1932

Abstract

▪ Abstract 

About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.

Loading

Article metrics loading...

/content/journals/10.1146/annurev.genet.37.110801.143214
2004-12-15
2024-10-03
Loading full text...

Full text loading...

/deliver/fulltext/ge/38/1/annurev.genet.37.110801.143214.html?itemId=/content/journals/10.1146/annurev.genet.37.110801.143214&mimeType=html&fmt=ahah

Literature Cited

  1. Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS. et al. 2001. Mitochondrial DNA sequences in ancient Australians: implications for modern human origins. Proc. Natl. Acad. Sci. USA 98:537–42 [Google Scholar]
  2. Allard MW, Young D, Huyen Y. 1995. Detecting dinosaur DNA. Science 268:1192 [Google Scholar]
  3. Andrews LB, Buenger N, Bridge J, Rosenow L, Stoney D. et al. 2004. Constructing ethical guidelines for biohistory. Science 304:215–16 [Google Scholar]
  4. Arriaza BT, Salo W, Aufderheide AC, Holcomb TA. 1995. Pre-Columbian tuberculosis in Northern Chile—molecular and skeletal evidence. Am. J. Phys. Anthropol. 98:37–45 [Google Scholar]
  5. Austin JJ, Ross AJ, Smith AB, Fortey RA, Thomas RH. 1997. Problems of reproducibility—does geologically ancient DNA survive in amber-preserved insects. Proc. R. Soc. London Ser. B 264:467–74 [Google Scholar]
  6. Bailey JF, Richards MB, Macaulay VA, Colson IB, James IT. et al. 1996. Ancient DNA suggests a recent expansion of European cattle from a diverse wild progenitor species. Proc. R. Soc. London Ser. B 263:1467–73 [Google Scholar]
  7. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A. 2002. Dynamics of Pleistocene population extinctions in Beringian brown bears. Science 295:2267–70 [Google Scholar]
  8. Barnes I, Young JPW, Dobney KM. 2000. DNA-based identification of goose species from two archaeological sites in Lincolnshire. J. Archaeolog. Sci. 27:91–100 [Google Scholar]
  9. Bensasson D, Zhang DX, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 16:314–21 [Google Scholar]
  10. Bunce M, Worthy TH, Ford T, Hoppitt W, Willerslev E. et al. 2003. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425:172–75 [Google Scholar]
  11. Burger J, Rosendahl W, Loreille O, Hemmer H, Eriksson T. et al. 2004. Molecular phylogeny of the extinct cave lion Panthera leo spelaea. Mol. Phylogenet. Evol. 30:841–49 [Google Scholar]
  12. Cano RJ, Borucki MK. 1995. Revival and identification of bacterial-spores in 25-million-year-old to 40-million-year-old Dominican amber. Science 268:1060–64 [Google Scholar]
  13. Cano RJ, Poinar HN, Pieniazek NJ, Acra A, Poinar GO. 1993. Amplification and sequencing of DNA from a 120–135-million-year-old weevil. Nature 363:536–38 [Google Scholar]
  14. Caramelli D, Lalueza-Fox C, Vernesi C, Lari M, Casoli A. et al. 2003. Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. Proc. Natl. Acad. Sci. USA 100:6593–97 [Google Scholar]
  15. Collins MJ, Waite ER, van Duin ACT. 1999. Predicting protein decomposition: the case of aspartic-acid racemization kinetics. Philos. Trans. R. Soc. London Ser. B 354:51–64 [Google Scholar]
  16. Colson IB, Richards MB, Bailey JF, Sykes BC, Hedges REM. 1997. DNA analysis of seven human skeletons excavated from the terp of Wijnaldum. J. Archaeolog. Sci. 24:911–17 [Google Scholar]
  17. Constable JJ, Packer C, Collins DA, Pusey AE. 1995. Nuclear DNA from primate dung. Nature 373:393 [Google Scholar]
  18. 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 409:704–7 [Google Scholar]
  19. Cooper A, Mourer-Chauvire C, Chambers GK, von Haeseler A, Wilson AC, Pääbo S. 1992. Independent origins of New Zealand moas and kiwis. Proc. Natl. Acad. Sci. USA 89:8741–44 [Google Scholar]
  20. Cooper A, Poinar HN. 2000. Ancient DNA: Do it right or not at all. Science 289:1139 [Google Scholar]
  21. Debruyne R, Barriel V, Tassy P. 2003. Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae. Mol. Phylogenet. Evol. 26:421–34 [Google Scholar]
  22. Desalle R, Gatesy J, Wheeler W, Grimaldi D. 1992. DNA sequences from a fossil termite in Oligomiocene amber and their phylogenetic implications. Science 257:1933–36 [Google Scholar]
  23. Donoghue HD, Spigelman M, Zias J, Gernaey-Child AM, Minnikin DE. 1998. Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old. Lett. Appl. Microbiol. 27:265–69 [Google Scholar]
  24. Drancourt M, Aboudharam G, Signoli M, Dutour O, Raoult D. 1998. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia. Proc. Natl. Acad. Sci. USA 95:12637–40 [Google Scholar]
  25. Duarte C, Mauricio J, Pettitt PB, Souto P, Trinkaus E. et al. 1999. The early Upper Paleolithic human skeleton from the Abrigo do Lagar Velho (Portugal) and modern human emergence in Iberia. Proc. Natl. Acad. Sci. USA 96:7604–9 [Google Scholar]
  26. Eglinton G, Logan GA. 1991. Molecular preservation. Philos. Trans. R. Soc. London Ser. B 333:315–27 discussion 27–28 [Google Scholar]
  27. Endicott P, Gilbert MTP, Stringer C, Lalueza-Fox C, Willerslev E. et al. 2003. The genetic origins of the Andaman Islanders. Am. J. Hum. Genet. 72:178–84 [Google Scholar]
  28. Enflo P, Hawks J, Wolpoff M. 2001. A simple reason why Neanderthal ancestry can be consistent with current DNA information. Am. J. Phys. Anthropol. 114:62 [Google Scholar]
  29. Fish SA, Shepherd TJ, McGenity TJ, Grant WD. 2002. Recovery of 16S ribosomal RNA gene fragments from ancient halite. Nature 417:432–36 [Google Scholar]
  30. Fletcher HA, Donoghue HD, Holton J, Pap I, Spigelman M. 2003. Widespread occurrence of Mycobacterium tuberculosis DNA from 18th–19th century Hungarians. Am. J. Phys. Anthropol. 120:144–52 [Google Scholar]
  31. Friedberg EC, Walker GC, Siede W. 1995. DNA Repair and Mutagenesis Washington, DC: ASM Press698pp. [Google Scholar]
  32. Gilbert MTP, Cuccui J, White W, Lynnerup N, Titball RW. et al. 2004. Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. Microbiology-Sgm 150:341–54 [Google Scholar]
  33. Gilbert MTP, Hansen AJ, Willerslev E, Rudbeck L, Barnes I. et al. 2003. Characterization of genetic miscoding lesions caused by postmortem damage. Am. J. Hum. Genet. 72:48–61 [Google Scholar]
  34. Gilbert MTP, Willerslev E, Hansen AJ, Barnes I, Rudbeck L. et al. 2003. Distribution patterns of postmortem damage in human mitochondrial DNA. Am. J. Hum. Genet. 72:32–47 [Google Scholar]
  35. Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M. et al. 1990. Chloroplast DNA sequence from a miocene Magnolia species. Nature 344:656–58 [Google Scholar]
  36. Goloubinoff P, Pääbo S, Wilson AC. 1993. Evolution of maize inferred from sequence diversity of an adh2 gene segment from archaeological specimens. Proc. Natl. Acad. Sci. USA 90:1997–2001 [Google Scholar]
  37. Greenwood AD, Castresana J, Feldmaier-Fuchs G, Pääbo S. 2001. A molecular phylogeny of two extinct sloths. Mol. Phylogenet. Evol. 18:94–103 [Google Scholar]
  38. Greenwood AD, Capelli C, Possnert G, Pääbo S. 1999. Nuclear DNA sequences from Late Pleistocene megafauna. Mol. Biol. Evol. 16:1466–73 [Google Scholar]
  39. Greenwood AD, Lee F, Capelli C, DeSalle R, Tikhonov A. et al. 2001. Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives. Mol. Biol. Evol. 18:840–47 [Google Scholar]
  40. Haas CJ, Zink A, Molnar E, Szeimies U, Reischl U. et al. 2000. Molecular evidence for different stages of tuberculosis in ancient bone samples from Hungary. Am. J. Phys. Anthropol. 113:293–304 [Google Scholar]
  41. Haddrath O, Baker AJ. 2001. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R Soc. London Ser. B 268:939–45 [Google Scholar]
  42. Hadly EA, Kohn MH, Leonard JA, Wayne RK. 1998. A genetic record of population isolation in pocket gophers during Holocene climatic change. Proc. Natl. Acad. Sci. USA 95:6893–96 [Google Scholar]
  43. Hagelberg E, Thomas MG, Cook CE Jr., Sher AV, Baryshnikov GF, Lister AM. 1994. DNA from ancient mammoth bones. Nature 370:333–34 [Google Scholar]
  44. Hale ML, Lurz PW, Shirley MD, Rushton S, Fuller RM, Wolff K. 2001. Impact of landscape management on the genetic structure of red squirrel populations. Science 293:2246–48 [Google Scholar]
  45. Handt O, Höss M, Krings M, Pääbo S. 1994. Ancient DNA: methodological challenges. Experientia 50:524–29 [Google Scholar]
  46. Handt O, Krings M, Ward RH, Pääbo S. 1996. The retrieval of ancient human DNA sequences. Am. J. Hum. Genet. 59:368–76 [Google Scholar]
  47. Handt O, Richards M, Trommsdorf M, Kilger C, Simanainen J. et al. 1994. Molecular genetic analyses of the Tyrolean Ice Man. Science 264:1775–78 [Google Scholar]
  48. Hänni C, Begue A, Laudet V, Stehelin D, Brousseau T. et al. 1995. Molecular typing of Neolithic human bones. J. Archaeolog. Sci. 22:649–58 [Google Scholar]
  49. Hänni C, Laudet V, Stehelin D, Taberlet P. 1994. Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing. Proc. Natl. Acad. Sci. USA 91:12336–40 [Google Scholar]
  50. Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P. 2001. Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol. 18:262–65 [Google Scholar]
  51. Hardy C, Callou C, Vigne JD, Casane D, Dennebouy N. et al. 1995. Rabbit mitochondrial DNA diversity from prehistoric to modern times. J. Mol. Evol. 40:227–37 [Google Scholar]
  52. Hawks JD, Wolpoff MH. 2001. The accretion model of Neandertal evolution. Evolution 55:1474–85 [Google Scholar]
  53. Hedges SB, Schweitzer MH. 1995. Detecting dinosaur DNA. Science 268:1191–92 [Google Scholar]
  54. Henikoff S. 1995. Detecting dinosaur DNA. Science 268:1192 [Google Scholar]
  55. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. 1984. DNA sequences from the quagga, an extinct member of the horse family. Nature 312:282–84 [Google Scholar]
  56. Hofreiter M, Betancourt JL, Sbriller AP, Markgraf V, McDonald HG. 2003. Phylogeny, diet, and habitat of an extinct ground sloth from Cuchillo Cura, Neuquen Province, southwest Argentina. Quat. Res. 59:364–78 [Google Scholar]
  57. Hofreiter M, Capelli C, Krings M, Waits L, Conard N. et al. 2002. Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of Late Pleistocene cave bears. Mol. Biol. Evol. 19:1244–50 [Google Scholar]
  58. Hofreiter M, Jaenicke V, Serre D, Haeseler Av Pääbo S. 2001. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29:4793–99 [Google Scholar]
  59. Hofreiter M, Mead JI, Martin P, Poinar HN. 2003. Molecular caving. Curr. Biol. 13:R693–95 [Google Scholar]
  60. Hofreiter M, Poinar HN, Spaulding WG, Bauer K, Martin PS. et al. 2000. A molecular analysis of ground sloth diet through the last glaciation. Mol. Ecol. 9:1975–84 [Google Scholar]
  61. Hofreiter M, Rabeder G, Jaenicke-Despres V, Withalm G, Nagel D. et al. 2004. Evidence for reproductive isolation between cave bear populations. Curr. Biol. 14:40–43 [Google Scholar]
  62. Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S. 2001. Ancient DNA. Nat. Rev. Genet. 2:353–59 [Google Scholar]
  63. Hofreiter M, Vigilant L. 2003. Ancient human DNA: phylogenetic applications. In Nature Encyclopedia of the Human Genome ed. DN Cooper pp. 116–19 London: Nature Publ. Group [Google Scholar]
  64. Höss M, Dilling A, Currant A, Pääbo S. 1996. Molecular phylogeny of the extinct ground sloth Mylodon darwinii. Proc. Natl. Acad. Sci. USA 93:181–85 [Google Scholar]
  65. Höss M, Jaruga P, Zastawny TH, Dizdaroglu M, Pääbo S. 1996. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24:1304–7 [Google Scholar]
  66. Höss M, Kohn M, Pääbo S, Knauer F, Schröder W. 1992. Excrement analysis by PCR. Nature 359:199 [Google Scholar]
  67. Höss M, Pääbo S, Vereshchagin NK. 1994. Mammoth DNA sequences. Nature 370:333 [Google Scholar]
  68. Huynen L, Millar CD, Scofield RP, Lambert DM. 2003. Nuclear DNA sequences detect species limits in ancient moa. Nature 425:175–78 [Google Scholar]
  69. Jaenicke-Despres V, Buckler ES, Smith BD, Gilbert MTP, Cooper A. et al. 2003. Early allelic selection in maize as revealed by ancient DNA. Science 302:1206–8 [Google Scholar]
  70. Jans MME, Nielsen-Marsh CM, Smith CI, Collins MJ, Kars H. 2004. Characterisation of microbial attack on archaeological bone. J. Archaeolog. Sci. 31:87–95 [Google Scholar]
  71. Jones M. 2003. Ancient DNA in pre-Columbian archaeology: a review. J. Archaeolog. Sci. 30:629–35 [Google Scholar]
  72. Kahila Bar-Gal G, Khalaily H, Mader O, Ducos P, Kolska Horwitz L. 2002. Ancient DNA evidence for the transition from wild to domestic status in Neolithic goats: a case study from the site of Abu Gosh, Israel. Ancient Biomolecules 4:9–17 [Google Scholar]
  73. Kohn MH, Wayne RK. 1997. Facts from feces revisited. Trends Ecol. Evol. 12:223–27 [Google Scholar]
  74. Kolmann CJ, Tuross N. 2000. Ancient DNA analysis of human populations. Am. J. Phys. Anthropol. 111:5–23 [Google Scholar]
  75. Koon HEC, Nicholson RA, Collins MJ. 2003. A practical approach to the identification of low temperature heated bone using TEM. J. Archaeolog. Sci. 13:1393–99 [Google Scholar]
  76. Krajewski C, Buckley L, Westerman M. 1997. DNA phylogeny of the marsupial wolf resolved. Proc. R. Soc. London Ser. B 264:911–17 [Google Scholar]
  77. Krajewski C, Driskell AC, Baverstock PR, Braun MJ. 1992. Phylogenetic relationships of the thylacine (Mammalia: Thylacinidae) among dasyuroid marsupials: evidence from cytochrome b DNA sequences. Proc. R. Soc. London Ser. B 250:19–27 [Google Scholar]
  78. Krings M, Capelli C, Tschentscher F, Geisert H, Meyer S. et al. 2000. A view of Neandertal genetic diversity. Nat. Genet. 26:144–46 [Google Scholar]
  79. Krings M, Geisert H, Schmitz RW, Krainitzki H, Pääbo S. 1999. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl. Acad. Sci. USA 96:5581–85 [Google Scholar]
  80. Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S. 1997. Neandertal DNA sequences and the origin of modern humans. Cell 90:19–30 [Google Scholar]
  81. Lambert DM, Ritchie PA, Millar CD, Holland B, Drummond AJ, Baroni C. 2002. Rates of evolution in ancient DNA from Adelie penguins. Science 295:2270–73 [Google Scholar]
  82. Larson S, Jameson R, Etnier M, Fleming M, Bentzen P. 2002. Loss of genetic diversity in sea otters (Enhydra lutris) associated with the fur trade of the 18th and 19th centuries. Mol Ecol. 11:1899–903 [Google Scholar]
  83. Leonard JA, Wayne RK, Cooper A. 2000. Population genetics of Ice Age brown bears. Proc. Natl. Acad. Sci. USA 97:1651–54 [Google Scholar]
  84. Leonard JA, Wayne RK, Wheeler J, Valadez R, Guillen S, Vila C. 2002. Ancient DNA evidence for Old World origin of New World dogs. Science 298:1613–16 [Google Scholar]
  85. Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature 362:709–15 [Google Scholar]
  86. Lindahl T. 1993. Recovery of antediluvian DNA. Nature 365:700 [Google Scholar]
  87. Lindahl T, Karlstro O. 1973. Heat-induced depyrimidination of deoxyribonucleic acid in neutral solution. Biochemistry 12:5151–54 [Google Scholar]
  88. Lindahl T, Nyberg B. 1972. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11:3610 [Google Scholar]
  89. Logan GA, Smiley CJ, Eglinton G. 1995. Preservation of fossil leaf waxes in association with their source tissues, Clarkia, Northern Idaho, USA. Geochim. Cosmochim. Acta 59:751–63 [Google Scholar]
  90. 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. 11:200–3 [Google Scholar]
  91. Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley J. 2002. A single domestication for maize shown by multilocus microsatellite genotyping. Proc. Natl. Acad. Sci. USA 99:6080–84 [Google Scholar]
  92. Miller CR, Waits LP. 2003. The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): implications for conservation. Proc. Natl. Acad. Sci. USA 100:4334–39 [Google Scholar]
  93. Morin PA, Chambers KE, Boesch C, Vigilant L. 2001. Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol. Ecol. 10:1835–44 [Google Scholar]
  94. Navidi W, Arnheim N, Waterman MS. 1992. A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR—statistical considerations. Am. J. Hum. Genet. 50:347–59 [Google Scholar]
  95. Nielsen-Marsh CM, Hedges REM, Mann T, Collins MJ. 2000. A preliminary investigation of the application of differential scanning calorimetry to the study of collagen degradation in archaeological bone. Thermochim. Acta 365:129–39 [Google Scholar]
  96. Nordborg M. 1998. On the probability of Neanderthal ancestry. Am. J. Hum. Genet. 63:1237–40 [Google Scholar]
  97. Noro M, Masuda R, Dubrovo IA, Yoshida MC, Kato M. 1998. 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. 46:314–26 [Google Scholar]
  98. Oota H, Saitou N, Matsushita T, Ueda S. 1995. A genetic-study of 2,000-year-old human remains from Japan using mitochondrial DNA sequences. Am. J. Phys. Anthropol. 98:133–45 [Google Scholar]
  99. Oota H, Saitou N, Matsushita T, Ueda S. 1999. 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. 64:250–58 [Google Scholar]
  100. Orlando L, Bonjean D, Bocherens H, Thenot A, Argant A. et al. 2002. Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Mol. Biol. Evol. 19:1920–33 [Google Scholar]
  101. Ovchinnikov IV, Götherström A, Romanova GP, Kharitonov VM, Liden K, Goodwin W. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404:490–93 [Google Scholar]
  102. Ozawa T, Hayashi S, Mikhelson VM. 1997. Phylogenetic position of mammoth and Steller's sea cow within Tethytheria demonstrated by mitochondrial DNA sequences. J. Mol. Evol. 44:406–13 [Google Scholar]
  103. Pääbo S. 1985. Molecular cloning of ancient Egyptian mummy DNA. Nature 314:644–45 [Google Scholar]
  104. Pääbo S. 1989. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl. Acad. Sci. USA 86:1939–43 [Google Scholar]
  105. Pääbo S. 1990. Amplifying ancient DNA. In PCR-Protocols and Applications—A Laboratory Manual ed. MA Innis, DH Gelfand, JJ Sninsky, TJ White pp. 159–66 San Diego: Academic [Google Scholar]
  106. Pääbo S, Wilson AC. 1988. Polymerase chain reaction reveals cloning artefacts. Nature 334:387–88 [Google Scholar]
  107. Pääbo S, Wilson AC. 1991. Miocene DNA sequences—a dream come true. Curr. Biol. 1:45–46 [Google Scholar]
  108. Paxinos EE, James HF, Olson SL, Sorenson MD, Jackson J, Fleischer RC. 2002. MtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose (Branta canadensis). Proc. Natl. Acad. Sci. USA 99:1399–404 [Google Scholar]
  109. Pergams ORW, Barnes WM, Nyberg D. 2003. Rapid change in mouse mitochondrial DNA. Nature 423:397 [Google Scholar]
  110. Pertoldi C, Hansen MM, Loeschcke V, Madsen AB, Jacobsen L, Baagoe H. 2001. Genetic consequences of population decline in the European otter (Lutra lutra): an assessment of microsatellite DNA variation in Danish otters from 1883 to 1993. Proc. R. Soc. London Ser. B 268:1775–81 [Google Scholar]
  111. Piperno DR, Flannery KV. 2001. The earliest archaeological maize (Zea mays L.) from highland Mexico: new accelerator mass spectrometry dates and their implications. Proc. Natl. Acad. Sci. USA 98:2101–3 [Google Scholar]
  112. Poinar H, Kuch M, McDonald G, Martin P, Pääbo S. 2003. Nuclear gene sequences from a Late Pleistocene sloth coprolite. Curr. Biol. 12:1150–52 [Google Scholar]
  113. Poinar HN, Cano RJ, Poinar GO. 1993. DNA from an extinct plant. Nature 363:677 [Google Scholar]
  114. Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA. et al. 1998. Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281:402–6 [Google Scholar]
  115. Poinar HN, Höss M, Bada JL, Pääbo S. 1996. Amino acid racemization and the preservation of ancient DNA. Science 272:864–66 [Google Scholar]
  116. Poinar HN, Kuch M, Sobolik KD, Barnes I, Stankiewicz AB. et al. 2001. A molecular analysis of dietary diversity for three archaic Native Americans. Proc. Natl. Acad. Sci. USA 98:4317–22 [Google Scholar]
  117. Poinar HN, Stankiewicz BA. 1999. Protein preservation and DNA retrieval from ancient tissues. Proc. Natl. Acad. Sci. USA 96:8426–31 [Google Scholar]
  118. Pusch CM, Bachmann L. 2004. Spiking of contemporary human template DNA with ancient DNA extracts induces mutations under PCR and generates nonauthentic mitochondrial sequences. Mol. Biol. Evol. 21:957–64 [Google Scholar]
  119. 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 97:12800–3 [Google Scholar]
  120. Reid AH, Fanning TG, Hultin JV, Taubenberger JK. 1999. Origin and evolution of the 1918 “Spanish” influenza virus hemagglutinin gene. Proc. Natl. Acad. Sci. USA 96:1651–56 [Google Scholar]
  121. Richards MB, Sykes BC, Hedges REM. 1995. Authenticating DNA extracted from ancient skeletal remains. J. Archaeolog. Sci. 22:291–99 [Google Scholar]
  122. Ritchie PA, Millar CD, Gibb GC, Baroni C, Lambert DM. 2004. Ancient DNA enables timing of the Pleistocene origin and Holocene expansion of two Adelie penguin lineages in Antarctica. Mol. Biol. Evol. 21:240–48 [Google Scholar]
  123. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R. et al. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–91 [Google Scholar]
  124. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT. et al. 1985. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–54 [Google Scholar]
  125. Salo WL, Aufderheide AC, Buikstra J, Holcomb TA. 1994. Identification of Mycobacterium tuberculosis DNA in a Pre-Columbian Peruvian mummy. Proc. Natl. Acad. Sci. USA 91:2091–94 [Google Scholar]
  126. Savolainen P, Zhang YP, Luo J, Lundeberg J, Leitner T. 2002. Genetic evidence for an East Asian origin of domestic dogs. Science 298:1610–11 [Google Scholar]
  127. Schaaper RM, Kunkel TA, Loeb LA. 1983. Infidelity of DNA-synthesis associated with bypass of apurinic sites. Proc. Natl. Acad. Sci. USA 80:487–91 [Google Scholar]
  128. Schmitz RW, Serre D, Bonani G, Feine S, Hillgruber F. et al. 2002. The Neandertal type site revisited: interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc. Natl. Acad. Sci. USA 99:13342–47 [Google Scholar]
  129. Serre D, Hofreiter M, Pääbo S. 2004. Mutations induced by ancient DNA extracts. Mol. Biol. Evol. 21:1463–67 [Google Scholar]
  130. Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M. et al. 2004. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol. 2:313–17 [Google Scholar]
  131. Shapiro R. 1981. Damage to DNA caused by hydrolysis. In Chromosome Damage and Repair ed. E Seeberg, K Kleppe pp. 3–12 New York: Plenum [Google Scholar]
  132. Sidow A, Wilson AC, Pääbo S. 1991. Bacterial DNA in Clarkia fossils. Philos. Trans. R. Soc. London Ser. B 333:429–32 discussion 32–33 [Google Scholar]
  133. Smith CI, Chamberlain AT, Riley MS, Cooper A, Stringer CB, Collins MJ. 2001. Neanderthal DNA. Not just old but old and cold. Nature 410:771–72 [Google Scholar]
  134. Smith CI, Chamberlain AT, Riley MS, Stringer C, Collins MJ. 2003. The thermal history of human fossils and the likelihood of successful DNA amplification. J. Hum. Evol. 45:203–17 [Google Scholar]
  135. Soltis PS, Soltis DE, Smiley CJ. 1992. An rbcl sequence from a Miocene Taxodium (Bald Cypress). Proc. Natl. Acad. Sci. USA 89:449–51 [Google Scholar]
  136. Stankiewicz B, Poinar H, Briggs D, Evershed R, Poinar G. 1998. Chemical preservation of plants and insects in natural resins. Proc. R. Soc. London Ser. B 265:641–47 [Google Scholar]
  137. Stone AC, Stoneking M. 1993. Ancient DNA from a Pre-Columbian Amerindian population. Am. J. Phys. Anthropol. 92:463–71 [Google Scholar]
  138. Stone AC, Stoneking M. 1998. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the new world. Am. J. Hum. Genet. 62:1153–70 [Google Scholar]
  139. Stone AC, Stoneking M. 1999. Analysis of ancient DNA from a prehistoric Amerindian cemetery. Philos. Trans. R. Soc. London Ser. B 354:153–59 [Google Scholar]
  140. Stringer C. 2002. Modern human origins: progress and prospects. Philos. Trans. R. Soc. London Ser. B 357:563–79 [Google Scholar]
  141. Stringer CB, Andrews P. 1988. Genetic and fossil evidence for the origin of modern humans. Science 239:1263–68 [Google Scholar]
  142. Suarez AV, Tsutsui ND. 2004. The value of museum collections for research and society. BioScience 54:66–74 [Google Scholar]
  143. Thalmann O, Hebler J, Poinar HN, Pääbo S, Vigilant L. 2004. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol. Ecol. 13:321–35 [Google Scholar]
  144. Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC. et al. 2003. Genetic affinities of the Andaman Islanders, a vanishing human population. Curr. Biol. 13:86–93 [Google Scholar]
  145. Thomas MG, Hagelberg E, Jone HB, Yang Z, Lister AM. 2000. Molecular and morphological evidence on the phylogeny of the Elephantidae. Proc. R. Soc. London Ser. B 267:2493–500 [Google Scholar]
  146. Thomas RH, Schaffner W, Wilson AC, Pääbo S. 1989. DNA phylogeny of the extinct marsupial wolf. Nature 340:465–67 [Google Scholar]
  147. Thomas WK, Pääbo S, Villablanca FX, Wilson AC. 1990. Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens. J. Mol. Evol. 31:101–12 [Google Scholar]
  148. Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5:123–35 [Google Scholar]
  149. Trinkaus E. 2001. The Neandertal paradox. In Neanderthals and Modern Humans in Late Pleistocene Eurasia ed. C Finlayson pp. 73–74 Gibraltar: Gibraltar Museum [Google Scholar]
  150. Trinkaus E, Duarte C. 2000. The hybrid child from Portugal. Sci. Am. 282:102–3 [Google Scholar]
  151. Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT. et al. 2001. Genetic evidence for Near-Eastern origins of European cattle. Nature 410:1088–91 [Google Scholar]
  152. Vanderkuyl AC, Kuiken CL, Dekker JT, Perizonius WRK, Goudsmit J. 1995. Nuclear counterparts of the cytoplasmic mitochondrial 12S ribosomal-RNA gene—a problem of ancient DNA and molecular phylogenies. J. Mol. Evol. 40:652–57 [Google Scholar]
  153. Vasan S, Zhang X, Kapurniotu A, Bernhagen J, Teichberg S. et al. 1996. An agent cleaving glucose-derived protein crosslinks in vitro and in vivo. Nature 382:275–78 [Google Scholar]
  154. Vernesi C, Di Benedetto G, Caramelli D, Secchieri E, Simoni L. et al. 2001. Genetic characterization of the body attributed to the evangelist Luke. Proc. Natl. Acad. Sci. USA 98:13460–63 [Google Scholar]
  155. Vigilant L, Hofreiter M, Siedel H, Boesch C. 2001. Paternity and relatedness in wild chimpanzee communities. Proc. Natl. Acad. Sci. USA 98:12890–95 [Google Scholar]
  156. Vila C, Leonard J, Götherström A, Marklund S, Sandberg K. et al. 2001. Widespread origins of domestic horse lineages. Science 291:474–77 [Google Scholar]
  157. Vila C, Savolainen P, Maldonado JE, Amorim IR, Rice JE. et al. 1997. Multiple and ancient origins of the domestic dog. Science 276:1687–89 [Google Scholar]
  158. Vreeland RH, Rosenzweig WD, Powers DW. 2000. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407:897–900 [Google Scholar]
  159. Wandeler P, Smith S, Morin PA, Pettifor RA, Funk SM. 2003. Patterns of nuclear DNA degeneration over time—a case study in historic teeth samples. Mol. Ecol. 12:1087–93 [Google Scholar]
  160. Wang RL, Stec A, Hey J, Lukens L, Doebley J. 1999. The limits of selection during maize domestication. Nature 398:236–39 [Google Scholar]
  161. Watanabe T, Ishiguro N, Nakano M, Takamiya H, Matsui A, Hongo H. 2002. Prehistoric introduction of domestic pigs onto the Okinawa islands: ancient mitochondrial DNA evidence. J. Mol. Evol. 55:222–31 [Google Scholar]
  162. Watanabe T, Ishiguro N, Okumura N, Nakano M, Matsui A. et al. 2001. Ancient mitochondrial DNA reveals the origin of Sus scrofa from Rebun Island, Japan. J. Mol. Evol. 52:281–89 [Google Scholar]
  163. Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES. 2002. Genetic diversity and selection in the maize starch pathway. Proc. Natl. Acad. Sci. USA 99:12959–62 [Google Scholar]
  164. Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP. et al. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300:791–95 [Google Scholar]
  165. Willerslev E, Hansen AJ, Poinar HN. 2004. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol. Evol. 19:141–47 [Google Scholar]
  166. Willerslev E, Hansen AJ, Ronn R, Brand TB, Barnes I. et al. 2004. Long-term persistence of bacterial DNA. Curr. Biol. 14:R9–10 [Google Scholar]
  167. Wisely SM, Buskirk SW, Fleming MA, McDonald DB, Ostrander EA. 2002. Genetic diversity and fitness in black-footed ferrets before and during a bottleneck. J. Hered. 93:231–37 [Google Scholar]
  168. Wolpoff MH, Hawks J, Caspari R. 2000. Multiregional, not multiple origins. Am. J. Phys. Anthropol. 112:129–36 [Google Scholar]
  169. Wolpoff MH, Hawks J, Frayer DW, Hunley K. 2001. Modern human ancestry at the peripheries: a test of the replacement theory. Science 291:293–97 [Google Scholar]
  170. Woodward SR, Weyand NJ, Bunnell M. 1994. DNA sequence from Cretaceous period bone fragments. Science 266:1229–32 [Google Scholar]
  171. Yang H, Golenberg EM, Shoshani J. 1996. Phylogenetic resolution within the Elephantidae using fossil DNA sequences from the American mastodon (Mammut americanum) as an outgroup. Proc. Natl. Acad. Sci. USA 93:1190–94 [Google Scholar]
  172. Yao YG, Kong QP, Man XY, Bandelt HJ, Zhang YP. 2003. Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA. Mol. Biol. Evol. 20:214–19 [Google Scholar]
  173. Zink A, Haas CJ, Reischl U, Szeimies U, Nerlich AG. 2001. Molecular analysis of skeletal tuberculosis in an ancient Egyptian population. J. Med. Microbiol. 50:355–66 [Google Scholar]
  174. Zink AR, Grabner W, Reischl U, Wolf H, Nerlich AG. 2003. Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt. Epidemiol. Infect. 130:239–49 [Google Scholar]
  175. Zischler H, Hoss M, Handt O, von Haeseler A, van der Kuyl AC, Goudsmit J. 1995. Detecting dinosaur DNA. Science 268:1192–93 [Google Scholar]
  176. Pääpbo S, Irwin DM, Wilson AC. 1990. DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem. 265:4718–21 [Google Scholar]
/content/journals/10.1146/annurev.genet.37.110801.143214
Loading
/content/journals/10.1146/annurev.genet.37.110801.143214
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error