Kopalny DNA czyli lekcja z przeszłości

• Authors: Marta Gajewska , Wiesław Bogdanowicz

Title variants

EN

Ancient DNA - lesson from the past

• Languages of publication: PL EN

Abstracts

EN

Under certain conditions small amounts of DNA can survive for long periods of time and may be used as substrates in the polymerase chain reaction (PCR) for the study of phylogeny and population genetics of extinct animals and plants. About 20 years ago, DNA sequences were separately described from the quagga and an ancient Egyptian individual; what made these DNA sequences exceptional was that they were derived from 140- and 2,400-year-old specimens. More recently, ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes such as extinct horses, cave bears, woolly mammoths, the moa, and Neanderthal. In the past few years, this approach has been extended to the study of infectious disease in ancient mummies from Egypt and South America; they suggested a butchery pattern indicative of a human population under resource stress, revealed dietary habits of ancient animals, and helped to understand how climatic change impacts biological diversity. However, the field of aDNA is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. Deeper understanding of these processes and the effects of damage on aDNA templates has started to provide a more robust basis for research. DNA sequencing of the entire mitochondrial cytochrome b of Myotis myotis sensu lato in our molecular laboratory allowed the comparison of aDNA sequences (dating back to ca. 830 years BP) with those of modern bats to assess their genetic relationships. Initial results have revealed surprisingly complex population histories, and indicate that modern studies may give misleading impressions about even the recent evolutionary past.

• Journal: Kosmos
• Year: 2006
• Volume: 55
• Issue: 1
• Pages: 117-128

Dates

published

2006

Contributors

author

Marta Gajewska

• Muzeum i Instytut Zoologii PAN, Wilcza 64, 00-679 Warszawa, Polska

author

Wiesław Bogdanowicz

• Muzeum i Instytut Zoologii PAN, Wilcza 64, 00-679 Warszawa, Polska

References

• Abel O., 1920. Lehrbuch der Paläozoologie. Verlag von Gustav Fischer, Jena.
• Adcock G. J., Dennis E. S., Easteal S., Huttley G. A., Jermiin L. S., Peacock J., Thorne A., 2001. Mitochondrial DNA sequences in ancient Australians: Implication for modern human origins. Proc. Natl. Acad. Sci. USA 98, 537-542.
• Barnes I., Matheus P., Shapiro B., Jensen D., Cooper A., 2002. Dynamics of Pleistocene population extinctions in Beringian brown bears. Science 295, 2267-2270.
• Buick T. L., 1931. The mystery of the moa. Thomas Avery & Sons Ltd., New Plymouth, New Zealand.
• Bunce M., Worthy T. H., Ford T., Hoppitt W., Willerslev E., Drummond A., Cooper A., 2003. Extreme reserved sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425, 172-175.
• Burger J., Hummel S., Herrmann B., 2000. Palaeogenetics and cultural heritage. Species determination and STR-genotyping from ancient DNA in art and artifacts. Thermochim. Acta 365, 141-146.
• Burger J., Rosendahl W., Loreille O., Hemmer H., Eriksson T., Götherström A., Hiller J., Collins M., Wess T., Alt K. W., 2004. Molecular phylogeny of the extinct cave lion Panthera leo spelaea. Mol. Phylogenet. Evol. 30, 841-849.
• Cano R. J., Poinar H. N., Pieniazek N.J., Acra A., Poinar G. O. Jr, 1993. Amplification and sequencing of DNA from a 120-135-million-year-old weevil. Nature 363, 536-538.
• Capellini E., Chiarelli B., Sineo L., Casoli A., Di Gioia A., Vernesi C., Biella M. C., Caramelli D., 2004. Biomolecular study of the human remains from tomb 5859 in the Etruscan necropolis of Monterozzi, Tarquinia (Viterbo, Italy). J. Archeol. Sci. 31, 603-612.
• Clisson I., Keyser C., Francfort H. P., Crubezy E., Samashev Z., Ludes B. 2002. Genetic analysis of human remains from a double inhumation in a frozen kurgan in Kazakhstan (Berel site, Early 3rd Century BC). Int. J. Legal. Med. 116, 304-308.
• Cooper A., Wayne R., 1998. New uses for old DNA. Curr. Opinion Biotechnol. 9, 49-53.
• Cooper A., Lalueza- Fox C., Anderson S., Rambaut A., Austin J., Ward R. 2001. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409, 704-707.
• Debruyne R., Barriel V., Tassy P., 2002. Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae. Mol. Phylogenet. Evol. 26, 421-434.
• Drancourt M., Raoult D., 2002. Molecular insights into the history of plague. Microbes Infect. 4, 105-109.
• Endicott P., Gilert T. P., Stringer C., Lalueza-Fox C., Willerslev E., Hansen A. J., Cooper A., 2003. The genetic origin of the Andaman Islanders. Am. J. Hum. Genet. 72, 178-184.
• Gilbert M. T. P., Wilson A. S., Bunce M., Hansen A. J., Willerslev E., Shapiro B., Higham T. F. G., Richards M. P., O'Connell T. C., Tobin D. J., Janaway R. C., Cooper A., 2004. Ancient mitochondrial DNA from hair. Curr. Biol. 14, 463-464.
• Gill P., Ivanov P. L., Kimpton C., Piercy R., Benson N., Tully G., Evett I., Hagelberg E., Sullivan K. 1994. Identification of the remains of the Romanov family by DNA analysis. Nat. Genet. 6, 130-135.
• Golenberg E. M., Giannasi D. E., Clegg M. T., Smiley C. J., Durbin M., Henderson D., Zurawski G. 1990. Chloroplast DNA sequence from a Miocene Magnolia species. Nature 344, 656-658.
• Greenwood A. D., Castresana J., Feldmaier-Fuchs G., Pääbo S., 2001. A molecular phylogeny of two extinct sloths. Mol. Phylogenet. Evol. 18, 94-103.
• Grzybowski T., Czarny J., Woźniak M., Miścicka- Śliwka D. 2001. Sequencing of mtDNA region V from a 2300 years old Egyptian mummy. [W:] Mummy. Results of interdisciplinary examination of the Egyptian mummy of Aset-iri-khet-es from the Archeological Museum in Cracow. Polish Academy of Arts and Sciences, Kraków, 117-126.
• Hagelberg E., Thomas M.G., Cook C. E. Jr, Sher A. V., Baryshnikov G. F., Lister A. M., 1994. DNA from ancient mammoth bones. Nature 370, 333-334.
• Hauser L., Adcock G. J., Smith P. J., Bernal Ramirez J. H., Carvallo G. R., 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc. Natl. Acad. Sci. USA 99, 11742-11747.
• Hebsgaard M. B., Phillips M. J., Willerslev E., 2005. Geologically ancient DNA: fact or artefact? Trends in Microbiol. 13, 212-220.
• Higuchi R., Bowman B., Freiberger M., Ryder O. A., Wilson A. C., 1984. DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282-284.
• Hofreiter M., Capelli C., Krings M., Waits L., Conard N., Münzel S., Rabeder G., Nagel D., Paunovic M., Jambrĕsić G., Meyer S., Weiss G., Pääbo S., 2002. Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of Late Pleistocene cave bears. Mol. Biol. Evol. 19, 1244-1250.
• Hofreiter M., Serre D., Rohland N., Rabeder G., Nagel D., Conard N., Münzel S., Pääbo S., 2004. Lack of phylogeography in European mammals before the last glaciation. Proc. Natl. Acad. Sci. USA 101, 12963-12968.
• Holdaway R. N., Jacomb C., 2000. Rapid extinction of the moas (aves: Dinornithiformes): model, test, and implications. Science 287, 2250-2254.
• Höss M., Pääbo S., Vereshchagin N. K., 1994. Mammoth DNA sequences. Nature 370, 333.
• Hyunen L., Millar C. D., Scifield R. P., Lambert D. M., 2003 Nuclear DNA sequences detect species limits in ancient moa. Nature 425, 175-178.
• Jansen T., Forster P., Levine M. P., Oelke H., Hurles M., Renfrew C., Weber J., Olek K., 2002. Mitochondrial DNA and the origins of the domestic horse. Proc. Natl. Acad. Sci. USA 99, 10905-10910.
• Jehaes E., Toprak K., Vanderhyeden N., Pfeiffer H., Cassiman J.J., Brinkmann B., Decorte R. 2001. Pitfalls in the analysis of mitochondrial DNA from ancient specimens and the consequences for forensic DNA analysis: the historical case of the putative heart of Louis XVII. Int. J. Legal. Med. 115, 135-141
• Jones M., 2003. Ancient DNA in pre-Columbian archaeology: a review. J. Arch. Sci. 30, 629-635.
• Karanth K. P., Delefosse T., Rakotosamimanana B., Parsons T. J., Yoder A. D., 2005. Ancient DNA from giant extinct lemurs comfirms single origin of Malagasy primates. Proc. Natl. Acad. Sci. USA 102, 5090-5095.
• Kuehn R., Ludt C. J., Schroeder W., Rottmann O., 2005. Molecular phylogeny of Megaloceros giganteus - the giant deer or just a giant red deer? Zool. Sci. 22, 1031-1044.
• Lambert D.M., Ritchie P. A., Millar C. D., Holland B., Drummond A. J., Baroni C., 2002. Rates of evolution in ancient DNA from Adelie penguins. Nature 295, 2270-2273.
• Lambert D. M., Baker A., Huynen L., Haddrath O., Hebert P. D. H., Millar C. D., 2005. Is a large scale DNA-based inventory of ancient life possible? J. Heredity 96, 1-6.
• Larcombe L. A., Nickerson P., Hoppa R. D., Matheson C., 2005. Detection of a single nucleotide polymorphism in the IL-6 promoter region of ancient nuclear DNA. Infect. Genet. Evol. 5, 117-22.
• Lindahl T., 1993. Instability and decay of the primary structure of DNA. Nature 362, 709-715.
• Lindhal T., 1997. Facts and artifacts of ancient DNA. Cell 90, 1-3.
• Lydolph M. C., Jacobsen J., Arctander P., Gilbert M. T. P., Gilichinsky D. A., Hansen A. J., Willerslev E., Lange L., 2006. Beringian paleoecology inferred from permafrost-preserved fungal DNA. Appl. Env. Microbiol. 71, 1012-1017.
• MacPhee R. D. L., Tikhonov A. N., Mol D., Greenwood A. D., 2005. Late Quaternary loss of genetic diversity in muskox (Ovibos). BMC Evol. Biol., 5, 49.
• Matheson C. D., Loy T. H., 2001. Genetic sex identification of 9400-year-old human skull samples from Çayönü Tepesi, Turkey. J. Arch. Sci. 28, 569-575.
• Matisoo-Smith E., Robins J. H., 2004. Origins and dispersal of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat. Proc. Natl. Acad. Sci. USA 101, 9167-9172.
• Newman M. E., Parboosingh J. S., Bridge P. J., Ceri H., 2002. Identification of archeological animal bone by PCR/DNA analysis. J. Arch. Sci. 29, 77-84.
• Olson L. E., Hassanin A., 2003. Contamination and chimerism are perpetuating the legend of the snake-eating cow with twisted horns (Pseudonovibos spiralis). A case of study of the pitfalls of ancient DNA. Mol. Plylogenet. Evol. 27, 545-548.
• Ovchinnikov I. V., Götherström A., Romanova G. P., Kharitonov V. M., Lidén K., Goodwin W. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404, 490-493.
• Ozawa T., Hayashi S., Mikhelson V. M., 1997. Phylogenetic position of mammoth and Steller's sea cow with Tethythetria demonstrated by mitochondrial DNA sequences. J. Mol. Evol. 44, 406-413.
• Pääbo S., 1985. Molecular cloning of Ancient Egyptian mummy DNA. Nature 314, 644-645.
• Pääbo S., 1989. Ancient DNA: extraction, characterization, molecular cloning and enzymatic amplification. Proc. Natl. Acad. Sci. USA 86, 1939-1943.
• Pääbo S., Gifford J. A., Wilson A. C., 1988. Mitochondrial DNA sequences from a 7000-year old brain. Nucl. Acid Res. 16, 9775-9787.
• Poinar H. N., 2003 The top 10 list: criteria of authenticity for DNA from ancient and forensic samples. Intern. Congress Ser. 1239, 575-579.
• Poinar H. N., Hofreiter M., Spaulding W. G., Martin P. S., Stankiewicz B. A., Bland H., Evershed R. P., Possnert G., Pääbo S., 1998. Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281, 402-406.
• Poinar H. N., Schwarz C., Qi J., Shapiro B., Macphee R. D., Buigues B., Tikhonov A., Huson D. H., Tomsho L. P., Auch A., Rampp M., Miller W., Schuster S. C. 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311, 392-394.
• Richards M. B., Sykes B. C. 1995. Authenticating DNA extracted from ancient skeletal remains. J. Arch. Sci. 22, 291-299.
• Rogaev E. I., Moliaka Y. K., Malyarchuk B. A., Kondrashov F. A., Derenko M. V., Chumakov I., Grigorenko A. P., 2006. Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLOS Biology 4, 0001-0007.
• Schultes T., Hummel S., Herrmann B., 1999. Amplification of Y chromosomal STRs from ancient skeletal material. Hum. Genet. 104, 164-166.
• Serre D., Langaney A., Chech M., Teschler-Nicola M., Paunovic M., Mennecier P., Hofreiter M., Possnert G., Pääbo S. 2004. No evidence of Neanderthal mtDNA contribution to Early Modern Humans. PLOS Biology 2, 313-317.
• Shapiro B., Cooper A., 2003. Beringia as an Ice Age genetic museum. Quarternary Res. 60, 94-100.
• Thomas R. H., Schaffner W., Wilson A.C., Pääbo S., 1989. DNA phylogeny of the extinct marsupial wolf. Nature 340, 465-467.
• Vernesi C., Di Benedetto G., Caramelli D., Secchieri E., Simoni L., Katti E., Malaspina P., Noveletto A., Marin V. T. W., Barbujani G., 2001. Genetic characterization of the body attributed to the evangelist Luke. Proc. Natl. Acad. Sci. USA 98, 13460-13463.
• Vreeland R. H., Rosenzweig W. D., Powers D. W., 2000. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407, 897-900.
• Weinstock J., Willerslev E., Sher A., Tong W., Ho S. Y. W., Rubenstein D., Storer J., Burns J., Martin L., Bravi C., Prieto A., Froese D., Scott E., Xulong L., 2005. Evolution, systematics, and phylogeography of Pleistocene horses in the new world: A molecular perspective. PLOS Biol. 3 (8), e241.
• Willerslev E., Cooper A., 2005. Ancient DNA. Proc. R. Soc. London, B 272, 3-16.
• Willerslev E., Hansen A.J., Christensen B., Steffensen J. P., Arctander P., 1999. Diversity of Holocene life forms in fossil glacier ice. Proc. Natl. Acad. Sci. USA 96, 8017-8021.
• Willerslev E., Hansen A. J., Binladen J., Brand T. B., Shapiro B., Bunce M., Wiuf C., Gilichinsky D. A., Cooper A., 2003. Diverse plant and animal genetic records from Holocene and Pleisocene sediments. Science 300, 791-795.
• Woodward S. R., Weyand N. J., Bunnell M., 1994. DNA sequence from Cretaceous Period bone fragments. Science 266, 1229-1232.