Molecular anthropology: Touching the past through ancient DNA retrieval. Methodological aspects

Henryk W. Witas

doi:10.18778/1898-6773.64.03

Authors

Henryk W. Witas Molecular Biology Unit, Institute of Pediatrics, Medical University of Łódź, Sporna 36/50, 91-736 Łódź, Poland

DOI:

https://doi.org/10.18778/1898-6773.64.03

Keywords:

molecular biology, PCR, restriction analysis, sequencing, aDNA, mtDNA, Neandertals

Abstract

The revolution which introduced new techniques of molecular biology applied to DNA analysis enormously accelerated the progress in most areas of medicine and biology. Techniques such as polymerase chain reaction (PCR), restriction analysis and sequencing are widely used for diagnosis of a number of diseases, for genetic screening, phylogenetic analysis and population studies. Moreover, it became possible to study genetic relationships of extinct to contemporary organisms and even to follow evolutionary events. Variation in DNA sequences, especially that of humans, is fascinating not only for our own sake, but also because of the inferences that can be drawn from it about our recent evolution, demography and movements. Selected problems arising during ancient DNA (aDNA) isolation and analysis are discussed. Environment and time related factors altering the structure of nucleic acids as well as contamination of isolated material are among methodological problems that arise during the procedure of isolation and processing of aDNA. Resolving them is of great importance for the authentication of the identified sequences. Most common informative targets of aDNA are presented and among them mtDNA, and the sequences localized within nuclear DNA. The first, as well as the most important findings in the field are mentioned.

Downloads

Download data is not yet available.

References

AHERN T., A.M. KLIBANOV, 1985, The mechanism of irreversible enzyme inactivation at 100C, Science, 228, 1280-84
View in Google Scholar DOI: https://doi.org/10.1126/science.4001942

AUSTIN J.J., A.J. ROSS, A.B. SMITH, R.A. FORTEY, R.H. THOMAS, 1997a, Problems with reproducibility – does geologically ancient DNA survive in amber-preserved insects? Proc. R. Soc. Lond. B., 264, 467-474
View in Google Scholar DOI: https://doi.org/10.1098/rspb.1997.0067

AUSTIN J.J., A.B. SMITH, R.H. THOMAS, 1997b, Paleontology in a molecular world: The search for the authentic ancient DNA, Trends Ecol. Evol., 12, 303-306
View in Google Scholar DOI: https://doi.org/10.1016/S0169-5347(97)01102-6

BERTRANPETIT J., 2000, Genome, diversity and origins: The Y chromosome as a storyteller, Proc. Natl. Acad. Sci. USA, 97, 6927-29
View in Google Scholar DOI: https://doi.org/10.1073/pnas.97.13.6927

BREIMER L.H., T. LINDAHL, 1985, Thymine lesions produced by ionizing radiation in double-stranded DNA, Biochemistry, 24, 4018-22
View in Google Scholar DOI: https://doi.org/10.1021/bi00336a032

BRINKMANN B., A. SAJANTILA, H.W. GOEDDE, H. MATSUMOTO, K. NISHI, P. WIEGAND, 1996, Population genetic comparisons among eight populations using allele frequency and sequence data from three microsatellite loci, Eur. J. Hum. Genet., 4, 175-182
View in Google Scholar DOI: https://doi.org/10.1159/000472192

BROWN T.A., 1999, Genomes, BIOS Scientific Publ., Oxford
View in Google Scholar

BROWN T.A., 2001, Genomy, (Polish edition), Wyd. Naukowe PWN, Warszawa
View in Google Scholar

BROWN T.A., D. NELSON, J.S. VOGEL, J.R. SOUTHON, 1988, Improved collagen extraction by modified Longin method, Radiocarbon, 30, 171-177
View in Google Scholar DOI: https://doi.org/10.1017/S0033822200044118

BROWN W.M., M. GEORGE JR., A.C. WILSON, 1979, Rapid evolution of animal mitochondrial DNA, Proc. Natl. Acad. Sci. USA, 76, 1967-71
View in Google Scholar DOI: https://doi.org/10.1073/pnas.76.4.1967

CANN R.L., M. STONEKING, A.C. WILSON, 1987, Mitochondrial DNA and human evolution, Nature, 325, 31-36
View in Google Scholar DOI: https://doi.org/10.1038/325031a0

COOPER A., 1994, DNA from museum specimens, [in:] Ancient DNA, B. Herrmann & S. Hummel (eds.), Springer Verlag, New York, pp. 149-165
View in Google Scholar DOI: https://doi.org/10.1007/978-1-4612-4318-2_10

DE KNIJFF P., 2000, Messages through bottlenecks: on the combined use of slow and fast evolving polymorphic markers on human Y chromosome, Am. J. Hum. Genet., 67, 1055-61
View in Google Scholar DOI: https://doi.org/10.1016/S0002-9297(07)62935-8

DENIRO M.J., 1985, Postmortem preservation and alteration of in vivo bone collagen isotope ratios in relation to palaeodietary reconstruction, Nature, 317, 806-809
View in Google Scholar DOI: https://doi.org/10.1038/317806a0

DIZDAROGLU M., 1991, Chemical determination of free radical-induced damage to DNA, Free Radical Biol. Med., 10, 225-242
View in Google Scholar DOI: https://doi.org/10.1016/0891-5849(91)90080-M

DIZDAROGLU M., 1992, Oxidative damage to DNA in mammalian chromatin, Mutat. Res., 275, 331-342
View in Google Scholar DOI: https://doi.org/10.1016/0921-8734(92)90036-O

DORAN G.H., D.N. DICKEL, W.A. BALLINGER JR., F.O. AGEE, P.J. LAIPIS, W.W. HAUSWIRTH, 1986, 8000 year old human brain tissue: Anatomical, cellular and molecular analysis, Nature, 323, 803-806
View in Google Scholar DOI: https://doi.org/10.1038/323803a0

DORIT R.L., H. AKASHI, W. GILBERT, 1995, Absence of polymorphism at the ZFY locus on the human Y chromosome, Science, 268, 1183-85
View in Google Scholar DOI: https://doi.org/10.1126/science.7761836

FOSTER E.A., M.A. JOBLING, P.G. TAYLOR, P. DONNELLY, et al., 1998, Jefferson fathered slaves last child, Nature, 396, 27-28
View in Google Scholar DOI: https://doi.org/10.1038/23835

FREDERICO L.A., T.A. KUNKEL, B.R. SHAW, 1990, A sensitive genetic assay for the detection of cytosine deamination: Determination of rate constants and the activation energy, Biochemistry 29, 2532-37
View in Google Scholar DOI: https://doi.org/10.1021/bi00462a015

GILES R.E., H. BLANC, H.M. CANN, D.C. WALLACE, 1980, Maternal inheritance of human mitochondrial DNA, Proc. Natl. Acad. Sci. USA, 77, 6715-19
View in Google Scholar DOI: https://doi.org/10.1073/pnas.77.11.6715

GREENWOOD A.D., C. CAPELLI, G. POSSNERT, S. PÄÄBO, 1999, Nuclear DNA sequences from late Pleistocene megafauna, Mol. Biol. Evol., 16, 1466-73
View in Google Scholar DOI: https://doi.org/10.1093/oxfordjournals.molbev.a026058

HAGELBERG E., B. SYKES, R. HEDGES, 1989, Ancient bone DNA amplified, Nature, 342, 485
View in Google Scholar DOI: https://doi.org/10.1038/342485a0

HAMADA H., M.G. PETRINO, T. KAKUNAGA, 1982, A novel repeated element with Z-DNA forming potential is widely found inevolutionary diverse eukaryotic genomes, Proc. Natl. Acad. Sci. USA, 79, 6465-69
View in Google Scholar DOI: https://doi.org/10.1073/pnas.79.21.6465

HAMMER M.F., T. KARAFET, A. RASANAYAGAM, E.T. WOOD, et al., 1998, Out of Africa and back again: Nested cladistic analysis of human Y chromosome variation, Mol. Biol. Evol., 15, 427-441
View in Google Scholar DOI: https://doi.org/10.1093/oxfordjournals.molbev.a025939

HAMMER M.F., A.J. REDD, E.T. WOOD, M.R. BONNER, et al., 2000, Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes, Proc. Natl. Acad. Sci. USA, 97, 6769-74
View in Google Scholar DOI: https://doi.org/10.1073/pnas.100115997

HANDT O., M. HÓSS, M. KRINGS, S. PÄÄBO, 1994, Ancient DNA: Methodological challenges, Experientia, 50, 524-529
View in Google Scholar DOI: https://doi.org/10.1007/BF01921720

HANDT O., M. KRINGS, R.H. WARD, S. PÄÄBO, 1996, The retrieval of ancient human DNA sequences, Am. J. Hum. Genet., 59, 368-376
View in Google Scholar

HERRMANN B., S. HUMMEL, 1993, Recovery and analysis of genetic material from paleontological, archeological museum, and forensic specimens, [in:] Ancient DNA, B. Herrmann & S. Hummel (eds.), Springer Verlag, New York, pp. 1-12
View in Google Scholar

HERRMANN B., S. HUMMEL, 1997, Genetic analysis of past populations by DNA studies, [in:] Advances in research on DNA polymorphisms, ISFH Hakone Symposium Program Committee (eds.), Toyoshoten, Tokyo, pp. 33-47
View in Google Scholar

HIGUCHI R., B. BOWMAN, M. FREIBERGER, O.A. RYDER, A.C. WILSON, 1984, DNA sequences from a quagga an extinct member of the horse family, Nature, 312, 282-284
View in Google Scholar DOI: https://doi.org/10.1038/312282a0

HOFREITER M., H. N. POINAR, W.G. SPAULDING, K. BAUER, P.S. MARTIN, G. POSSNERT, S. PÄÄBO, 2000, A molecular analysis of ground sloth diet through the last glaciation, Mol. Ecol., 9, 1975-84
View in Google Scholar DOI: https://doi.org/10.1046/j.1365-294X.2000.01106.x

HORAI S., K. HAYASAKA, K. MURAYAMA, N. WATE, H. KOIKE, N. NAKAI, 1989, DNA amplification from ancient human skeletal remains and their sequence analysis, Proc. Jap. Acad., 65, 229-233
View in Google Scholar DOI: https://doi.org/10.2183/pjab.65.229

HÓSS M., P. JARUGA, T.H. ZASTAWNY, M. DIZDAROGLU, S. PÄÄBO, 1996, DNA damage and DNA sequence retrieval from ancient tissue, Nucleic Acid Res., 24, 1304-07
View in Google Scholar DOI: https://doi.org/10.1093/nar/24.7.1304

INGMAN M., H. KAESSMANN, S. PÄÄBO, U. GYLLENSTEN, 2000, Mitochondrial genome variation and the origin of modern humans, Nature, 408, 708-713
View in Google Scholar DOI: https://doi.org/10.1038/35047064

JOBLING M.A., C. TYLER-SMITH, 1995, Fathers and sons: The Y-chromosome and human evolution, Trends Genet., 11, 449-456
View in Google Scholar DOI: https://doi.org/10.1016/S0168-9525(00)89144-1

KASAI H., S. NISHIMURA, 1984, Hydroxylation of deoxyguanosine at the C-8 position by ascorbic acid and other reducing agents, Nucleic Acid Res., 12, 2137-45
View in Google Scholar DOI: https://doi.org/10.1093/nar/12.4.2137

KOLMAN C.J., N. TUROSS, 2000, Ancient DNA analysis of human populations, Am. J. Phys. Anthropol., 111, 5-23
View in Google Scholar DOI: https://doi.org/10.1002/(SICI)1096-8644(200001)111:1<5::AID-AJPA2>3.0.CO;2-3

KRINGS M., C. CAPELLI, F. TSCHENTSCHER, H. GEISERT, et al., 2000, A view of Neandertal genetic diversity, Nature Genet., 26, 144-146
View in Google Scholar DOI: https://doi.org/10.1038/79855

KRINGS M., H. GEISERT, R.W. SCHMITZ, H. KRAINITZKI, S. PÄÄBO, 1999, DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen, Proc. Natl. Acad. Sci. USA, 96, 5581-85
View in Google Scholar DOI: https://doi.org/10.1073/pnas.96.10.5581

KRINGS M., A. STONE, R.W. SCHMITZ, H. KRAINITZKI, M. STONEKING, S. PÄÄBO, 1997, Neandertal DNA sequences and the origin of modern humans, Cell, 90, 19-30
View in Google Scholar DOI: https://doi.org/10.1016/S0092-8674(00)80310-4

LAWLOR D.A., C.D. DICKEL, W.W. HAUSWIRTH, P. PARHAM, 1991, Ancient HLA genes from 7,500-year old archaeological remains, Nature, 349, 785-788
View in Google Scholar DOI: https://doi.org/10.1038/349785a0

LINDAHL T., 1993, Instability and decay of the primary structure of DNA, Nature, 362, 709-715
View in Google Scholar DOI: https://doi.org/10.1038/362709a0

LOEB L.A., 1994, Microsatellite instability: Marker of a mutator phenotype in cancer, Cancer Res., 54, 5059-63
View in Google Scholar

MADDISON D.R., M. RUVOLO, D.L. SWOFFORD, 1992, Geographic origins of human mitochondrial DNA: Phylogenetic evidence from control region sequences, Syst. Biol., 41, 111-124
View in Google Scholar DOI: https://doi.org/10.1093/sysbio/41.1.111

MIESFELD R., M. KRISTAL, N. ARNHEIM, 1981, A member of a new repeated sequence family which is conserved throughout eucaryotic evolution is founded between the human delta globin genes, Nucleic Acid Res., 9, 5931-47
View in Google Scholar DOI: https://doi.org/10.1093/nar/9.22.5931

MULLIS K.B., F.A. FALOONA, 1987, Specific synthesis of DNA in vitro via a polymerasecatalyzed chain reaction, Methods Enzymol., 155, 335-350
View in Google Scholar DOI: https://doi.org/10.1016/0076-6879(87)55023-6

NORDBORG M., 1998, On the probability of Neanderthal ancestry, Am. J. Hum. Genet., 63, 1237-40
View in Google Scholar DOI: https://doi.org/10.1086/302052

OLIVO P.D., M.J. VAN DE WALLE, P.J. LAIPIS, W.W. HOUSEWIRTH, 1983, Nucleotide sequence evidence for rapid genotypic shifts in the bovine mitochondrial DNA D-loop, Nature, 306, 400-402
View in Google Scholar DOI: https://doi.org/10.1038/306400a0

OVCHINNIKOV I.V., A. GÓTHERSTRÓM, G.P. ROMANOWA, V.M. KHARITONOV, K. LIDEN, W. GOODWIN, 2000, Molecular analysis of Neanderthal DNA from the northern Caucasus, Nature, 404, 490-493
View in Google Scholar DOI: https://doi.org/10.1038/35006625

PÄÄBO S., 1985a, Preservation of DNA in ancient Egyptian mummies, J. Arch. Sci., 12, 411-417
View in Google Scholar DOI: https://doi.org/10.1016/0305-4403(85)90002-0

PÄÄBO S., 1985b, Molecular cloning of ancient Egyptian mummy DNA, Nature, 314, 644-645
View in Google Scholar DOI: https://doi.org/10.1038/314644a0

PÄÄBO S., 1986, Molecular genetic investigations of ancient human remains, Cold Spring Harbour Symp. Quant. Biol., 51, 441-446
View in Google Scholar DOI: https://doi.org/10.1101/SQB.1986.051.01.053

PÄÄBO S., 1989, Ancient DNA: Extraction, characterization, molecular cloning, and enzymatic amplification, Proc. Natl. Acad. Sci. USA, 86, 1939-1943
View in Google Scholar DOI: https://doi.org/10.1073/pnas.86.6.1939

PÄÄBO S., 1995, The Y chromosome and the origin of all of us, Science, 268, 1141-42
View in Google Scholar DOI: https://doi.org/10.1126/science.7761828

POINAR H.N., M. HÓSS, J.L. BADA, S. PÄÄBO, 1996, Amino acid racemization and the preservation of ancient DNA, Science, 272, 864-866
View in Google Scholar DOI: https://doi.org/10.1126/science.272.5263.864

SHEN P., F. WANG, P.A. UNDERHILL, C. FRANCO, et al., 2000, Population genetic implications from sequence variation in four Y chromosomal genes, Proc. Natl. Acad. Sci. USA, 97, 7354-59
View in Google Scholar DOI: https://doi.org/10.1073/pnas.97.13.7354

SIDOW A., A.C. WILSON, S. PÄÄBO, 1991, Bacterial DNA in Clarkia fossils, Philos. Trans. R. Soc. Lond. B., 333, 429-433
View in Google Scholar DOI: https://doi.org/10.1098/rstb.1991.0093

STANKIEWICZ B., H. POINAR, D. BRIGGS, R. EVERSHED, G. POINAR, 1998, Chemical presentation of plants and insects in natural resins, Proc. R. Soc. Lond. B., 265, 641-647
View in Google Scholar DOI: https://doi.org/10.1098/rspb.1998.0342

TAMURA K., M. NEI, 1993, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees, Mol. Biol. Evol., 10, 512-526
View in Google Scholar

WEBER J.L., P.E. MAY, 1989, Abundant class of human DNA polymorphism which can be typed using polymerase chain reaction, Am. J. Hum. Genet., 44, 388-396
View in Google Scholar

WEBER J.L., C. WONG, 1993, Mutation of human short tandem repeats, Hum. Mol. Genet., 2, 1123-28
View in Google Scholar DOI: https://doi.org/10.1093/hmg/2.8.1123

WIEGAND P., T. BAJANOWSKI, B. BRINKMANN, 1993, DNA typing of debris from fingernails, Int. J. Legal Med., 106, 81-83
View in Google Scholar DOI: https://doi.org/10.1007/BF01225045