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Setting Up an Ancient DNA Laboratory

  • Tara L. Fulton
  • Beth ShapiroEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1963)

Abstract

Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential is high for contamination of ancient samples, ancient DNA extracts, and genomic sequencing libraries prepared from these extracts with non-degraded DNA from the present-day environment. To minimize the risk of contamination in ancient DNA environments, experimental protocols specific to handling ancient specimens, including those that outline the design and layout of laboratory space, have been introduced. Here, we outline challenges associated with working with ancient samples, including providing guidelines for setting up a new ancient DNA laboratory. We also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination of ancient DNA experiments with exogenous sources of DNA.

Key words

Ancient DNA aDNA DNA damage Laboratory setup Contamination Subsampling Sample preparation Guidelines 

References

  1. 1.
    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(5991):282–284CrossRefGoogle Scholar
  2. 2.
    Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA et al (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle-cell Anemia. Science 230(4732):1350–1354CrossRefGoogle Scholar
  3. 3.
    Paabo S, Higuchi RG, Wilson AC (1989) Ancient DNA and the polymerase chain-reaction—the emerging field of molecular archaeology. J Biol Chem 264(17):9709–9712PubMedGoogle Scholar
  4. 4.
    Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M et al (2010) A draft sequence of the Neandertal genome. Science 328(5979):710–722CrossRefGoogle Scholar
  5. 5.
    Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K et al (2014) Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513(7518):409–413CrossRefGoogle Scholar
  6. 6.
    Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M, Pietrusewsky M et al (2018) Ancient genomes document multiple waves of migration in southeast Asian prehistory. Science 361(6397):92–95CrossRefGoogle Scholar
  7. 7.
    Edwards CJ, Bollongino R, Scheu A, Chamberlain A, Tresset A, Vigne JD et al (2007) Mitochondrial DNA analysis shows a near eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proc R Soc B-Biol Sci 274(1616):1377–1385CrossRefGoogle Scholar
  8. 8.
    Larson G, Liu RR, Zhao XB, Yuan J, Fuller D, Barton L et al (2010) Patterns of east Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci U S A 107(17):7686–7691CrossRefGoogle Scholar
  9. 9.
    Leonard JA, Wayne RK, Wheeler J, Valadez R, Guillén S, Vilà C (2002) Ancient DNA evidence for Old World origin of New World dogs. Science 298:1613–1616CrossRefGoogle Scholar
  10. 10.
    Goloubinoff P, Paabo S, Wilson AC (1993) Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. Proc Natl Acad Sci U S A 90(5):1997–2001CrossRefGoogle Scholar
  11. 11.
    Gaunitz C, Fages A, Hanghoj K, Albrechtsen A, Khan N, Schubert M et al (2018) Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 360(6384):111–114CrossRefGoogle Scholar
  12. 12.
    Schubert M, Jonsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A et al (2014) Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A 111(52):E5661–E5669CrossRefGoogle Scholar
  13. 13.
    Stiller M, Baryshnikov G, Bocherens H, d'Anglade AG, Hilpert B, Munzel SC et al (2010) Withering away-25,000 years of genetic decline preceded cave bear extinction. Mol Biol Evol 27(5):975–978CrossRefGoogle Scholar
  14. 14.
    Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV et al (2004) Rise and fall of the Beringian steppe bison. Science 306(5701):1561–1565CrossRefGoogle Scholar
  15. 15.
    Campos PF, Willerslev E, Sher A, Orlando L, Axelsson E, Tikhonov A et al (2010) Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc Natl Acad Sci U S A 107(12):5675–5680CrossRefGoogle Scholar
  16. 16.
    Leonard JA, Wayne RK, Cooper A (2000) Population genetics of ice age brown bears. Proc Natl Acad Sci U S A 97(4):1651–1654CrossRefGoogle Scholar
  17. 17.
    Pinsky ML, Newsome SD, Dickerson BR, Fang Y, Van Tuinen M, Kennett DJ et al (2010) Dispersal provided resilience to range collapse in a marine mammal: insights from the past to inform conservation biology. Mol Ecol 19(12):2418–2429PubMedGoogle Scholar
  18. 18.
    Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ et al (2017) Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science 358(6365):951–954CrossRefGoogle Scholar
  19. 19.
    Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, Bininda-Emonds ORP et al (2002) Flight of the dodo. Science 295(5560):1683CrossRefGoogle Scholar
  20. 20.
    Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M et al (2009) Revising the recent evolutionary history of equids using ancient DNA. Proc Natl Acad Sci U S A 106(51):21754–21759CrossRefGoogle Scholar
  21. 21.
    Krause J, Unger T, Nocon A, Malaspinas AS, Kolokotronis SO, Stiller M et al (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol 8:220CrossRefGoogle Scholar
  22. 22.
    Heintzman PD, Zazula GD, Cahill JA, Reyes AV, MacPhee RD, Shapiro B (2015) Genomic data from extinct north American Camelops revise camel evolutionary history. Mol Biol Evol 32(9):2433–2440CrossRefGoogle Scholar
  23. 23.
    Meyer M, Palkopoulou E, Baleka S, Stiller M, Penkman KEH, Alt KW et al (2017) Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution. eLife 6:e25413CrossRefGoogle Scholar
  24. 24.
    Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362(6422):709–715CrossRefGoogle Scholar
  25. 25.
    Pääbo S (1989) Ancient DNA—extraction, characterization, molecular-cloning, and enzymatic amplification. P Natl Acad Sci USA 86(6):1939–1943CrossRefGoogle Scholar
  26. 26.
    Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, Buigues B et al (2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311(5759):392–394CrossRefGoogle Scholar
  27. 27.
    Hoss M, Jaruga P, Zastawny TH, Dizdaroglu M, Paabo S (1996) DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res 24(7):1304–1307CrossRefGoogle Scholar
  28. 28.
    Rohland N, Pollack JL, Nagel D, Beauval C, Airvaux J, Paabo S et al (2005) The population history of extant and extinct hyenas. Mol Biol Evol 22(12):2435–2443CrossRefGoogle Scholar
  29. 29.
    Hofreiter M (2008) Long DNA sequences and large data sets: investigating the quaternary via ancient DNA. Quat Sci Rev 27(27–28):2586–2592CrossRefGoogle Scholar
  30. 30.
    Lindahl T (1993) Recovery of antediluvian DNA. Nature 365(6448):700CrossRefGoogle Scholar
  31. 31.
    Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S (2001) Ancient DNA. Nat Rev Genet 2(5):353–359CrossRefGoogle Scholar
  32. 32.
    Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N et al (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38:645–679CrossRefGoogle Scholar
  33. 33.
    Willerslev E, Cooper A (2005) Ancient DNA. Proc R Soc B-Biol Sci 272(1558):3–16CrossRefGoogle Scholar
  34. 34.
    Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B et al (2013) Complete mitochondrial genome sequence of a middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A 110(39):15758–15763CrossRefGoogle Scholar
  35. 35.
    Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M et al (2013) Recalibrating Equus evolution using the genome sequence of an early middle Pleistocene horse. Nature 499(7456):74–78CrossRefGoogle Scholar
  36. 36.
    Leonard JA, Shanks O, Hofreiter M, Kreuz E, Hodges L, Ream W et al (2007) Animal DNA in PCR reagents plagues ancient DNA research. J Archaeol Sci 34(9):1361–1366CrossRefGoogle Scholar
  37. 37.
    Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20(10):541–544CrossRefGoogle Scholar
  38. 38.
    Handt O, Hoss M, Krings M, Paabo S (1994) Ancient DNA—methodological challenges. Experientia 50(6):524–529CrossRefGoogle Scholar
  39. 39.
    Cooper A, Poinar HN (2000) Ancient DNA: do it right or not at all. Science 289(5482):1139CrossRefGoogle Scholar
  40. 40.
    Poinar HN, Hoss M, Bada JL, Paabo S (1996) Amino acid racemization and the preservation of ancient DNA. Science 272(5263):864–866CrossRefGoogle Scholar
  41. 41.
    Collins MJ, Penkman KE, Rohland N, Shapiro B, Dobberstein RC, Ritz-Timme S et al (2009) Is amino acid racemization a useful tool for screening for ancient DNA in bone? Proc Biol Sci 276(1669):2971–2977CrossRefGoogle Scholar
  42. 42.
    Handt O, Krings M, Ward RH, Paabo S (1996) The retrieval of ancient human DNA sequences. Am J Hum Genet 59(2):368–376PubMedPubMedCentralGoogle Scholar
  43. 43.
    Hebsgaard MB, Phillips MJ, Willerslev E (2005) Geologically ancient DNA: fact or artefact? Trends Microbiol 13(5):212–220CrossRefGoogle Scholar
  44. 44.
    Huson DH, Weber N (2013) Microbial community analysis using MEGAN. Methods Enzymol 531:465–485CrossRefGoogle Scholar
  45. 45.
    Willerslev E, Hansen AJ, Poinar HN (2004) Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol Evol 19(3):141–147CrossRefGoogle Scholar
  46. 46.
    Griffiths AJF (2005) Introduction to genetic analysis, 8th edn. W.H. Freeman and Co, New York, p 782. xviGoogle Scholar
  47. 47.
    Kemp BM, Smith DG (2005) Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int 154(1):53–61CrossRefGoogle Scholar
  48. 48.
    Gilbert MTP, Hansen AJ, Willerslev E, Turner-Walker G, Collins M (2006) Insights into the processes behind the contamination of degraded human teeth and bone samples with exogenous sources of DNA. Int J Osteoarchaeol 16(2):156–164CrossRefGoogle Scholar
  49. 49.
    Sampietro ML, Gilbert MTP, Lao O, Caramelli D, Lari M, Bertranpetit J et al (2006) Tracking down human contamination in ancient human teeth. Mol Biol Evol 23(9):1801–1807CrossRefGoogle Scholar
  50. 50.
    Salamon M, Tuross N, Arensburg B, Weiner S (2005) Relatively well preserved DNA is present in the crystal aggregates of fossil bones. Proc Natl Acad Sci U S A 102(39):13783–13788CrossRefGoogle Scholar
  51. 51.
    Gilbert MTP, Menez L, Janaway RC, Tobin DJ, Cooper A, Wilson AS (2006) Resistance of degraded hair shafts to contaminant DNA. Forensic Sci Int 156(2–3):208–212CrossRefGoogle Scholar
  52. 52.
    Rasmussen M, Li YR, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I et al (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463(7282):757–762CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Environment and Climate Change CanadaEdmontonCanada
  2. 2.Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUSA

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