Vegetation History and Archaeobotany

, Volume 24, Issue 1, pp 207–214 | Cite as

Recent advances in ancient DNA research and their implications for archaeobotany

  • Terence A. Brown
  • Enrico Cappellini
  • Logan Kistler
  • Diane L. Lister
  • Hugo R. Oliveira
  • Nathan Wales
  • Angela SchlumbaumEmail author


The scope and ambition of biomolecular archaeology is undergoing rapid change due to the development of new ‘next generation’ sequencing (NGS) methods for analysis of ancient DNA in archaeological specimens. These methods have not yet been applied extensively to archaeobotanical material but their utility has been demonstrated with desiccated, waterlogged and charred remains. The future use of NGS is likely to open up new areas of investigation that have been difficult or impossible with the traditional approach to aDNA sequencing. Species identification should become more routine with archaeobotanical explants, not just with charred grain but with most if not all species likely to be encountered in an archaeobotanical setting. Distinctions between different subspecies groups such as cereal landraces will also be possible in the near future. Phenotypic characterization, in which aDNA sequencing is used to infer the biological characteristics of an archaeological specimen, will become possible, improving our understanding of traits such as flowering behaviour of cereals, and when combined with studies of preserved RNA and protein will enable complex phenotypes such as environmental tolerance and nutritional quality to be assessed. The sequencing of entire ancient plant genomes is also likely to have significant impact. As with past studies of ancient plant DNA, realization of the new potential provided by NGS will require productive collaboration between archaeologists and geneticists within the archaeobotanical research community.


Ancient DNA Charred plant remains Desiccated plant remains Genomes Next generation DNA sequencing Phenotype characterization Species identification Waterlogged plant remains 



This paper is dedicated to Franco Rollo, who passed away on 3rd September 2014. Franco was the first to identify preserved nucleic acids in plant remains. His work in the 1980s and early 1990s ensured that biomolecular archaeobotany developed into the rigorous and respected discipline that it has now become.


  1. Allaby RG, O’Donoghue K, Sallares R, Jones MK, Brown TA (1997) Evidence for the survival of ancient DNA in charred wheat seeds from European archaeological sites. Anc Biomol 1:119–129Google Scholar
  2. Allaby RG, Banerjee M, Brown TA (1999) Evolution of the high-molecular-weight glutenin loci of the A, B, D and G genomes of wheat. Genome 42:296–307CrossRefGoogle Scholar
  3. Allaby RG, Gutaker R, Clarke A et al (2014) Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Phil Trans R Soc B 279:4,727–4,733Google Scholar
  4. Ávila-Arcos MC, Cappellini E, Romero-Navarro JA et al (2011) Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Sci Rep 1:74CrossRefGoogle Scholar
  5. Blatter R, Jacomet S, Schlumbaum A (2002) Spelt-specific alleles in HMW glutenin genes from modern and historical European spelt (Triticum spelta L.). Theor Appl Genet 104:329–337CrossRefGoogle Scholar
  6. Brown TA (1999) How ancient DNA may help in understanding the origin and spread of agriculture. Phil Trans R Soc B 354:89–98CrossRefGoogle Scholar
  7. Brown TA, Brown KA (2011) Biomolecular archaeology: an introduction. Wiley-Blackwell, New YorkCrossRefGoogle Scholar
  8. Bunning SL, Jones G, Brown TA (2012) Next generation sequencing of DNA in 3300-year-old charred cereal grains. J Archaeol Sci 39:2,780–2,784CrossRefGoogle Scholar
  9. Cappellini E, Gilbert MTP, Geuna F et al (2010) A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97:205–217CrossRefGoogle Scholar
  10. Fordyce L, Ávila-Arcos MC, Rasmussen M et al (2013) Deep sequencing of RNA from ancient maize kernels. PLoS ONE 8(1):e50961CrossRefGoogle Scholar
  11. Freitas FO, Bandel G, Allaby RG, Brown TA (2003) DNA from primitive maize landraces and archaeological remains: implications for the domestication of maize and its expansion into South America. J Archaeol Sci 30:901–908CrossRefGoogle Scholar
  12. Goloubinoff P, Pääbo S (1993) Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. Proc Natl Acad Sci USA 90:1,997–2,001CrossRefGoogle Scholar
  13. Green RE, Briggs AW, Krause J et al (2009) The Neandertal genome and ancient DNA authenticity. EMBO J 28:2,494–2,502CrossRefGoogle Scholar
  14. Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447:418–424CrossRefGoogle Scholar
  15. Jaenicke-Després V, Buckler ES, Smith BD et al (2003) Early allelic selection in maize as revealed by ancient DNA. Science 302:1,206–1,208CrossRefGoogle Scholar
  16. Jones G, Valamoti S, Charles M (2000) Early crop diversity: a “new” glume wheat from northern Greece. Veget Hist Archaeobot 9:133–146CrossRefGoogle Scholar
  17. Jones G, Jones H, Charles MP et al (2012) Phylogeographic analysis of barley DNA as evidence for the spread of Neolithic agriculture through Europe. J Archaeol Sci 39:3,230–3,238CrossRefGoogle Scholar
  18. Jones G, Charles MP, Jones MK et al (2013) DNA evidence for multiple introductions of barley into Europe following dispersed domestications in Western Asia. Antiquity 87:701–713Google Scholar
  19. Kistler L, Shapiro B (2011) Ancient DNA confirms a local origin of domesticated chenopod in eastern North America. J Archaeol Sci 38:3,549–3,554CrossRefGoogle Scholar
  20. Kistler L, Montenegro A, Smith BD et al (2014) Transoceanic drift and the domestication of African bottle gourds in the Americas. Proc Natl Acad Sci USA 118(8):2,937–2,941CrossRefGoogle Scholar
  21. Leino M, Boström E, Hagenblad J (2013) Twentieth-century changes in the genetic composition of Swedish field pea metapopulations. Heredity 110:338–346CrossRefGoogle Scholar
  22. Li CX, Lister DL, Li HJ et al (2011) Ancient DNA analysis of desiccated wheat grains excavated from a Bronze Age cemetery in Xinjiang. J Archaeol Sci 38:115–119CrossRefGoogle Scholar
  23. Lia VV, Confalonieri VA, Ratto N et al (2007) Microsatellite markers provide insights into the genetic constitution of ancient maize in southern South America. Proc R Soc Lond B 274:545–554CrossRefGoogle Scholar
  24. Lister DL, Jones H, Jones MK, O’Sullivan DM, Cockram J (2013) Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform. Taxon 62:779–789CrossRefGoogle Scholar
  25. Llamas B, Holland ML, Chen K et al (2012) High-resolution analysis of cytosine methylation in ancient DNA. PLoS ONE 7(1):e30226CrossRefGoogle Scholar
  26. Manen JF, Bouby L, Dalnoki O et al (2003) Microsatellites from archaeological Vitis vinifera seeds allow a tentative assignment of the geographical origin of ancient cultivars. J Archaeol Sci 30:721–729CrossRefGoogle Scholar
  27. Martin MD, Cappellini E, Samaniego JA (2013) Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat Comm 4(2):172Google Scholar
  28. O’Donoghue K, Brown TA, Carter JF, Evershed RP (1994) Detection of nucleotide bases in ancient seeds using gas chromatography/mass spectrometry and gas chromatography/mass spectrometry/mass spectrometry. Rapid Comm Mass Spectrom 8:503–508CrossRefGoogle Scholar
  29. O’Donoghue K, Clapham A, Evershed RP, Brown TA (1996) Remarkable preservation of biomolecules in ancient radish seeds. Proc R Soc Lond B 263:541–547CrossRefGoogle Scholar
  30. Oliveira HR, Civáň P, Morales J et al (2012) Ancient DNA in archaeological wheat grains: preservation conditions and the study of pre-Hispanic agriculture on the island of Gran Canaria (Spain). J Archaeol Sci 39:828–835CrossRefGoogle Scholar
  31. Palmer SA, Moore JD, Clapham AJ, Rose P, Allaby RG (2009) Archaeogenetic evidence of ancient Nubian barley evolution from six to two-row indicates local adaptation. PLoS ONE 4(7):e6301CrossRefGoogle Scholar
  32. Palmer SA, Clapham AJ, Rose P et al (2012a) Archaeogenomic evidence of punctuated genome evolution in Gossypium. Mol Biol Evol 29:2,031–2,038CrossRefGoogle Scholar
  33. Palmer SA, Smith O, Allaby RG (2012b) The blossoming of plant archaeogenetics. Ann Anat 194:146–156CrossRefGoogle Scholar
  34. Rollo F (1985) Characterisation by molecular hybridization of RNA fragments isolated from ancient (1400 bc) seeds. Theor Appl Genet 71:330–333Google Scholar
  35. Schlumbaum A, Edwards CJ (2013) Ancient DNA research on wetland archaeological evidence. In: Menotti F, O’Sullivan A (eds) The Oxford handbook of wetland archaeology. Oxford University Press, Oxford, pp 569–583Google Scholar
  36. Schlumbaum A, Neuhaus J-M, Jacomet S (1998) Coexistence of tetraploid and hexaploid naked wheat in a Neolithic lake dwelling of central Europe: evidence from morphology and ancient DNA. J Archaeol Sci 25:1,111–1,118CrossRefGoogle Scholar
  37. Schlumbaum A, Tensen M, Jaenicke-Després V (2008) Ancient plant DNA in archaeobotany. Veget Hist Archaeobot 17:233–244CrossRefGoogle Scholar
  38. Shapiro B, Hofreiter M (2010) Analysis of ancient human genomes. BioEssays 32:388–391CrossRefGoogle Scholar
  39. Shapiro B, Hofreiter M (2014) A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343:1,236,573CrossRefGoogle Scholar
  40. Skoglund P, Northoft BH, Shunkov MV et al (2014) Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1414542111 Google Scholar
  41. Smith O, Manning K, Clapham AJ et al. (2010) Detection of epigenesis in archaeogenetic systems. In: Abstracts, fourth international symposium on biomolecular archaeology, p 104Google Scholar
  42. Smith O, Clapham A, Rose P et al (2014) A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological barley stripe mosaic virus. Sci Rep 4:5,559Google Scholar
  43. Wales N, Anderson K, Cappellini E et al (2014) Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLoS ONE 9(1):e86827CrossRefGoogle Scholar
  44. Yoshida K, Schuenemann VJ, Cano LM et al. (2013) The rise and fall of the Phytophora infestans lineage that triggered the Irish potato famine. eLIFE 2:e00731Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Terence A. Brown
    • 1
  • Enrico Cappellini
    • 2
  • Logan Kistler
    • 3
  • Diane L. Lister
    • 4
  • Hugo R. Oliveira
    • 5
  • Nathan Wales
    • 2
  • Angela Schlumbaum
    • 6
    Email author
  1. 1.Faculty of Life Sciences, Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK
  2. 2.Centre for GeoGeneticsUniversity of CopenhagenCopenhagen KDenmark
  3. 3.Department of AnthropologyPennsylvania State UniversityUniversity ParkUSA
  4. 4.McDonald Institute for Archaeological ResearchUniversity of CambridgeCambridgeUK
  5. 5.Research Centre in Biodiversity and Genetic ResourcesVairãoPortugal
  6. 6.Integrative Prähistorische und Naturwissenschaftliche ArchäologieBaselSwitzerland

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