Ancient DNA

Proceedings of the Royal Society B: Biological Sciences

Volumn 272, Issue 1558, 2005, Pages 3-16

  Willerslev, Eske ^a   Cooper, Alan ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Ancient DNA; Archaeology; DNA damage and repair; Palaeoecology; Palaeontology; Population genetics

Indexed keywords

DNA; DNA FRAGMENT; MITOCHONDRIAL DNA;

ARCHAEOLOGY; DNA; MOLECULAR ANALYSIS; PALEOECOLOGY; PALEONTOLOGY; POPULATION GENETICS;

ARCHEOLOGY; CONTAMINATION; DNA DAMAGE; DNA REPAIR; DNA TEMPLATE; GENE SEQUENCE; GENOME; HOLOCENE; PALEOECOLOGY; PALEONTOLOGY; PHENOTYPE; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW; SEDIMENT; SPECIES EXTINCTION;

MAMMALIA;

EID: 17044388603     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2004.2813     Document Type: Review

References (141)

1. Adcock, G. J., Dennis, E. S., Easteal, S., Huttley, G. A., Jermin, L. S., Peacock, W. J. & Thorne, A. 2001 Mitochondrial DNA sequences in ancient Australians: implications for modern human origins. Proc. Natl Acad. Sci. USA 98, 537-542.
2. Anderson, P. M., Bartlein, P. J. & Brubaker, L. B. 1994 An early Wisconsin to present history of tundra vegetation in north-western Alaska (U.S.A.). Quatern. Res. 41, 306-315.
3. Austin, J. J., Ross, A. J., Smith, A. B., Fortey, R. A. & Thomas, R. H. 1997a Problems of reproducibility-does geologically ancient DNA survive in amber-preserved insects? Proc. R. Soc. Lond. B 264, 467-474. (doi:10.1098/rspb.1997.0067)
4. Austin, J. J., Smith, A. B. & Thomas, R. H. 19976 Palaeontology in a molecular world: the search for authentic ancient DNA. Trends Ecol. Evol. 12, 303-306.
5. Avise, J. C. 2000 Phylogeography; the history and formation of species. Cambridge, MA: Harvard University Press.
6. Banerjee, M. & Brown, T. A. 2002 Preservation of nuclear but not chloroplast DNA in archaeological assemblages of charred wheat grains. Ancient Biomol. 4, 59-63.
7. Barnes, I., Matheus, P., Shapiro, B., Jensen, D. & Cooper, A. 2002 Dynamics of Pleistocene population extinctions in Beringian brown bears. Science 295, 2267-2270.
8. Brown, T. A. 1999 How ancient DNA may help in understanding the origin and spread of agriculture. Phil. Trans. R. Soc. Lond. B 354, 89-98. (doi:10.1098/rstb.1999.0362)
9. Brown, P., Sutikna, T., Morwood, M. J., Soejono, R. P., Jatmiko, Wayhu Saptomo, E. & Rokus Awe Due 2004 A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia, Nature 431, 1055-1061. (doi:10.1038/ nature02999)
10. Bunce, M., Worthy, T. H., Ford, T., Hoppitt, W., Willerslev, E., Drummond, A. & Cooper, A. 2003 Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425, 172-175.
11. Cano, R. J. & Borucki, M. K. 1995 Revival and identification of bacterial spores in 25-million-year-old to 40-million-year-old Dominican amber. Science 268, 1060-1064.
12. Cano, R. J., Poinar, H. N. & Poinar Jr, G. O. 1992a Isolation and partial characterisation of DNA from the bee Proplebeia dominicana (Apidae: Hymenoptera) in 25-40 million year old amber. Med. Sci. Res. 20, 249-251.
13. Cano, R. J., Poinar, H. N., Roublik, D. W. & Poinar Jr, G. O. 1992b Enzymatic amplification and nucleotide sequencing of portions of the 18S rRNA gene of the bee Proplebeia dominicana (Apidae: Hymenoptera) isolated from 25-40 million year old Dominican amber. Med. Sci. Res. 20, 619-622.
14. Cano, R. J., Poinar, H. N., Pieniezak, N. S. & Poinar Jr, G. O. 1993 Enzymatic amplification and nucleotide sequencing of DNA from 120-135 million year old weevil. Nature 363, 536-538.
15. Cano, R. J., Tiefenbrunner, F., Ubaldi, M., Del Cueto, C., Luciani, S., Cox, T., Orkand, P., Kunzel, K. H. & Rollo, F. 2000 Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman. Am. J. Phys. Anthropol. 112, 297-309.
16. Caramelli, D. (and 10 others) 2003 Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. Proc. Natl Acad. Sci. USA 100, 6593-6597.
17. Christner, B. C., Mosley-Thompson, E., Thompson, L. G. & Reeve, J. N. 2001 Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environ. Microbiol. 3, 570-577.
18. Collins, M. J., Waite, E. R. & van Duin, A. C. T. 1999 Predicting protein decomposition: the case of aspartic-acid racemization kinetics. Phil. Trans. R. Soc. Lond. B 354, 51-64. (doi:10.1098/rstb.1999.0359)
19. Collins, M. J., Nielsen-Marsh, C., Hiller, J., Smith, C. I., Roberts, J. P., Prigodich, R. V., Wess, T. J., Csapo, J., Millard, A. R. & Turner Walker, G. 2002 The survival of organic matter in bone. Archaeometry 44, 383-394.
20. Cooper, A. 1993 DNA from museum specimens. In Ancient DNA (ed. B. Herrmann & S. Hummel), pp. 149-165. New York: Springer.
21. Cooper, A. 1997 Ancient DNA: how do you really know when you have it? Am. J. Hum. Genet. 60, 1001-1002.
22. Cooper, A. & Poinar, H. N. 2001 Ancient DNA: do it right or not at all. Science 18, 289.
23. Cooper, A., Rhymer, J. D., James, H. F., Olson, S. L., McIntosh, C. E., Sorenson, M. D. & Fleischer, R. C. 1996 Ancient DNA and island endemics. Nature 381, 484.
24. Cooper, A., Rambaut, A., Macaulay, V., Willerslev, E., Hansen, A. J. & Stringer, C. 2001a Human origins and ancient human DNA. Science 292, 1655-1656.
25. Cooper, A., Lalueza-Fox, C., Anderson, S., Rambaut, A., Austin, J. & Ward, R. 2001b Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409, 704-707.
26. Cooper, A., Drummond, A. J. & Willerslev, E. 2004 Would the real Neandertal please stand up? Curr. Biol. 14, R463-R464.
27. DePriest, P. T., Ivanova, N. V., Fahselt, D., Alstrup, V. & Gargas, A. 2000 Sequences of psychrophilic fungi amplified from glacier-preserved ascolichens. Can. J. Bot. 78, 1450-1459.
28. DeSalle, R. 1994 Implications of ancient DNA for phylogenetic studies. Experientia 50, 543-550.
29. DeSalle, R., Gatesy, J., Wheeler, W. & Grimaldi, D. 1992 DNA Sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science 257, 1933-1936.
30. DeSalle, R., Barcia, M. & Wray, C. 1993 PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus). Experientia 49, 906-909.
31. Di Bernardo, G., Del Gaudio, S., Cammarota, M., Galderisi, U., Cascino, A. & Cipollaro, M. 2002 Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains. Nucleic Acids Res. 30, e16.
32. Endicott, P., Gilbert, M. T. P., Stringer, C., Lalueza-Fox, C., Willerslev, E., Hansen, A. J. & Cooper, A. 2003 The genetic origins of the Andaman Islanders. Am. J. Hum. Genet. 72, 178-184.
33. Fenchel, T., Esteban, G. F. & Finlay, B. J. 1997 Local versus global diversity of microorganisms: cryptic diversity of ciliated Protozoa. Oikos 80, 220-225.
34. Finlay, J. F. 2002 Global dispersal of free-living microbial eukaryote species. Science 296, 1061-1063.
35. Fish, S. A., Shepherd, T. J., McGenity, T. J. & Grant, W. D. 2002 Recovery of 16S ribosomal RNA gene fragments from ancient halite. Nature 417, 432-436.
36. Fisher, D. A. 2000 Internal layers in an 'accublation' ice cap: a test for flow. Icarus 144, 289-294.
37. Fletcher, H. A., Donoghue, H. D., Holton, J., Pap, I. & Spigelman, M. 2003 Widespread occurrence of Mycobacterium tuberculosis DNA from 18th-19th century Hungarians. Am. J. Phys. Anthropol. 120, 144-152.
38. Geiger, T. & Clarke, S. 1987 Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation. J. Biol. Chem. 262, 785-794.
39. Geigl, E.-M. 2002 On the circumstances surrounding the preservation and analysis of very old DNA. Archaeometry 44, 337-342.
40. Gilbert, M. T. P., Willerslev, E., Hansen, A. J., Barnes, I., Rudbeck, L., Lynnerup, N. & Cooper, A. 2003a Distribution patterns of post-mortem damage in human mitochondrial DNA. Am. J. Hum. Genet. 72, 32-47.
41. Gilbert, M. T. P., Hansen, A. J., Willerslev, E., Barnes, I., Rudbeck, L., Lynnerup, N. & Cooper, A. 2003b Characterisation of genetic miscoding lesions caused by post-mortem damage. Am. J. Hum. Genet. 72, 48-61.
42. Gilbert, M. T. P. (and 10 others) 2004a Ancient mitochondrial DNA from hair. Curr. Biol. 14, R463-R464.
43. Gilbert, M. T. P., Cuccui, J., White, W., Lynnerup, N., Titball, R. W., Cooper, A. & Prentice, M. B. 2004b Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. Microbiology 150, 341-354.
44. Gilbert, M. T. P., Barnes, I., Collins, M. J., Smith, C., Eklund, J., Goudsmit, J., Poinar, H. & Cooper, A. 2005a News and comments: the long-term survival of ancient DNA in Egypt: response to Zink and Nerlich. Am. J. Phys. Anthropol. (In the press.)
45. Gilbert, M. T. P. (and 14 others) 2005b Biochemical and physical correlates of DNA contamination in archaeological bones and teeth. J. Arch. Sci. (In the press.)
46. Goldstein, P. E. & DeSalle, R. 2003 Calibrating phylogenetic species formation in a threatened species using DNA from historical specimens. Mol. Ecol. 12, 1993-1998.
47. Golenberg, E. M., Giannassi, D. E., Clegg, M. T., Smiley, C. J., Durbin, M., Henderson, D. & Zurawski, G. 1990 Chloroplast DNA from a Miocene Magnolia species. Nature 344, 656-658.
48. Graur, D. & Pupko, T. 2001 The Permian bacterium that isn't. Mol. Biol. Evol. 18, 1143-1146.
49. Greenwood, A. D., Capelli, C., Possnert, G. & Pääbo, S. 1999 Nuclear DNA sequences from late Pleistocene megafauna. Mol. Biol. Evol. 16, 1466-1473.
50. Greenwood, A. D., Lee, F., Capelli, C., DeSalle, R., Tikhonov, A., Marx, P. A. & MacPhee, R. D. E. 2001 Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives. Mol. Biol. Evol. 18, 840-847.
51. Guthrie, R. D. 1990 Frozen Fauna of the mammoth steppe: the story of blue babe. The University of Chicago Press.
52. Gutiérrez, G. & Marín, A. 1998 The most ancient DNA recovered from an amber-preserved specimen may not be as ancient as it seems. Mol. Biol. Evol. 15, 926-929.
53. Haddrath, O. & Baker, A. J. 2001 Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R. Soc. Lond. B 268, 939-945. (doi:10.1098/rspb.2001.1587)
54. Handt, O., Höss, M., Krings, M. & Pääbo, S. 1994 Ancient DNA: methodological challenges. Experientia 50, 524-529.
55. Handt, O., Krings, M., Ward, R. H. & Pääbo, S. 1996 The retrieval of ancient human DNA sequences. Am. J. Hum. Genet. 59, 376-386.
56. Hansen, A. J. & Willerslev, E. 2002 Perspectives for DNA studies on polar ice cores. In The Patagonian icefields: a unique natural laboratory for environmental and climate change studies (ed. G. Casassa, et al.), pp. 17-29. Kluwer Academic/Plenum Publishers.
57. Hansen, A. J., Willerslev, E., Wiuf, C., Mourier, T. & Arctander, P. 2001 Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol. 18, 262-265.
58. Hansen, A. J., Willerslev, E., Mørk, S., Hedegaard, M. M., Rønn, R. & Jeffares, D. C. 2002 JAWS: just add water system - a device for detection of nucleic acids in the Martian ice caps. In Proc. 2nd Eur. Workshop on Exo/Astrobiology Graz, Austria (ESA SP-518, November 2002) (ed. H. Lacoste), pp. 309-311. ESA Publication Division, ESTEC.
59. Hauswirth, W. W., Dickel, C. D., Rowold, D. J. & Hauswirth, M. A. 1994 Inter- and intra-population studies of ancient humans. Experientia 50, 585-591.
60. Herrmann, B. & Hummel, S. 1996 Ancient DNA. New York: Springer.
61. 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.
62. Hofreiter, M., Jaenicke, V., Serre, S., von Haeseler, A. & Pääbo, S. 2001a DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29, 4793-4799.
63. Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M. & Pääbo, S. 2001b Ancient DNA. Nature Rev. Genet. 2, 353-360.
64. Hofreiter, M. (and 12 others) 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.
65. Hofreiter, M., Mead, J. I., Martin, P. & Poinar, N. H. 2003 Molecular caving. Curr. Biol. 13, 693-695.
66. Hofreiter, M., Rabeder, G., Jaenicke-Després, V., Withalm, G., Nagel, D., Paunovic, M., Jambresiç, G. & Pääbo, S. 2004 Evidence for reproductive isolation between cave bear populations. Curr. Biol. 14, 40-43.
67. Horneck, G., Bücker, H. & Reitz, G. 1994 Long-term survival of bacterial spores in space. Adv. Space Res. 14, 41-45.
68. Höss, M., Pääbo, S. & Vereshchagin, N. K. 1994 Mammoth DNA sequences. Nature 370, 333.
69. Höss, M., Jaruga, P., Zastawny, T. H., Dizdaroglu, M. & Pääbo, S. 1996 DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24, 1304-1307.
70. Huynen, L. C., Millar, D., Scofield, R. P. & Lambert, D. M. 2003 Nuclear DNA sequences detect species limits in ancient moa. Nature 425, 175-178.
71. Jaenicke-Després, V., Buckler, E., Smith, B. D., Gilbert, M. T. P., Cooper, A., Doebley, J. & Pääbo, S. 2003 Early allelic selection in maize as revealed by ancient DNA. Science 302, 1206-1208.
72. Kennedy, M. J., Reader, S. L. & Swierczynski, L. M. 1994 Preservation records of microorganisms: evidence of the tenacity of life. Microbiology 140, 2513-2529.
73. Kim, S., Soltis, D. E., Soltis, P. S. & Sue, Y. 2004 DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae). Am. J. Bot. 91, 615-620.
74. Kolman, C. & Tuross, N. 2000 Ancient DNA analysis of human populations. Am. J. Phys. Anthropol. 111, 5-23.
75. Krings, M., Stone, A., Schmilz, R. W., Krainitzki, H., Stoneking, M. & Pääbo, S. 1997 Neandertal DNA sequences and the origin of modern humans. Cell 90, 19-30.
76. Krings, M., Geisert, H., Schmitz, R., Krainitzki, H. & Pääbo, S. 1999 DNA sequence of the mitochondrial hypervariable region II from the Neanderthal type specimen. Proc. Natl Acad. Sci. USA 96, 5581-5585.
77. Krings, M., Capelli, C., Tschentscher, F., Geisert, H., Meyer, S., von Haeseler, A., Grossschmidt, K., Possnert, G., Paunovic, M. & Pääbo, S. 2000 A view of Neandertal genetic diversity. Nature Genet. 26, 144-146.
78. Kwok, S. & Higuchi, R. 1989 Avoiding false positives with PCR. Nature 339, 237-238.
79. Lambert, D. M., Ritchie, P. A., Millar, C. D., Holland, B. J., Drummond, A. & Baroni, C. 2001 Rates of evolution in ancient DNA from Adélie penguins. Science 295, 2270-2273.
80. Leonard, J. A., Wayne, R. K. & Cooper, A. 2000 Population genetics of Ice Age brown bears. Proc. Natl Acad. Sci. USA 97, 1651-1654.
81. Leonard, J. A., Wayne, R. K., Wheeler, J., Valadez, R., Guillén, S. & Vilà, C. 2002 Ancient DNA evidence for old world origin of new world dogs. Science 298, 1613-1616.
82. Lindahl, T. 1993 Instability and decay of the primary structure of DNA. Nature 362, 709-715.
83. Loreille, O., Orlando, L., Patou-Mathis, M., Philippe, M., Taberlet, P. & Hänni, C. 2001 Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr. Biol. 11, 200-203.
84. Lorenz, M. G. & Wackernagel, W. 1994 Bacterial transfer by natural genetic transformation in the environment. Microbiol. Rev. 58, 563-602.
85. Lydolph, M. C., Jacobsen, J., Arctander, P., Gilbert, M. T. P., Gilicinsky, D. A., Hansen, A. J., Willerslev, E. & Lange, L. 2004 Beringian paleoecology inferred from permafrost-preserved fungi DNA. Appl. Environ. Microbiol. (In the press.)
86. Ma, L.-J., Rogers, S. O., Catranis, C. M. & Starmer, W. T. 1999 Detection and characterization of ancient fungi entrapped in glacial ice. Mycologia 92, 286-295.
87. Maca-Meyer, N., Arnay, M., Rando, J. C., Flores, C., Gonzaléz, A. M., Cabrera, V. M. & Larruga, J. M. 2004 Ancient mtDNA analysis and the origin of the Guanches. Eur. J. Hum. Genet. 12, 155-162.
88. Marota, I., Basile, C., Ubaldi, M. & Rollo, F. D. 2002 DNA decay rate in papyri and human remains from Egyptian archaeological sites. Am. J. Phys. Anthropol. 117, 310-318.
89. Martin, P. S. 1984 Prehistoric overkill: the global model. In Quaternary extinctions (ed. P. S. Martin & R. G. Klein), pp. 345-403. Tucson, AZ: University of Arizona Press.
90. Morwood, M. J. (and 13 others) 2004 Archaeology and age of a new hominin from Flores in eastern Indonesia. Nature 431, 1087-1091.
91. Mourier, T., Hansen, A. J., Willerslev, E. & Arctander, P. 2001 The human genome project reveals a continuous transfer of evenly distributed large mitochondrial fragments to the nucleus. Mol. Biol. Evol. 18, 1833-1837.
92. Nicholson, W. L., Munakata, N., Horneck, G., Melosh, H. J. & Setlow, P. 2000 Resistance of bacterial endospores to extreme terrestrial and extraterrestrial environments. Mol. Bio. Rev. 64, 548-572.
93. Nickle, D. C., Learn, G. H., Rain, M. W., Mullins, J. I. & Mittler, J. E. 2002 Curiously modern DNA for a '250 million-year-old' bacterium. J. Mol. Evol. 54, 134-137.
94. Nielsen-Marsh, C. M., Ostrom, P. H., Gandhi, H., Shapiro, B., Cooper, A., Hauschka, P. V. & Collins, M. J. 2002 Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka. Geology 30, 1099-1102.
95. O'Donoghue, K., Clapham, A., Evershed, R. P. & Brown, T. A. 1996 Remarkable preservation of biomolecules in ancient radish seeds. Proc. R. Soc. Lond. B 263, 541-547.
96. Orlando, L., Leonard, J. A., Thenot, A., Laudet, V., Guerin, G. & Hänni, C. 2003 Ancient DNA analysis reveals woolly rhino evolutionary relationships. Mol. Phylogenet. Evol. 28, 76-90.
97. Ovchinnikov, I., Götherström, A., Romanova, G., Kharitonov, V., Lidén, K. & Goodwin, W. 2000 Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404, 490-493.
98. Pääbo, S. 1985 Molecular cloning of ancient Egyptian mummy DNA. Nature 314, 644-645.
99. Pääbo, S. 1989 Ancient DNA; extraction, characterization, molecular cloning and enzymatic amplification. Proc. Natl Acad. Sci. USA 86, 1939-1943.
100. Pääbo, S. & Wilson, A. C. 1988 Polymerase chain reaction reveals cloning artefacts. Nature 334, 387-388.
101. Pääbo, S., Higuchi, R. G. & Wilson, A. C. 1989 Ancient DNA and the polymerase chain reaction. J. Biol. Chem. 264, 9709-9712.
102. Poinar, H. N. & Stankiewicz, B. A. 1999 Protein preservation and DNA retrieval from ancient tissues. Proc. Natl Acad. Sci. USA 96, 8426-8431.
103. Poinar, H. N., Poinar Jr, G. O. & Cano, R. J. 1993 DNA from an extinct plant. Nature 363, 677.
104. Poinar, H. N., Höss, M., Bada, J. L. & Pääbo, S. 1996 Amino acid racemization and the preservation of ancient DNA. Science 272, 864-866.
105. Poinar, H. N., Hofreiter, M., Spaulding, G. S., Martin, P. S., Stankiewicz, A. B., 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.
106. Poinar, H. N., Kuch, M., McDonald, G., Martin, P. & Pääbo, S. 2003 Nuclear gene sequences from a Late Pleistocene sloth coprolite. Curr. Biol. 13, 1150-1152.
107. Priscu, J. C. (and 11 others) 1999 Geomicrobiology of subglacial ice above Lake Vostok, Antarctica. Science 286, 2141-2144.
108. Pusch, C. M. & Bachmann, L. 2004 Spiking of contemporary human template DNA with ancient DNA extracts induces mutations under PCR and generates non-authentic mitochondrial sequences. Mol. Biol. Evol. 211, 957-964.
109. Raoult, D., Aboudharam, G., Crubezy, E., Larrouy, G., Ludes, B. & Drancourt, M. 2000 Molecular identification by 'suicide PCR' of Yersinia pestis as the agent of medieval black death. Proc. Natl Acad. Sci. USA 97, 12 800-12 803.
110. Reid, A. H., Fanning, T. G., Hultin, J. V. & Taubenberger, J. K. 1999 Origin and evolution of the 1918 'Spanish' influenza virus hemagglutinin gene. Proc. Natl Acad. Sci. USA 96, 1651-1656.
111. Richards, M., Sykes, B. & Hedges, R. 1995 Authenticating DNA extracted from ancient skeletal remains. J. Archeol. Sci. 22, 291-299.
112. Ritchie, P. A., Millar, C. D., Gibb, G. C., Baroni, C. & Lambert, D. M. 2004 Ancient DNA enables timing of the Pleistocene origin and Holocene expansion of two Adélie penguin lineages in Antarctica. Mol. Biol. Evol. 21, 240-248.
113. Rollo, F. S. & Amici, A. 1991 Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize. Genet. Res. 58, 193-201.
114. Rollo, F. & Marota, I. 1999 How microbial ancient DNA, found in association with human remains, can be interpreted. Phil. Trans. R. Soc. Lond. B 354, 111-119. (doi:10.1098/rstb.1999.0364)
115. Rollo, F., Sassaroli, S. & Ubaldi, M. 1995 Molecular phylogeny of the fungi of the iceman's grass clothing. Curr. Genet. 28, 289-297.
116. Rollo, F., Ubaldi, M., Ermini, L. & Marota, I. 2002 Ötzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proc. Natl Acad. Sci. USA 99, 12594-12599.
117. Rothschild, B. M., Martin, L. D., Lev, G., Bercovier, H., Bar-Gal, G. K., Greenblatt, C., Donoghue, H., Spigelman, M. & Brittain, D. 2001 Mycobacterium tuberculosis complex DNA from an extinct bison dated 17,000 years before the present. Clin. Infect. Dis. 33, 305-311.
118. Schmitz, R. W., Serre, D., Bonani, G., Feine, S., Hillgruber, F., Krainitzki, H., Pääbo, S. & Smith, F. H. 2002 The Neandertal type-site revisited: interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc. Natl Acad. Sci. USA 99, 13 342-13 347.
119. Serre, D., Langaney, A., Chech, M., Teschler-Nicola, M., Paunovic, M., Mennecier, P., Hofreiter, M., Possnert, G. & Pääbo, S. 2004a No evidence of Neandertal mtDNA contribution to early modern humans. PLOS Biol. 2, 313-317.
120. Serre, D., Hofreiter, M. & Pääbo, S. 2004b Mutations induced by ancient DNA extracts? Mol. Biol. Evol. 21, 1463-1467.
121. Shapiro, B. (and 25 others) 2004 The impact of large-scale climate change on genetic diversity in large mammal populations. Science. (In the press.)
122. Shi, T., Reeves, R. H., Gilichinsky, D. A. & Friedmann, E. I. 1997 Characterization of viable bacteria in Siberian permafrost by 16S rDNA sequencing. Microbiol. Ecol. 33, 169-179.
123. Shi-yi, H. 1997 A cytological study of plasmid inheritance in angiosperms. Acta Botanica Sinica 391, 363-371.
124. Sidow, A., Wilson, A. C. & Pääbo, S. 1991 Bacterial DNA in Clarkia fossils. Phil. Trans. R. Soc. Lond. B 333, 429-433.
125. Smith, C. I., Chamberlain, A. T., Riley, M. S., Cooper, A., Stringer, C. B. & Collins, M. J. 2001 Neanderthal DNA: not just old but old and cold? Nature 10, 771-772.
126. Soltis, P. S., Soltis, D. E. & Smiley, C. J. 1992 An rbcL sequence from a Miocene Taxodium (bald cypress). Proc. Natl Acad. Sci. USA 89, 449-451.
127. Thomas, R. H., Schaffner, W., Wilson, A. C. & Pääbo, S. 1989 DNA phylogeny of the extinct marsupial wolf. Nature 340, 465-467.
128. Vila, C., Leonard, J. A., Gotherstrom, A., Marklund, S., Sandberg, K., Liden, K., Wayne, R. K. & Ellegren, H. 2001 Widespread origins of domestic horse lineages. Science 291, 474-477.
129. Vorobyova, E., Soina, V., Gorlenko, M., Minkovskaya, N., Zalinova, N., Mamukelashvili, A., Gilichinsky, D. A., Rivkina, E. & Vishnivetskaya, T. 1997 The deep cold biosphere: facts and hypotheses. FEMS Microbiol. Rev. 20, 277-290.
130. Vreeland, R. H. & Rosenzweig, W. D. 2002 The question of uniqueness of ancient bacteria. J. Ind. Microbiol. Biotechnol. 28, 32-41.
131. 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.
132. Ward, D. M., Bateson, M. M., Weller, R. & Ruff-Roberts, A. L. 1992 Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microbial Ecol. 12, 219-286.
133. 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.
134. Willerslev, E., Hansen, A. J., Brand, T. B., Binladen, J., Gilbert, M. T. P., Shapiro, B., Bunce, M., Wiuf, C., Gilichinsky, D. A. & Cooper, A. 2003a Diverse plant and animal DNA from Holocene and Pleistocene sedimentary records. Science 300, 792-795.
135. Willerslev, E., Hansen, A. J., Rønn, R. & Nielsen, O. J. 2003b Panspermia-true or false? Lancet 362, 406.
136. Willerslev, E., Hansen, A. J., Brand, T. B., Rønn, R., Barnes, I., Wiuf, C., Gilichinsky, D. A., Mitchell, D. & Cooper, A. 2004a Long-term persistence of bacterial DNA. Curr. Biol. 14, R9-R10.
137. Willerslev, E., Hansen, A. J. & Poinar, H. N. 2004b Isolation of nucleic acids and cultures from ice and permafrost. Trends Ecol. Evol. 19, 141-147.
138. Woodward, S. R., Weyand, N. J. & Bunell, M. 1994 DNA sequence from Cretaceous period bone fragments. Science 266, 1229-1232.
139. Zink, A., Haas, C. J., Reischl, U., Szeimies, U. & Nerlich, A. G. 2001 Molecular analysis of skeletal tuberculosis in an ancient Egyptian population. J. Med. Microbiol. 50, 355-366.
140. Zischler, H., Höss, M., Handt, O., von Haeseler, A., van der Kuyl, A. C., Goudsmit, J. & Pääbo, S. 1995a Detecting dinosaur DNA. Science 268, 1192-1193.
141. Zischler, H., Geisert, H., von Haeseler, A. & Pääbo, S. 2003a A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans. Nature 378, 489-492.