1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Plant Biology
  4. Volume 71, 2020
  5. Article

Annual Review of Plant Biology

Volume 71, 2020

Ancient Plant Genomics in Archaeology, Herbaria, and the Environment

Abstract

The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.

Keyword(s): ancient plant DNA, archaeobotany, archaeogenomics, environmental ancient DNA, herbarium collections, paleogenomics
Loading

Article metrics loading...

/content/journals/10.1146/annurev-arplant-081519-035837
2020-04-29
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/arplant/71/1/annurev-arplant-081519-035837.html?itemId=/content/journals/10.1146/annurev-arplant-081519-035837&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Adams RP, Sharma LN 2010. DNA from herbarium specimens. I. Correlation of DNA size with specimen age. Phytologia 92:346–53
     [Google Scholar]
  2. 2. 
    Allaby RG, Jones MK, Brown TA 1994. DNA in charred wheat grains from the Iron Age hillfort at Danebury, England. Antiquity 68:258126–32
     [Google Scholar]
  3. 3. 
    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. 1:2119–29
     [Google Scholar]
  4. 4. 
    Allaby RG, Smith O, Kistler L 2018. Archaeogenomics and crop adaptation. Paleogenomics C Lindqvist, R Rajora 189–203 Cham, Switz.: Springer
     [Google Scholar]
  5. 5. 
    Allaby RG, Ware RL, Kistler L 2019. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evol. Appl. 12:129–37
     [Google Scholar]
  6. 6. 
    Allentoft ME, Collins M, Harker D, Haile J, Oskam CL et al. 2012. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B 279:17484724–33
     [Google Scholar]
  7. 7. 
    Alsos IG, Lammers Y, Yoccoz NG, Jørgensen T, Sjögren P et al. 2018. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLOS ONE 13:4e0195403
     [Google Scholar]
  8. 8. 
    Ames M, Spooner DM 2008. DNA from herbarium specimens settles a controversy about origins of the European potato. Am. J. Bot. 95:2252–57
     [Google Scholar]
  9. 9. 
    Anderson-Carpenter LL, McLachlan JS, Jackson ST, Kuch M, Lumibao CY, Poinar HN 2011. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC Evol. Biol. 11:30
     [Google Scholar]
  10. 10. 
    Ávila-Arcos MC, Cappellini E, Romero-Navarro JA, Wales N, Moreno-Mayar JV et al. 2011. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA. Sci. Rep. 1:74
     [Google Scholar]
  11. 11. 
    Bakker FT, Lei D, Yu J, Mohammadin S, Wei Z et al. 2016. Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline. Biol. J. Linn. Soc. Lond. 117:133–43
     [Google Scholar]
  12. 12. 
    Beaman RS, Cellinese N. 2012. Mass digitization of scientific collections: new opportunities to transform the use of biological specimens and underwrite biodiversity science. Zookeys 209:7–17
     [Google Scholar]
  13. 13. 
    Besnard G, Christin P-A, Malé P-JG, Lhuillier E, Lauzeral C et al. 2014. From museums to genomics: Old herbarium specimens shed light on a C3 to C4 transition. J. Exp. Bot. 65:226711–21
     [Google Scholar]
  14. 14. 
    Besnard G, Gaudeul M, Lavergne S, Muller S, Rouhan G et al. 2018. Herbarium-based science in the twenty-first century. Bot. Lett. 165:3–4323–27
     [Google Scholar]
  15. 15. 
    Bieker VC, Martin MD. 2018. Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections. Bot. Lett. 165:3–4409–18
     [Google Scholar]
  16. 16. 
    Bilinski P, Albert PS, Berg JJ, Birchler JA, Grote MN et al. 2018. Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. PLOS Genet 14:5e1007162
     [Google Scholar]
  17. 17. 
    Boast AP, Weyrich LS, Wood JR, Metcalf JL, Knight R, Cooper A 2018. Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. PNAS 115:71546–51
     [Google Scholar]
  18. 18. 
    Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J et al. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. PNAS 104:3714616–21
     [Google Scholar]
  19. 19. 
    Brown TA, Allaby RG, Sallares R, Jones G 1998. Ancient DNA in charred wheats: taxonomic identification of mixed and single grains. Anc. Biomol. 2:2185–93
     [Google Scholar]
  20. 20. 
    Brown TA, Cappellini E, Kistler L, Lister DL, Oliveira HR et al. 2015. Recent advances in ancient DNA research and their implications for archaeobotany. Veg. Hist. Archaeobot. 24:1207–14
     [Google Scholar]
  21. 21. 
    Bunning SL, Jones G, Brown TA 2012. Next generation sequencing of DNA in 3300-year-old charred cereal grains. J. Archaeol. Sci. 39:82780–84
     [Google Scholar]
  22. 22. 
    Campos PF, Craig OE, Turner-Walker G, Peacock E, Willerslev E, Gilbert MTP 2012. DNA in ancient bone—Where is it located and how should we extract it?. Ann. Anat. 194:17–16
     [Google Scholar]
  23. 23. 
    Cappellini E, Gilbert MTP, Geuna F, Fiorentino G, Hall A et al. 2010. A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97:2205–17
     [Google Scholar]
  24. 24. 
    Carøe C, Gopalakrishnan S, Vinner L, Mak SST, Sinding MHS et al. 2018. Single-tube library preparation for degraded DNA. Methods Ecol. Evol. 9:2410–19
     [Google Scholar]
  25. 25. 
    Clarke CL, Edwards ME, Brown AG, Gielly L, Lammers Y et al. 2019. Holocene floristic diversity and richness in northeast Norway revealed by sedimentary ancient DNA (sedaDNA) and pollen. Boreas 48:2299–316
     [Google Scholar]
  26. 26. 
    Cooper A, Poinar HN. 2000. Ancient DNA: Do it right or not at all. Science 289:54821139
     [Google Scholar]
  27. 27. 
    Cota-Sánchez JH, Remarchuk K, Ubayasena K 2006. Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue. Plant Mol. Biol. Rep. 24:2161
     [Google Scholar]
  28. 28. 
    Cubero OF, Crespo A, Fatehi J, Bridge PD 1999. DNA extraction and PCR amplification method suitable for fresh, herbarium-stored, lichenized, and other fungi. Plant Syst. Evol. 216:3–4243–49
     [Google Scholar]
  29. 29. 
    da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P et al. 2015. The origin and evolution of maize in the American Southwest. Nat. Plants 1:14003
     [Google Scholar]
  30. 30. 
    Dabney J, Knapp M, Glocke I, Gansauge M-T, Weihmann A et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. PNAS 110:3915758–63
     [Google Scholar]
  31. 31. 
    Délye C, Deulvot C, Chauvel B 2013. DNA analysis of herbarium specimens of the grass weed Alopecurus myosuroides reveals herbicide resistance pre-dated herbicides. PLOS ONE 8:10e75117
     [Google Scholar]
  32. 32. 
    Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:11–15
     [Google Scholar]
  33. 33. 
    Elbaum R, Melamed-Bessudo C, Tuross N, Levy AA, Weiner S 2009. New methods to isolate organic materials from silicified phytoliths reveal fragmented glycoproteins but no DNA. Quat. Int. 193:1–211–19
     [Google Scholar]
  34. 34. 
    Erickson DL, Smith BD, Clarke AC, Sandweiss DH, Tuross N 2005. An Asian origin for a 10,000-year-old domesticated plant in the Americas. PNAS 102:5118315–20
     [Google Scholar]
  35. 35. 
    Erkens RHJ, Cross H, Maas JW, Hoenselaar K, Chatrou LW 2008. Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA. Blumea 53:2407–28
     [Google Scholar]
  36. 36. 
    Exposito-Alonso M, Becker C, Schuenemann VJ, Reiter E, Setzer C et al. 2018. The rate and potential relevance of new mutations in a colonizing plant lineage. PLOS Genet 14:2e1007155
     [Google Scholar]
  37. 37. 
    Fordyce SL, Ávila-Arcos MC, Rasmussen M, Cappellini E, Romero-Navarro JA et al. 2013. Deep sequencing of RNA from ancient maize kernels. PLOS ONE 8:1e50961
     [Google Scholar]
  38. 38. 
    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. 30:7901–8
     [Google Scholar]
  39. 39. 
    Fricker EJ, Spigelman M, Fricker CR 1997. The detection of Escherichia coli DNA in the ancient remains of Lindow Man using the polymerase chain reaction. Lett. Appl. Microbiol. 24:5351–54
     [Google Scholar]
  40. 40. 
    Fuller DQ, Denham T, Arroyo-Kalin M, Lucas L, Stevens CJ et al. 2014. Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. PNAS 111:176147–52
     [Google Scholar]
  41. 41. 
    Fulton TL, Shapiro B. 2019. Setting up an ancient DNA laboratory. Methods Mol. Biol. 1963:1–13
     [Google Scholar]
  42. 42. 
    Gansauge M-T, Gerber T, Glocke I, Korlević P, Lippik L et al. 2017. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res 45:10e79
     [Google Scholar]
  43. 43. 
    Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I 2005. Assessing ancient DNA studies. Trends Ecol. Evol. 20:10541–44
     [Google Scholar]
  44. 44. 
    Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM et al. 2009. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotech. 27:2182–89
     [Google Scholar]
  45. 45. 
    Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M et al. 1990. Chloroplast DNA sequence from a Miocene Magnolia species. Nature 344:656–58
     [Google Scholar]
  46. 46. 
    Goloubinoff P, Pääbo S, Wilson AC 1993. Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. PNAS 90:51997–2001
     [Google Scholar]
  47. 47. 
    Graham CH, Ferrier S, Huettman F, Moritz C, Peterson AT 2004. New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol. Evol. 19:9497–503
     [Google Scholar]
  48. 48. 
    Grass RN, Heckel R, Puddu M, Paunescu D, Stark WJ 2015. Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54:82552–55
     [Google Scholar]
  49. 49. 
    Green EJ, Speller CF. 2017. Novel substrates as sources of ancient DNA: prospects and hurdles. Genes 8:7180
     [Google Scholar]
  50. 50. 
    Gutaker RM, Burbano HA. 2017. Reinforcing plant evolutionary genomics using ancient DNA. Curr. Opin. Plant Biol. 36:38–45
     [Google Scholar]
  51. 51. 
    Gutaker RM, Reiter E, Furtwängler A, Schuenemann VJ, Burbano HA 2017. Extraction of ultrashort DNA molecules from herbarium specimens. Biotechniques 62:276–79
     [Google Scholar]
  52. 52. 
    Gutaker RM, Weiß CL, Ellis D, Anglin NL, Knapp S et al. 2019. The origins and adaptation of European potatoes reconstructed from historical genomes. Nat. Ecol. Evol. 3:1093–101
     [Google Scholar]
  53. 53. 
    Haber M, Mezzavilla M, Xue Y, Tyler-Smith C 2016. Ancient DNA and the rewriting of human history: be sparing with Occam's razor. Genome Biol 17:11
     [Google Scholar]
  54. 54. 
    Hansson MC, Foley BP. 2008. Ancient DNA fragments inside Classical Greek amphoras reveal cargo of 2400-year-old shipwreck. J. Archaeol. Sci. 35:51169–76
     [Google Scholar]
  55. 55. 
    Hart ML, Forrest LL, Nicholls JA, Kidner CA 2016. Retrieval of hundreds of nuclear loci from herbarium specimens. Taxon 65:51081–92
     [Google Scholar]
  56. 56. 
    Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC 1984. DNA sequences from the quagga, an extinct member of the horse family. Nature 312:282–84
     [Google Scholar]
  57. 57. 
    Iñiguez AM, Reinhard K, Carvalho Gonçalves ML, Ferreira LF, Araújo A, Paulo Vicente AC 2006. SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites. Int. J. Parasitol. 36:131419–25
     [Google Scholar]
  58. 58. 
    Jaenicke-Despres V, Buckler ES, Smith BD, Gilbert MTP, Cooper A et al. 2003. Early allelic selection in maize as revealed by ancient DNA. Science 302:56481206–8
     [Google Scholar]
  59. 59. 
    Johnson MG, Pokorny L, Dodsworth S, Botigué LR, Cowan RS et al. 2019. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Syst. Biol. 68:4594–606
     [Google Scholar]
  60. 60. 
    Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L 2013. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29:131682–84
     [Google Scholar]
  61. 61. 
    Jørgensen T, Kjær KH, Haile J, Rasmussen M, Boessenkool S et al. 2012. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding. Mol. Ecol. 21:81980–88
     [Google Scholar]
  62. 62. 
    Kapusta A, Suh A, Feschotte C 2017. Dynamics of genome size evolution in birds and mammals. PNAS 114:8E1460–69
     [Google Scholar]
  63. 63. 
    Kennett DJ, Thakar HB, VanDerwarker AM, Webster DL, Culleton BJ et al. 2017. High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras. PNAS 114:349026–31
     [Google Scholar]
  64. 64. 
    Kistler L, Maezumi SY, Gregorio de Souza J, Przelomska NAS, Malaquias Costa F et al. 2018. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 362:64201309–13
     [Google Scholar]
  65. 65. 
    Kistler L, Montenegro Á, Smith BD, Gifford JA, Green RE et al. 2014. Transoceanic drift and the domestication of African bottle gourds in the Americas. PNAS 111:82937–41
     [Google Scholar]
  66. 66. 
    Kistler L, Newsom LA, Ryan TM, Clarke AC, Smith BD, Perry GH 2015. Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication. PNAS 112:4915107–12
     [Google Scholar]
  67. 67. 
    Kistler L, Shapiro B. 2011. Ancient DNA confirms a local origin of domesticated chenopod in eastern North America. J. Archaeol. Sci. 38:123549–54
     [Google Scholar]
  68. 68. 
    Kistler L, Ware R, Smith O, Collins M, Allaby RG 2017. A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Res 45:116310–20
     [Google Scholar]
  69. 69. 
    Konrade L, Shaw J, Beck J 2019. A rangewide herbarium-derived dataset indicates high levels of gene flow in black cherry (Prunus serotina). Ecol. Evol. 9:3975–85
     [Google Scholar]
  70. 70. 
    Korneliussen TS, Albrechtsen A, Nielsen R 2014. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinform 15:356
     [Google Scholar]
  71. 71. 
    Korpelainen H, Pietiläinen M. 2019. The effects of sample age and taxonomic origin on the success rate of DNA barcoding when using herbarium material. Plant Syst. Evol. 305:4319–24
     [Google Scholar]
  72. 72. 
    Krause J, Unger T, Noçon A, Malaspinas A-S, Kolokotronis S-O et al. 2008. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol. Biol. 8:220
     [Google Scholar]
  73. 73. 
    Kumagai M, Kanehara M, Shoda S, Fujita S, Onuki S et al. 2016. Rice varieties in archaic East Asia: reduction of its diversity from past to present times. Mol. Biol. Evol. 33:102496–505
     [Google Scholar]
  74. 74. 
    Leitch IJ, Bennett MD. 1997. Polyploidy in angiosperms. Trends Plant Sci 2:12470–76
     [Google Scholar]
  75. 75. 
    Leitch IJ, Johnston E, Pellicer J, Hidalgo O, Bennett M 2019. Plant DNA C-values Database, London, United Kingdom, updated April 2019, retrieved August 12, 2019. https://cvalues.science.kew.org/
  76. 76. 
    Li H, Durbin R 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:141754–60
     [Google Scholar]
  77. 77. 
    Lindahl T 1993. Instability and decay of the primary structure of DNA. Nature 362:709–15
     [Google Scholar]
  78. 78. 
    Loreille O, Roumat E, Verneau O, Bouchet F, Hänni C 2001. Ancient DNA from Ascaris: extraction amplification and sequences from eggs collected in coprolites. Int. J. Parasitol. 31:101101–6
     [Google Scholar]
  79. 79. 
    Martin MD, Cappellini E, Samaniego JA, Zepeda ML, Campos PF et al. 2013. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun. 4:2172
     [Google Scholar]
  80. 80. 
    Martin MD, Vieira FG, Ho SYW, Wales N, Schubert M et al. 2016. Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans. Mol. Biol. Evol. 33:2478–91
     [Google Scholar]
  81. 81. 
    Mascher M, Schuenemann VJ, Davidovich U, Marom N, Himmelbach A et al. 2016. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat. Genet. 48:1089–93
     [Google Scholar]
  82. 82. 
    Matheson CD, Gurney C, Esau N, Lehto R 2010. Assessing PCR inhibition from humic substances. Open Enzym. Inhib. J. 3:38–45
     [Google Scholar]
  83. 83. 
    Matsuoka Y, Vigouroux Y, Goodman MM, G JS, Buckler E, Doebley J 2002. A single domestication for maize shown by multilocus microsatellite genotyping. PNAS 99:96080–84
     [Google Scholar]
  84. 84. 
    Meyer M, Kircher M 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010:6pdb.prot5448
     [Google Scholar]
  85. 85. 
    Miller W, Drautz DI, Ratan A, Pusey B, Qi J et al. 2008. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:7220387–90
     [Google Scholar]
  86. 86. 
    Muñoz-Rodríguez P, Carruthers T, Wood JRI, Williams BRM, Weitemier K et al. 2018. Reconciling conflicting phylogenies in the origin of sweet potato and dispersal to Polynesia. Curr. Biol. 28:81246–56.e12
     [Google Scholar]
  87. 87. 
    Murray DC, Pearson SG, Fullagar R, Chase BM, Houston J et al. 2012. High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens. Quat. Sci. Rev. 58:135–45
     [Google Scholar]
  88. 88. 
    Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F et al. 2011. Genetic structure and domestication history of the grape. PNAS 108:93530–35
     [Google Scholar]
  89. 89. 
    Nielsen R, Paul JS, Albrechtsen A, Song YS 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12:443–51
     [Google Scholar]
  90. 90. 
    Nistelberger HM, Smith O, Wales N, Star B, Boessenkool S 2016. The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains. Sci. Rep. 6:37347
     [Google Scholar]
  91. 91. 
    Olofsson JK, Bianconi M, Besnard G, Dunning LT, Lundgren MR et al. 2016. Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait. Mol. Ecol. 25:246107–23
     [Google Scholar]
  92. 92. 
    Olofsson JK, Cantera I, Van de Paer C, Hong‐Wa C, Zedane L et al. 2019. Phylogenomics using low‐depth whole genome sequencing: a case study with the olive tribe. Mol. Ecol. Resour. 19:4877–92
     [Google Scholar]
  93. 93. 
    Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A et al. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499:745674–78
     [Google Scholar]
  94. 94. 
    Pääbo S 1989. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. PNAS 86:61939–43
     [Google Scholar]
  95. 95. 
    Palmer SA, Clapham AJ, Rose P, Freitas FO, Owen BD et al. 2012. Archaeogenomic evidence of punctuated genome evolution in Gossypium. Mol. Biol. Evol 29:82031–38
     [Google Scholar]
  96. 96. 
    Palmer SA, Smith O, Allaby RG 2012. The blossoming of plant archaeogenetics. Ann. Anat. 194:1146–56
     [Google Scholar]
  97. 97. 
    Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y et al. 2017. Ancient plant DNA in lake sediments. New Phytol 214:3924–42
     [Google Scholar]
  98. 98. 
    Parducci L, Nota K, Wood J 2018. Reconstructing past vegetation communities using ancient DNA from lake sediments. Paleogenomics C Lindqvist, O Rajora 163–87 Cham, Switz.: Springer
     [Google Scholar]
  99. 99. 
    Parducci L, Suyama Y, Lascoux M, Bennett KD 2005. Ancient DNA from pollen: a genetic record of population history in Scots pine. Mol. Ecol. 14:92873–82
     [Google Scholar]
  100. 100. 
    Pearsall DM 2000. Paleoethnobotany: A Handbook of Procedures San Diego: Academic 2nd ed .
  101. 101. 
    Pedersen MW, Ginolhac A, Orlando L, Olsen J, Andersen K et al. 2013. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa. Quat. Sci. Rev. 75:161–68
     [Google Scholar]
  102. 102. 
    Pedersen MW, Ruter A, Schweger C, Friebe H, Staff RA et al. 2016. Postglacial viability and colonization in North America's ice-free corridor. Nature 537:45–49
     [Google Scholar]
  103. 103. 
    Piperno DR. 2016. Phytolith radiocarbon dating in archaeological and paleoecological research: a case study of phytoliths from modern Neotropical plants and a review of the previous dating evidence. J. Archaeol. Sci. 68:54–61
     [Google Scholar]
  104. 104. 
    Piperno DR, Flannery KV. 2001. The earliest archaeological maize (Zea mays L.) from highland Mexico: new accelerator mass spectrometry dates and their implications. PNAS 98:42101–3
     [Google Scholar]
  105. 105. 
    Piperno DR, Ranere AJ, Holst I, Iriarte J, Dickau R 2009. Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico. PNAS 106:135019–24
     [Google Scholar]
  106. 106. 
    Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA et al. 1998. Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281:5375402–6
     [Google Scholar]
  107. 107. 
    Poinar HN, Schwarz C, Qi J, Shapiro B, MacPhee RDE et al. 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311:5759392–94
     [Google Scholar]
  108. 108. 
    Pont C, Wagner S, Kremer A, Orlando L, Plomion C, Salse J 2019. Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 20:29
     [Google Scholar]
  109. 109. 
    Pyke GH, Ehrlich PR. 2010. Biological collections and ecological/environmental research: a review, some observations and a look to the future. Biol. Rev. Camb. Philos. Soc. 85:2247–66
     [Google Scholar]
  110. 110. 
    Ramos-Madrigal J, Runge AKW, Bouby L, Lacombe T, Samaniego Castruita JA et al. 2019. Palaeogenomic insights into the origins of French grapevine diversity. Nat. Plants 5:6595–603
     [Google Scholar]
  111. 111. 
    Ramos-Madrigal J, Smith BD, Moreno-Mayar JV, Gopalakrishnan S, Ross-Ibarra J et al. 2016. Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Curr. Biol. 26:233195–201
     [Google Scholar]
  112. 112. 
    Rasmussen M, Cummings LS, Gilbert MTP, Bryant V, Smith C et al. 2009. Response to comment by Goldberg et al. on “DNA from pre-Clovis human coprolites in Oregon, North America”. Science 325:5937148
     [Google Scholar]
  113. 113. 
    Reinhard KJ, Bryant VM. 1992. Coprolite analysis: a biological perspective on archaeology. Archaeol. Method Theory 4:245–88
     [Google Scholar]
  114. 114. 
    Rogers SO, Bendich AJ. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol. Biol. 5:269–76
     [Google Scholar]
  115. 115. 
    Rohland N, Glocke I, Aximu-Petri A, Meyer M 2018. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat. Protoc. 13:112447–61
     [Google Scholar]
  116. 116. 
    Rohland N, Harney E, Mallick S, Nordenfelt S, Reich D 2014. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. B 370:166020130624
     [Google Scholar]
  117. 117. 
    Rohland N, Hofreiter M 2007. Comparison and optimization of ancient DNA extraction. Biotechniques 42:3343–52
     [Google Scholar]
  118. 118. 
    Rollo F. 1985. Characterisation by molecular hybridization of RNA fragments isolated from ancient (1400 B.C.) seeds. Theor. Appl. Genet. 71:2330–33
     [Google Scholar]
  119. 119. 
    Rollo F, Amici A, Salvi R, Garbuglia A 1988. Short but faithful pieces of ancient DNA. Nature 335:6193774
     [Google Scholar]
  120. 120. 
    Rollo F, Ubaldi M, Ermini L, Marota I 2002. Ötzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. PNAS 99:2012594–99
     [Google Scholar]
  121. 121. 
    Roullier C, Benoit L, McKey DB, Lebot V 2013. Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. PNAS 110:62205–10
     [Google Scholar]
  122. 122. 
    Sablok G, Amiryousefi A, He X, Hyvönen J, Poczai P 2019. Sequencing the plastid genome of giant ragweed (Ambrosia trifida, Asteraceae) from a herbarium specimen. Front. Plant Sci. 10:218
     [Google Scholar]
  123. 123. 
    Sánchez Barreiro F, Vieira FG, Martin MD, Haile J, Gilbert MTP, Wales N 2016. Characterizing restriction enzyme‐associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom‐designed RNA probes. Mol. Ecol. Resour. 17:209–20
     [Google Scholar]
  124. 124. 
    Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA et al. 2015. Gut microbiome of an 11th Century A.D. pre-Columbian Andean mummy. PLOS ONE 10:9e0138135
     [Google Scholar]
  125. 125. 
    Särkinen T, Staats M, Richardson JE, Cowan RS, Bakker FT 2012. How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLOS ONE 7:8e43808
     [Google Scholar]
  126. 126. 
    Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S 2012. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLOS ONE 7:3e34131
     [Google Scholar]
  127. 127. 
    Schubert M, Ginolhac A, Lindgreen S, Thompson JF, AL-Rasheid KAS et al. 2012. Improving ancient DNA read mapping against modern reference genomes. BMC Genom 13:178
     [Google Scholar]
  128. 128. 
    Scott MF, Botigué LR, Brace S, Stevens CJ, Mullin VE et al. 2019. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat. Plants 5:1120–28
     [Google Scholar]
  129. 129. 
    Seersholm FV, Pedersen MW, Søe MJ, Shokry H, Mak SST et al. 2016. DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago. Nat. Commun. 7:13389
     [Google Scholar]
  130. 130. 
    Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT et al. 2013. Ligation bias in Illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLOS ONE 8:10e78575
     [Google Scholar]
  131. 131. 
    Shapiro B, Hofreiter M 2012. Preface. Ancient DNA: Methods and Protocols B Shapiro, M Hofreiter v–vii New York: Springer
     [Google Scholar]
  132. 132. 
    Shepherd L, Perrie L. 2014. Genetic analyses of herbarium material: Is more care required?. Taxon 63:5972–73
     [Google Scholar]
  133. 133. 
    Skoglund P, Mathieson I. 2018. Ancient genomics of modern humans: the first decade. Annu. Rev. Genom. Hum. Genet. 19:381–404
     [Google Scholar]
  134. 134. 
    Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S et al. 2014. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. PNAS 111:62229–34
     [Google Scholar]
  135. 135. 
    Slon V, Hopfe C, Weiß CL, Mafessoni F, De La Rasilla M et al. 2017. Neandertal and Denisovan DNA from Pleistocene sediments. Science 356:6338605–8
     [Google Scholar]
  136. 136. 
    Smith O, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG 2014a. A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Sci. Rep. 4:4003
     [Google Scholar]
  137. 137. 
    Smith O, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG 2014b. Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci. Rep. 4:5559
     [Google Scholar]
  138. 138. 
    Smith O, Momber G, Bates R, Garwood P, Fitch S et al. 2015. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science 347:6225998–1001
     [Google Scholar]
  139. 139. 
    Smith O, Nicholson WV, Kistler L, Mace E, Clapham A et al. 2019. A domestication history of dynamic adaptation and genomic deterioration in Sorghum. Nat. Plants 5:369–79
     [Google Scholar]
  140. 140. 
    Smith O, Palmer SA, Clapham AJ, Rose P, Liu Y et al. 2017. Small RNA activity in archeological barley shows novel germination inhibition in response to environment. Mol. Biol. Evol. 34:102555–62
     [Google Scholar]
  141. 141. 
    Staats M, Cuenca A, Richardson JE, Vrielink-van Ginkel R, Petersen G et al. 2011. DNA damage in plant herbarium tissue. PLOS ONE 6:12e28448
     [Google Scholar]
  142. 142. 
    Stahlschmidt MC, Collin TC, Fernandes DM, Bar-Oz G, Belfer-Cohen A et al. 2019. Ancient mammalian and plant DNA from late quaternary stalagmite layers at Solkota Cave, Georgia. Sci. Rep. 9:6628
     [Google Scholar]
  143. 143. 
    Stankiewicz BA, Poinar HN, Briggs DEG, Evershed RP, Poinar GO 1998. Chemical preservation of plants and insects in natural resins. Proc. R. Soc. B 265:1397641–47
     [Google Scholar]
  144. 144. 
    Sutton M, Malik M, Ogram A 1996. Experiments on the determination of gender from coprolites by DNA analysis. J. Archaeol. Sci. 23:2263–67
     [Google Scholar]
  145. 145. 
    Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R et al. 2017. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357:6350512–15
     [Google Scholar]
  146. 146. 
    Tulig M, Tarnowsky N, Bevans M, Kirchgessner A, Thiers BM 2012. Increasing the efficiency of digitization workflows for herbarium specimens. Zookeys 209:103–13
     [Google Scholar]
  147. 147. 
    Vallebueno-Estrada M, Rodríguez-Arévalo I, Rougon-Cardoso A, Martínez González J, García Cook A et al. 2016. The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding. PNAS 113:4914151–56
     [Google Scholar]
  148. 148. 
    Van de Paer C, Hong-Wa C, Jeziorski C, Besnard G 2016. Mitogenomics of Hesperelaea, an extinct genus of Oleaceae. Gene 594:2197–202
     [Google Scholar]
  149. 149. 
    Vandepitte K, de Meyer T, Helsen K, van Acker K, Roldán-Ruiz I et al. 2014. Rapid genetic adaptation precedes the spread of an exotic plant species. Mol. Ecol. 23:92157–64
     [Google Scholar]
  150. 150. 
    VanDerwarker AM, Bardolph DN, Hoppa KM, Thakar HB, Martin LS et al. 2016. New world paleoethnobotany in the new millennium (2000–2013). J. Archaeol. Res. 24:2125–77
     [Google Scholar]
  151. 151. 
    Wagner S, Lagane F, Seguin-Orlando A, Schubert M, Leroy T et al. 2018. High-throughput DNA sequencing of ancient wood. Mol. Ecol. 27:51138–54
     [Google Scholar]
  152. 152. 
    Wales N, Akman M, Watson RHB, Sánchez Barreiro F, Smith BD et al. 2019. Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement. Evol. Appl. 12:138–53
     [Google Scholar]
  153. 153. 
    Wales N, Andersen K, Cappellini E, Ávila-Arcos MC, Gilbert MTP 2014. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLOS ONE 9:1e86827
     [Google Scholar]
  154. 154. 
    Wales N, Kistler L. 2019. Extraction of ancient DNA from plant remains. Ancient DNA: Methods and Protocols B Shapiro, A Barlow, PD Heintzman, M Hofreiter, JLA Paijmans, AER Soares 45–55 New York: Springer
     [Google Scholar]
  155. 155. 
    Wales N, Ramos Madrigal J, Cappellini E, Carmona Baez A, Samaniego Castruita JA et al. 2016. The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. J. Archaeol. Sci. 72:57–70
     [Google Scholar]
  156. 156. 
    Webber WB, Ernest LJ, Vangapandu S 2011. Mercury exposures in university herbarium collections. J. Chem. Heal. Saf. 18:29–12
     [Google Scholar]
  157. 157. 
    Weiß CL, Schuenemann VJ, Devos J, Shirsekar G, Reiter E et al. 2016. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. R. Soc. Open Sci. 3:6160239
     [Google Scholar]
  158. 158. 
    Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB et al. 2007. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317:5834111–14
     [Google Scholar]
  159. 159. 
    Willerslev E, Davison J, Moora M, Zobel M, Coissac E et al. 2014. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506:748647–51
     [Google Scholar]
  160. 160. 
    Willerslev E, Hansen AJ, Binladen J, Tina B, Gilbert MTP et al. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300:5620791–95
     [Google Scholar]
  161. 161. 
    Winkel T, Aguirre MG, Arizio CM, Aschero CA, del Pilar Babot M et al. 2018. Discontinuities in quinoa biodiversity in the dry Andes: an 18-century perspective based on allelic genotyping. PLOS ONE 13:12e0207519
     [Google Scholar]
  162. 162. 
    Wood JR, Crown A, Cole TL, Wilmshurst JM 2016. Microscopic and ancient DNA profiling of Polynesian dog (kurī) coprolites from northern New Zealand. J. Archaeol. Sci. Rep. 6:496–505
     [Google Scholar]
  163. 163. 
    Woodward SR, Weyand NJ, Bunnell M 1994. DNA sequence from Cretaceous period bone fragments. Science 266:51881229–32
     [Google Scholar]
  164. 164. 
    Yoshida K, Sasaki E, Kamoun S 2015. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects. Front. Plant Sci. 6:771
     [Google Scholar]
  165. 165. 
    Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B et al. 2013. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife 2:e00731
     [Google Scholar]
  166. 166. 
    Zhou Y, Minio A, Massonnet M, Solares E, Lv Y et al. 2019. Structural variants, hemizygosity and clonal propagation in grapevines. bioRxiv 508119. https://doi.org/10.1101/508119
    [Crossref]
  167. 167. 
    Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT et al. 2015. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci. Rep. 5:16498
     [Google Scholar]
/content/journals/10.1146/annurev-arplant-081519-035837
Loading
Ancient Plant Genomics in Archaeology, Herbaria, and the Environment
Annual Review of Plant Biology 71, 605 (2020); https://doi.org/10.1146/annurev-arplant-081519-035837
/content/journals/10.1146/annurev-arplant-081519-035837
/content/journals/10.1146/annurev-arplant-081519-035837
Loading

Data & Media loading...

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error