Recent advances in ancient DNA research and their implications for archaeobotany

Vegetation History and Archaeobotany

Volumn 24, Issue 1, 2015, Pages 207-214

  Brown, Terence A ^a   Cappellini, Enrico ^b   Kistler, Logan ^c   Lister, Diane L ^d   Oliveira, Hugo R ^e   Wales, Nathan ^b   Schlumbaum, Angela ^f  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^f Integrative prähistorische und naturwissenschaftliche Archäologie   (Switzerland)

Author keywords

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

Indexed keywords

EID: 84921937432     PISSN: 09396314     EISSN: 16176278     Source Type: Journal    
DOI: 10.1007/s00334-014-0489-4     Document Type: Review

References (44)

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 1:119–129
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 42:296–307
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 279:4,727–4,733
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 1:74
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 104:329–337
6. Brown TA (1999) How ancient DNA may help in understanding the origin and spread of agriculture. Phil Trans R Soc B 354:89–98
7. Brown TA, Brown KA (2011) Biomolecular archaeology: an introduction. Wiley-Blackwell, New York
8. Bunning SL, Jones G, Brown TA (2012) Next generation sequencing of DNA in 3300-year-old charred cereal grains. J Archaeol Sci 39:2,780–2,784
9. Cappellini E, Gilbert MTP, Geuna F et al (2010) A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97:205–217
10. Fordyce L, Ávila-Arcos MC, Rasmussen M et al (2013) Deep sequencing of RNA from ancient maize kernels. PLoS ONE 8(1):e50961
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 30:901–908
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 90:1,997–2,001
13. Green RE, Briggs AW, Krause J et al (2009) The Neandertal genome and ancient DNA authenticity. EMBO J 28:2,494–2,502
14. Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447:418–424
15. Jaenicke-Després V, Buckler ES, Smith BD et al (2003) Early allelic selection in maize as revealed by ancient DNA. Science 302:1,206–1,208
16. Jones G, Valamoti S, Charles M (2000) Early crop diversity: a “new” glume wheat from northern Greece. Veget Hist Archaeobot 9:133–146
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 39:3,230–3,238
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 87:701–713
19. Kistler L, Shapiro B (2011) Ancient DNA confirms a local origin of domesticated chenopod in eastern North America. J Archaeol Sci 38:3,549–3,554
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):2,937–2,941
21. Leino M, Boström E, Hagenblad J (2013) Twentieth-century changes in the genetic composition of Swedish field pea metapopulations. Heredity 110:338–346
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 38:115–119
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 274:545–554
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 62:779–789
25. Llamas B, Holland ML, Chen K et al (2012) High-resolution analysis of cytosine methylation in ancient DNA. PLoS ONE 7(1):e30226
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 30:721–729
27. Martin MD, Cappellini E, Samaniego JA (2013) Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat Comm 4(2):172
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 8:503–508
29. O’Donoghue K, Clapham A, Evershed RP, Brown TA (1996) Remarkable preservation of biomolecules in ancient radish seeds. Proc R Soc Lond B 263:541–547
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 39:828–835
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):e6301
32. Palmer SA, Clapham AJ, Rose P et al (2012a) Archaeogenomic evidence of punctuated genome evolution in Gossypium. Mol Biol Evol 29:2,031–2,038
33. Palmer SA, Smith O, Allaby RG (2012b) The blossoming of plant archaeogenetics. Ann Anat 194:146–156
34. Rollo F (1985) Characterisation by molecular hybridization of RNA fragments isolated from ancient (1400 bc) seeds. Theor Appl Genet 71:330–333
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 569–583
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 25:1,111–1,118
37. Schlumbaum A, Tensen M, Jaenicke-Després V (2008) Ancient plant DNA in archaeobotany. Veget Hist Archaeobot 17:233–244
38. Shapiro B, Hofreiter M (2010) Analysis of ancient human genomes. BioEssays 32:388–391
39. Shapiro B, Hofreiter M (2014) A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343:1,236,573
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
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 104
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 4:5,559
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):e86827
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:e00731