Movatterモバイル変換

[0]ホーム
URL:

Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Advertisement

European Journal of Human Genetics
  • Article
  • Published:

Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity

European Journal of Human Geneticsvolume 13, pages1106–1112 (2005)Cite this article

Abstract

Research into ancient mitochondrial DNA is plagued by contamination, post mortem damage, and other artefacts. The stringent set of controls suggested by Cooper and Poinar a few years ago are, however, rarely followed in practice, and even when applied carefully, these criteria need not be sufficient to guarantee authenticity. The fairly relaxed prerequisites now common for ancient population studies have opened the door for all kinds of contamination and sequencing errors to enter ancient mtDNA data. To reject or question authenticity of particular sequencing resultsa posteriori, one can follow similar strategies of focused database comparisons that have proven to be effective and successful in the case of flawed modern mtDNA data.

Similar content being viewed by others

Log in or create a free account to read this content

Gain free access to this article, as well as selected content from this journal and more onnature.com

or

References

  1. Kaestle FA, Horsburgh KA : Ancient DNA in anthropology: methods, applications, and ethics.Yearbk Phys Anthrop 2002;45: 92–130.

    Article  Google Scholar 

  2. Richards MB, Sykes BC, Hedges REM : Authenticating DNA extracted from ancient skeletal remains.J Arch Sci 1995;22: 291–299.

    Article  Google Scholar 

  3. Nicholls H : Ancient DNA comes of age.PLoS Biol 2005;3: e56.

    Article PubMed PubMed Central  Google Scholar 

  4. Abbott A : Anthropologists cast doubt on human DNA evidence.Nature 2003;423: 468.

    Article CAS PubMed  Google Scholar 

  5. Yang DY, Eng B, Saunders SR : Hypersensitive PCR, ancient human mtDNA, and contamination.Hum Biol 2003;75: 355–364.

    Article PubMed  Google Scholar 

  6. Gilbert MTP, Willerslev E, Hansen AJet al: Distribution patterns of postmortem damage in human mitochondrial DNA.Am J Hum Genet 2003a;72: 32–47, 779 (erratum).

    Article CAS PubMed  Google Scholar 

  7. Gilbert MTP, Hansen AJ, Willerslev Eet al: Characterization of genetic miscoding lesions caused by postmortem damage.Am J Hum Genet 2003b;72: 48–61.

    Article CAS PubMed  Google Scholar 

  8. Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V : The fingerprint of phantom mutations in mitochondrial DNA data.Am J Hum Genet 2002;71: 1150–1160.

    Article CAS PubMed PubMed Central  Google Scholar 

  9. Herrnstadt C, Preston G, Howell N : Errors, phantom and otherwise, in human mtDNA sequences.Am J Hum Genet 2003;72: 1585–1586.

    Article CAS PubMed PubMed Central  Google Scholar 

  10. Zischler H, Geisert H, von Haeseler A, Pääbo S : A nuclear ‘fossil’ of the mitochondrial D-loop and the origin of modern humans.Nature 1995;378: 489–492.

    Article CAS PubMed  Google Scholar 

  11. Wallace DC, Stugard C, Murdock D, Schurr T, Brown MD : Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations.Proc Natl Acad Sci USA 1997;94: 14900–14905.

    Article CAS PubMed PubMed Central  Google Scholar 

  12. Tully LA, Parsons TJ, Steighner RJ, Holland MM, Marino MA, Prenger VL : A sensitive denaturing gradient-gel electrophoresis assay reveals a high frequency of heteroplasmy in hypervariable region 1 of the human mtDNA control region.Am J Hum Genet 2000;67: 432–443.

    Article CAS PubMed PubMed Central  Google Scholar 

  13. Hänni C, Laudet V, Coll J, Stehelin D : An unusual mitochondrial DNA sequence variant from an Egyptian mummy.Genomics 1994;22: 487–489.

    Article PubMed  Google Scholar 

  14. Cooper AR, Poinar H : Ancient DNA; do it right or not at all.Science 2000;289: 1139.

    Article CAS PubMed  Google Scholar 

  15. Adcock G, Dennis E, Easteal Set al: Mitochondrial DNA sequences in ancient Australians: implications for modern human origins.Proc Natl Acad Sci USA 2001;98: 537–542.

    Article CAS PubMed PubMed Central  Google Scholar 

  16. Cooper A, Rambaut A, Macaulay V, Willerslev E, Hansen AJ, Stringer C : Human origins and ancient human DNA.Science 2001;292: 1655–1656.

    Article CAS PubMed  Google Scholar 

  17. Cooper A, Drummond AJ, Willerslev E: Ancient DNA : would the real Neandertal please stand up?Curr Biol 2004;14: R431–R433.

    Article CAS PubMed  Google Scholar 

  18. Serre D, Langaney A, Chech Met al: No evidence of Neandertal mtDNA contribution to early modern humans.PloS Biol 2004;2: 0313–0317.

    Article CAS  Google Scholar 

  19. Ovchinnikov IV, Goodwin W : Ancient human DNA from Sungir?J Hum Evol 2003;44: 389–392.

    Article PubMed  Google Scholar 

  20. Barbujani G, Bertorelle G : Were Cro-Magnons too like us for DNA to tell?Nature 2003;424: 127.

    Article CAS PubMed  Google Scholar 

  21. Pääbo S, Poinar H, Serre Det al: Genetic analyses from ancient DNA.Annu Rev Genet 2004;38: 645–679.

    Article PubMed  Google Scholar 

  22. Bandelt H-J, Herrnstadt C, Yao Y-Get al: Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats.Ann Hum Genet 2003;67: 512–524.

    Article CAS PubMed  Google Scholar 

  23. Kolman CJ, Tuross N : Ancient DNA analysis of human populations.Am J Phys Anthrop 2000;111: 5–23.

    Article CAS PubMed  Google Scholar 

  24. Bandelt H-J, Salas A, Lutz-Bonengel S : Artificial recombination in forensic mtDNA population databases.Int J Legal Med 2004;118: 267–273.

    Article CAS PubMed  Google Scholar 

  25. Izagirre N, de la Rúa 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 1999;65: 199–207.

    Article CAS PubMed PubMed Central  Google Scholar 

  26. Roychoudhury S, Roy S, Dey Bet al: Fundamental genomic unity of ethnic India is revealed by analysis of mitochondrial DNA.Curr Sci 2000;79: 1182–1192.

    Google Scholar 

  27. Bandelt H-J, Macaulay V, Richards M : Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA.Mol Phylogenet Evol 2000;16: 8–28.

    Article CAS PubMed  Google Scholar 

  28. Yao Y, Zhang Y : Pitfalls in the analysis of ancient human mtDNA.Chinese Sci Bull 2003;48: 826–830.

    Article CAS  Google Scholar 

  29. Stenico M, Nigro L, Bertorelle Get al: High mitochondrial sequence diversity in linguistic isolates of the Alps.Am J Hum Genet 1996;59: 1363–1375.

    CAS PubMed PubMed Central  Google Scholar 

  30. Vernesi C, Fuselli S, Castrì L, Bertorelle G, Barbujani G : Mitochondrial diversity in linguistic isolates of the Alps: a reappraisal.Hum Biol 2002;74: 725–730.

    Article PubMed  Google Scholar 

  31. Vernesi C, Di Benedetto G, Caramelli Det al: Genetic characterization of the body attributed to the evangelist Luke.Proc Natl Acad Sci USA 2001;98: 13460–13463.

    Article CAS PubMed PubMed Central  Google Scholar 

  32. Di Benedetto G, Ergüven A, Stenico Met al: DNA diversity and population admixture in Anatolia.Am J Phys Anthrop 2001;115: 144–156.

    Article CAS PubMed  Google Scholar 

  33. Bandelt H-J, Lahermo P, Richards M, Macaulay V : Detecting errors in mtDNA data by phylogenetic analysis.Int J Legal Med 2001;115: 64–69.

    Article CAS PubMed  Google Scholar 

  34. Parson W, Brandstätter A, Alonso Aet al: The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives.Forensic Sci Int 2004;139: 215–226.

    Article CAS PubMed  Google Scholar 

  35. Yao Y-G, Bravi CM, Bandelt H-J : A call for mtDNA data quality control in forensic science.Forensic Sci Int 2004;141: 1–6.

    Article CAS PubMed  Google Scholar 

  36. Szibor R, Michael M : Correct mitochondrial L-strand sequencing after C-stretches.Int J Legal Med 1999;112: 348–349.

    Article CAS PubMed  Google Scholar 

  37. Imaizumi K, Parsons TJ, Yoshino M, Holland MM : A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals.Int J Legal Med 2002;116: 68–73.

    Article CAS PubMed  Google Scholar 

  38. Ricaut F-X, Keyser-Tracqui C, Cammaert L, Crubézy E, Ludes B : Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons.Am J Phys Anthrop 2004;123: 351–360.

    Article PubMed  Google Scholar 

  39. Vona G, Falchi A, Moral P, Calò CM, Varesi L : Mitochondrial sequence variation in the Guahibo Amerindian population from Venezuela.Am J Phys Anthropol 2005;127: 361–369.

    Article PubMed  Google Scholar 

  40. Brandstätter A, Sänger T, Lutz-Bonengel Set al: Phantom mutation hotspots in human mitochondrial DNA.Electrophoresis 2005, in press.

  41. Grzybowski T, Malyarchuk BA, Czarny J, Miścicka-Śliwka D, Kotzbach R : High levels of mitochondrial DNA heteroplasmy in single hair roots: reanalysis and revision.Electrophoresis 2003;24: 1159–1165.

    Article CAS PubMed  Google Scholar 

  42. Brandstätter A, Parson W : Mitochondrial DNA heteroplasmy or artefacts — a matter of the amplification strategy?Int J Legal Med 2003;117: 180–184.

    Article PubMed  Google Scholar 

  43. García-Bour J, Pérez-Pérez A, Álvarez Set al: Early population differentiation in extinct aborigines from Tierra del Fuego-Patagonia: ancient mtDNA sequences and Y-chromosome STR characterization.Am J Phys Anthrop 2004;123: 361–370.

    Article PubMed  Google Scholar 

  44. Salas A, Richards M, De la Fe Tet al: The making of the African mtDNA landscape.Am J Hum Genet 2002;71: 1082–1111.

    Article CAS PubMed PubMed Central  Google Scholar 

  45. Rickards O, Martínez-Labarga C, Lum JK, De Stefano GF, Cann RL : mtDNA history of the Cayapa Amerinds of Ecuador: detection of additional founding lineages for the Native American populations.Am J Hum Genet 1999;65: 519–530.

    Article CAS PubMed PubMed Central  Google Scholar 

  46. Alves-Silva J, da Silva Santos M, Guimarães PEet al: The ancestry of Brazilian mtDNA lineages.Am J Hum Genet 2000;67: 444–461, 775 (erratum).

    Article CAS PubMed PubMed Central  Google Scholar 

  47. Moraga ML, Rocco P, Miquel JFet al: Mitochondrial DNA polymorphisms in Chilean aboriginal populations: implications for the peopling of the southern cone of the continent.Am J Phys Anthropol 2000;113: 19–29.

    Article CAS PubMed  Google Scholar 

  48. Monson KL, Miller KWP, Wilson MR, DiZinno JA, Budowle B : The mtDNA population database: an integrated software and database resource for forensic comparison.Forensic Sci Comm 2002;4: No. 2.

  49. Hagelberg E, Goldman N, Lió Pet al: Evidence for mitochondrial DNA recombination in a human population of island Melanesia.Proc R Soc Lond B 1999;266: 485–492.

    Article CAS  Google Scholar 

  50. Montiel R, Malgosa A, Francalacci P : Authenticating ancient human mitochondrial DNA.Hum Biol 2001;73: 689–713.

    Article CAS PubMed  Google Scholar 

  51. Caramelli D, Lalueza-Fox C, Vernesi Cet al: Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans.Proc Natl Acad Sci USA 2003;100: 6593–6597.

    Article CAS PubMed PubMed Central  Google Scholar 

  52. Herrnstadt C, Elson JL, Fahy Eet al: Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups.Am J Hum Genet 2002;70: 1152–1171, 71: 448–449 (erratum).

    Article CAS PubMed PubMed Central  Google Scholar 

  53. Vernesi C, Caramelli D, Dupanloup Iet al: The Etruscans: a population-genetic study.Am J Hum Genet 2004;74: 694–704.

    Article CAS PubMed PubMed Central  Google Scholar 

  54. Maca-Meyer N, González AM, Pestano J, Flores C, Larruga JM, Cabrera VM : Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography.BMC Genet 2003;4: 15.

    Article PubMed PubMed Central  Google Scholar 

  55. Achilli A, Rengo C, Magri Cet al: The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool.Am J Hum Genet 2004;75: 910–918.

    Article CAS PubMed PubMed Central  Google Scholar 

  56. Meyer S, Weiss G, von Haeseler A : Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA.Genetics 1999;152: 1103–1110.

    CAS PubMed PubMed Central  Google Scholar 

  57. Barbujani G, Vernesi C, Caramelli D, Castrì L, Lalueza-Fox C, Bertorelle G : Etruscan artifacts: much ado about nothing.Am J Hum Genet 2004;75: 923–927.

    Article CAS PubMed Central  Google Scholar 

  58. Miller K, Dawson J :Mitochondrial DNA concordance. Version 2.0 (1998), Available:http://www.bioanth.cam.ac.uk/mtDNA/.

  59. Wittig H :D-Loop Base. Forensische Datenbank nichtcodierender mitochondrialer DNA-Sequenzen. Eine Analyse von 850 mtDNA-Sequenzen zentraleuropäischer Kaukasoider. Magdeburg: Dissertation, Otto-von-Guericke-Universität, 2000.

    Google Scholar 

  60. Forster P, Calì F, Röhl Aet al: Continental and subcontinental distributions of mtDNA control region types.Int J Legal Med 2002;116: 99–108.

    Article PubMed  Google Scholar 

  61. Belyaeva O, Bermisheva M, Khrunin Aet al: Mitochondrial DNA variations in Russian and Belorussian populations.Hum Biol 2003;75: 647–660.

    Article PubMed  Google Scholar 

  62. Taylor RW, McDonnell MT, Blakely ELet al: Genotypes from patients indicate no paternal mitochondrial DNA contribution.Ann Neurol 2003;54: 521–524.

    Article CAS PubMed  Google Scholar 

  63. Derenko MV, Grzybowski T, Malyarchuk BAet al: Diversity of mitochondrial DNA lineages in South Siberia.Ann Hum Genet 2003;67: 397–411.

    Article  Google Scholar 

  64. Tajima A, Sun C-S, Pan I-H, Ishida T, Saitou N, Horai S : Mitochondrial DNA polymorphisms in nine aboriginal groups of Taiwan: implications for the population history of aboriginal Taiwanese.Hum Genet 2003;113: 24–33.

    CAS PubMed  Google Scholar 

  65. Poetsch M, Wittig H, Krause D, Lignitz E : Mitochondrial diversity of a northeast German population sample.Forensic Sci Int 2003;137: 125–132.

    Article CAS PubMed  Google Scholar 

  66. Pinto F, González AM, Hernández M, Larruga JM, Cabrera VM : Genetic relationship between the Canary Islanders and their African and Spanish ancestors inferred from mitochondrial DNA sequences.Ann Hum Genet 1996;60: 321–330.

    Article CAS PubMed  Google Scholar 

  67. Rando JC, Pinto F, González AMet al: Mitochondrial DNA analysis of northwest African populations reveals genetic exchanges with European, near-eastern, and sub-Saharan populations.Ann Hum Genet 1998;62: 531–550.

    Article CAS PubMed  Google Scholar 

  68. Bandelt H-J : Etruscan artifacts.Am J Hum Genet 2004;75: 919–920.

    Article CAS PubMed PubMed Central  Google Scholar 

  69. Malyarchuk BA, Rogozin IB : On the Etruscan mtDNA contribution to modern humans.Am J Hum Genet 2004;75: 920–923.

    Article CAS PubMed PubMed Central  Google Scholar 

  70. Keyser-Tracqui C, Crubézy E, Ludes B : Nuclear and mitochondrial DNA analysis of a 2,000-year-old necropolis in the Egyin Gol valley of Mongolia.Am J Hum Genet 2003;73: 247–260.

    Article CAS PubMed PubMed Central  Google Scholar 

  71. Lalueza-Fox C, Gilbert MTP, Martínez-Fuentes AJ, Calafell F, Bertranpetit J : Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Caribbean.Am J Phys Anthrop 2003;121: 97–108.

    Article CAS PubMed  Google Scholar 

  72. Maca-Meyer N, Arnay M, Rando JCet al: Ancient mtDNA analysis and the origin of the Guanches.Europ J Human Genet 2004;12: 155–162.

    Article CAS  Google Scholar 

  73. Hummel S (ed):Ancient DNA typing: methods, strategies and applications. Berlin, Heidelberg: Springer-Verlag, 2003.

    Book  Google Scholar 

  74. Brown TA, Brown KA : Book review of ‘Susanne Hummel (editor) Ancient DNA typing: methods, strategies and applications, Springer-Verlag, Berlin, Heidelberg, 2003’.Hum Genet 2003;114: 124–125.

    Article  Google Scholar 

  75. Handt O, Krings M, Ward RH, Pääbo S : The retrieval of ancient human DNA sequences.Am J Hum Genet 1996;59: 368–376.

    CAS PubMed PubMed Central  Google Scholar 

  76. Gilbert MTP, Bandelt H-J, Hofreiter M, Barnes I : Assessing ancient DNA studies.Trends Ecol Evol 2005, in press.

Download references

Acknowledgements

I thank Antonio Salas and Yong-Gang Yao for advice as well as for literature and database searches.

Author information

Authors and Affiliations

  1. Fachbereich Mathematik, Universität Hamburg, Hamburg, Germany

    Hans-Jürgen Bandelt

Authors
  1. Hans-Jürgen Bandelt

Corresponding author

Correspondence toHans-Jürgen Bandelt.

Rights and permissions

About this article

Cite this article

Bandelt, HJ. Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity.Eur J Hum Genet13, 1106–1112 (2005). https://doi.org/10.1038/sj.ejhg.5201476

Download citation

Keywords

This article is cited by

Search

Advanced search

Quick links

[8]ページ先頭
©2009-2026 Movatter.jp