Using palaeoenvironmental DNA to reconstruct past environments: Progress and prospects

Journal of Quaternary Science

Volumn 29, Issue 7, 2014, Pages 610-626

  Rawlence, Nicolas J ^a,b   Lowe, David J ^a   Wood, Jamie R ^c   Young, Jennifer M ^d   Churchman, G Jock ^d   Huang, Yu Tuan ^a   Cooper, Alan ^d  

^a UNIVERSITY OF WAIKATO   (New Zealand)

^b UNIVERSITY OF OTAGO   (New Zealand)

^c LANDCARE RESEARCH   (New Zealand)

^d UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Ancient DNA; Archaeology; Environmental DNA; Palaeoecology; Palaeoenvironmental DNA; PalEnDNA; Quaternary

Indexed keywords

ARCHAEOLOGY; DNA; PALEOECOLOGY; PALEOENVIRONMENT; QUATERNARY; RECONSTRUCTION; TAPHONOMY;

EID: 84923867737     PISSN: 02678179     EISSN: 10991417     Source Type: Journal    
DOI: 10.1002/jqs.2740     Document Type: Review

References (197)

1. Adler CJ, Haak W, Donlon D, et al. 2011. Survival and recovery of DNA from ancient teeth and bones. Journal of Archaeological Science 38: 956-964.
2. Adler CJ, Dobney K, Weyrich LS, et al. 2013. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nature Genetics 45: 450-455.
3. Ahrens RJ, Arnold RW. 2012. Soil Taxonomy. In Handbook of Soil Sciences. 2nd edn Vol. 1, Huang PM, Li Y, Sumner ME (eds). CRC Press: Boca Raton; 31.1-31.13.
4. Allen MF, Crisafulli CM, Morris SJ, et al. 2005. Mycorrhizae and Mount St. Helens: story of a symbiosis. In Ecological Responses to the 1980 Eruption of Mount St. Helens, Dale VH, Swanson FJ, Crisafulli CM (eds). Springer: New York; 221-231.
5. Allentoft ME, Collins M, Harker D, et al. 2012. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society of London Series B 279: 4724-4733.
6. Alley RB, Andrews JT, Brigham-Grette J, et al. 2010. History of the Greenland Ice Sheet: paleoclimatic insights. Quaternary Science Reviews 29: 1728-1756.
7. Alloway BV, Lowe DJ, Larsen G, et al. 2013. Tephrochronology. In The Encyclopaedia of Quaternary Science. 2nd edn, Vol. 4, Elias SA, Mock CJ (eds). Elsevier: London; 277-304.
8. Alvarez AJ, Khanna M, Toranzos GA, et al. 1998. Amplification of DNA bound on clay minerals. Molecular Ecology 7: 775-778.
9. Anderson-Carpenter LL, McLachlan JS, Jackson ST, et al. 2011. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC Evolutionary Biology 11: 30.
10. Andersen K, Bird KL, Rasmussen M, et al. 2012. Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity. Molecular Ecology 21: 1966-1979.
11. Arnold LJ, Roberts RG, MacPhee RDE, et al. 2011. Paper II - dirt, dates and DNA: OSL and radiocarbon chronologies of perennially frozen sediments in Siberia, and their implications for sedimentary ancient DNA studies. Boreas 40: 417-445.
12. Austin JJ, Ross AJ, Smith AB, et al. 1997. Problems of reproducibility - does geologically ancient DNA survive in amber-preserved insects? Proceedings of the Royal Society of London Series B 264: 467-474.
13. Banks NG, Hoblitt RP. 1981. Summary of temperature studies of 1980 deposits. In The 1980 Eruptions of Mount St. Helens, Washington, Lipma PW, Mullineaux DR (eds). Geological Survey, Professional Paper 1250: 295-313.
14. Bennett KD, Parducci L. 2006. DNA from pollen: principles and potential. The Holocene 16: 1031-1034.
15. Birks HH, Birks HJB. 2006. Multi-proxy studies in palaeolimnology. Vegetation History and Archaeobotany 15: 235-251.
16. Birks HJB, Heiri O, Seppä H, et al. 2010. Strengths and weaknesses of quantitative climate reconstructions based on late-Quaternary biological proxies. Open Ecology Journal 3: 68-110.
17. Bissett A, Gibson JAE, Jarman SN, et al. 2005. Isolation, amplification, and identification of ancient copepod DNA from lake sediments. Limnology and oceanography. Methods 3: 533-542.
18. Boessenkool S, Epp LS, Haile J, et al. 2012. Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Molecular Ecology 8: 1806-1815.
19. Boessenkool S, McGlynn G, Epp LS, et al. 2014. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity. Conservation Biology 28: 446-455.
20. Bohmann K, Evans A, Gilbert MTP, et al. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology and Evolution 29: 358-367.
21. Brotherton P, Endicott P, Sanchez JJ, et al. 2007. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Research 35: 5717-5728.
22. Bunce M, Worthy TH, Phillips MJ, et al. 2009. The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proceedings of the National Academy of Science of the United States of America 106: 20646-20651.
23. Calvignac-Spencer S, Merkel K, Kutzner N, et al. 2013. Carrion fly derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Molecular Ecology 22: 915-924.
24. Campos PF, Willerslev E, Mead JI, et al. 2010. Molecular identification of the extinct mountain goat, Oreamnos harringtoni (Bovidae). Boreas 39: 18-23.
25. Cano RJ, Poinar H, Poinar G. 1992. Isolation and partial characterisation of DNA from the bee Proplebeia dominicana (Apidae: Hymenoptera) in 25-40 million year old amber. Medical Science Research 20: 249-251.
26. Chan YL, Lacey EA, Pearson OP, et al. 2005. Ancient DNA reveals Holocene loss of genetic diversity in a South American rodent. Biology Letters 1: 423-426.
27. Churchman GJ, Lowe DJ. 2012. Alteration, formation, and occurrence of minerals in soils. In Handbook of Soil Sciences. 2nd edn. Vol. 1, Huang PM, Li Y, Sumner ME (eds). CRC Press: Boca Raton; 20.1-20.72.
28. Clack AA, MacPhee RDE, Poinar HN. 2012a. Mylodon darwinii DNA sequences from ancient fecal hair shafts. Annals of Anatomy 194: 26-30.
29. Clack AA, MacPhee RDE, Poinar HN. 2012b. Case study: ancient sloth DNA recovered from hairs preserved in paleofeces. In Ancient DNA. Methods in Molecular Biology 840, Shapiro B, Hofreiter M (eds). Springer: New York; 51-56.
30. Clarkson BR, Patel RN, Clarkson BD. 1988. Composition and structure of forest overwhelmed at Pureora, central North Island, New Zealand, during the Taupo eruption (c. A.D. 130). Journal of the Royal Society of New Zealand 18: 417-436.
31. Coffey KT, Schmitt AK, Ford A, et al. 2014. Volcanic ash provenance from zircon dust with an application to Maya pottery. Geology 42: 595-598.
32. Coolen MJL, Gibson JAE. 2009. Ancient DNA in lake sediment records. PAGES News 17: 104-106.
33. Cooper A, Poinar HN. 2000. Ancient DNA: do it right or not at all. Science 289: 1139.
34. Cooper A, Mourer-Chauviré C, Chambers GK, et al. 1992. Independent origins of New Zealand moas and kiwis. Proceedings of the National Academy of Science of the United States of America 89: 8741-8744.
35. Corinaldesi C, Beolchini F, Dell'anno A. 2008. Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences. Molecular Ecology 17: 3939-3951.
36. 230Th disequilibrium and (U-Th)/He zircon ages. Earth and Planetary Science Letters 349-350: 240-250.
37. D'Anjou RM, Bradley RS, Balascio NL, et al. 2012. Climate impacts on human settlement and agricultural activities in northern Norway revealed through sediment biogeochemistry. Proceedings of the National Academy of Sciences of the United States of America 109: 20332-20337.
38. D'Costa VM, King CE, Kalan L, et al. 2011. Antibiotic resistance is ancient. Nature 477: 457-461.
39. de Bruyn M, Hoelzel AR, Carvalho GR, et al. 2011. Faunal histories from Holocene ancient DNA. Trends in Ecology and Evolution 26: 405-413.
40. de la Fuente C, Flores S, Moraga M. 2013. DNA from human ancient bacteria: a novel source of genetic evidence from archaeological dental calculus. Archaeometry 55: 766-778.
41. Demuro M, Arnold LJ, Froese DG, et al. 2013. OSL dating of loess deposits bracketing Sheep Creek tephra beds, northwest Canada: dim and problematic single-grain OSL characteristics and their effect on multi-grain age estimates. Quaternary Geochronology 15: 67-87.
42. Drummond AJ, Rambaut A, Shapiro B, et al. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution 22: 1185-1192.
43. Epp LS, Boessenkool S, Bellemain EP, et al. 2012. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology 21: 1821-1833.
44. Fridriksson S. 1987. Plant colonization of a volcanic island, Surtsey, Iceland. Arctic and Alpine Research 19: 425-431.
45. Giguet-Covex C, Pansu J, Arnaud F, et al. 2014. Long livestock farming history and human landscape shaping revealed by lake sediment DNA. Nature Communications 5: 3211.
46. Gilbert MTP, Bandelt HJ, Hofreiter M, et al. 2005. Assessing ancient DNA studies. Trends in Ecology and Evolution 20: 541-5544.
47. Gilbert MTP, Tomsho LP, Rendulic S, et al. 2007. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science 317: 1927-1930.
48. Gilbert MTP, Jenkins DL, Götherstrom A, et al. 2008. DNA from pre-Clovis human coprolites in Oregon, North America. Science 320: 786-789.
49. Gilbert MTP, Jenkins DL, Higham TFG, et al. 2009. Response to comment by Poinar et al. on 'DNA from pre-Clovis human coprolites in Oregon, North America'. Science 325: 148.
50. Goldberg P, Berna F, Macphail RI. 2009. Comment on 'DNA from pre-Clovis human coprolites in Oregon, North America'. Science 325: 148.
51. Gould BA, León B, Buffen AM, et al. 2010. Evidence of a high-Andean, mid-Holocene plant community: an ancient DNA analysis of glacially preserved remains. American Journal of Botany 97: 1579-1584.
52. Green RE, Krause J, Ptak SE, et al. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330-336.
53. Green RE, Briggs AW, Krause J, et al. 2009. The Neandertal genome and ancient DNA authenticity. EMBO Journal 28: 2494-2502.
54. Green RE, Krause J, Briggs AW, et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722.
55. Gugerli F, Parducci L, Petit RJ. 2005. Ancient plant DNA: review and prospects. New Phytologist 166: 409-418.
56. Gugerli F, Alvarez N, Tinner W. 2013. A deep dig - hindsight on Holocene vegetation composition from ancient environmental DNA. Molecular Ecology 22: 3433-3436.
57. Haile J. 2012. Ancient DNA extraction from soils and sediment. In Ancient DNA. Methods in Molecular Biology 840, Shapiro B, Hofreiter M (eds). Springer: New York; 57-63.
58. Haile J, Holdaway R, Oliver K, et al. 2007. Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution 24: 982-989.
59. Haile J, Froese DG, MacPhee RDE, et al. 2009. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Science of the United States of America 106: 22352-22357.
60. Haouchar D, Haile J, McDowell MC, et al. 2014. Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene-Holocene cave deposit on Kangaroo Island, South Australia. Quaternary Science Reviews 84: 56-64.
61. Hansen AJ, Mitchell DL, Wiuf C, et al. 2006. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173: 1175-1179.
62. Hebsgaard MB, Phillips MJ, Willerslev E. 2005. Geologically ancient DNA: fact or artefact? Trends in Microbiology 13: 212-220.
63. Hebsgaard MB, Gilbert MTP, Arneborg J, et al. 2009. 'The farm beneath the sand' - an archaeological case study on ancient 'dirt' DNA. Antiquity 83: 430-444.
64. Herrera A, Cockell CS. 2007. Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction. Journal of Microbiological Methods 70: 1-12.
65. Hewitt AE. 2010. New Zealand Soil Classification, 3rd edn. Landcare Research Science Series 1: 1-136.
66. Higham TFG, Anderson AJ, Jacomb C. 1999. Dating the first New Zealanders: the chronology of Wairau Bar. Antiquity 73: 420-427.
67. Higuchi RG, Bowman B, Freiberger M, et al. 1984. DNA sequences from the quagga, an extinct member of the horse family. Nature 312: 282-284.
68. Hofreiter M, Poinar HN, Spaulding WG, et al. 2000. A molecular analysis of ground sloth diet through the last glaciation. Molecular Ecology 9: 1975-1984.
69. Hofreiter M, Betancourt JL, Sbriller AP, et al. 2003a. Phylogeny, diet, and habitat of an extinct ground sloth from Cuchillo Cura, Neuquén Province, southwest Argentina. Quaternary Research 59: 364-378.
70. Hofreiter M, Mead JI, Martin P, et al. 2003b. Molecular caving. Current Biology 13: R693-R695.
71. Hogg AG, Higham TFG, Lowe DJ, et al. RM 2003. A wiggle-match date for Polynesian settlement of New Zealand. Antiquity 77: 116-125.
72. 14C calibration data set. The Holocene 22: 439-449.
73. Holmsgaard PN, Norman A, Hede SC, et al. 2011. Bias in bacterial diversity as a result of Nycodenz extraction from bulk soil. Soil Biology and Biochemistry 43: 2152-2159.
74. Huang Y-T, Churchman GJ, Lowe DJ, et al. 2012. Evaluating the character and preservation of DNA within allophane clusters in buried soils on Holocene tephras, northern New Zealand. In Proceedings, Combined Australian Regolith Geoscientists Association and Australian Clay Minerals Society Conference: Mildura (Victoria, Australia), 7-9 February 2012, Churchman GJ, Cresswell R, Singh B (eds); 121-124.
75. Huang Y-T, Lowe DJ, Churchman GJ, et al. 2014. Carbon storage and DNA adsorption in allophanic soils and paleosols. In Soil Carbon. Progress in Soil Science Series, Hartemink AE, McSweeney K (eds). Springer: New York; 163-172.
76. Hudspith VA, Scott AC, Wilson CJN, et al. 2010. Charring of woods by volcanic processes: an example from the Taupo ignimbrite, New Zealand. Palaeogeography, Palaeoclimatology, Palaeoecology 291: 40-51.
77. Iñiguez AM, Araújo A, Ferreira LF, et al. 2003a. Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach. Memorias do Instituto Oswaldo Cruz 98 (Suppl I): 63-65.
78. Iñiguez A, Reinhard KJ, Araujo A, et al. 2003b. Enteriobius vermicularis: ancient DNA from North and South American human coprolites. Memorias do Instituto Oswaldo Cruz 98 (Suppl I): 67-69.
79. Iñiguez AM, Reinhard K, Carvalho Gonçalves MLC, et al. 2006. SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites. International Journal for Parasitology 36: 1419-1425.
80. James HF, Burney DA. 1997. The diet and ecology of Hawaii's extinct flightless waterfowl: evidence from coprolites. Biological Journal of the Linnean Society 62: 279-297.
81. Jenkins DL, Davis LG, Stafford TW, et al. 2012. Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves. Science 337: 223-228.
82. Johnson SS, Hebsgaard MB, Christensen TR, et al. 2007. Ancient bacteria show evidence of DNA repair. Proceedings of the National Academy of Science of the United States of America 104: 14401-14405.
83. Jørgensen T, Haile J, Möller P, et al. 2012a. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability. Molecular Ecology 21: 1989-2003.
84. Jørgensen T, Kjaer KH, Haile J, et al. 2012b. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding. Molecular Ecology 21: 1980-1988.
85. Kemp BM, Monroe C, Smith DG. 2006. Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts. Journal of Archaeological Science 33: 1680-1689.
86. Knapp M, Hofreiter M. 2010. Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes 1: 227-243.
87. Knauth S, Schmidt H, Tippkötter R. 2013. Comparison of commercial kits for the extraction of DNA from paddy soils. Letters in Applied Microbiology 56: 222-228.
88. Krüttli A, Bouwman A, Akgül G, et al. 2014. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central Europe. PLOS ONE 9: e86251.
89. Kuch M, Rohland N, Betancourt JL, et al. 2002. Molecular analysis of an 11700-year-old rodent midden from the Atacama Desert, Chile. Molecular Ecology 11: 913-924.
90. Kuch M, Poinar HN. 2012. Extraction of DNA from paleofeces. In Ancient DNA. Methods in Molecular Biology 840, Shapiro B, Hofreiter M (eds). Springer: New York; 37-42.
91. Kuzmina SA, Sher AV, Edwards ME, et al. 2011. The Late Pleistocene environment of the eastern west Beringia based on the principal section at the Main River, Chukotka. Quaternary Science Reviews 30: 2091-2106.
92. Larson G, Cucchi T, Fujita M, et al. 2007. Phylogeny and ancient DNA of Sus provides insights into Neolithic expansion in island Southeast Asia and Oceania. Proceedings of the National Academy of Sciences of the United States of America 104: 4834-4839.
93. Lejzerowicz F, Esling P, Majewski W, et al. 2013. Ancient DNA complements microfossil record in deep-sea subsurface sediments. Biology Letters 9: 20130283.
94. Leles D, Araújo A, Ferreira LF, et al. 2008. Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times. Memorias do Instituto Oswaldo Cruz 103: 106-108.
95. Letts B, Fulton TL, Stiller M, et al. 2012. Ancient DNA reveals genetic continuity in mountain woodland caribou of the Mackenzie and Selwyn Mountains, Northwest Territories, Canada. Arctic 65 (Suppl 1): 80-94.
96. Limburg PA, Weider LJ. 2002. 'Ancient' DNA in the resting egg bank of a microcrustacean can serve as a palaeolimnological database. Proceedings of the Royal Society of London Series B 269: 281-287.
97. Lindahl T. 1993a. Instability and decay of the primary structure of DNA. Nature 362: 709-715.
98. Lindahl T. 1993b. Recovery of antediluvian DNA. Nature 365: 700.
99. Lloyd-Jones G, Hunter DWF. 2001. Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biology and Biochemistry 33: 2053-2059.
100. Loreille O, Roumat E, Verneau O, et al. 2001. Ancient DNA from Ascaris: extraction amplification and sequences from eggs collected in coprolites. International Journal for Parasitology 31: 1101-1106.
101. Lowe DJ. 1988. Stratigraphy, age, composition, and correlation of Late Quaternary tephras interbedded with organic sediments in Waikato lakes, North Island, New Zealand. New Zealand Journal of Geology and Geophysics 31: 125-165.
102. Lowe DJ. 2011. Tephrochronology and its application: a review. Quaternary Geochronology 6: 107-153.
103. Lowe DJ, Palmer DJ. 2005. Andisols of New Zealand and Australia. Journal of Integrated Field Science 2: 39-65.
104. Lowe DJ, Wilson CJN, Newnham RM, et al. 2010. Dating the Kawakawa/Oruanui eruption: comment on "Optical luminescence dating of a loess section containing a critical tephra marker horizon, SW North Island of New Zealand" by R. Grapes et al. Quaternary Geochronology 5: 493-496.
105. Lowe DJ, Blaauw M, Hogg AG, et al. 2013. Ages of 24 widespread tephras erupted since 30 000 years ago in New Zealand, with re-evaluation of the timing and palaeoclimatic implications of the late-glacial cool episode recorded at Kaipo bog. Quaternary Science Reviews 74: 170-194.
106. Luciani S, Fornaciari G, Rickards O, et al. 2006. Molecular characterization of a pre-Columbian mummy and in situ coprolite. American Journal of Physical Anthropology 129: 620-629.
107. Lydolph MC, Jacobsen J, Arctander P, et al. 2005. Beringian paleoecology inferred from permafrost-preserved fungal DNA. Applied and Environmental Microbiology 71: 1012-1017.
108. Ma LT, Rogers SO, Catranis CM, et al. 2000. Detection and characterization of ancient fungi entrapped in glacial ice. Mycologia 92: 286-295.
109. Madeja J, Wacnik A, Zyga A, et al. 2009. Bacterial ancient DNA as an indicator of human presence in the past: its correlation with palynological and archaeological data. Journal of Quaternary Science 24: 317-321.
110. Madeja J, Wacnik A, Wypasek E, et al. 2010. Integrated palynological and molecular analyses of Late Holocene deposits from lake Milkowskie (NE Poland): verification of local human impact on environment. Quaternary International 220: 147-152.
111. Magyari EK, Major A, Bálint M, et al. 2011. Population dynamics and genetic changes of Picea abies in the south Carpathians revealed by pollen and ancient DNA analyses. BMC Evolutionary Biology 11: 66.
112. Marková S, Černý M, Rees DJ, et al. 2006. Are they still viable? Physical conditions and abundance of Daphnia pulicaria resting eggs in sediment cores from lakes in the Tatra mountains. Biologia 61 (Suppl): S135-S146.
113. Matisoo-Smith E, Roberts K, Welikala N, et al. 2008. Recovery of DNA and pollen from New Zealand lake sediments. Quaternary International 184: 139-149.
114. McClelland E, Wilson CJN, Bardot L. 2004. Paleotemperature determinations for the 1.8-ka Taupo ignimbrite, New Zealand, and implications for the emplacement history of a high-velocity pyroclastic flow. Bulletin of Volcanology 66: 492-513.
115. McDaniel PA, Lowe DJ, Arnalds O, et al. 2012. Andisols. In Handbook of Soil Sciences. 2nd edn, Vol. 1, Huang PM, Li Y, Sumner ME (eds). CRC Press: Boca Raton; 33.29-33.48.
116. Metcalf JL, Ursell LK, Knight R. 2014. Ancient human oral plaque preserves a wealth of biological data. Nature Genetics 46: 321-323.
117. Meyer M, Kircher M, Gansauge MT, et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222-226.
118. Mitchell D, Willerslev E, Hansen AJ. 2005. Damage and repair of ancient DNA. Mutation Research 571: 265-276.
119. Mitchell KJ, Llamas B, Soubrier J, et al. 2014. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science 344: 898-900.
120. Munch K, Boomsma W, Huelsenbeck JP, et al. 2008a. Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology 57: 750-757.
121. Munch K, Boomsma W, Willerslev E, et al. 2008b. Fast phylogenetic DNA barcoding. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 363: 3997-4002.
122. Newnham RM, de Lange PJ, Lowe DJ. 1995. Holocene vegetation, climate, and history of a raised bog complex, northern New Zealand, based on palynology, plant macrofossils and tephrochronology. Holocene 5: 267-282.
123. Orlando L, Ginolhac A, Zhang G, et al. 2013. Recalibrating Equus evolution using the genome sequence of an early middle Pleistocene horse. Nature 499: 74-78.
124. Oskam CL, Haile J, McLay E, et al. 2010. Fossil avian eggshell preserves ancient DNA. Proceedings of the Royal Society of London Series B 277: 1991-2000.
125. Pääbo S. 1985. Molecular cloning of ancient Egyptian mummy DNA. Nature 314: 644-645.
126. Pääbo S, Poinar H, Serre D, et al. 2004. Genetic analyses from ancient DNA. Annual Review of Genetics 38: 645-679.
127. Parducci L, Suyama Y, Lascoux M, et al. 2005. Ancient DNA from pollen: a genetic record of population history in Scots pine. Molecular Ecology 14: 2873-2882.
128. Parducci L, Matetovici I, Fontana SL, et al. 2013. Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia. Molecular Ecology 22: 3511-3524.
129. Paffetti D, Vettori C, Caramelli D, et al. 2007. Unexpected presence of Fagus orientalis complex in Italy as inferred from 45, 000-year-old DNA pollen samples from Venice lagoon. BMC Evolutionary Biology 7 (Suppl): S6.
130. Park JS, Vreeland RH, Cho BC, et al. 2009. Haloarchaeal diversity in 23, 121 and 419 MYA salts. Geobiology 7: 515-523.
131. Pedersen MW, Ginolhac A, Orlando L, et al. 2013. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa. Quaternary Science Reviews 75: 161-168.
132. Poinar HN, Hofreiter M, Spaulding WG, et al. 1998. Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281: 402-406.
133. Poinar HN, Kuch M, Sobolik KD, et al. 2001. A molecular analysis of dietary diversity for three archaic Native Americans. Proceedings of the National Academy of Science of the United States of America 98: 4317-4322.
134. Poinar H, Kuch M, McDonald G, et al. 2003. Nuclear gene sequences from a Late Pleistocene sloth coprolite. Current Biology 13: 1150-1152.
135. Poinar H, Fiedel S, King CE, et al. 2009. Comment on 'DNA from pre-Clovis human coprolites in Oregon, North America'. Science 325: 148.
136. Ponnamperuma C, Young RS, Caren LD. 1967. Some chemical and microbiological studies of Surtsey. Surtsey Research Progress Report (Surtsey Research Society, Iceland) 3: 70-780.
137. Prüfer K, Racimo F, Patterson N, et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43-49.
138. Rai H, Yokoyama S, Hashimoto S, et al. 2010. A restriction factor of direct DNA extraction from volcanic ash soils. In Proceedings 19th World Congress of Soil Science, Symposium 2.5.1 Extracellular proteins and nucleic acids in soil, Gilkes RJ, Prakongkep N (eds); 1-4. Website http://www.iuss.org/.
139. Rasmussen M, Cummings LS, Gilbert MTP, et al. 2009. Response to Comment by Goldberg et al. on "DNA from Pre-Clovis Human Coprolites in Oregon, North America". Science 325: 148.
140. Rawlence NJ, Cooper A. 2013. Youngest reported radiocarbon age of a moa (Aves: Dinornithiformes) dated from a natural site in New Zealand. Journal of the Royal Society of New Zealand 43: 100-107.
141. Rawlence NJ, Wood JR, Armstrong KN, et al. 2009. DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa. Proceedings of the Royal Society of London Series B 276: 3395-3402.
142. Reinhard KJ, Chaves SM, Jones JG, et al. 2008. Evaluating chloroplast DNA in prehistoric Texas coprolites: medicinal, dietary, or ambient ancient DNA? Journal of Archaeological Science 35: 1748-1755.
143. Reyes AV, Zazula GD, Kuzmina S, et al. 2011. Identification of last interglacial deposits in eastern Beringia: a cautionary note from the Palisades, interior Alaska. Journal of Quaternary Science 26: 345-352.
144. Rizzi E, Lari M, Gigli E, et al. 2012. Ancient DNA studies: new perspectives on old samples. Genetics, Selection, Evolution: GSE 44: 1-19.
145. Rollo F, Ubaldi M, Ermini L, et al. 2002. Otzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proceedings of the National Academy of Science of the United States of America 99: 12594-12599.
146. Saeki K, Sakai M, Wada S. 2010. DNA adsorption on synthetic and natural allophanes. Applied Clay Science 50: 493-497.
147. Sawyer S, Krause J, Guschanski K, et al. 2012. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLOS ONE 7: e34131.
148. Shapiro B, Drummond AJ, Rambaut A, et al. 2004. Rise and fall of the Beringian Steppe Bison. Science 306: 1561-1565.
149. Shi T, Reeves RH, Gilichinsky DA, et al. 1997. Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing. Microbial Ecology 33: 169-179.
150. Sirocko F, Dietrich S, Veres D, et al. 2013. Multi-proxy dating of Holocene maar lakes and Pleistocene dry maar sediments in the Eifel, Germany. Quaternary Science Reviews 62: 56-76.
151. Smith HG. 1985. The colonization of volcanic tephra on Deception Island by protozoa: long-term trends. British Antarctic Surveys Bulletin 66: 19-33.
152. Smith CI, Chamberlain AT, Riley MS, et al. 2001. Not just old, but old and cold. Nature 410: 771-772.
153. Smith CI, Chamberlain AT, Riley MS, et al. 2003. The thermal history of human fossils and the likelihood of successful DNA amplification. Journal of Human Evolution 45: 203-217.
154. Sønstebø JH, Gielly L, Brysting AK, et al. 2010. Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources 10: 1009-1018.
155. Speller CF, Kemp BM, Wyatt SD, et al. 2010. Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication. Proceedings of the National Academy of Science of the United States of America 107: 2807-2812.
156. Stoof-Leichsenring KR, Epp LS, Trauth MH, et al. 2012. Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation. Molecular Ecology 21: 1918-1930.
157. Suyama Y, Kawamuro K, Kinoshita I, et al. 1996. DNA sequence from a fossil pollen of Abies spp. from Pleistocene peat. Genes and Genetic Systems 71: 145-149.
158. Suyama Y, Gunnarsson U, Parducci L. 2008. Analysis of short DNA fragments from Holocene peatmoss samples. The Holocene 18: 1003-1006.
159. Taberlet P, Coissac E, Pompanon F, et al. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 35: e14.
160. Taberlet P, Coissac E, Hajibabaei M, et al. 2012a. Environmental DNA. Molecular Ecology 21: 1789-1793.
161. Taberlet P, Prud'Homme SM, Campione E, et al. 2012b. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular Ecology 21: 1816-1820.
162. Thomsen PF, Elias S, Gilbert MTP, et al. 2009. Non-destructive sampling of ancient insect DNA. PLOS ONE 4: e5048.
163. Thomson VA, Lebrasseur O, Austin JJ, et al. 2014a. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proceedings of the National Academy of Sciences 111: 4826-4831.
164. Thomson VA, Lebrasseur O, Austin JJ, et al. 2014b. Reply to Beavan, Bryant, and Storey and Matisoo-Smith: Ancestral Polynesian 'D' haplotypes reflect authentic Pacific chicken lineages. Proceedings of the National Academy of Sciences 111: E3585-E3586.
165. Tito RY, Knights D, Metcalf J, et al. 2012. Insights from characterizing extinct human gut microbiomes. PLOS ONE 7: e51146.
166. Tringe SG, von Mering C, Kobayashi A, et al. 2005. Comparative metagenomics of microbial communities. Science 308: 554-557.
167. VanderHoek R, Nelson RC. 2007. Ecological road blocks on a constrained landscape: the cultural effects of catastrophic Holocene volcanism on the Alaska Peninsula, southwest Alaska. In Living Under the Shadow: Cultural Impacts of Volcanic Eruptions, Grattan J, Torrence R (eds). Left Coast Press: Walnut Creek; 133-152.
168. van Geel B, Aptroot A, Baittinger C, et al. 2008. The ecological implications of a Yakutian mammoth's last meal. Quaternary Research 69: 361-376.
169. van Geel B, Guthrie RD, Altmann JG, et al. 2011. Mycological evidence of coprophagy from the feces of an Alaskan late glacial mammoth. Quaternary Science Reviews 30: 2289-2303.
170. van Geel B, Fisher DC, Rountrey AN, et al. 2012. Palaeo-environmental and dietary analysis of intestinal contents of a mammoth calf (Yamal Peninsula, northwest Siberia). Quaternary Science Reviews 30: 3935-3946.
171. van Geel B, Protopopov A, Bull I, et al. 2014. Multiproxy diet analysis of the last meal of an Early Holocene Yakutian bison. Journal of Quaternary Science 29: 261-268.
172. Vestheim H, Jarman SN. 2008. Blocking primers to enhance PCR amplification of rare sequences in mixed samples: a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology 5: 12.
173. Vishnivetskaya TA, Petrova MA, Urbance J, et al. 2006. Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. Astrobiology 6: 400-414.
174. Vreeland RH, Rosenzweig WD, Powers DW. 2000. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407: 897-900.
175. Wales N, Andersen K, Cappellini E, et al. 2014. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains. PLOS ONE 9: e86827.
176. Wall JD, Kim SK. 2007. Inconsistencies in Neanderthal genomic DNA sequences. PLOS Genetics 3: 1862-1866.
177. Warinner C, Rodrigues JFM, Vyas R, et al. 2014. Pathogens and host immunity in the ancient human oral cavity. Nature Genetics 46: 336-344.
178. Willerslev E, Cooper A. 2005. Ancient DNA. Proceedings of the Royal Society of London Biological Series 272: 3-16.
179. Willerslev E, Hansen AJ, Christensen B, et al. 1999. Diversity of Holocene life forms in fossil glacier ice. Proceedings of the National Academy of Science of the United States of America 96: 8017-8021.
180. Willerslev E, Hansen AJ, Binladen J, et al. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300: 791-795.
181. Willerslev E, Hansen AJ, Poinar HN. 2004. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends in Ecology and Evolution 19: 141-147.
182. Willerslev E, Cappellini E, Boomsma W, et al. 2007. Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317: 111-114.
183. Willerslev E, Davison J, Moora M, et al. 2014. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506: 47-51.
184. Wilmshurst JM, Anderson AJ, Higham TFG, et al. 2008. Dating the late prehistoric dispersal of Polynesians to New Zealand using the commensal Pacific rat. Proceedings of the National Academy of Sciences of the United States of America 105: 7676-7680.
185. Wilmshurst JM, Moar NT, Wood JR, et al. 2014. Use of pollen and ancient DNA as conservation baselines for offshore islands in New Zealand. Conservation Biology 28: 202-212.
186. Wood JR. 2007. Moa gizzard content analyses: further information on the diets of Dinornis robustus and Emeus crassus, and the first evidence for the diet of Pachyornis elephantopus (Aves: Dinornithiformes). Records of the Canterbury Museum 21: 27-39.
187. Wood JR, Rawlence NJ, Rogers GM, et al. 2008. Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes). Quaternary Science Reviews 27: 2593-2602.
188. Wood JR, Wilmshurst JM, Wagstaff SJ, et al. 2012a. High-resolution coproecology: using coprolites to reconstruct the habits and habitats of New Zealand's extinct upland moa (Megalapteryx didinus). PLOS ONE 7: e40025.
189. Wood JR, Wilmshurst JM, Worthy TH, et al. 2012b. First coprolites evidence for the diet of Anomalopteryx didiformis, an extinct forest ratite from New Zealand. New Zealand Journal of Ecology 36: 164-170.
190. Wood JR, Wilmshurst JM, Worthy TH, et al. 2012c. A lost link between a flightless parrot and a parasitic plant and the potential role of coprolites in conservation paleobiology. Conservation Biology 26: 1091-1099.
191. Wood JR, Wilmshurst JM, Rawlence NJ, et al. 2013a. A megafauna's microfauna: gastrointestional parasites of New Zealand's extinct moa (Aves: Dinornithiformes). PLOS ONE 8: e57315.
192. Wood JR, Wilmshurst JM, Richardson SJ, et al. 2013b. Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes). Proceedings of the National Academy of Sciences of the United States of America 110: 16910-16915.
193. Woodward SR, Weyand NJ, Bunnell M. 1994. DNA sequence from Cretaceous period bone fragments. Science 266: 1229-1232.
194. Xu Z-, Jiang XD, Wang GZ, et al. 2011. DNA extraction, amplification and analysis of the 28S rRNA portion in sediment-buried copepod DNA in the Great Wall Bay and Xihu Lake, Antarctica. Journal of Plankton Research 33: 917-925.
195. Yoccoz NG, Bråthen KA, Gielly L, et al. 2012. DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology 21: 3647-3655.
196. Young JM, Rawlence NJ, Weyrich LS, et al. 2014. Limitations and recommendations for successful DNA extraction from forensic soil samples: a review. Science and Justice: Journal of the Forensic Science Society 54: 238-244.
197. Zischler H, Hoss M, Handt O, et al. 1995. Detecting dinosaur DNA. Science 268: 1192-1193.