Ancient Plant DNA

Encyclopedia of Quaternary Science: Second Edition

Volumn , Issue , 2013, Pages 705-715

  Wales, N ^a   Allaby, R ^b   Willerslev, E ^c   Gilbert, M T P ^b  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Ancient DNA; Contamination; Coprolite; Core; Degradation; DNA; Paleogenetics; Permafrost; Phylogenetics; Plant; Pollen; Preservation; Sediment; Seed; Wood

Indexed keywords

EID: 84900335370     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-444-53643-3.00202-8     Document Type: Chapter

References (71)

1. Allaby R.G., Banerjee M., Brown T.A. Evolution of the high-molecular-weight glutenin loci of the A, B, D and G genomes of wheat. Genome 1999, 42:296-307.
2. Vila-Arcos M.C., Cappellini E., Romero-Navarro J.A., et al. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Scientific Reports 2011, 1:74.
3. Blatter R.H.E., Jacomet S., Schulmbaum A. Spelt-specific alleles in HMW glutenin genes from modern and historical European spelt (Triticum spelta L.). Theoretical and Applied Genetics 2002, 104:329-337.
4. Briggs A.W., Good J.M., Green R.E., et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 2009, 325:318-321.
5. Brown T.A. How ancient DNA may help in understanding the origin and spread of agriculture. Proceedings of the Royal Society B 1999, 354:89-98.
6. Burbano H.A., Hodges E., Green R.E., et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 2010, 328:723-725.
7. Burger J., Hummel S., Herrmann B. Palaeogenetics and cultural heritage. Species determination and STR-genotyping from ancient DNA in art and artefacts. Thermochimica Acta 2000, 365:141-146.
8. Callaway E. Taking molecular snaps of ancient crops. Nature News 2010, Published, online 13 September 2010. 10.1038/news.2010.464.
9. Campbell K.L., Roberts J.E.E., Watson L.N., et al. Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics 2010, 42:536-540.
10. Cappellini E., Gilbert M., Geuna F., et al. A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 2010, 97:205-217.
11. Chen K., Rajewsky N. The evolution of gene regulation by transcription factors and microRNAs. Nature Reviews Genetics 2007, 8:93-103.
12. Deguilloux M.-F., Pemonge M.-H., Petit R.J. Novel perspectives in wood certification and forensics: Dry wood as a source of DNA. Proceedings of the Royal Society B 2002, 269:1039-1046.
13. Deguilloux M.-F., Pemonge M.-H., Petit R.J. DNA-based control of oak wood geographic origin in the context of the cooperage industry. Annals of Forest Science 2004, 61:97-104.
14. Drabkova L., Kirschner J., Vlcek C. Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. Plant Molecular Biology Reporter 2002, 20:161-175.
15. Dumolin-Lapegue S., Pemonge H.-M., Gielly L., Taberlet P., Petit R.J. Amplification of oak DNA from ancient and modern wood. Molecular Ecology 1999, 8:2137-2140.
16. Elbaum R., Melamed-Bessudo C., Boaretto E., et al. Ancient olive DNA in pits: Preservation, amplification and sequence analysis. Journal of Archaeological Science 2006, 33:77-88.
17. Elbaum R., Melamed-Bessudo C., Tuross N., Levy A.A., Weiner S. New methods to isolate organic materials from silicified phytoliths reveal fragmented glycoproteins but no DNA. Quaternary International 2009, 193:11-19.
18. Erickson D.L., Smith B.D., Clarke A.C., Sandweiss D.H., Tuross N. An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:18315-18320.
19. Fortea J., de la Rasilla M., García-Tabernero A., Gigli E., Rosas A., Lalueza-Fox C. Excavation protocol of bone remains for Neandertal DNA analysis in El Sidrón Cave (Asturias, Spain). Journal of Human Evolution 2008, 55:353-357.
20. Freitas F.O., Bendel G., Allaby R.G., Brown T.A. DNA from primitive maize landraces and archaeological remains, implications for the domestication of maize and its expansion into South America. Journal of Archaeological Science 2003, 30:901-908.
21. Gilbert M.T.P., Bandelt H.J., Hofreiter M., Barnes I. Assessing ancient DNA studies. Trends in Ecology and Evolution 2005, 20:541-544.
22. Gilbert M.T.P., Jenkins D.L., Gotherstrom A., et al. DNA from pre-Clovis human coprolites in Oregon, North America. Science 2008, 320:786-789.
23. Golenberg E.M., Giannasi D.E., Clegg M.T., et al. Chloroplast DNA sequence from a Miocene Magnolia species. Nature 1990, 344:656-658.
24. Gould B.A., Leon B., Buffen A.M., Thompson L.G. Evidence of a high-Andean, mid-Holocene plant community: An ancient DNA analysis of glacially preserved remains. American Journal of Botany 2010, 97:1579-1584.
25. Green R.E., Krause J., Briggs A.W., et al. A draft sequence of the Neandertal genome. Science 2010, 328:710-722.
26. Gugerli F., Parducci L., Petit R.J. Ancient plant DNA, review and prospects. New Phytologist 2005, 166:409-418.
27. Haile J., Holdaway R., Oliver K., et al. Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor?. Molecular Biology and Evolution 2007, 24:982-989.
28. Hansson M.C., Foley B.P. Ancient DNA fragments inside Classical Greek amphoras reveal cargo of 2400-year-old shipwreck. Journal of Archaeological Science 2008, 35:1169-1176.
29. Hebsgaard M.B., Gilbert M.T.P., Arneborg J., et al. 'The Farm Beneath the Sand' - An archaeological case study on ancient 'dirt' DNA. Antiquity 2009, 83:430-444.
30. Hebsgaard M.B., Phillips M.J., Willerslev E. Geologically ancient DNA: Fact or artefact?. Trends in Microbiology 2005, 13:212-220.
31. Hofreiter M., Serre D., Poinar H.N., Kuch M., Pääbo S. Ancient DNA. Nature Reviews Genetics 2001, 2:353-359.
32. Jaenicke-Després V., Buckler E.S., Smith B.D., et al. Early allelic selection in maize as revealed by ancient DNA. Science 2003, 302:1206-1208.
33. Kim S., Soltis D.E., Soltis P.S., Suh Y. DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae). American Journal of Botany 2004, 91:615-620.
34. Knapp M., Hofreiter M. Next generation sequencing of ancient DNA: Requirements, strategies and perspectives. Genes 2010, 1:227-243.
35. Küch M., Rohland N., Betancourt J.L., Latorre C., Steppan S., Poinar H.N. Molecular analysis of an 11,700-year-old rodent midden from the Atacama Desert, Chile. Molecular Ecology 2002, 11:913-924.
36. Li W., Brlansky R.H., Hartung J.S. Amplification of DNA of Xanthomonas axonopodis pv. citri from historic citrus canker herbarium specimens. Journal of Microbiological Methods 2006, 65:237-246.
37. Li C., Lister D.L., Li H., et al. Ancient DNA analysis of desiccated wheat grains excavated from a Bronze Age cemetery in Xinjiang. Journal of Archaeological Science 2011, 38:115-119.
38. Lia V.V., Confalonieri V.A., Ratto N., et al. Microsatellite typing of ancient maize: Insights into the history of agriculture in southern South America. Proceedings of the Royal Society B 2007, 274:545-554.
39. Liepelt S., Sperisen C., Deguilloux M., et al. Authenticated DNA from ancient wood remains. Annals of Botany 2006, 98:1107-1111.
40. Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993, 362:709-715.
41. Manen J.-F., Bouby L., Dalnoki O., Marinval P., Turgay M., Schlumbaum A. Microsatellites from archaeological Vitis vinifera seeds allow a tentative assignment of the geographical origin of ancient cultivars. Journal of Archaeological Science 2003, 30:721-729.
42. Marota I., Basile C., Ubaldi M., Rollo F. DNA decay rate in papyri and human remains from Egyptian archaeological sites. American Journal of Physical Anthropology 2002, 117:310-318.
43. Millar C.D., Huynen L., Subramanian S., Mohandesan E., Lambert D.M. New developments in ancient genomics. Trends in Ecology and Evolution 2008, 23(7):386-393.
44. Miller W., Drautz D.I., Ratan A., et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 2008, 456:387-390.
45. Mukherjee A., Roy S., De Bera S., et al. Results of molecular analysis of an archaeological hemp (Cannabis sativa L.) DNA sample from North West China. Genetic Resources and Crop Evolution 2008, 55:481-485.
46. Pääbo S., Wilson A.C. Miocene DNA sequences - A dream come true?. Current Biology 1991, 1:45-46.
47. Paffetti D., Vettori C., Caramelli D., et al. Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon. BMC Evolutionary Biology 2007, 7:S6.
48. Palmer S.A., Moore J.D., Clapham A.J., Rose P., Allaby R.G. Archaeogenetic evidence of ancient Nubian Barley evolution from six to two-row indicates local adaptation. PLoS One 2009, 4:e6301. 10.1371/journal.pone.0006301.
49. Palmer S.A., Smith O., Allaby R.G. The blossoming of plant archaeogenetics. Annals of Anatomy 2012, 194:146-156.
50. Panieri G., Lugli S., Manzi V., Roveri M., Schreiber B.C., Palinska K.A. Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy. Geobiology 2010, 8:101-111.
51. Parducci L., Suyama Y., Lascoux M., Bennett K.D. Ancient DNA from pollen, a genetic record of population history in Scots pine. Molecular Ecology 2005, 14:2873-2882.
52. Poinar H.N., Hofreiter M., Spaulding W.G., et al. Molecular coproscopy: Dung and diet of the extinct Ground Sloth Nothrotheriops shastensis. Science 1998, 281:402-406.
53. Poinar H.N., Kuch M., Sobolik K.D., et al. A molecular analysis of dietary diversity for three archaic Native Americans. Proceedings of the National Academy of Sciences of the United States of America 2001, 98:4317-4322.
54. Poinar H.N., Schwarz C., Qi J., et al. Metagenomics to paleogenomics: Large-scale sequencing of Mammoth DNA. Science 2006, 311:392-394.
55. Raniello R., Procaccini G. Ancient DNA in the seagrass Posidonia oceanica. Marine Ecology Progress Series 2002, 227:269-273.
56. Rasmussen M., Cummings L.S., Gilbert M.T.P., et al. Response to comment by Goldberg et al. on 'DNA from pre-Clovis human coprolites in Oregon, North America'. Science 2009, 325:148.
57. Reinhard K.J., Chaves S.M., Jones J.G., Iñiguez A.M. Evaluating chloroplast DNA in prehistoric Texas coprolites: Medicinal, dietary, or ambient ancient DNA?. Journal of Archaeological Science 2008, 35:1748-1755.
58. Ristaino J.B., Groves C.T., Parra G. PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 2001, 411:695-697.
59. Roberts C., Ingham S. Using ancient DNA analysis in palaeopathology: A critical analysis of published papers, with recommendations for future work. International Journal of Osteoarchaeology 2008, 18:600-613.
60. Rollo F., Ubaldi M., Ermini L., Marota I. ötzi's last meals, DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:12594-12599.
61. Sallon S., Solowey E., Cohen Y., et al. Germination, genetics, and growth of an ancient date seed. Science 2008, 320:1464.
62. Saltonstall K. Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:2445-2449.
63. Schlumbaum A., Tensen M., Jaenicke-Després V. Ancient plant DNA in archaeobotany. Vegetation History and Archaeobotany 2008, 17:233-244.
64. Sidow A., Wilson A.C., Pääbo S. Bacterial DNA in Clarkia fossils. Philosophical Transactions of the Royal Society B 1991, 333:429-433.
65. Taberlet P., Coissac E., Pompanon F., et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 2007, 35:e14.
66. Tanaka K., Honda T., Ishikawa R. Rice archaeological remains and the possibility of DNA archaeology: Examples from Yayoi and Heian periods of Northern Japan. Archaeological and Anthropological Sciences 2010, 2:69-78.
67. Tringe S.G., Rubin E.M. Metagenomics: DNA sequencing of environmental samples. Nature Reviews Genetics 2005, 6:805-814.
68. van Geel B., Aptroot A., Baittinger C., et al. The ecological implications of a Yakutian mammoth's last meal. Quaternary Research 2008, 69:361-376.
69. Willerslev E., Cappellini E., Boomsma W., et al. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 2007, 317:111-114.
70. Willerslev E., Cooper A. Ancient DNA. Proceedings of the Royal Society B 2005, 272:3-16.
71. Willerslev E., Hansen A.J., Binladen J., et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 2003, 300:791-795.