecules for ancient genome sequencing[J]. Genome Res, 2014,24(9):1543-1549
doi: 10.1101/gr.174201.114 URL pmid: 25081630 |
[33] | Geigl E. On the circumstances surrounding the preservation and analysis of very old DNA[J]. Archaeometry, 2002, 44337-342 |
[34] | Höss M, Dilling A, Currant A, et al. Molecular phylogeny of the extinct ground sloth mylodon darwinii[J]. Proceedings of the National Academy of Sciences of the United States of America, 1996, 93181-185 |
[35] | Hansen AJ, Mitchell DL, Wiuf C, et al. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments[J]. Genetics, 2006, 1731175-1179 |
[36] | Hofreiter M, Jaenicke V, Serre D, et al. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient dna[J]. Nucleic Acids Research, 2001, 294793-4799 |
[37] | Rohland N, Hofreiter M. Comparison and optimization of ancient DNA extraction[J]. BioTechniques, 2007, 42343-352 |
[38] | Tebbe CC, Vahjen W. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast[J]. Appl Environ Microbiol, 1993, 592657-2665 |
[39] | Tuross N. The biochemistry of ancient DNA in bone[J]. Experientia, 1994, 50530-535 |
[40] | Li R, Liriano L. A bone sample cleaning method using trypsin for the isolation of DNA[J]. Leg Med (Tokyo), 2011,13(6):304-308 |
[41] | Kemp BM, Smith DG. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth[J]. Forensic Sci Int, 2005,154(1):53-61 |
[42] |
Barta JL, Monroe C, Kemp BM. Further evaluation of the efficacy of contamination removal from bone surfaces[J]. Forensic Sci Int, 2013,231(1-3):340-348
doi: 10.1016/j.forsciint.2013.06.004 URL pmid: 23890658 |
[43] |
Salamon M, Tuross N, Arensburg B, et al. Relatively well preserved DNA is present in the crystal aggregates of fossil bones[J]. PNAS, 2005,102(39):13783-13788
URL pmid: 16162675 |
[44] |
Malmstrom H, Svensson EM, Gilbert MT, et al. More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA[J]. Mol Biol Evol, 2007,24(4):998-1004
doi: 10.1093/molbev/msm015 URL pmid: 17255122 |
[45] | Dabney J, Knapp M, Glocke I, et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013,110(39):15758-15763 |
[46] |
Hajdinjak M, Fu QM, Hubner A, et al. Reconstructing the genetic history of late Neanderthals[J]. Nature, 2018
URL pmid: 33208969 |
[47] | Ginolhac A, Vilstrup J, Stenderup J, et al. Improving the performance of true single molecule sequencing for ancient DNA[J]. BMC Genomics, 2012,13177 |
[48] | Peter B. Damgaard AM, Hannes Schroeder, Ludovic Orlando,, Eske Willerslev MEA. Improving access to endogenous DNA in ancient bones and teeth[J]. Scientific Reports, 2015,511184 |
[49] | Sikora M, Pitulko VV, Sousa VC, et al. The population history of northeastern Siberia since the Pleistocene[J]. Nature, 2019,570(7760):182-188 |
[50] | Bernardi G. Chromatography of Nucleic Acids on Hydroxyapatite[J]. Nature, 1965, 206779-783 |
[51] | Grunenwald A, Keyser C, Sautereau AM, et al. Adsorption of DNA on biomimetic apatites: Toward the understanding of the role of bone and tooth mineral on the preservation of ancient DNA[J]. Appl Surf Sci, 2014, 292867-875 |
[52] | Persson P. A method to recover DNA from ancient bones[J]. Ancient DNA Newsl, 1992, 125-27 |
[53] | Götherström A, Lidén K. A modified DNA extraction method for bone and teeth[J]. Laborativ Arkeologi, 1996, 953-56 |
[54] | Bajorath J, Saenger W, Pal GP. Autolysis and inhibition of proteinase K, a subtilisin-related serine proteinase isolated from the fungus Tritirachium album Limber[J]. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, 1988,954:176-182 |
[55] | 刘杨柳, 武小芳, 胡树样, 等. 蛋白酶K的性质及其在核酸提取中的应用[J]. 食品研究与开发, 2017,38(10):196-199 |
[56] | Hofreiter M, Rabeder G, Jaenicke-Despres V, et al. Evidence for reproductive isolation between cave bear populations[J]. Curr Biol, 2004,14(1):40-43 |
[57] |
Rohland N, Hofreiter M. Ancient DNA extraction from bones and teeth[J]. Nature protocols, 2007,2(7):1756-1762
doi: 10.1038/nprot.2007.247 URL pmid: 17641642 |
[58] |
Yang DY, Eng B, Waye JS, et al. Improved DNA extraction from Ancient Bones Using Silica-Based Spin Columns[J]. American Journal of Physical Anthropology, 1998,105(4):539-543
doi: 10.1002/(SICI)1096-8644(199804)105:4<539::AID-AJPA10>3.0.CO;2-1 URL pmid: 9584894 |
[59] |
Juras A, Makarowicz P, Chylenski M, et al. Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations[J]. Am J Phys Anthropol, 2020,172(2):176-188
doi: 10.1002/ajpa.24057 URL pmid: 32297323 |
[60] |
Rohland N, Siedel H, Hofreiter M. A rapid column-based ancient DNA extraction method for increased sample throughput[J]. Molecular ecology resources, 2010,10(4):677-683
doi: 10.1111/j.1755-0998.2009.02824.x URL pmid: 21565072 |
[61] | Sullivan NO, Posth C, Coia V, et al. Ancient genome-wide analyses infer kinship structure[J]. Science Advance, 2018, 4 eaao1262 |
[62] |
Gaudio D, Fernandes DM, Schmidt R, et al. Genome-Wide DNA from Degraded Petrous Bones and the Assessment of Sex and Probable Geographic Origins of Forensic Cases[J]. Sci Rep, 2019,9(1):8226
doi: 10.1038/s41598-019-44638-w URL pmid: 31160682 |
[63] | 杨百全, 王利君, 遇长青, 等. 磁珠法回收纯化 DNA样本[J]. 中国法医学杂志, 2006,21:10-11 |
[64] |
Zhao J, Liu FE, Lin S, et al. Investigation on maternal lineage of a Neolithic group from northern Shaanxi based on ancient DNA[J]. Mitochondrial DNA A DNA Mapp Seq Anal, 2017,28(5):732-739
URL pmid: 27246811 |
[65] |
Kalmár T, Bachrati CZ, Marcsik A, et al. A simple and efficient method for PCR amplifiable DNA extraction from ancient bones[J]. Nucleic Acids Research, 2000,28(12):E67
doi: 10.1093/nar/28.12.e67 URL pmid: 10871390 |
[66] |
Orlando L, Ginolhac A, Raghavan M, et al. True single-molecule DNA sequencing of a pleistocene horse bone[J]. Genome Res, 2011,21(10):1705-1719
doi: 10.1101/gr.122747.111 URL |
[67] | Rohland N, Siedel H, Hofreiter M. Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens[J]. BioTechniques, 2004, 36814-821 |
[68] |
Hervella M, Iniguez MG, Izagirre N, et al. Nondestructive methods for recovery of biological material from human teeth for DNA extraction[J]. J Forensic Sci, 2015,60(1):136-141
doi: 10.1111/1556-4029.12568 URL pmid: 25047360 |
[69] | Gomes C, Palomo-Díez S, Roig J, et al. Nondestructive extraction DNA method from bones or teeth, true or false?[J]. Forensic Science International: Genetics Supplement Series, 2015, 5e279-e282 |
[1] | ZHANG Ming, PING Wanjing, YANG Melinda Anna, FU Qiaomei. Ancient genomes reveal the complex genetic history of Prehistoric Eurasian modern humans [J]. Acta Anthropologica Sinica, 2023, 42(03): 412-421. |
[2] | DING Manyu, HE Wei, WANG Tianyi, Shargan Wangdue, ZHANG Ming, CAO Peng, LIU Feng, DAI Qingyan, FU Qiaomei. A study of the mitochondrial genome of ancient inhabitants from the Latuotanggu cemetery, Tibet, China [J]. Acta Anthropologica Sinica, 2021, 40(01): 1-11. |
[3] | WANG Tianyi, ZHAO Dongyue, ZHANG Ming, QIAO Shiyu, YANG Fan, WAN Yang, YANG Ruowei, CAO Peng, LIU Feng, FU Qiaomei. Ancient DNA capture techniques and genetic study progress of early southern China populations [J]. Acta Anthropologica Sinica, 2020, 39(04): 680-694. |
[4] | LI Chunxiang, ZHANG Fan, MA Pengcheng, WANG Lixin, CUI Yinqiu. Ancient mitogenomes reveals Holocene human population history in the Nenjiang River valley [J]. Acta Anthropologica Sinica, 2020, 39(04): 695-705. |
[5] | ZHANG Yajun, ZHANG Xu, ZHAO Xin, TONG Tao, LI Linhui. Craniometric evidence and ancient DNA analysis of the population origin of Ngari prefecture of Tibet Autonomous Region between 3rd and 4th century AD [J]. Acta Anthropologica Sinica, 2020, 39(03): 435-449. |
[6] | ZHANG Ming, FU Qiaomei. Prehistoric interbreeding between archaic human groups and anatomically modern humans [J]. Acta Anthropologica Sinica, 2018, 37(02): 206-218. |
[7] | WEN Shaoqing, WANG Chuanchao, AO Xue, WEI Lanhai, TONG Xinzhu, WANG Lingxiang, WANG ZhanFeng, HAN Sheng, LI Hui. Ancient DNA supports Emperor Cao’s paternal genetic lineage belonging to haplogroup O2 [J]. Acta Anthropologica Sinica, 2016, 35(04): 617-625. |
[8] | ZHANG Peng-yin; XU Zhi; XU Bo-song; TAN Jing-ze; ZHOU Hui; JIN Li; HAN Kang-xin. Genetic analysis of people who lived in Shangsunjiazhai, Datong Qinghai as revealed by mitochondrial DNA [J]. Acta Anthropologica Sinica, 2013, 32(02): 204-218. |
[9] | YANG Dong-ya. Contamination contorls and detection in ancient DNA studies [J]. Acta Anthropologica Sinica, 2003, 22(02): 163-173. |
[10] | Zhao Lingxia, Susanne Hummel, Cadja Lassen et al.. Ancient DNA extraction from Neolithic human skeletal remains and PCR based amplification of the X-Y homologous amelogenin gene [J]. Acta Anthropologica Sinica, 1996, 15(03): 200-209. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||