Ancient DNA (original) (raw)

References

  1. Höss, M., Jaruga, P., Zastawny, T. H., Dizdaroglu, M. & Pääbo, S. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24, 1304–1307 (1996).
    Article PubMed PubMed Central Google Scholar
  2. Pääbo, S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl Acad. Sci. USA 86, 1939–1943 (1989).
    Article PubMed PubMed Central Google Scholar
  3. Pääbo, S. & Wilson, A. C. Miocene DNA sequences — a dream come true? Curr. Biol. 1, 45–46 (1991).
    Article PubMed Google Scholar
  4. Lindahl, T. Instability and decay of the primary structure of DNA. Nature 362, 709–715 (1993). Provides a comprehensive review of DNA damage that includes what is expected to occur in archaeological and palaeontological specimens.
    Article CAS PubMed Google Scholar
  5. Collins, M. Neanderthal DNA: not just old but old and cold. Nature (in the press).
  6. Thomas, W. K., Pääbo, S., Villablanca, F. X. & Wilson, A. C. Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens. J. Mol. Evol. 31, 101–112 (1990).
    Article CAS PubMed Google Scholar
  7. Groombridge, J. J., Jones, C. G., Bruford, M. W. & Nichols, R. A. 'Ghost' alleles of the Mauritius kestrel. Nature 403 , 616 (2000).
    Article CAS PubMed Google Scholar
  8. Cooper, A. et al. Ancient DNA and island endemics. Nature 381, 484 (1996).
    Article CAS PubMed Google Scholar
  9. Thomas, R. H., Schaffner, W., Wilson, A. C. & Pääbo, S. DNA phylogeny of the extinct marsupial wolf. Nature 340, 465–467 (1989).
    Article CAS PubMed Google Scholar
  10. Krajewski, C., Driskell, A. C., Baverstock, P. R. & Braun, M. J. Phylogenetic relationships of the thylacine (Mammalia: Thylacinidae) among dasyuroid marsupials: evidence from cytochrome b DNA sequences. Proc. R. Soc. Lond. B 250, 19–27 (1992).
    Google Scholar
  11. Christidis, L., Leeton, P. R. & Westerman, M. Were bowerbirds part of the New Zealand fauna? Proc. Natl Acad. Sci. USA 93, 3898– 3901 (1996); erratum 93, 14992 (1996).
    Article CAS PubMed PubMed Central Google Scholar
  12. Krajewski, C., Buckley, L. & Westerman, M. DNA phylogeny of the marsupial wolf resolved. Proc. R. Soc. Lond. B 264, 911–917 (1997).
    Article Google Scholar
  13. Handt, O., Höss, M., Krings, M. & Pääbo, S. Ancient DNA: methodological challenges. Experientia 50, 524–529 (1994).
    Article CAS PubMed Google Scholar
  14. Höss, M., Handt, O. & Pääbo, S. in The Polymerase Chain Reaction (eds Mullis, K., Ferre, F. & Gibbs, R.) 257–264 (Birkhauser, Boston, Massachusetts, 1994).
    Book Google Scholar
  15. Greenwood, A., Capelli, C., Possnert, G. & Pääbo, S. Nuclear DNA sequences from Late Pleistocene megafauna. Mol. Biol. Evol. 16, 1466–1473 ( 1999).
    Article CAS PubMed Google Scholar
  16. Lawlor, D. A., Dickel, C. D., Hauswirth, W. W. & Parham, P. Ancient HLA genes from 7,500-year-old archaeological remains. Nature 349, 785–788 ( 1991).
    Article CAS PubMed Google Scholar
  17. Poinar, H. N., Höss, M., Bada, J. L. & Pääbo, S. Amino acid racemization and the preservation of ancient DNA. Science 272, 864–866 ( 1996).Presents amino-acid analysis as a tool to substantiate claims that DNA can (or cannot) survive in ancient organic remains.
    Article CAS PubMed Google Scholar
  18. Poinar, H. N. & Stankiewicz, B. A. Protein preservation and DNA retrieval from ancient tissues. Proc. Natl Acad. Sci. USA 96, 8426–8431 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  19. Handt, O., Krings, M., Ward, R. H. & Pääbo, S. The retrieval of ancient human DNA sequences. Am. J. Hum. Genet. 59, 368–376 (1996).
    CAS PubMed PubMed Central Google Scholar
  20. Morin, P., Chambers, K., Boesch, C. & Vigilant, L. Quantitative DNA analysis from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol. Ecol. 10 (in the press).
  21. Lindahl, T. Recovery of antediluvian DNA. Nature 365, 700 (1993).
    Article CAS PubMed Google Scholar
  22. Austin, J. J., Ross, A. J., Smith, A. B., Fortey, R. A. & Thomas, R. H. Problems of reproducibility — does geologically ancient DNA survive in amber-preserved insects? Proc. R. Soc. Lond. B 264, 467–474 (1997).
    Article Google Scholar
  23. Austin, J. J., Smith, A. B. & Thomas, R. H. Paleontology in a molecular world: the search for authentic ancient DNA. Trends Ecol. Evol. 12, 303–306 (1997).
    Article CAS PubMed Google Scholar
  24. Stankiewicz, B., Poinar, H., Briggs, D., Evershed, R. & Poinar, G. Chemical preservation of plants and insects in natural resins. Proc. R. Soc. Lond. B 265, 641– 647 (1998).
    Article Google Scholar
  25. Sidow, A., Wilson, A. C. & Pääbo, S. Bacterial DNA in Clarkia fossils. Phil. Trans. R. Soc. Lond. B 333, 429–433 (1991).
    Google Scholar
  26. Zischler, H., Geisert, H., von Haeseler, A. & Pääbo, S. A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans . Nature 378, 489–492 (1995).
    Article CAS PubMed Google Scholar
  27. Cooper, A. et al. Independent origins of New Zealand moas and kiwis. Proc. Natl Acad. Sci. USA 89, 8741– 8744 (1992).
    Article CAS PubMed PubMed Central Google Scholar
  28. Cooper, A. et al. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409, 704 –707 (2001).The first determination of complete mitochondrial DNAs from fossil remains.
    Article CAS PubMed Google Scholar
  29. Leonard, J. A., Wayne, R. K. & Cooper, A. From the cover: population genetics of ice age brown bears. Proc. Natl Acad. Sci. USA 97, 1651 –1654 (2000).
    Article CAS PubMed PubMed Central Google Scholar
  30. Pääbo, S. Of bears, conservation genetics, and the value of time travel. Proc. Natl Acad. Sci. USA 97, 1320– 1321 (2000).
    Article PubMed PubMed Central Google Scholar
  31. Vila, C. et al. Widespread origins of domestic horse lineages. Science 291, 474–477 ( 2001).
    Article CAS PubMed Google Scholar
  32. Loreille, O. et al. Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr. Biol. 11, 200–203 (2001).
    Article CAS PubMed Google Scholar
  33. Krings, M. et al. Neandertal DNA sequences and the origin of modern humans. Cell 90, 19–30 ( 1997).The first determination of a Neanderthal mitochondrial DNA sequence, including an extensive set of controls to support the authenticity of DNA sequence.
    Article CAS PubMed Google Scholar
  34. Krings, M., Geisert, H., Schmitz, R. W., Krainitzki, H. & Pääbo, S. DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen. Proc. Natl Acad. Sci. USA 96, 5581–5585 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  35. Ingman, M., Kaessmann, H., Pääbo, S. & Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 408, 708–713 ( 2000).
    Article CAS PubMed Google Scholar
  36. Adcock, G. et al. Mitochondrial DNA sequences in ancient Australians: implications for modern human origins. Proc. Natl Acad. Sci. USA 98, 537–542 (2001).
    Article CAS PubMed PubMed Central Google Scholar
  37. Pääbo, S. Human evolution. Trends Cell Biol. 9, M13 –M16 (1999).
    Article PubMed Google Scholar
  38. Kaessmann, H., Wiebe, V., Weiss, G. & Pääbo, S. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nature Genet. 27, 155–156 (2001).
    Article CAS PubMed Google Scholar
  39. Ovchinnikov, I. V. et al. Molecular analysis of Neanderthal DNA from the northern Caucasus . Nature 404, 490–493 (2000).
    Article CAS PubMed Google Scholar
  40. Krings, M. et al. A view of Neandertal genetic diversity. Nature Genet. 26, 144–146 ( 2000).
    Article CAS PubMed Google Scholar
  41. Rogers, A. R. & Harpending, H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552–569 ( 1992).
    CAS PubMed Google Scholar
  42. Höss, M., Kohn, M., Pääbo, S., Knauer, F. & Schröder, W. Excrement analysis by PCR . Nature 359, 199 ( 1992).
    Article PubMed Google Scholar
  43. Kohn, M., Knauer, F., Stoffella, A., Schröder, W. & Pääbo, S. Conservation genetics of the European brown bear — a study using excremental PCR of nuclear and mitochondrial sequences. Mol. Ecol. 4, 95 –103 (1995).
    Article CAS PubMed Google Scholar
  44. Kohn, M. H. et al. Estimating population size by genotyping faeces. Proc. R. Soc. Lond. B 266, 657–663 (1999).
    Article Google Scholar
  45. Vasan, S. et al. An agent cleaving glucose-derived protein crosslinks in vitro and in vivo. Nature 382, 275 –278 (1996).
    Article CAS PubMed Google Scholar
  46. Poinar, H. N. et al. Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281 , 402–406 (1998).
    Article CAS PubMed Google Scholar
  47. Hansen, R. M. Shasta ground sloth food habits, Rampart Cave, Arizona. Paleobiology 4, 302–319 ( 1978).
    Article Google Scholar
  48. Hofreiter, M. et al. A molecular analysis of ground sloth diet through the last glaciation. Mol. Ecol. 9, 1975– 1984 (2000).A diachronical study of ground sloth diet over almost 20,000 years, illustrating the usefulness of coprolites for molecular studies.
    Article CAS PubMed Google Scholar
  49. Poinar, H. et al. A molecular analysis of dietary diversity for three archaic Native Americans. Proc. Natl Acad. Sci. USA 98, 4317–4322.
  50. Klein, R. The Human Career 2nd edn (Chicago Univ. Press, Chicago, 1999).
  51. Monsalve, M. V., Cardenas, F., Guhl, F., Delaney, A. D. & Devine, D. V. Phylogenetic analysis of mtDNA lineages in South American mummies. Ann. Hum. Genet. 60, 293 –303 (1996).
    Article CAS PubMed Google Scholar
  52. Izagirre, N. & de la Rua, C. An mtDNA analysis in ancient Basque populations: implications for haplogroup V as a marker for a major paleolithic expansion from southwestern Europe. Am. J. Hum. Genet. 65, 199–207 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  53. Oota, H., Saitou, N., Matsushita, T. & Ueda, S. Molecular genetic analysis of remains of a 2,000-year-old human population in China — and its relevance for the origin of the modern Japanese population . Am. J. Hum. Genet. 64, 250– 258 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  54. Schultes, T., Hummel, S. & Herrmann, B. Amplification of Y-chromosomal STRs from ancient skeletal material. Hum. Genet. 104, 164– 166 (1999).
    Article CAS PubMed Google Scholar
  55. Wang, L. et al. Genetic structure of a 2,500-year-old human population in China and its spatiotemporal changes. Mol. Biol. Evol. 17 , 1396–1400 (2000).
    Article CAS PubMed Google Scholar
  56. Higuchi, R., Bowman, B., Freiberger, M., Ryder, O. A. & Wilson, A. C. DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282–284 (1984).
    Article CAS PubMed Google Scholar
  57. Janczewski, D. N., Yuhki, N., Gilbert, D. A., Jefferson, G. T. & O'Brien, S. J. Molecular phylogenetic inference from saber-toothed cat fossils of Rancho La Brea. Proc. Natl Acad. Sci. USA 89, 9769–9773 ( 1992).
    Article CAS PubMed PubMed Central Google Scholar
  58. Hagelberg, E. et al. DNA from ancient mammoth bones. Nature 370, 333–334 (1994).
    Article CAS PubMed Google Scholar
  59. Höss, M., Pääbo, S. & Vereshchagin, N. K. Mammoth DNA sequences. Nature 370, 333 (1994).
    Article PubMed Google Scholar
  60. Yang, H., Golenberg, E. M. & Shsoshani, J. Phylogenetic resolution within the Elephantidae using fossil DNA sequences from the American mastodon (Mammut americanum) as an outgroup. Proc. Natl Acad. Sci. USA 93, 1190–1194 (1996).
    Article CAS PubMed PubMed Central Google Scholar
  61. Ozawa, T., Hayashi, S. & Mikhelson, V. M. Phylogenetic position of mammoth and Steller's sea cow within Tethytheria demonstrated by mitochondrial DNA sequences . J. Mol. Evol. 44, 406– 413 (1997).
    Article CAS PubMed Google Scholar
  62. Noro, M., Masuda, R., Dubrovo, I. A., Yoshida, M. C. & Kato, M. Molecular phylogenetic inference of the woolly mammoth Mammuthus primigenius, based on complete sequences of mitochondrial cytochrome b and 12S ribosomal RNA genes. J. Mol. Evol. 46, 314–326 (1998).
    Article CAS PubMed Google Scholar
  63. Hänni, C., Laudet, V., Stehelin, D. & Taberlet, P. Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing . Proc. Natl Acad. Sci. USA 91, 12336– 12340 (1994).
    Article PubMed PubMed Central Google Scholar
  64. Robinson, T. J., Bastos, A. D., Halanych, K. M. & Herzig, B. Mitochondrial DNA sequence relationships of the extinct blue antelope Hippotragus leucophaeus. Naturwissenschaften 83 , 178–182 (1996).
    CAS PubMed Google Scholar
  65. Höss, M., Dilling, A., Currant, A. & Pääbo, S. Molecular phylogeny of the extinct ground sloth Mylodon darwinii. Proc. Natl Acad. Sci. USA 93, 181– 185 (1996).
    Article PubMed PubMed Central Google Scholar
  66. Bailey, J. F. et al. Ancient DNA suggests a recent expansion of European cattle from a diverse wild progenitor species. Proc. R. Soc. Lond. B 263, 1467–1473 (1996).
    Google Scholar
  67. Trewick, S. A. Flightlessness and phylogeny amongst endemic rails (aves: Rallidae) of the New Zealand region. Phil. Trans. R. Soc. Lond. B 352 , 429–446 (1996).
    Google Scholar
  68. Houde, P., Cooper, A., Leslie, E., Strand, A. E. & Montano, G. A. in Avian Molecular Evolution Systems and Systematics (ed. Mindell, D. P.) 121–158 (Academic, London, 1997).
    Book Google Scholar
  69. Westerman, M., Springer, M. S., Dixon, J. & Krajewski, C. Molecular relationships of the extinct pig-footed bandicoot Chaeropus ecaudatus (Marsupialia: Perameloidea) using 12S rRNA sequences. J. Mamm. Evol. 6, 271–288 ( 1999).
    Article Google Scholar
  70. Sorenson, M. D. et al. Relationships of the extinct moa-nalos, flightless Hawaiian waterfowl, based on ancient DNA. Proc. R. Soc. Lond. B 266, 2187–2193 (1999).
    Article Google Scholar
  71. Lalueza-Fox, C., Bertranpetit, J., Alcover, J. A., Shailer, N. & Hagelberg, E. Mitochondrial DNA from Myotragus balearicus, an extinct bovid from the Balearic Islands. J. Exp. Zool. 288, 56–62 ( 2000).
    Article CAS PubMed Google Scholar

Download references