{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T19:19:54Z","timestamp":1790709594613,"version":"4.1.0"},"reference-count":273,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2017,7,13]],"date-time":"2017-07-13T00:00:00Z","timestamp":1499904000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000267","name":"Arts and Humanities Research Council","doi-asserted-by":"publisher","award":["AH\/N005015\/1"],"award-info":[{"award-number":["AH\/N005015\/1"]}],"id":[{"id":"10.13039\/501100000267","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively \u201cnovel\u201d. Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and\/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.<\/jats:p>","DOI":"10.3390\/genes8070180","type":"journal-article","created":{"date-parts":[[2017,7,13]],"date-time":"2017-07-13T10:31:57Z","timestamp":1499941917000},"page":"180","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":60,"title":["Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles"],"prefix":"10.3390","volume":"8","author":[{"given":"Eleanor","family":"Green","sequence":"first","affiliation":[{"name":"BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7128-9903","authenticated-orcid":false,"given":"Camilla","family":"Speller","sequence":"additional","affiliation":[{"name":"BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2017,7,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/312282a0","article-title":"DNA sequences from the quagga, an extinct member of the horse family","volume":"312","author":"Higuchi","year":"1984","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/0305-4403(85)90002-0","article-title":"Preservation of DNA in ancient Egyptian mummies","volume":"12","year":"1985","journal-title":"J. Archaeol. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/314644a0","article-title":"Molecular cloning of Ancient Egyptian mummy DNA","volume":"314","year":"1985","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1038\/323803a0","article-title":"Anatomical, cellular and molecular analysis of 8000-year-old human brain tissue from the Windover archaeological site","volume":"323","author":"Doran","year":"1986","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"9775","DOI":"10.1093\/nar\/16.20.9775","article-title":"Mitochondrial DNA sequences from a 7000-year old brain","volume":"16","author":"Gifford","year":"1988","journal-title":"Nucleic Acids Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1073\/pnas.86.6.1939","article-title":"Ancient DNA: Extraction, characterization, molecular cloning, and enzymatic amplification","volume":"86","year":"1989","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/0305-4403(90)90049-B","article-title":"Recovery and analysis of human genetic material from mummified tissue and bone","volume":"17","author":"Thuesen","year":"1990","journal-title":"J. Archaeol. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1002\/ajpa.1330330509","article-title":"Study of nucleic acids isolated from ancient remains","volume":"33","author":"Rogan","year":"1990","journal-title":"Am. J. Phys. Anthropol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1038\/342485a0","article-title":"Ancient bone DNA amplified","volume":"342","author":"Hagelberg","year":"1989","journal-title":"Nature"},{"key":"ref_10","first-page":"365","article-title":"Amplification de fragments d\u2019ADN mitochondrial \u00e0 partir de dents et d\u2019os humains anciens","volume":"310","author":"Laudet","year":"1990","journal-title":"Comptes Rendus de l\u2019Acad\u00e9mie des Sciences"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"229","DOI":"10.2183\/pjab.65.229","article-title":"DNA Amplification from Ancient Human Skeletal Remains and Their Sequence Analysis","volume":"65","author":"Horai","year":"1989","journal-title":"Proc. Jpn. Acad. Ser. B Phys. Biol. Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.ajhg.2013.10.002","article-title":"Pulling out the 1%: Whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries","volume":"93","author":"Carpenter","year":"2013","journal-title":"Am. J. Hum. Genet."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1111\/j.1755-0998.2009.02824.x","article-title":"A rapid column-based ancient DNA extraction method for increased sample throughput","volume":"10","author":"Rohland","year":"2010","journal-title":"Mol. Ecol. Resour."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"15758","DOI":"10.1073\/pnas.1314445110","article-title":"Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments","volume":"110","author":"Dabney","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1002\/(SICI)1096-8644(199804)105:4<539::AID-AJPA10>3.0.CO;2-1","article-title":"Technical note: Improved DNA extraction from ancient bones using silica-based spin columns","volume":"105","author":"Yang","year":"1998","journal-title":"Am. J. Phys. Anthropol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Pinhasi, R., Fernandes, D., Sirak, K., Novak, M., Connell, S., Alpaslan-Roodenberg, S., Gerritsen, F., Moiseyev, V., Gromov, A., and Raczky, P. (2015). Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0129102"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"5257","DOI":"10.1038\/ncomms6257","article-title":"Genome flux and stasis in a five millennium transect of European prehistory","volume":"5","author":"Gamba","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Hansen, H.B., Damgaard, P.B., Margaryan, A., Stenderup, J., Lynnerup, N., Willerslev, E., and Allentoft, M.E. (2017). Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0170940"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1016\/j.jas.2010.11.010","article-title":"Survival and recovery of DNA from ancient teeth and bones","volume":"38","author":"Adler","year":"2011","journal-title":"J. Archaeol. Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1126\/science.1188046","article-title":"Targeted investigation of the Neandertal genome by array-based sequence capture","volume":"328","author":"Burbano","year":"2010","journal-title":"Science"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1007\/s10592-014-0606-z","article-title":"Ancient DNA reveals prehistoric habitat fragmentation and recent domestic introgression into native wild reindeer","volume":"15","author":"Flagstad","year":"2014","journal-title":"Conserv. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jas.2013.07.026","article-title":"Searching for Scandinavians in Pre-Viking Scotland: Molecular Fingerprinting of Early Medieval Combs","volume":"41","author":"Ashby","year":"2014","journal-title":"J. Archaeol. Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/335774a0","article-title":"Short but faithful pieces of ancient DNA","volume":"335","author":"Rollo","year":"1988","journal-title":"Nature"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1007\/BF01921727","article-title":"DNA in wheat seeds from European archaeological sites","volume":"50","author":"Brown","year":"1994","journal-title":"Experientia"},{"key":"ref_25","first-page":"119","article-title":"Evidence for the survival of ancient DNA in charred wheat seeds from European archaeological sites","volume":"1","author":"Allaby","year":"1997","journal-title":"Anc. Biomol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1139\/g98-114","article-title":"Evolution of the high molecular weight glutenin loci of the A, B, D, and G genomes of wheat","volume":"42","author":"Allaby","year":"1999","journal-title":"Genome"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1016\/S0305-4403(02)00269-8","article-title":"DNA from primitive maize landraces and archaeological remains: Implications for the domestication of maize and its expansion into South America","volume":"30","author":"Freitas","year":"2003","journal-title":"J. Archaeol. Sci."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1126\/science.1089056","article-title":"Early allelic selection in maize as revealed by ancient DNA","volume":"302","author":"Buckler","year":"2003","journal-title":"Science"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Palmer, S.A., Moore, J.D., Clapham, A.J., Rose, P., and Allaby, R.G. (2009). Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0006301"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2780","DOI":"10.1016\/j.jas.2012.04.012","article-title":"Next generation sequencing of DNA in 3300-year-old charred cereal grains","volume":"39","author":"Bunning","year":"2012","journal-title":"J. Archaeol. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"20130377","DOI":"10.1098\/rstb.2013.0377","article-title":"Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops","volume":"370","author":"Allaby","year":"2014","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3195","DOI":"10.1016\/j.cub.2016.09.036","article-title":"Genome Sequence of a 5310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication","volume":"26","author":"Smith","year":"2016","journal-title":"Curr. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1038\/ng.3611","article-title":"Genomic analysis of 6000-year-old cultivated grain illuminates the domestication history of barley","volume":"48","author":"Mascher","year":"2016","journal-title":"Nat. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"37347","DOI":"10.1038\/srep37347","article-title":"The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains","volume":"6","author":"Nistelberger","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.jas.2016.12.001","article-title":"Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds","volume":"78","author":"Hagenblad","year":"2017","journal-title":"J. Archaeol. Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1016\/S0305-4403(03)00002-5","article-title":"Degradation of DNA in artificially charred wheat seeds","volume":"30","author":"Threadgold","year":"2003","journal-title":"J. Archaeol. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"18315","DOI":"10.1073\/pnas.0509279102","article-title":"An Asian origin for a 10,000-year-old domesticated plant in the Americas","volume":"102","author":"Erickson","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.aanat.2011.03.012","article-title":"The blossoming of plant archaeogenetics","volume":"194","author":"Palmer","year":"2012","journal-title":"Ann. Anat."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1073\/pnas.90.5.1997","article-title":"Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens","volume":"90","author":"Goloubinoff","year":"1993","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_40","first-page":"545","article-title":"Microsatellite typing of ancient maize: Insights into the history of agriculture in southern South America","volume":"274","author":"Lia","year":"2007","journal-title":"Proc. Biol. Sci."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1016\/j.jas.2005.04.002","article-title":"Morphological and genetic studies of waterlogged Prunus species from the Roman vicus Tasgetium (Eschenz, Switzerland)","volume":"32","author":"Pollmann","year":"2005","journal-title":"J. Archaeol. Sci."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1266\/ggs.71.145","article-title":"DNA sequence from a fossil pollen of Abies spp. from Pleistocene peat","volume":"71","author":"Suyama","year":"1996","journal-title":"Genes Genet. Syst."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1111\/j.1365-294X.2005.02644.x","article-title":"Ancient DNA from pollen: A genetic record of population history in Scots pine","volume":"14","author":"Parducci","year":"2005","journal-title":"Mol. Ecol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1471-2148-7-S2-S6","article-title":"Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon","volume":"7","author":"Paffetti","year":"2007","journal-title":"BMC Evol. Biol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/s10681-005-5814-7","article-title":"Morphological and molecular analysis of common millet (P. miliaceum) cultivars compared to an aDNA sample from the 15th century (Hungary)","volume":"146","author":"Gyulai","year":"2005","journal-title":"Euphytica"},{"key":"ref_46","first-page":"14","article-title":"Molecular diversity of common millet (P. miliaceum) compared to archaeological samples excavated from the 4th and 15th centuries","volume":"1","author":"Gyulai","year":"2006","journal-title":"Hung. Agric. Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1079\/SSR2006251","article-title":"Seed remains of common millet from the 4th (Mongolia) and 15th (Hungary) centuries: AFLP, SSR and mtDNA sequence recoveries","volume":"16","author":"Gyulai","year":"2006","journal-title":"Seed Sci. Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"3549","DOI":"10.1016\/j.jas.2011.08.023","article-title":"Ancient DNA confirms a local origin of domesticated chenopod in eastern North America","volume":"38","author":"Kistler","year":"2011","journal-title":"J. Archaeol. Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s001220100680","article-title":"Spelt-specific alleles in HMW glutenin genes from modern and historical European spelt (Triticum spelta L.)","volume":"104","author":"Blatter","year":"2002","journal-title":"Theor. Appl. Genet."},{"key":"ref_50","first-page":"65","article-title":"Little Evidence for the Preservation of a Single-Copy Gene in Charred Archaeological Wheat","volume":"4","author":"Blatter","year":"2002","journal-title":"Anc. Biomol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1179\/009346907791071610","article-title":"Quids and aprons: Ancient DNA from artifacts from the American Southwest","volume":"32","author":"LeBlanc","year":"2007","journal-title":"J. Field Archaeol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1016\/j.jas.2005.12.012","article-title":"Genetic analysis of archaeological wood remains: First results and prospects","volume":"33","author":"Deguilloux","year":"2006","journal-title":"J. Archaeol. Sci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1093\/aob\/mcl188","article-title":"Authenticated DNA from ancient wood remains","volume":"98","author":"Liepelt","year":"2006","journal-title":"Ann. Bot."},{"key":"ref_54","first-page":"225","article-title":"Improved direct PCR screen for bacterial colonies: Wooden toothpicks inhibit PCR amplification","volume":"18","author":"Lee","year":"1995","journal-title":"Biotechniques"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"38","DOI":"10.2174\/1874940201003010038","article-title":"Assessing PCR inhibition from humic substances","volume":"3","author":"Matheson","year":"2010","journal-title":"Open Enzym. Inhib. J."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.jas.2017.01.010","article-title":"TaqMan qPCR pushes boundaries for the analysis of millennial wood","volume":"79","author":"Grasse","year":"2017","journal-title":"J. Archaeol. Sci."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1111\/j.1755-0998.2010.02855.x","article-title":"Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate","volume":"10","author":"Gielly","year":"2010","journal-title":"Mol. Ecol. Resour."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.jas.2006.09.002","article-title":"The survival of PCR-amplifiable DNA in cow leather","volume":"34","author":"Vuissoz","year":"2007","journal-title":"J. Archaeol. Sci."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1016\/j.jas.2009.12.025","article-title":"Ancient DNA, a Neolithic legging from the Swiss Alps and the early history of goat","volume":"37","author":"Schlumbaum","year":"2010","journal-title":"J. Archaeol. Sci."},{"key":"ref_60","first-page":"227","article-title":"Mitochondrial and nuclear DNA from (pre) historic hide-derived material","volume":"3","author":"Burger","year":"2001","journal-title":"Anc. Biomol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1927","DOI":"10.1126\/science.1146971","article-title":"Whole-genome shotgun sequencing of mitochondria from ancient hair shafts","volume":"317","author":"Gilbert","year":"2007","journal-title":"Science"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/nature08835","article-title":"Ancient human genome sequence of an extinct Palaeo-Eskimo","volume":"463","author":"Rasmussen","year":"2010","journal-title":"Nature"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.jas.2014.10.028","article-title":"Ancient DNA unravels the truth behind the controversial GUS Greenlandic Norse fur samples: The bison was a horse, and the muskox and bears were goats","volume":"53","author":"Sinding","year":"2015","journal-title":"J. Archaeol. Sci."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1007\/s12520-011-0055-2","article-title":"Characterising the potential of sheep wool for ancient DNA analyses","volume":"3","author":"Brandt","year":"2011","journal-title":"Archaeol. Anthropol. Sci."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"3750","DOI":"10.1016\/j.jas.2012.06.020","article-title":"Minimally destructive DNA extraction from archaeological artefacts made from whale baleen","volume":"39","author":"Sinding","year":"2012","journal-title":"J. Archaeol. Sci."},{"key":"ref_66","first-page":"345","article-title":"Sex determination of baleen whale artefacts: Implications for ancient DNA use in zooarchaeology","volume":"10","author":"Sinding","year":"2016","journal-title":"J. Archaeol. Sci. Rep."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1007\/s00414-005-0521-4","article-title":"Microsatellite genotyping of DNA isolated from claws left on tanned carnivore hides","volume":"119","author":"Hedmark","year":"2005","journal-title":"Int. J. Legal Med."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Willerslev, E., Gilbert, M.T.P., Binladen, J., Ho, S.Y.W., Campos, P.F., Ratan, A., Tomsho, L.P., da Fonseca, R.R., Sher, A., and Kuznetsova, T.V. (2009). Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol. Biol., 9.","DOI":"10.1186\/1471-2148-9-95"},{"key":"ref_69","first-page":"502","article-title":"Searching for DNA in museum specimens: A comparison of sources in a mammal species","volume":"10","author":"Revilla","year":"2009","journal-title":"Mol. Ecol. Resour."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Herrmann, B., and Hummel, S. (1994). Genomic DNA from Museum Bird Feathers. Ancient DNA, Springer.","DOI":"10.1007\/978-1-4612-4318-2"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1093\/auk\/120.4.982","article-title":"Microsatellite amplification from museum feather samples: Effects of fragment size and template concentration on genotyping errors","volume":"120","author":"Sefc","year":"2003","journal-title":"Auk"},{"key":"ref_72","first-page":"84","article-title":"An overlooked DNA source for non-invasive genetic analysis in birds","volume":"36","author":"Negro","year":"2004","journal-title":"J. Avian Biol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/2041-2223-2-16","article-title":"Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations","volume":"2","author":"Speller","year":"2011","journal-title":"Investig. Genet."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"2741","DOI":"10.1093\/molbev\/msr107","article-title":"Ancient DNA recovers the origins of M\u0101ori feather cloaks","volume":"28","author":"Hartnup","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"ref_75","unstructured":"Crabtree, D.E. (1972). An Introduction to Flintworking, Idaho State University Museum. Idaho State University Museum Occasional Paper No. 28."},{"key":"ref_76","first-page":"87","article-title":"Verifying the reliability of lithic use-wear assessments by \u201cblind tests\u201d: The low-power approach","volume":"7","author":"Odell","year":"1980","journal-title":"J. Field Archaeol."},{"key":"ref_77","unstructured":"Keeley, L.H. (1980). Experimental Determination of Stone Tool Uses: A Microwear Analysis, University of Chicago Press."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1126\/science.220.4603.1269","article-title":"Prehistoric blood residues: Detection on tool surfaces and identification of species of origin","volume":"220","author":"Loy","year":"1983","journal-title":"Science"},{"key":"ref_79","first-page":"119","article-title":"The Identification of Protein Residues on Lithic Artifacts from a Stratified Boreal Forest Site","volume":"13","author":"Newman","year":"1989","journal-title":"Can. J. Archaeol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1080\/00438243.1993.9980227","article-title":"The artifact as site: An example of the biomolecular analysis of organic residues on prehistoric tools","volume":"25","author":"Loy","year":"1993","journal-title":"World Archaeol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1006\/jasc.1996.0144","article-title":"Recovery of Mammalian DNA from Middle Paleolithic Stone Tools","volume":"24","author":"Hardy","year":"1997","journal-title":"J. Archaeol. Sci."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1006\/jasc.2000.0628","article-title":"Recovery of Protein and DNA Trapped in Stone Tool Microcracks","volume":"28","author":"Shanks","year":"2001","journal-title":"J. Archaeol. Sci."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.jas.2004.06.004","article-title":"DNA from ancient stone tools and bones excavated at Bugas-Holding, Wyoming","volume":"32","author":"Shanks","year":"2005","journal-title":"J. Archaeol. Sci."},{"key":"ref_84","first-page":"416","article-title":"Ancient DNA: Do it right or not at all","volume":"5482","author":"Poinar","year":"2000","journal-title":"Science"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1016\/j.jas.2006.10.023","article-title":"Animal DNA in PCR reagents plagues ancient DNA research","volume":"34","author":"Leonard","year":"2007","journal-title":"J. Archaeol. Sci."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/0305-4403(92)90016-V","article-title":"Verifying the reliability of blood residue analysis on archaeological tools","volume":"19","author":"Kooyman","year":"1992","journal-title":"J. Archaeol. Sci."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1006\/jasc.2001.0757","article-title":"The Removal of Protein from Mineral Surfaces: Implications for Residue Analysis of Archaeological Materials","volume":"29","author":"Craig","year":"2002","journal-title":"J. Archaeol. Sci."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1006\/jasc.1996.0027","article-title":"Protein Identification of Blood Residues on Experimental Stone Tools","volume":"23","author":"Tuross","year":"1996","journal-title":"J. Archaeol. Sci."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1017\/S0003598X00081011","article-title":"Blood residue analysis of 90,000-year-old stone tools from Tabun Cave, Israel","volume":"66","author":"Loy","year":"1992","journal-title":"Antiquity"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1017\/S0003598X00064280","article-title":"Survival and detection of blood residues on stone tools","volume":"69","author":"Eisele","year":"1995","journal-title":"Antiquity"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1006\/jasc.1996.0011","article-title":"Blood from Stones? Some Methodological and Interpretive Problems in Blood Residue Analysis","volume":"23","author":"Fiedel","year":"1996","journal-title":"J. Archaeol. Sci."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Adamiak, J., Otlewska, A., Tafer, H., Lopandic, K., Gutarowska, B., Sterflinger, K., and Pi\u00f1ar, G. (2017). First evaluation of the microbiome of built cultural heritage by using the Ion Torrent next generation sequencing platform. Int. Biodeterior. Biodegrad.","DOI":"10.1016\/j.ibiod.2017.01.040"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"979","DOI":"10.3389\/fmicb.2015.00979","article-title":"Metabolomic and high-throughput sequencing analysis-modern approach for the assessment of biodeterioration of materials from historic buildings","volume":"6","author":"Gutarowska","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_94","first-page":"187","article-title":"The survival of food residues: New methods of analysis, interpretation and application","volume":"77","author":"Evershed","year":"1992","journal-title":"Proc. Br. Acad."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1111\/j.1475-4754.1993.tb01036.x","article-title":"Quantification and distribution of lipid in archaeological ceramics: Implications for sampling potsherds for organic residue analysis and the classification of vessel use","volume":"35","author":"Charters","year":"1993","journal-title":"Archaeometry"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"2027","DOI":"10.1098\/rspb.1998.0536","article-title":"Free and bound fatty acid oxidation products in archaeological ceramic vessels","volume":"265","author":"Regert","year":"1998","journal-title":"Proc. R. Soc. B"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1017\/S0003598X00113316","article-title":"Direct detection of maize in pottery residues via compound specific stable carbon isotope analysis","volume":"78","author":"Reber","year":"2004","journal-title":"Antiquity"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"S226","DOI":"10.1007\/s00239-003-0031-2","article-title":"Evidence for S. cerevisiae fermentation in ancient wine","volume":"57","author":"Cavalieri","year":"2003","journal-title":"J. Mol. Evol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1016\/j.jas.2007.08.009","article-title":"Ancient DNA fragments inside Classical Greek amphoras reveal cargo of 2400-year-old shipwreck","volume":"35","author":"Hansson","year":"2008","journal-title":"J. Archaeol. Sci."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.jas.2011.09.025","article-title":"Aspects of ancient Greek trade re-evaluated with amphora DNA evidence","volume":"39","author":"Foley","year":"2012","journal-title":"J. Archaeol. Sci."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.jas.2017.01.005","article-title":"Ritual complexity in a past community revealed by ancient DNA analysis of pre-colonial terracotta items from Northern Ghana","volume":"79","author":"Robinson","year":"2017","journal-title":"J. Archaeol. Sci."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1038\/362709a0","article-title":"Instability and Decay of the Primary Structure of DNA","volume":"362","author":"Lindahl","year":"1993","journal-title":"Nature"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.aanat.2011.07.003","article-title":"DNA in ancient bone\u2014Where is it located and how should we extract it?","volume":"194","author":"Campos","year":"2012","journal-title":"Ann. Anat."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"e17092","DOI":"10.7554\/eLife.17092","article-title":"Protein sequences bound to mineral surfaces persist into deep time","volume":"5","author":"Demarchi","year":"2016","journal-title":"eLife"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"20130376","DOI":"10.1098\/rstb.2013.0376","article-title":"A new era in palaeomicrobiology: Prospects for ancient dental calculus as a long-term record of the human oral microbiome","volume":"370","author":"Warinner","year":"2015","journal-title":"Philos. Trans. R. Soc. B"},{"key":"ref_106","first-page":"643","article-title":"Formation and inhibition of dental calculus","volume":"40","author":"Schroeder","year":"1969","journal-title":"J. Periodontol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1177\/154411130201300506","article-title":"Supragingival calculus: Formation and control","volume":"13","author":"Jin","year":"2002","journal-title":"Crit. Rev. Oral Biol. Med."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1016\/j.jas.2011.03.020","article-title":"Ancient bacterial DNA (aDNA) in dental calculus from archaeological human remains","volume":"38","author":"Preus","year":"2011","journal-title":"J. Archaeol. Sci."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/ng.2536","article-title":"Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions","volume":"45","author":"Adler","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"16498","DOI":"10.1038\/srep16498","article-title":"Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification","volume":"5","author":"Ziesemer","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1002\/ajpa.22960","article-title":"Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus","volume":"160","author":"Ozga","year":"2016","journal-title":"Am. J. Phys. Anthropol."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nature21674","article-title":"Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus","volume":"544","author":"Weyrich","year":"2017","journal-title":"Nature"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/ng.2906","article-title":"Pathogens and host immunity in the ancient human oral cavity","volume":"46","author":"Warinner","year":"2014","journal-title":"Nat. Genet."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"7104","DOI":"10.1038\/srep07104","article-title":"Direct evidence of milk consumption from ancient human dental calculus","volume":"4","author":"Warinner","year":"2014","journal-title":"Sci. Rep."},{"key":"ref_115","doi-asserted-by":"crossref","unstructured":"Velsko, I.M., Overmyer, K.A., Speller, C., Collins, M., Loe, L., Frantz, L.A.F., Martinez, J.B.R., Chavez, E., Klaus, L., and Sankaranarayanan, K. (2017). The dental calculus metabolome in modern and historic samples. bioRxiv, 136176.","DOI":"10.1101\/136176"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.jhevol.2014.10.016","article-title":"Ancient human microbiomes","volume":"79","author":"Warinner","year":"2015","journal-title":"J. Hum. Evol."},{"key":"ref_117","first-page":"5","article-title":"Ancient DNA analysis of dental calculus","volume":"6","author":"Weyrich","year":"2014","journal-title":"J. Hum. Evol."},{"key":"ref_118","unstructured":"Hunt, A.P., Mil\u00e0n, J., Lucas, S.G., and Spielmann, J.A. (2012). Early processes in the fossilization of terrestrial feces to coprolites, and microstructure preservation. Vertebrate Coprolites: Bulletin 57, New Mexico Museum of Natural History and Science."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1126\/science.281.5375.402","article-title":"Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis","volume":"281","author":"Poinar","year":"1998","journal-title":"Science"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"4317","DOI":"10.1073\/pnas.061014798","article-title":"A molecular analysis of dietary diversity for three archaic Native Americans","volume":"98","author":"Poinar","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1016\/S0960-9822(03)00450-0","article-title":"Nuclear gene sequences from a late pleistocene sloth coprolite","volume":"13","author":"Poinar","year":"2003","journal-title":"Curr. Biol."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"1975","DOI":"10.1046\/j.1365-294X.2000.01106.x","article-title":"A molecular analysis of ground sloth diet through the last glaciation","volume":"9","author":"Hofreiter","year":"2000","journal-title":"Mol. Ecol."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1126\/science.1154116","article-title":"DNA from Pre-Clovis Human Coprolites in Oregon, North America","volume":"320","author":"Gilbert","year":"2008","journal-title":"Science"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.1218443","article-title":"Clovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves","volume":"337","author":"Jenkins","year":"2012","journal-title":"Science"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1016\/j.jas.2006.02.015","article-title":"Repeat silica extraction: A simple technique for the removal of PCR inhibitors from DNA extracts","volume":"33","author":"Kemp","year":"2006","journal-title":"J. Archaeol. Sci."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"2593","DOI":"10.1016\/j.quascirev.2008.09.019","article-title":"Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes)","volume":"27","author":"Wood","year":"2008","journal-title":"Quat. Sci. Rev."},{"key":"ref_127","first-page":"164","article-title":"First coprolite evidence for the diet of Anomalopteryx didiformis, an extinct forest ratite from New Zealand","volume":"36","author":"Wood","year":"2012","journal-title":"N. Z. J. Ecol."},{"key":"ref_128","doi-asserted-by":"crossref","unstructured":"Wood, J.R., Wilmshurst, J.M., Wagstaff, S.J., Worthy, T.H., Rawlence, N.J., and Cooper, A. (2012). High-Resolution Coproecology: Using Coprolites to Reconstruct the Habits and Habitats of New Zealand\u2019s Extinct Upland Moa (Megalapteryx didinus). PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0040025"},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"16910","DOI":"10.1073\/pnas.1307700110","article-title":"Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes)","volume":"110","author":"Wood","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"2807","DOI":"10.1073\/pnas.0909724107","article-title":"Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication","volume":"107","author":"Speller","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1111\/j.1523-1739.2012.01931.x","article-title":"A lost link between a flightless parrot and a parasitic plant and the potential role of coprolites in conservation paleobiology","volume":"26","author":"Wood","year":"2012","journal-title":"Conserv. Biol."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1590\/S0074-02762003000900013","article-title":"Enterobius vermicularis: Ancient DNA from North and South American human coprolites","volume":"98","author":"Reinhard","year":"2003","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.1016\/j.ijpara.2006.07.005","article-title":"SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites","volume":"36","author":"Reinhard","year":"2006","journal-title":"Int. J. Parasitol."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1590\/S0074-02762008005000004","article-title":"Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: New scenery of ascariasis in pre-Colombian South America times","volume":"103","author":"Leles","year":"2008","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_135","first-page":"496","article-title":"Microscopic and ancient DNA profiling of Polynesian dog (kur\u012b) coprolites from northern New Zealand","volume":"6","author":"Wood","year":"2016","journal-title":"J. Archaeol. Sci. Rep."},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Rivera-Perez, J.I., Cano, R.J., Narganes-Storde, Y., Chanlatte-Baik, L., and Toranzos, G.A. (2015). Retroviral DNA Sequences as a Means for Determining Ancient Diets. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0144951"},{"key":"ref_137","doi-asserted-by":"crossref","unstructured":"Tito, R.Y., Macmil, S., Wiley, G., Najar, F., Cleeland, L., Qu, C., Wang, P., Romagne, F., Leonard, S., and Ruiz, A.J. (2008). Phylotyping and functional analysis of two ancient human microbiomes. PLoS ONE, 3.","DOI":"10.1371\/journal.pone.0003703"},{"key":"ref_138","doi-asserted-by":"crossref","unstructured":"Tito, R.Y., Knights, D., Metcalf, J., Obregon-Tito, A.J., Cleeland, L., Najar, F., Roe, B., Reinhard, K., Sobolik, K., and Belknap, S. (2012). Insights from characterizing extinct human gut microbiomes. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0051146"},{"key":"ref_139","doi-asserted-by":"crossref","unstructured":"Cano, R.J., Rivera-Perez, J., Toranzos, G.A., Santiago-Rodriguez, T.M., Narganes-Storde, Y.M., Chanlatte-Baik, L., Garc\u00eda-Rold\u00e1n, E., Bunkley-Williams, L., and Massey, S.E. (2014). Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0106833"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.quascirev.2016.02.018","article-title":"A protocol for subsampling Late Quaternary coprolites for multi-proxy analysis","volume":"138","author":"Wood","year":"2016","journal-title":"Quat. Sci. Rev."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1128\/AEM.03242-13","article-title":"Viruses in a 14th-century coprolite","volume":"80","author":"Appelt","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1126\/science.159.3820.1199","article-title":"Human stones","volume":"159","author":"Lonsdale","year":"1968","journal-title":"Science"},{"key":"ref_143","doi-asserted-by":"crossref","unstructured":"G\u0142adykowska-Rzeczycka, J.J., and Nowakowski, D. (2014). A biological stone from a medieval cemetery in Poland. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0109096"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"e01337-14","DOI":"10.1128\/mBio.01337-14","article-title":"Recovery of a medieval Brucella melitensis genome using shotgun metagenomics","volume":"5","author":"Kay","year":"2014","journal-title":"mBio"},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"e20983","DOI":"10.7554\/eLife.20983","article-title":"A molecular portrait of maternal sepsis from Byzantine Troy","volume":"6","author":"Devault","year":"2017","journal-title":"eLife"},{"key":"ref_146","first-page":"425","article-title":"Macromolecules in Mollusc Shells and Their Functions in Biomineralization","volume":"304","author":"Weiner","year":"1984","journal-title":"Philos. Trans. R. Soc. B"},{"key":"ref_147","unstructured":"Marin, F., Marie, B., Hamada, S.B., Ramos-Silva, P., Le Roy, N., Guichard, N., Wolf, S.E., Montagnani, C., Joubert, C., and Piquemal, D. (2013). Shellome\u2019: Proteins involved in mollusk shell biomineralization-diversity, functions. Recent Adv. Pearl Res., 149\u2013166."},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/1040-6182(89)90011-6","article-title":"Amino acid geochronology: Resolution and precision in carbonate fossils","volume":"1","author":"Miller","year":"1989","journal-title":"Quat. Int."},{"key":"ref_149","unstructured":"Hare, P.E., King, K., and Hoering, I.C. (1980). Amino acid geochronology: Integrity of the carbonate matrix and potential of molluscan fossils. Biogeochemistry of Amino Acids, John Wiley & Sons."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"2958","DOI":"10.1016\/j.quascirev.2007.06.034","article-title":"Testing the aminostratigraphy of fluvial archives: The evidence from intra-crystalline proteins within freshwater shells","volume":"26","author":"Penkman","year":"2007","journal-title":"Quat. Sci. Rev."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.quaint.2010.05.029","article-title":"Amino acid racemization dating of marine shells: A mound of possibilities","volume":"239","author":"Demarchi","year":"2011","journal-title":"Quat. Int."},{"key":"ref_152","doi-asserted-by":"crossref","unstructured":"Demarchi, B., O\u2019Connor, S., de Lima Ponzoni, A., de Almeida Rocha Ponzoni, R., Sheridan, A., Penkman, K., Hancock, Y., and Wilson, J. (2014). An integrated approach to the taxonomic identification of prehistoric shell ornaments. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0099839"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1111\/gbi.12087","article-title":"Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium","volume":"12","author":"Lejzerowicz","year":"2014","journal-title":"Geobiology"},{"key":"ref_154","first-page":"3665","article-title":"Palaeoceanographic changes in Hornsund Fjord (Spitsbergen, Svalbard) over the last millennium: New insights from ancient DNA","volume":"11","author":"Lejzerowicz","year":"2015","journal-title":"Clim. Past Discuss."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1093\/mollus\/eyw011","article-title":"Reviving Gal\u00e1pagos snails: Ancient DNA extraction and amplification from shells of probably extinct endemic land snails","volume":"82","author":"Villanea","year":"2016","journal-title":"J. Molluscan"},{"key":"ref_156","doi-asserted-by":"crossref","unstructured":"Der Sarkissian, C., Pichereau, V., Dupont, C., Ils\u00f8e, P.C., Perrigault, M., Butler, P., Chauvaud, L., Eir\u00edksson, J., Scourse, J., and Paillard, C. (2017). Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol. Ecol. Resour.","DOI":"10.1111\/1755-0998.12679"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1038\/nature06204","article-title":"Early human use of marine resources and pigment in South Africa during the Middle Pleistocene","volume":"449","author":"Marean","year":"2007","journal-title":"Nature"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1098\/rstb.1992.0092","article-title":"Pleistocene geochronology and palaeothermometry from protein diagenesis in ostrich eggshells: Implications for the evolution of modern humans","volume":"337","author":"Miller","year":"1992","journal-title":"Philos. Trans. R. Soc. B"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1126\/science.248.4951.60","article-title":"Dating Pleistocene archaeological sites by protein diagenesis in ostrich eggshell","volume":"248","author":"Brooks","year":"1990","journal-title":"Science"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"752","DOI":"10.2307\/1369183","article-title":"Reconstructing Avian Diets Using Stable-Carbon and Nitrogen Isotope Analysis of Egg Components: Patterns of Isotopic Fractionation and Turnover","volume":"97","author":"Hobson","year":"1995","journal-title":"Condor"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1007\/s10592-005-9040-6","article-title":"A comparison of sample types varying in invasiveness for use in DNA sex determination in an endangered population of greater Sage-Grouse (Centrocercus uropihasianus)","volume":"6","author":"Bush","year":"2005","journal-title":"Conserv. Genet."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1111\/j.1471-8286.2007.02042.x","article-title":"Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA","volume":"8","author":"Lee","year":"2008","journal-title":"Mol. Ecol. Resour."},{"key":"ref_163","first-page":"1991","article-title":"Fossil avian eggshell preserves ancient DNA","volume":"277","author":"Oskam","year":"2010","journal-title":"Proc. Biol. Sci."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/j.1755-0998.2008.02214.x","article-title":"A nondestructive method for obtaining maternal DNA from avian eggshells and its application to embryonic viability determination in herring gulls (Larus argentatus)","volume":"9","author":"Egloff","year":"2009","journal-title":"Mol. Ecol. Resour."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.ympev.2017.01.005","article-title":"Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell","volume":"109","author":"Grealy","year":"2017","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1126\/science.1251981","article-title":"Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution","volume":"344","author":"Mitchell","year":"2014","journal-title":"Science"},{"key":"ref_167","doi-asserted-by":"crossref","unstructured":"Schierwater, B., Streit, B., Wagner, G.P., and DeSalle, R. (1994). Analysis of DNA from natural history museum collections. Molecular Ecology and Evolution: Approaches and Applications. Experientia Supplementum, vol 69, Birkh\u00e4user.","DOI":"10.1007\/978-3-0348-7527-1"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1093\/jmammal\/gyv178","article-title":"Natural history collections-based research: Progress, promise, and best practices","volume":"97","author":"McLean","year":"2016","journal-title":"J. Mammal."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"R463","DOI":"10.1016\/j.cub.2004.06.008","article-title":"Ancient mitochondrial DNA from hair","volume":"14","author":"Gilbert","year":"2004","journal-title":"Curr. Biol."},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Thomsen, P.F., Elias, S., Gilbert, M.T.P., Haile, J., Munch, K., Kuzmina, S., Froese, D.G., Sher, A., Holdaway, R.N., and Willerslev, E. (2009). Non-destructive sampling of ancient insect DNA. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0005048"},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1080\/00032719.2010.506939","article-title":"DNA Extraction from Orthoptera Museum Specimens","volume":"44","author":"Tagliavia","year":"2011","journal-title":"Anal. Lett."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"e00731","DOI":"10.7554\/eLife.00731","article-title":"The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine","volume":"2","author":"Yoshida","year":"2013","journal-title":"eLife"},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1111\/mec.12675","article-title":"Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance","volume":"23","author":"Martin","year":"2014","journal-title":"Mol. Ecol."},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"160239","DOI":"10.1098\/rsos.160239","article-title":"Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens","volume":"3","author":"Schuenemann","year":"2016","journal-title":"R. Soc. Open Sci."},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"76","DOI":"10.2144\/000114517","article-title":"Extraction of ultrashort DNA molecules from herbarium specimens","volume":"62","author":"Gutaker","year":"2017","journal-title":"Biotechniques"},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1080\/00837792.2017.1313383","article-title":"Herbarium genomics: Skimming and plastomics from archival specimens","volume":"72","author":"Bakker","year":"2017","journal-title":"Webbia"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1016\/j.jas.2009.12.036","article-title":"A flock of sheep, goats and cattle: Ancient DNA analysis reveals complexities of historical parchment manufacture","volume":"37","author":"Campana","year":"2010","journal-title":"J. Archaeol. Sci."},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"20130379","DOI":"10.1098\/rstb.2013.0379","article-title":"Paging through history: Parchment as a reservoir of ancient DNA for next generation sequencing","volume":"370","author":"Teasdale","year":"2015","journal-title":"Philos. Trans. R. Soc. B"},{"key":"ref_179","doi-asserted-by":"crossref","unstructured":"Lech, T. (2016). Ancient DNA in historical parchments\u2014Identifying a procedure for extraction and amplification of genetic material. Genet. Mol. Res., 15.","DOI":"10.4238\/gmr.15028661"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1023\/A:1018776925261","article-title":"Archive contributions to a molecular phylogeography of the toad Bufo calamita in Britain","volume":"36","author":"Beebee","year":"1998","journal-title":"Biochem. Genet."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1002\/1096-9896(2000)9999:9999<::AID-PATH768>3.0.CO;2-C","article-title":"An assessment of the long-term preservation of the DNA of a bacterial pathogen in ethanol-preserved archival material","volume":"192","author":"Barnes","year":"2000","journal-title":"J. Pathol."},{"key":"ref_182","first-page":"283","article-title":"Long-term DNA survival in ethanol-preserved archival material","volume":"83","author":"Spigelman","year":"2001","journal-title":"Ann. R. Coll. Surg. Engl."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1017\/S1477200005001891","article-title":"Extraction of nuclear DNA from bone of skeletonized and fluid-preserved museum specimens","volume":"4","author":"Stuart","year":"2006","journal-title":"Syst. Biodivers."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"245","DOI":"10.3897\/zookeys.365.5787","article-title":"Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol","volume":"365","author":"Miller","year":"2013","journal-title":"Zookeys"},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"9402","DOI":"10.1021\/ja00074a005","article-title":"DNA interstrand cross-linking by formaldehyde: Nucleotide sequence preference and covalent structure of the predominant cross-link formed in synthetic oligonucleotides","volume":"115","author":"Huang","year":"1993","journal-title":"J. Am. Chem. Soc."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S0027-5107(97)00314-X","article-title":"DNA damage caused by common cytological fixatives","volume":"401","author":"Douglas","year":"1998","journal-title":"Mutat. Res. Fundam. Mol. Mech. Mutagen."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1071\/IS04039","article-title":"The effects of preservatives and temperatures on arachnid DNA","volume":"19","author":"Vink","year":"2005","journal-title":"Invertebr. Syst."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1742-9994-5-18","article-title":"DNA damage in preserved specimens and tissue samples: A molecular assessment","volume":"5","author":"Zimmermann","year":"2008","journal-title":"Front. Zool."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/S0002-9440(10)64472-0","article-title":"Effect of fixatives and tissue processing on the content and integrity of nucleic acids","volume":"161","author":"Srinivasan","year":"2002","journal-title":"Am. J. Pathol."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1177\/39.3.1704393","article-title":"Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction","volume":"39","author":"Johnson","year":"1991","journal-title":"J. Histochem. Cytochem."},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1016\/S0002-9440(10)65461-2","article-title":"A high frequency of sequence alterations is due to formalin fixation of archival specimens","volume":"155","author":"Williams","year":"1999","journal-title":"Am. J. Pathol."},{"key":"ref_192","unstructured":"Tang, E. (2006). Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collections: Workshop Summary, National Academies Press."},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.ab.2013.04.006","article-title":"Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues","volume":"439","author":"Paireder","year":"2013","journal-title":"Anal. Biochem."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.ab.2009.08.016","article-title":"High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil","volume":"395","author":"Lin","year":"2009","journal-title":"Anal. Biochem."},{"key":"ref_195","doi-asserted-by":"crossref","unstructured":"Ruane, S., and Austin, C.C. (2017). Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens. Mol. Ecol. Res.","DOI":"10.1111\/1755-0998.12655"},{"key":"ref_196","doi-asserted-by":"crossref","unstructured":"Hykin, S.M., Bi, K., and McGuire, J.A. (2015). Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0141579"},{"key":"ref_197","doi-asserted-by":"crossref","unstructured":"H\u00fchns, M., Erbersdobler, A., Obliers, A., and R\u00f6penack, P. (2017). Identification of HPV Types and Mycobacterium Tuberculosis Complex in Historical Long-Term Preserved Formalin Fixed Tissues in Different Human Organs. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0170353"},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"233","DOI":"10.2144\/000113362","article-title":"Direct PCR amplification and sequencing of specimens\u2019 DNA from preservative ethanol","volume":"48","author":"Shokralla","year":"2010","journal-title":"Biotechniques"},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/syt018","article-title":"Next-generation museomics disentangles one of the largest primate radiations","volume":"62","author":"Guschanski","year":"2013","journal-title":"Syst. Biol."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"20140266","DOI":"10.1098\/rsbl.2014.0266","article-title":"Rodents of the Caribbean: Origin and diversification of hutias unravelled by next-generation museomics","volume":"10","author":"Fabre","year":"2014","journal-title":"Biol. Lett."},{"key":"ref_201","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/aob\/mcw208","article-title":"Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar","volume":"119","author":"Silva","year":"2017","journal-title":"Ann. Bot."},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"6310","DOI":"10.1093\/nar\/gkx361","article-title":"A new model for ancient DNA decay based on paleogenomic meta-analysis","volume":"45","author":"Kistler","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/S0047-2484(03)00106-4","article-title":"The thermal history of human fossils and the likelihood of successful DNA amplification","volume":"45","author":"Smith","year":"2003","journal-title":"J. Hum. Evol."},{"key":"ref_204","first-page":"4724","article-title":"The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils","volume":"279","author":"Allentoft","year":"2012","journal-title":"Proc. R. Soc. Lond. B Biol. Sci."},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1111\/1475-4754.t01-1-00071","article-title":"The survival of organic matter in bone: A review","volume":"44","author":"Collins","year":"2002","journal-title":"Archaeometry"},{"key":"ref_206","doi-asserted-by":"crossref","first-page":"368","DOI":"10.2144\/000114364","article-title":"New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA","volume":"59","author":"Wales","year":"2015","journal-title":"Biotechniques"},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"14616","DOI":"10.1073\/pnas.0704665104","article-title":"Patterns of damage in genomic DNA sequences from a Neandertal","volume":"104","author":"Briggs","year":"2007","journal-title":"Proc.Natl. Acad. Sci. USA"},{"key":"ref_208","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.crvi.2017.03.002","article-title":"Effects of different preservation methods on inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) molecular markers in botanic samples","volume":"340","author":"Wang","year":"2017","journal-title":"C. R. Biol."},{"key":"ref_209","doi-asserted-by":"crossref","unstructured":"Staats, M., Cuenca, A., Richardson, J.E., Ginkel, R.V., Petersen, G., Seberg, O., and Bakker, F.T. (2011). DNA Damage in Plant Herbarium Tissue. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0028448"},{"key":"ref_210","first-page":"60","article-title":"Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA","volume":"147","author":"Atanesyan","year":"2017","journal-title":"Am. J. Clin. Pathol."},{"key":"ref_211","unstructured":"(2017, July 11). Thermal Age Web Tool. Available online: http:\/\/thermal-age.eu\/."},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jprot.2017.01.004","article-title":"Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites","volume":"158","author":"Wadsworth","year":"2017","journal-title":"J. Proteom."},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.1126\/science.1249274","article-title":"Biochemistry. Unlocking ancient protein palimpsests","volume":"343","author":"Cappellini","year":"2014","journal-title":"Science"},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.jas.2016.07.014","article-title":"Finding Britain\u2019s last hunter-gatherers: A new biomolecular approach to \u201cunidentifiable\u201d bone fragments utilising bone collagen","volume":"73","author":"Charlton","year":"2016","journal-title":"J. Archaeol. Sci."},{"key":"ref_215","first-page":"2971","article-title":"Is amino acid racemization a useful tool for screening for ancient DNA in bone?","volume":"276","author":"Collins","year":"2009","journal-title":"Proc. Biol. Sci."},{"key":"ref_216","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.jas.2014.02.005","article-title":"Proteomics evidence for kefir dairy in Early Bronze Age China","volume":"45","author":"Yang","year":"2014","journal-title":"J. Archaeol. Sci."},{"key":"ref_217","first-page":"547","article-title":"A preliminary investigation of DNA stability in bone during artificial diagenesis","volume":"168","author":"Waite","year":"1997","journal-title":"Bull. Soc. G\u00e9ol. Fr."},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.forsciint.2008.05.017","article-title":"Degradation of biomolecules in artificially and naturally aged teeth: Implications for age estimation based on aspartic acid racemization and DNA analysis","volume":"179","author":"Dobberstein","year":"2008","journal-title":"Forensic Sci. Int."},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/S0305-4403(03)00099-2","article-title":"Non-random DNA damage resulting from heat treatment: Implications for sequence analysis of ancient DNA","volume":"31","author":"Banerjee","year":"2004","journal-title":"J. Archaeol. Sci."},{"key":"ref_220","doi-asserted-by":"crossref","first-page":"S169","DOI":"10.1016\/S1344-6223(02)00102-5","article-title":"Extraction and amplification of nuclear and mitochondrial DNA from ancient and artificially aged bones","volume":"5","author":"Harbeck","year":"2003","journal-title":"Leg. Med."},{"key":"ref_221","first-page":"67","article-title":"Botanical remains: Utility in protein and DNA research","volume":"3","author":"Chalfoun","year":"1999","journal-title":"Anc. Biomol."},{"key":"ref_222","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/s00114-008-0478-5","article-title":"Preservation of ancient DNA in thermally damaged archaeological bone","volume":"96","author":"Ottoni","year":"2009","journal-title":"Naturwissenschaften"},{"key":"ref_223","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/365700a0","article-title":"Recovery of antediluvian DNA","volume":"365","author":"Lindahl","year":"1993","journal-title":"Nature"},{"key":"ref_224","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1007\/BF01921720","article-title":"Ancient DNA: Methodological challenges","volume":"50","author":"Handt","year":"1994","journal-title":"Experientia"},{"key":"ref_225","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1038\/35072071","article-title":"Ancient DNA","volume":"2","author":"Hofreiter","year":"2001","journal-title":"Nat. Rev. Genet."},{"key":"ref_226","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13323-015-0020-4","article-title":"Re-inventing ancient human DNA","volume":"6","author":"Knapp","year":"2015","journal-title":"Investig. Genet."},{"key":"ref_227","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.tree.2005.07.005","article-title":"Assessing ancient DNA studies","volume":"20","author":"Gilbert","year":"2005","journal-title":"Trends Ecol. Evol."},{"key":"ref_228","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1016\/S0531-5131(02)00624-6","article-title":"The top 10 list: Criteria of authenticity for DNA from ancient and forensic samples","volume":"1239","author":"Poinar","year":"2003","journal-title":"Int. Congr. Ser."},{"key":"ref_229","doi-asserted-by":"crossref","first-page":"5717","DOI":"10.1093\/nar\/gkm588","article-title":"Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions","volume":"35","author":"Brotherton","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_230","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1093\/bioinformatics\/btr347","article-title":"Mapdamage: Testing for damage patterns in ancient DNA sequences","volume":"27","author":"Ginolhac","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_231","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","article-title":"Mapdamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters","volume":"29","author":"Ginolhac","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_232","doi-asserted-by":"crossref","first-page":"2962","DOI":"10.1093\/bioinformatics\/btu410","article-title":"Bammds: A tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)","volume":"30","author":"Malaspinas","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_233","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_234","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1002\/bies.201000026","article-title":"Analysis of ancient human genomes","volume":"32","author":"Shapiro","year":"2010","journal-title":"Bioessays"},{"key":"ref_235","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1109\/MC.2002.1016901","article-title":"Genome sequence assembly: Algorithms and issues","volume":"35","author":"Pop","year":"2002","journal-title":"Computer"},{"key":"ref_236","doi-asserted-by":"crossref","unstructured":"Schmieder, R., and Edwards, R. (2011). Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0017288"},{"key":"ref_237","doi-asserted-by":"crossref","unstructured":"Longo, M.S., O\u2019Neill, M.J., and O\u2019Neill, R.J. (2011). Abundant human DNA contamination identified in non-primate genome databases. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0016410"},{"key":"ref_238","doi-asserted-by":"crossref","first-page":"e675","DOI":"10.7717\/peerj.675","article-title":"Unexpected cross-species contamination in genome sequencing projects","volume":"2","author":"Merchant","year":"2014","journal-title":"PeerJ"},{"key":"ref_239","doi-asserted-by":"crossref","unstructured":"Laurence, M., Hatzis, C., and Brash, D.E. (2014). Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0097876"},{"key":"ref_240","doi-asserted-by":"crossref","unstructured":"Warinner, C., Herbig, A., Mann, A., Fellows Yates, J.A., Wei\u00df, C.L., Burbano, H.A., Orlando, L., and Krause, J. (2017). A Robust Framework for Microbial Archaeology. Annu. Rev. Genom. Hum. Genet.","DOI":"10.1146\/annurev-genom-091416-035526"},{"key":"ref_241","doi-asserted-by":"crossref","unstructured":"Meyer, M., and Kircher, M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc., 6.","DOI":"10.1101\/pdb.prot5448"},{"key":"ref_242","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1111\/1755-0998.12470","article-title":"Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing","volume":"16","author":"Gamba","year":"2016","journal-title":"Mol. Ecol. Resour."},{"key":"ref_243","doi-asserted-by":"crossref","first-page":"2585","DOI":"10.1016\/j.jas.2008.04.011","article-title":"Improved methodology for extraction and amplification of DNA from single grains of charred wheat","volume":"35","author":"Giles","year":"2008","journal-title":"J. Archaeol. Sci."},{"key":"ref_244","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/978-1-61779-516-9_10","article-title":"Ancient DNA extraction from plants","volume":"840","author":"Kistler","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"ref_245","doi-asserted-by":"crossref","unstructured":"Telle, S., and Thines, M. (2008). Amplification of cox2 (approximately 620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases. PLoS ONE, 3.","DOI":"10.1371\/journal.pone.0003584"},{"key":"ref_246","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1093\/nar\/27.16.e12","article-title":"Optimisation of DNA and RNA extraction from archival formalin-fixed tissue","volume":"27","author":"Coombs","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"ref_247","unstructured":"Favreau, J., and Patalano, R. (2017). The Sustainability of Dental Calculus for Archaeological Research. Shallow Pasts, Endless Horizons: Sustainability & Archaeology. Proceedings of the 48th Annual Chacmool Conference, The Chacmool Archaeological Association of the University of Calgary."},{"key":"ref_248","first-page":"541","article-title":"Remarkable preservation of biomolecules in ancient radish seeds","volume":"263","author":"Clapham","year":"1996","journal-title":"Proc. Biol. Sci."},{"key":"ref_249","doi-asserted-by":"crossref","unstructured":"Krakov\u00e1, L., \u0160oltys, K., Otlewska, A., Pietrzak, K., Purkrtov\u00e1, S., Savick\u00e1, D., Pu\u0161k\u00e1rov\u00e1, A., Bu\u010dkov\u00e1, M., Szemes, T., and Budi\u0161, J. (2017). Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq). Int. Biodeterior. Biodegrad.","DOI":"10.1016\/j.ibiod.2017.02.015"},{"key":"ref_250","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1016\/j.tree.2007.08.017","article-title":"Back to the future: Museum specimens in population genetics","volume":"22","author":"Wandeler","year":"2007","journal-title":"Trends Ecol. Evol."},{"key":"ref_251","doi-asserted-by":"crossref","first-page":"6018","DOI":"10.1111\/mec.12516","article-title":"Unlocking the vault: Next-generation museum population genomics","volume":"22","author":"Bi","year":"2013","journal-title":"Mol. Ecol."},{"key":"ref_252","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/518292a","article-title":"Museums: The endangered dead","volume":"518","author":"Kemp","year":"2015","journal-title":"Nature"},{"key":"ref_253","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s12520-011-0067-y","article-title":"A Novel and Non-Destructive Approach for Zooms Analysis: Ammonium Bicarbonate Buffer Extraction","volume":"3","author":"Hollund","year":"2011","journal-title":"Archaeol. Anthropol. Sci."},{"key":"ref_254","doi-asserted-by":"crossref","first-page":"e279","DOI":"10.1016\/j.fsigss.2015.09.111","article-title":"Nondestructive extraction DNA method from bones or teeth, true or false?","volume":"5","author":"Gomes","year":"2015","journal-title":"Forensic Sci. Int. Genet."},{"key":"ref_255","doi-asserted-by":"crossref","unstructured":"Andersen, J.C., and Mills, N.J. (2012). DNA extraction from museum specimens of parasitic Hymenoptera. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0045549"},{"key":"ref_256","doi-asserted-by":"crossref","unstructured":"Gilbert, M.T.P., Moore, W., Melchior, L., and Worobey, M. (2007). DNA extraction from dry museum beetles without conferring external morphological damage. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0000272"},{"key":"ref_257","doi-asserted-by":"crossref","first-page":"15066","DOI":"10.1073\/pnas.1512264112","article-title":"Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting","volume":"112","author":"Fiddyment","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_258","first-page":"e79","article-title":"Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase","volume":"45","author":"Gansauge","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_259","doi-asserted-by":"crossref","first-page":"59115","DOI":"10.18632\/oncotarget.10827","article-title":"Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA","volume":"7","author":"Stiller","year":"2016","journal-title":"Oncotarget"},{"key":"ref_260","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/nature12788","article-title":"A mitochondrial genome sequence of a hominin from Sima de los Huesos","volume":"505","author":"Meyer","year":"2014","journal-title":"Nature"},{"key":"ref_261","doi-asserted-by":"crossref","first-page":"e09560","DOI":"10.7554\/eLife.09560","article-title":"Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa","volume":"4","author":"Berger","year":"2015","journal-title":"eLife"},{"key":"ref_262","doi-asserted-by":"crossref","unstructured":"Sender, R., Fuchs, S., and Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol., 14.","DOI":"10.1101\/036103"},{"key":"ref_263","doi-asserted-by":"crossref","first-page":"2316","DOI":"10.1126\/science.291.5512.2316b","article-title":"In a map for human life, count the microbes, too","volume":"291","author":"Davies","year":"2001","journal-title":"Science"},{"key":"ref_264","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.gde.2016.07.003","article-title":"Insights into human evolution from ancient and contemporary microbiome studies","volume":"41","author":"Schnorr","year":"2016","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_265","first-page":"532","article-title":"Incubation reduces microbial growth on eggshells and the opportunity for trans-shell infection","volume":"8","author":"Cook","year":"2005","journal-title":"Ecology"},{"key":"ref_266","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1111\/1462-2920.12471","article-title":"Unmasking the measles-like parchment discoloration: Molecular and microanalytical approach","volume":"17","author":"Sterflinger","year":"2015","journal-title":"Environ. Microbiol."},{"key":"ref_267","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1002\/bies.201300036","article-title":"Phenotypes from ancient DNA: Approaches, insights and prospects","volume":"35","author":"Fortes","year":"2013","journal-title":"Bioessays"},{"key":"ref_268","doi-asserted-by":"crossref","unstructured":"Llamas, B., Holland, M.L., Chen, K., Cropley, J.E., Cooper, A., and Suter, C.M. (2012). High-resolution analysis of cytosine methylation in ancient DNA. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0030226"},{"key":"ref_269","doi-asserted-by":"crossref","unstructured":"Smith, R.W.A., Monroe, C., and Bolnick, D.A. (2015). Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0125344"},{"key":"ref_270","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1126\/science.1250368","article-title":"Reconstructing the DNA methylation maps of the Neandertal and the Denisovan","volume":"344","author":"Gokhman","year":"2014","journal-title":"Science"},{"key":"ref_271","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1101\/gr.163592.113","article-title":"Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome","volume":"24","author":"Pedersen","year":"2014","journal-title":"Genome Res."},{"key":"ref_272","doi-asserted-by":"crossref","first-page":"5559","DOI":"10.1038\/srep05559","article-title":"Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process","volume":"4","author":"Smith","year":"2014","journal-title":"Sci. Rep."},{"key":"ref_273","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1126\/science.1256515","article-title":"An epigenetic window into the past?","volume":"345","author":"Orlando","year":"2014","journal-title":"Science"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/8\/7\/180\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:42:30Z","timestamp":1760208150000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/8\/7\/180"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,13]]},"references-count":273,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2017,7]]}},"alternative-id":["genes8070180"],"URL":"https:\/\/doi.org\/10.3390\/genes8070180","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,13]]}}}