Adler, C. J., Dobney, K., Weyrich, L. S., Kaidonis, J., Walker, A. W., Haak, W., Bradshaw, C. J. A., Townsend, G., Sołtysiak, A., Alt, K. W., and Parkhill, J. 2013. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial Revolutions. Nature Genetics 45(4):450–455.Google Scholar

Allentoft, M. E., Collins, M., Harker, D., Haile, J., Oskam, C. L., Hale, M. L., Campos, P. F., Samaniego, J. A., Gilbert, M. T. P., Willerslev, E., and Zhang, G. 2012. The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B: Biological Sciences 279(1748):4724–4733.CrossRefGoogle ScholarPubMed

Atkinson, Q. D. 2011. Phonemic diversity supports a serial founder effect model of language expansion from Africa. Science 332(6027):346–349.Google Scholar

Ballard, J. W. O. and Whitlock, M. C. 2004. The incomplete natural history of mitochondria. Molecular Ecology 13(4):729–744.Google Scholar

Balloux, F. 2010. The worm in the fruit of the mitochondrial DNA tree. Heredity 104(5):419.Google Scholar

Bollongino, R., Tresset, A., and Vigne, J.-D. 2008. Environment and excavation: Pre-lab impacts on ancient DNA analyses. Comptes Rendus Palevol 7(2–3):91–98.Google Scholar

Bollongino, R. and Vigne, J.-D. 2008. Temperature monitoring in archaeological animal bone samples in the Near East arid area, before, during and after excavation. Journal of Archaeological Science 35(4):873–881.Google Scholar

Bramanti, B., Thomas, M. G., Haak, W., Unterlaender, M., Jores, P., Tambets, K., Antanaitis-Jacobs, I. I., Haidle, M. N., Jankauskas, R., Kind, C. J., and Lueth, F. 2009. Genetic discontinuity between local hunter-gatherers and Central Europe’s first farmers. Science 326(5949):137–140.Google Scholar

Carpenter, M. L., Buenrostro, J. D., Valdiosera, C., Schroeder, H., Allentoft, M. E., Sikora, M., Rasmussen, M., Gravel, S., Guillén, S., Nekhrizov, G., and Leshtakov, K. 2013. Pulling out the 1%: Whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. The American Journal of Human Genetics 93(5):852–864.Google Scholar

Castelo, R., and Roverato, A. 2012. Inference of regulatory networks from microarray data with R and the bioconductor package qpgraph. Methods Molecular Biology. 802:215–233.Google Scholar

Collins, M. J., Nielsen-Marsh, C. M., Hiller, J., Smith, C. I., Roberts, J. P., Prigodich, R. V., Wess, T. J., Csapo, J., Millard, A. R., and Turner-Walker, G. 2002. The survival of organic matter in bone: A review. Archaeometry 44(3):383–394.Google Scholar

Cooper, A. and Poinar, H. N. 2000. Ancient DNA: Do it right or not at all. Science 289(5482):1139.Google Scholar

Eriksson, A. and Manica, A. 2012. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences 109(35):13956–13960.Google Scholar

Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., and Meyer, M. 2014. Genome sequence of a 45,000-year-old modern human from Western Siberia. Nature 514(7523):445–449.Google Scholar

Gerbault, P., Leonardi, M., Powell, A., Weber, C., Benecke, N., Burger, J., and Thomas, M. G. 2012. Domestication and migrations: Using mitochondrial DNA to infer domestication processes of goats and horses. In: `Kaiser, E., `Burger, J., and `Schier, W. (eds.) Population Dynamics in Prehistory and Early History, pp. 17–30. Berlin, Boston: De Gruyter.Google Scholar

Gilbert, M. T. P., Bandelt, H.-J., Hofreiter, M., and Barnes, I. 2005. Assessing ancient DNA studies. Trends in Ecology and Evolution 20(10):541–544.Google Scholar

Girdland Flink, L., Allen, R., Barnett, R., Malmström, H., Peters, J., Eriksson, J., Andersson, L., Dobney, K., and Larson, G. 2014. Establishing the validity of domestication genes using DNA from ancient chickens. Proceedings of the National Academy of Sciences 111(17):6184–6189.Google Scholar

Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., and Siepel, A. 2011. Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43(10):1031–1034.Google Scholar

Haile, J., Froese, D. G., MacPhee, R. D. E., Roberts, R. G., Arnold, L. J., Reyes, A. V., Rasmussen, M., Nielsen, R., Brook, B. W., Robinson, S., and Demuro, M. 2009. Ancient DNA reveals late survival of mammoth and horse in Interior Alaska. Proceedings of the National Academy of Sciences 106(52):22352–22357.Google Scholar

Horsburgh, K. A. 2008. Wild or domesticated? An ancient DNA approach to canid species identification in South Africa’s Western Cape Province. Journal of Archaeological Science 35(6):1474–1480.CrossRefGoogle Scholar

Knapp, M. and Hofreiter, M. 2010. Next generation sequencing of ancient DNA: Requirements, strategies and perspectives. Genes 1(2):227–243.Google Scholar

Korneliussen, T.S., Albrechtsen, A., and Nielsen, R., 2014. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15:356.Google Scholar

Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., and Pääbo, S. 2010. The complete mitochondrial DNA genome of an unknown hominin from Southern Siberia. Nature 464(7290):894–897.Google Scholar

Krause, J., Lalueza-Fox, C., Orlando, L., Enard, W., Green, R. E., Burbano, H. A., Hublin, J.-J., Hänni, C., Fortea, J., De La Rasilla, M., and Bertranpetit, J. 2007. The derived FOXP2 variant of modern humans was shared with Neandertals. Current Biology 17(21):1908–1912.Google Scholar

Lalueza-Fox, C., Römpler, H., Caramelli, D., Stäubert, C., Catalano, G., Hughes, D., Rohland, N., Pilli, E., Longo, L., Condemi, S., and De La Rasilla, M. 2007. A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318(5855):1453–1455.Google Scholar

Larson, G., Albarella, U., Dobney, K., Rowley-Conwy, P., Schibler, J., Tresset, A., Vigne, J.-D., Edwards, C. J., Schlumbaum, A., Dinu, A., and Bălăçsescu, A. 2007. Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Sciences 104(39):15276–15281.Google Scholar

Li, H. and Durbin, R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475(7357):493–496.Google Scholar

Lindahl, T. 1993. Instability and decay of the primary structure of DNA. Nature 362(6422):709–715.Google Scholar

Linz, B., Balloux, F., Moodley, Y., Manica, A., Liu, H., Roumagnac, P., Falush, D., Stamer, C., Prugnolle, F., van der Merwe, S. W., and Yamaoka, Y. 2007. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445(7130):915–918.Google Scholar

Llorente, M. G., Jones, E. R., Eriksson, A., Siska, V., Arthur, K. W., Arthur, J. W., Curtis, M. C., Stock, J. T., Coltorti, M., Pieruccini, P., and Stretton, S. 2015. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350(6262):820–822.Google Scholar

Loog, L., Thomas, M. G., Barnett, R., Allen, R., Sykes, N., Paxinos, P. D., Lebrasseur, O., Dobney, K., Peters, J., Manica, A., and Larson, G. 2017. Inferring allele frequency trajectories from ancient DNA indicates that selection on a chicken gene coincided with changes in medieval husbandry practices. Molecular Biology and Evolution 34(8):1981–1990.Google Scholar

Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G. A., Castanos, P., Cieslak, M., Lippold, S., Llorente, L., Malaspinas, A. S., and Slatkin, M. 2009. Coat color variation at the beginning of horse domestication. Science 324(5926):485.Google Scholar

Malmström, H., Gilbert, M. T. P., Thomas, M. G., Brandström, M., Storå, J., Molnar, P., Andersen, P. K., Bendixen, C., Holmlund, G., Götherström, A., and Willerslev, E. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Current Biology 19(20):1758–1762.CrossRefGoogle ScholarPubMed

McVean, G. 2009. A genealogical interpretation of principal components analysis. PLoS Genetics 5(10):e1000686.Google Scholar

Meyer, M., Fu, Q., Aximu-Petri, A., Glocke, I., Nickel, B., Arsuaga, J.-L., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., and Pääbo, S. 2014. A mitochondrial genome sequence of a hominin from Sima de Los Huesos. Nature 505(7483):403–406.CrossRefGoogle ScholarPubMed

Molina, J., Sikora, M., Garud, N., Flowers, J., Rubinstein, S., Reynolds, A., Huang, P., Jackson, S., Schaal, B. A., Bustamante, C. D., and Boyko, A. R. 2011. Molecular evidence for a single evolutionary origin of domesticated rice. Proceedings of the National Academy of Sciences 108(20):8351–8356.Google Scholar

Nielsen, R. 2004. Population genetic analysis of ascertained SNP data. Human Genomics 1(3):218.Google Scholar

Nielsen, R. and Beaumont, M. A. 2009. Statistical inferences in phylogeography. Molecular Ecology 18(6):1034–1047.Google Scholar

Olalde, I., Allentoft, M. E., Sánchez-Quinto, F., Santpere, G., Chiang, C. W. K., DeGiorgio, M., Prado-Martinez, J,. Rodríguez, J. A., Rasmussen, S., Quilez, J., and Ramírez, O. 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507(7491):225–228.Google Scholar

Oppenheimer, S. 2012. Out-of-Africa, the peopling of continents and islands: Tracing uniparental gene trees across the map. Philosophical Transactions of the Royal Society of London B: Biological Sciences 367(1590):770–784.Google Scholar

Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., and Johnson, P. L. 2013. Recalibrating Equus evolution using the genome sequence of an Early Middle Pleistocene horse. Nature 499(7456):74–78.Google Scholar

Oskam, C. L., Haile, J., McLay, E., Rigby, P., Allentoft, M. E., Olsen, M. E., Bengtsson, C., Miller, G. H., Schwenninger, J. L., Jacomb, C., and Walter, R. 2010. Fossil avian eggshell preserves ancient DNA. Proceedings of the Royal Society of London B: Biological Sciences 277(1690):1991–2000.Google ScholarPubMed

Ottoni, C., Girdland Flink, L., Evin, A., Georg, C., De Cupere, B., Van Neer, W., Bartosiewicz, L., Linderholm, A., Barnett, R., Peters, J., and Decorte, R. 2013. Pig domestication and human-mediated dispersal in Western Eurasia revealed through ancient DNA and geometric morphometrics. Molecular Biology and Evolution 30(4):824–832.Google Scholar

Palkopoulou, E., Mallick, S., Skoglund, P., Enk, J., Rohland, N., Li, H., Omrak, A., Vartanyan, S., Poinar, H., Götherström, A., and Reich, D. 2015. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Current Biology 25(10):1395–1400.Google Scholar

Pang, J.-F., Kluetsch, C., Zou, X.-J., Zhang, A. B., Luo, L.-Y., Angleby, H., Ardalan, A., Ekström, C., Sköllermo, A., Lundeberg, J., and Matsumura, S. 2009. mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Molecular Biology and Evolution 26(12):2849–2864.Google Scholar

Parducci, L., Suyama, Y., Lascoux, M., and Bennett, K. D. 2005. Ancient DNA from pollen: A genetic record of population history in Scots Pine. Molecular Ecology 14(9):2873–2882.Google Scholar

Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., and Reich, D. 2012. Ancient Admixture in Human History. Genetics 192:1065–1093.Google Scholar

Pickrell, J. K. and Reich, D. 2014. Toward a new history and geography of human genes informed by ancient DNA. Trends in Genetics 30(9):377–389.Google Scholar

Pinhasi, R., Fernandes, D., Sirak, K., Novak, M., Connell, S., Alpaslan-Roodenberg, S., Gerritsen, F., Moiseyev, V., Gromov, A., Raczky, P., and Anders, A. 2015. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS One 10(6):e0129102.Google Scholar

Poinar, H., Kuch, M., McDonald, G., Martin, P., and Pääbo, S. 2003. Nuclear gene sequences from a Late Pleistocene sloth coprolite. Current Biology 13(13):1150–1152.Google Scholar

Prendergast, M.E., Lipson, M., Sawchuk, E.A., Olalde, I., Ogola, C.A., Rohland, N., Sirak, K.A., Adamski, N., Bernardos, R., Broomandkhoshbacht, N., Callan, K., Culleton, B.J., Eccles, L., Harper, T.K., Lawson, A.M., Mah, M., Oppenheimer, J., Stewardson, K., Zalzala, F., Ambrose, S.H., Ayodo, G., Gates, H.L., Gidna, A.O., Katongo, M., Kwekason, A., Mabulla, A.Z.P., Mudenda, G.S., Ndiema, E.K., Nelson, C., Robertshaw, P., Kennett, D.J., Manthi, F.K., and Reich, D., 2019. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 365: eaaw6275.Google Scholar

Pritchard, J.K., Stephens, M., and Donnelly, P. 2000. Inference of Population Structure Using Multilocus Genotype Data. Genetics 155:945–959.Google Scholar

Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., De Filippo, C., and Li, H. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505(7481):43–49.CrossRefGoogle ScholarPubMed

Prugnolle, F., Manica, A., and Balloux, F. 2005. Geography predicts neutral genetic diversity of human populations. Current Biology 15(5):R159–160.Google Scholar

Ramachandran, S., Deshpande, O., Roseman, C. C., Rosenberg, N. A., Feldman, M. W., and Cavalli-Sforza, L. L. 2005. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences of the United States of America 102(44):15942–15947.Google Scholar

Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A, Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., and Kivisild, T. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334(6052):94–98.Google Scholar

Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L., and Maricic, T. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327):1053–1060.Google Scholar

Reich, D., Thangaraj, K., Patterson, N., Price, A. L., and Singh, L. 2009. Reconstructing Indian Population History. Nature 461(7263):489–494.Google Scholar

Rieux, A., Eriksson, A., Li, M., Sobkowiak, B., Weinert, L. A., Warmuth, V., Ruiz-Linares, A., Manica, A., and Balloux, F. 2014. Improved calibration of the human mitochondrial clock using ancient genomes. Molecular Biology and Evolution 31(10):2780–2792.Google Scholar

Rollo, F., Ubaldi, M., Ermini, L., and Marota, I. 2002. Ötzi’s last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proceedings of the National Academy of Sciences 99(20):12594–12599.Google Scholar

Rosenberg, N. A. and Nordborg, M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics 3(5):380–390.Google Scholar

Schiffels, S. and Durbin, R. 2014. Inferring human population size and separation history from multiple genome sequences. Nature Genetics 46(8):919–925.Google Scholar

Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Vicente, M., Steyn, M., Soodyall, H., Lombard, M., and Jakobsson, M., 2017. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358: 652–655.Google Scholar

Secher, B., Fregel, R., Larruga, J. M., Cabrera, V. M., Endicott, P., Pestano, J. J., and González, A. M. 2014. The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents. BMC Evolutionary Biology 14(1):109.Google Scholar

Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., and Goebel, T. 2014. Genomic structure in Europeans dating back at least 36,200 years. Science 346(6213):1113–1118.CrossRefGoogle Scholar

Skoglund, P., Ersmark, E., Palkopoulou, E., and Dalén, L. 2015. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Current Biology 25(11):1515–1519.Google Scholar

Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., and Jakobsson, M. 2014a. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proceedings of the National Academy of Sciences 111(6):2229–2234.Google Scholar

Skoglund, P., Sjödin, P., Skoglund, T., Lascoux, M., and Jakobsson, M. 2014b. Investigating population history using temporal genetic differentiation. Molecular Biology and Evolution 31(9):2516–2527.Google Scholar

Skoglund, P., Storå, J., Götherström, A., and Jakobsson, M. 2013. Accurate sex identification of ancient human memains using DNA shotgun sequencing. Journal of Archaeological Science 40(12):4477–4482.Google Scholar

Skoglund, P., Thompson, J. C., Prendergast, M. E., Mittnik, A., Sirak, K., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Peltzer, A., and Heinze, A. 2017. Reconstructing prehistoric African population structure. Cell 171(1):59–71.Google Scholar

Smith, C. I., Chamberlain, A. T., Riley, M. S., Stringer, C. B., and Collins, M. J. 2003. The thermal history of human fossils and the likelihood of successful DNA amplification. Journal of Human Evolution 45(3):203–217.Google Scholar

Stringer, C. B. 1974. A Multivariate Study of Cranial Variation in Middle and Upper Pleistocene Human Populations. Doctoral thesis, Universiy of Bristol.Google Scholar

Stringer, C. B. and Andrews, P. 1988. Genetic and fossil evidence for the origin of modern humans. Science 239(4845):1263–1268.Google Scholar

Sunnåker, M., Busetto, A. G., Numminen, E., Corander, J., Foll, M., and Dessimoz, C. 2013. Approximate Bayesian computation. PLoS Comput Biol 9(1):e1002803.Google Scholar

Sverrisdóttir, O. Ó., Timpson, A., Toombs, J., Lecoeur, C., Froguel, P., Carretero, J. M., Arsuaga Ferreras, J. L., Götherström, A., and Thomas, M. G. 2014. Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe. Molecular Biology and Evolution 31(4): 975-983.Google Scholar

Thalmann, O., Shapiro, B., Cui, P., Schuenemann, V. J., Sawyer, S. K., Greenfield, D. L., Germonpré, M. B., Sablin, M. V., López-Giráldez, F., Domingo-Roura, X., and Napierala, H. 2013. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342(6160):871–874.Google Scholar

Valdiosera, C. E., García, N., Anderung, C., Dalén, L., Crégut-Bonnoure, E., Kahlke, R.-D., Stiller, M., Brandström, M., Thomas, M. G., Arsuaga, J. L., and Götherström, A. 2007. Staying out in the cold: Glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears. Molecular Ecology 16(24):5140–5148.Google Scholar

Warmuth, V., Eriksson, A., Bower, M. A., Barker, G., Barrett, E., Hanks, B. K., Li, S., Lomitashvili, D., Ochir-Goryaeva, M., Sizonov, G. V., and Soyonov, V. 2012. Reconstructing the origin and spread of horse domestication in the Eurasian Steppe. Proceedings of the National Academy of Sciences 109(21):8202–8206.Google Scholar

Warmuth, V., Eriksson, A., Bower, M. A., Cañon, J., Cothran, G., Distl, O., Glowatzki-Mullis, M.-L., Hunt, H., Luís, C., do Mar Oom, M., and Yupanqui, I. T. 2011. European domestic horses originated in two Holocene refugia. PLoS One 6(3):e18194.Google Scholar

Weidenreich, F. 1940. Some problems dealing with ancient man. American Anthropologist 42(3):375–383.Google Scholar

Wilde, S., Timpson, A., Kirsanow, K., Kaiser, E., Kayser, M., Unterländer, M., Hollfelder, N., Potekhina, I. D., Schier, W., Thomas, M. G., and Burger, J. 2014. Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 Y. Proceedings of the National Academy of Sciences 111(13):4832–4837.Google Scholar

Wolpoff, M. H. 1989. Multiregional evolution: The fossil alternative to Eden. In: `Mellar, P. and `Stringer, C. (eds.) The Human Revolution, pp. 62–108. Princeton, NJ: Princeton University Press.Google Scholar

Yang, D. Y. and Watt, K. 2005. Contamination controls when preparing archaeological remains for ancient DNA analysis. Journal of Archaeological Science 32(3):331–336.Google Scholar

Abelson, P. H., 1954. Amino acids in fossils. Science 119(3096):576.Google Scholar

Altmeyer, W. et al. 2002. Method for qualitative and/or quantitative determination of gender, species, race and/or geographical origin of biological materials. Patent. Available at: http://google.com/patents/CA2452851A1?cl=zh (accessed June 29, 2019).Google Scholar

Asara, J. M. et al. 2007. Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316(5822):280–285.Google Scholar

Bada, J. L. 1991. Amino acid cosmogeochemistry. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 333(1268):349–358.Google Scholar

Bada, J. L. and Miller, S. L. 1968. Ammonium ion concentration in the primitive ocean. Science 159(3813):423–425.Google Scholar

Barker, A. 2011. Archaeological protein residues: New data for conservation science. Ethnobiology Letters 1:58–65.Google Scholar

Barker, A., Venables, B., Stevens, S. M. Jr., Seeley, K. W., Wang, P., and Wolverton, S. 2012. An optimized approach for protein residue extraction and identification from ceramics after cooking. Journal of Archaeological Method and Theory 19(3):407–439.Google Scholar

Becker, M. A., Willman, P., and Tuross, N. C. 1995. The U.S. First Ladies’ gowns: A biochemical study of silk preservation. Journal of the American Institute for Conservation 34(2):141–152.Google Scholar

Bern, M., Phinney, B. S., and Goldberg, D. 2009. Reanalysis of Tyrannosaurus rex mass spectra. Journal of Proteome Research 8(9):4328–4332.Google Scholar

Brandt, L. Ø., Schmidt, A. L., Mannering, U., Sarret, M., Kelstrup, C. D., Olsen, J. V., and Cappellini, E. 2014. Species identification of archaeological skin objects from Danish bogs: Comparison between mass spectrometry-based peptide sequencing and microscopy-based methods. PloS One 9(9):e106875.Google Scholar

Buckley, M. 2013. A molecular phylogeny of Plesiorycteropus reassigns the extinct mammalian order “Bibymalagasia.” PloS One 8(3):e59614.Google Scholar

Buckley, M. 2015. Ancient collagen reveals evolutionary history of the endemic South American “ungulates.” Proceedings of the Royal Society B-Biological Sciences 282(1806):20142671.Google Scholar

Buckley, M., Anderung, C., Penkman, K., Raney, B. J., Gotherstrom, A., Thomas-Oates, J., and Collins, M. J. 2008b. Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites. Journal of Archaeological Science 35:1756–1764.Google Scholar

Buckley, M., Collins, M., Thomas-Oates, J., and Wilson, J. C. 2009. Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry 23:3843–3854.Google Scholar

Buckley, M., Fraser, S., Herman, J., Melton, N. D., Mulville, J., and Palsdottir, A. H. 2014. Species identification of archaeological marine mammals using collagen fingerprinting. Journal of Archaeological Science 41:631–641.Google Scholar

Buckley, M. and Kansa, S. W. 2011. Collagen fingerprinting of archaeological bone and teeth remains from Domuztepe, South Eastern Turkey. Archaeological and Anthropological Sciences 3(3):271–280.Google Scholar

Kansa, S. W., Howard, S., Campbell, S., Thomas-Oates, J., and Collins, M. 2010. Distinguishing between archaeological sheep and goat bones using a single collagen peptide. Journal of Archaeological Science 37:13–20.Google Scholar

Buckley, M., Larkin, N., and Collins, M. 2011. Mammoth and mastodon collagen sequences: Survival and utility. Geochimica et Cosmochimica Acta 75(7):2007–2016.Google Scholar

Buckley, M., Melton, N. D., and Montgomery, J. 2013. Proteomics analysis of ancient food vessel stitching reveals >4000-year-old milk protein. Rapid Communications in Mass Spectrometry 27(4):531–538.CrossRefGoogle ScholarPubMed

Buckley, M. and Wadsworth, C. 2014. Proteome degradation in ancient bone: Diagenesis and phylogenetic potential. Palaeogeography, Palaeoclimatology, Palaeoecology 416:69–79.Google Scholar

Buckley, M., Walker, A., Ho, S. Y. W., Yang, Y., Smith, C., Ashton, P., Oates, J. T., Cappellini, E., Koon, H., Penkman, K., Elsworth, B., Ashford, D., Solazzo, C., Andrews, P., Strahler, J., Shapiro, B., Ostrom, P., Gandhi, H., Miller, W., Raney, B., Zylber, M. I., Gilbert, M. T. P., Prigodich, R. V., Ryan, M., Rijsdijk, K. F., Janoo, A., and Collins, M. J. 2008a. Comment on “protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.” Science 319:33.Google Scholar

Buckley, M., Warwood, S., Van Dongen, B., Kitchener, A. C., and Manning, P. L. 2017. A fossil protein chimera: Difficulties in discriminating dinosaur peptide sequences from modern cross-contamination. Proceedings of the Royal Society B-Biological Sciences 284:20170544.Google Scholar

Cappellini, E., Gilbert, M. T. P., Geuna, F., Fiorentino, G., Hall, A., Thomas-Oates, J., Ashton, P. D., Ashford, D. A., Arthur, P., Campos, P. F., Kool, J., Willerslev, E., and Collins, M. J. 2010. A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97:205–217.Google Scholar

Cappellini, E., Jensen, L. J., Szklarczyk, D., Ginolhac, A., Da Fonseca, R. a. R., Stafford, T. W., Holen, S. R., Collins, M. J., Orlando, L., Willerslev, E., Gilbert, M. T. P., and Olsen, J. V. 2012. Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins. Journal of Proteome Research 11:917–926.Google Scholar

Cattaneo, C., Gelsthorpe, K., Phillips, P., and Sokol, R. J. 1992. Detection of human proteins in buried blood using Elisa and monoclonal-antibodies – Towards the reliable species indentification of blood stains on buried material. Forensic Science International 57:139–146.Google Scholar

Chamberlain, P., Drewello, R., Korn, L., Bauer, W., Gough, T., Al-Fouzan, A., Collins, M., Van Doorn, N., Craig, O., and Heron, C. 2011. Construction of the Khoja Zaynuddin mosque: Use of animal glue modified with urine. Archaeometry 53:830–841.Google Scholar

Chambery, A., Di Maro, A., Sanges, C., Severino, V., Tarantino, M., Lamberti, A., Parente, A., and Arcari, P. 2009. Improved procedure for protein binder analysis in mural painting by LC-ESI/Q-q-TOF mass spectrometry: Detection of different milk species by casein proteotypic peptides. Analytical and Bioanalytical Chemistry 395:2281–2291.Google Scholar

Cleland, T. P., Schroeter, E. R., and Schweitzer, M. H. 2015. Biologically and diagenetically derived peptide modifications in moa collagens. Proceedings of the Royal Society B-Biological Sciences 282:20150015.Google Scholar

Collins, M. J., Nielsen-Marsh, C. M., Hiller, J., Smith, C. I., Roberts, J. P., Prigodich, R. V., Weiss, T. J., Csapo, J., Millard, A. R., and Turner-Walker, G. 2002. The survival of organic matter in bone: A review. Archaeometry 44:383–394.Google Scholar

Collins, M. J., Riley, M. S., Child, A. M., and Turnerwalker, G. 1995. A basic mathematical simulation of the chemical degradation of ancient collagen. Journal of Archaeological Science 22:175–183.Google Scholar

Corthals, A., Koller, A., Martin, D. W., Rieger, R., Chen, E. I., Bernaski, M., Recagno, G., and Davalos, L. M. 2012. Detecting the immune system response of a 500 year-old Inca mummy. PLoS One 7(7):e41244.Google Scholar

Craig, O. E. and Collins, M. J. 2000. An improved method for the immunological detection of mineral bound protein using hydrofluoric acid and direct capture. Journal of Immunological Methods 236(1–2):89–97.Google Scholar

Craig, O., Mulville, J., Pearson, M. P., Sokol, R., Gelsthorpe, K., Stacey, R., and Collins, M. 2000. Detecting milk proteins in ancient pots. Nature 408:312.Google Scholar

Dallongeville, S., Garnier, N., Casasola, D. B., Bonifay, M., Rolando, C., and Tokarski, C. 2011. Dealing with the identification of protein species in ancient amphorae. Analytical and Bioanalytical Chemistry 399:3053–3063.Google Scholar

Daniel, R. M., Dines, M., and Petach, H. H. 1996. The denaturation and degradation of stable enzymes at high temperatures. Biochemical Journal 317(Pt 1):1–11.Google Scholar

Demarchi, B. and Collins, M., 2014. Amino acid racemisation dating. In: `Rink, W. J and `Thompson, J. (eds.) Encyclopedia of Scientific Dating Methods, pp. 1–22. Springer Netherlands.Google Scholar

Demarchi, B., Hall, S., Roncal-Herrero, T., Freeman, C. L., Woolley, J., Crisp, M. K., Wilson, J., Fotakis, A., Fischer, R., Kessler, B. M., Jersie-Christensens, R. R., Olsen, J. V., Haile, J., Thomas, J., Marean, C. W., Parkington, J., Presslee, S., Lee-Thorp, J., Ditchfield, P., Hamilton, J. F., Ward, M. W., Wang, C. M., Shaw, M. D., Harrison, T., Dominguez-Rodrigo, M., Macpheel, R. D. E., Kwekason, A., Ecker, M., Horwitz, L. K., Chazan, M., Kroger, R., Thomas-Oates, J., Harding, J. H., Cappellini, E., Penkman, K., and Collins, M. J. 2016. Protein sequences bound to mineral surfaces persist into deep time. Elife 5:e17092.Google Scholar

Demarchi, B., O’Connor, S., Ponzoni, A. D., Ponzoni, R. D. 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(6):e99839.Google Scholar

Derbyshire, E., Harris, N., Boulter, D., and Jope, E. M. 1977. The extraction, composition and intra-cellular distribution of protein in early maize grains from an archaeological site in NE Arizona. New Phytologist 78:499–504.Google Scholar

Doberenz, A. R. and Wyckoff, R. W. 1967. Fine structure in fossil collagen. Proceedings of the National Academy of Sciences of the United States of America 57(3):539–541.Google Scholar

Domon, B. and Aebersold, R. 2006. Mass spectrometry and protein analysis. Science 312(5771):212–217.Google Scholar

Downs, E. F. and Lowenstein, J. M. 1995. Identification of archaeological blood proteins: A cautionary note. Journal of Archaeological Science 22(1):11–16.Google Scholar

El-Aneed, A., Cohen, A., and Banoub, J. 2009. Mass spectrometry, review of the basics: Electrospray, MALDI, and commonly used mass analyzers. Applied Spectroscopy Reviews 44(3):210–230.Google Scholar

Eöry, L., Gilbert, M. T. P., Li, C., Li, B., Archibald, A., Aken, B. L., Zhang, G. J., Jarvis, E., Flicek, P., and Burt, D. W. 2015. Avianbase: A community resource for bird genomics. Genome Biology 16:21.Google Scholar

Evershed, R. P. and Tuross, N. 1996. Proteinaceous material from potsherds and associated soils. Journal of Archaeological Science 23(3):429–436.Google Scholar

Fiddyment, S., Holsinger, B., Ruzzier, C., Devine, A., Binois, A., Albarella, U., Fischer, R., Nichols, E., Curtis, A., Cheese, E., Teasdale, M. D., Checkley-Scott, C., Milner, S. J., Rudy, K. M., Johnson, E. J., Vnoucek, J., Garrison, M., Mcgrory, S., Bradley, D. G., and Collins, M. J. 2015. Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proceedings of the National Academy of Sciences of the United States of America 112:15066–15071.Google Scholar

Heaton, K., Solazzo, C., Collins, M. J., Thomas-Oates, J., and Bergstrom, E. T. 2009. Towards the application of desorption electrospray ionisation mass spectrometry (DESI-MS) to the analysis of ancient proteins from artefacts. Journal of Archaeological Science 36(10):2145–2154.Google Scholar

Henzel, W. J., Watanabe, C., and Stults, J. T. 2003. Protein identification: The origins of peptide mass fingerprinting. Journal of the American Society for Mass Spectrometry 14(9):931–942.Google Scholar

Hill, R. C., Wither, M. J., Nemkov, T., Barrett, A., D’alessandro, A., Dzieciatkowska, M., and Hansen, K. C. 2015. Preserved proteins from extinct bison latifrons identified by tandem mass spectrometry: Hydroxylysine glycosides are a common feature of ancient collagen. Molecular and Cellular Proteomics 14 :1946–1958.Google Scholar

Hillenkamp, F., Karas, M., Beavis, R. C., and Chait, B. T. 1991. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Analytical chemistry 63(24):1193A–1203A.Google Scholar

Hollemeyer, K., Altmeyer, W., and Heinzle, E. 2002. Identification and quantification of feathers, down, and hair of avian and mammalian origin using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Analytical Chemistry 74(23):5960–5968.Google Scholar

Hollemeyer, K., Altmeyer, W., Heinzle, E., and Pitra, C. 2008. Species identification of Oetzi’s clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests. Rapid Communications in Mass Spectrometry 22(18):2751–2767.Google Scholar

Hollemeyer, K., Altmeyer, W., Heinzle, E., and Pitra, C. 2012. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry combined with multidimensional scaling, binary hierarchical cluster tree and selected diagnostic masses improves species identification of Neolithic keratin sequences from furs of the Tyrolean Iceman Oetzi. Rapid Communications in Mass Spectrometry 26(16):1735–1745.Google Scholar

Hong, C., Jiang, H. G., Lu, E. G., Wu, Y. F., Guo, L. H., Xie, Y. M., Wang, C. S., and Yang, Y. M. 2012. Identification of milk component in ancient food residue by proteomics. PLoS One 7(5):e37053.Google Scholar

Huq, N. L., Tseng, A., and Chapman, G. E. 1990. Partial amino acid sequence of osteocalcin from an extinct species of ratite bird. Biochemistry International 21(3):491–496.Google Scholar

Hyland, D. C., Tersak, J. M., Adovasio, J. M., and Siegel, M. I. 1990. Identification of the species of origin of residual blood on lithic material. American Antiquity 55(1):104–112.Google Scholar

Kirby, D. P., Buckley, M., Promise, E., Trauger, S. A., and Holdcraft, T. R. 2013. Identification of collagen-based materials in cultural heritage. The Analyst 138(17):4849–4858.Google Scholar

Kooyman, B., Newman, M. E., and Ceri, H. 1992. Verifying the reliability of blood residue analysis on archaeological tools. Journal of Archaeological Science 19(3):265–269.Google Scholar

Krizkova, M. C., Kuckova, S. H., Santrucek, J., and Hynek, R. 2014. Peptide mass mapping as an effective tool for historical mortar analysis. Construction and Building Materials 50:219–225.Google Scholar

Kuckova, S., Crhova, M., Vankova, L., Hnizda, A., Hynek, R., and Kodicek, M. 2009b. Towards proteomic analysis of milk proteins in historical building materials. International Journal of Mass Spectrometry 284:42–46.Google Scholar

Kuckova, S., Hynek, R., and Kodicek, M. 2007. Identification of proteinaceous binders used in artworks by MALDI-TOF mass spectrometry. Analytical and Bioanalytical Chemistry 388(1):201–206.Google Scholar

Kuckova, S., Hynek, R., and Kodicek, M., 2009a. Application of peptide mass mapping on proteins in historical mortars. Journal of Cultural Heritage 10(2):244–247.Google Scholar

Kuckova, S., Nemec, I., Hynek, R., Hradilova, J., and Grygar, T. 2005. Analysis of organic colouring and binding components in colour layer of art works. Analytical and Bioanalytical Chemistry 382(2):275–282.Google Scholar

Leach, J. D. and Mauldin, R. P. 1995. Additional comments on blood residue analysis in archaeology. Antiquity 69(266):1020–1022.Google Scholar

Lees, S. 1989. Some characteristics of mineralised collagen. In: Calcified Tissue, pp. 153–173. Topics in Molecular and Structural Biology. London: Macmillan.Google Scholar

Leo, G., Bonaduce, I., Andreotti, A., Marino, G., Pucci, P., Colombini, M. P., and Birolo, L. 2011. Deamidation at asparagine and glutamine as a major modification upon deterioration/aging of proteinaceous binders in mural paintings. Analytical Chemistry 83(6):2056–2064.Google Scholar

Lowenstein, J. M. 1981. Immunological reactions from fossil material. Philosophical Transactions of the Royal Society of London. Series B, Biological sciences 292(1057):143–149.Google Scholar

Loy, T. H. 1983. Prehistoric blood residues: Detection on tool surfaces and identification of species of origin. Science 220(4603):1269–1271.Google Scholar

Loy, T. H. 1994. Response. Science 266(5183):299–300.Google Scholar

Loy, T. H. and Hardy, B. L. 1992. Blood residue analysis of 90,000-year-old stone tools from Tabun Cave, Israel. Antiquity 66(250):24–35.Google Scholar

Maixner, F., Overath, T., Linke, D., Janko, M., Guerriero, G., Van Den Berg, B. H. J., Stade, B., Leidinger, P., Backes, C., Jaremek, M., Kneissl, B., Meder, B., Franke, A., Egarter-Vigl, E., Meese, E., Schwarz, A., Tholey, A., Zink, A., and Keller, A. 2013. Paleoproteomic study of the Iceman’s brain tissue. Cellular and Molecular Life Sciences 70(19):3709–3722.CrossRefGoogle ScholarPubMed

Malainey, M. E. 2011. Blood and protein residue analysis. In: `Malainey, M. E. (ed.) A Consumer’s Guide to Archaeological Science. Manuals in Archaeological Method, Theory and Technique, pp. 219–236. Springer New York.Google Scholar

Mann, K. and Mann, M. 2013. The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell. Proteome Science 11(1):40.Google Scholar

Frei, K. M., Mannering, U., Kristiansen, K., Allentoft, M. E., Wilson, A. S., Skals, I., Tridico, S., Nosch, M. L., Willerslev, E., Clarke, L., and Frei, R. 2015. Tracing the dynamic life story of a Bronze Age female. Scientific Reports 5:10431.Google Scholar

Mazel, V., Richardin, P., Debois, D., Touboul, D., Cotte, M., Brunelle, A., Walter, P., and Laprevote, O. 2007. Identification of ritual blood in African artifacts using TOF-SIMS and synchrotron radiation microspectroscopies. Analytical Chemistry 79(24):9253–9260.Google Scholar

Moini, M., Klauenberg, K., and Ballard, M. 2011. Dating silk by capillary electrophoresis mass spectrometry. Analytical Chemistry 83(19):7577–7581.Google Scholar

Nielsen-Marsh, C. M., Ostrom, P. H., Gandhi, H., Shapiro, B., Cooper, A., Hauschka, P. V., and Collins, M. J. 2002. Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka. Geology 30(12):1099–1102.Google Scholar

Nielsen-Marsh, C. M., Richards, M. P., Hauschka, P. V., Thomas-Oates, J. E., Trinkaus, E., Pettitt, P. B., Karavanic, I., Poinar, H., and Collins, M. J. 2005. Osteocalcin protein sequences of Neanderthals and modern primates. Proceedings of the National Academy of Sciences of the United States of America 102(12):4409–4413.Google Scholar

O’Connor, S., Solazzo, C., and Collins, M. 2015. Advances in identifying archaeological traces of horn and other keratinous hard tissues. Studies in Conservation 60(6):393–417.Google Scholar

Orlando, L., Ginolhac, A., Zhang, G. J., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P. L. F., Fumagalli, M., Vilstrup, J. T., Raghavan, M., Korneliussen, T., Malaspinas, A. S., Vogt, J., Szklarczyk, D., Kelstrup, C. D., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A. M. V., Cahill, J., Rasmussen, M., Wang, X. L., Min, J. M., Zazula, G. D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J. F., Weinstock, J., Gregersen, K., Roed, K. H., Eisenmann, V., Rubin, C. J., Miller, D. C., Antczak, D. F., Bertelsen, M. F., Brunak, S., Al-Rasheid, K. a. S., Ryder, O., Andersson, L., Mundy, J., Krogh, A., Gilbert, M. T. P., Kjaer, K., Sicheritz-Ponten, T., Jensen, L. J., Olsen, J. V., Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J., and Willerslev, E. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499(7456):74–78.Google Scholar

Ostrom, P. H., Schall, M., Gandhi, H., Shen, T. L., Hauschka, P. V., Strahler, J. R., and Gage, D. A. 2000. New strategies for characterizing ancient proteins using matrix-assisted laser desorption ionization mass spectrometry. Geochimica et Cosmochimica Acta 64(6):1043–1050.Google Scholar

Palmqvist, P., Grokke, D. R., Arribas, A., and Farina, R. A. 2003. Paleoecological reconstruction of a lower Pleistocene large mammal community using biogeochemical (δ13C, δ15N, δ18O, Sr: Zn) and ecomorphological approaches. Paleobiology 29(2):205–229.Google Scholar

Penkman, K. E. H., Kaufman, D. S., Maddy, D., and Collins, M. J. 2008. Closed-system behaviour of the intra-crystalline fraction of amino acids in mollusc shells. Quaternary Geochronology 3(1–2)2–25.Google Scholar

Penkman, K. E. H., Preece, R. C., Bridgland, D. R., Keen, D. H., Meijer, T., Parfitt, S. A., White, T. S., and Collins, M. J. 2013. An aminostratigraphy for the British Quaternary based on Bithynia opercula. Quaternary Science Reviews 61(C):111–134.Google Scholar

Peris-Vicente, J., Simo-Alfonso, E., Adelantado, J. V. G., and Carbo, M. T. D. 2005. Direct infusion mass spectrometry as a fingerprint of protein-binding media used in works of art. Rapid Communications in Mass Spectrometry 19(23):3463–3467.Google Scholar

Pevzner, P. A., Kim, S., and Ng, J. 2008. Comment on “Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.” Science 321(5892):1040.Google Scholar

Potter, B. A., Reuther, J. D., Lowenstein, J. M., and Scheuenstuhl, G. 2010. Assessing the reliability of pRIA for identifying ancient proteins from archaeological contexts. Journal of Archaeological Science 37(5):910–918.Google Scholar

Rao, H. Y., Li, B., Yang, Y. M., Ma, Q. L., and Wang, C. S. 2015. Proteomic identification of organic additives in the mortars of ancient Chinese wooden buildings. Analytical Methods 7(1):143–149.Google Scholar

Rasmussen, M., Li, Y. R., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, M. T. P., Wang, Y., Raghavan, M., Campos, P. F., Kamp, H. M., Wilson, A. S., Gledhill, A., Tridico, S., Bunce, M., Lorenzen, E. D., Binladen, J., Guo, X. S., Zhao, J., Zhang, X. Q., Zhang, H., Li, Z., Chen, M. F., Orlando, L., Kristiansen, K., Bak, M., Tommerup, N., Bendixen, C., Pierre, T. L., Gronnow, B., Meldgaard, M., Andreasen, C., Fedorova, S. A., Osipova, L. P., Higham, T. F. G., Ramsey, C. B., Hansen, T. V. O., Nielsen, F. C., Crawford, M. H., Brunak, S., Sicheritz-Ponten, T., Villems, R., Nielsen, R., Krogh, A., Wang, J., and Willerslev, E. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463(7282):757–762.Google Scholar

Rasmussen, K. L., Tenorio, A. L., Bonaduce, I., Colombini, M. P., Birolo, L., Galano, E., Amoresano, A., Doudna, G., Bond, A. D., Palleschi, V., Lorenzetti, G., Legnaioli, S., Van Der Plicht, J., and Gunneweg, J. 2012. The constituents of the ink from a Qumran inkwell: New prospects for provenancing the ink on the Dead Sea Scrolls. Journal of Archaeological Science 39(9):2956–2968.Google Scholar

Remington, S. J. 1994. Identifying species of origin from prehistoric blood residues. Science 266(5183):298–300.Google Scholar

Richter, K. K., Wilson, J., Jones, A. K. G., Buckley, M., van Doorn, N., and Collins, M. J. 2011. Fish’n chips: ZooMS peptide mass fingerprinting in a 96 well plate format to identify fish bone fragments. Journal of Archaeological Science, 38(7):1502–1510.Google Scholar

Rybczynski, N., Gosse, J. C., Harington, C. R., Wogelius, R. A., Hidy, A. J., and Buckley, M. 2013. Mid-Pliocene warm-period deposits in the high Arctic yield insight into camel evolution. Nature Communications 4:1550.Google Scholar

Sawafuji, R., Cappellini, E., Nagaoka, T., Fotakis, A. K., Jersie-Christensen, R. R., Olsen, J. V., Hirata, K., and Ueda, S. 2017. Proteomic profiling of archaeological human bone. Royal Society Open Science 4(6):161004.Google Scholar

Schmidt-Schultz, T. H. and Schultz, M. 2007. Well preserved non-collagenous extracellular matrix proteins in ancient human bone and teeth. International Journal of Osteoarchaeology 17(1):91–99.Google Scholar

Schroeter, E. R. and Cleland, T. P. 2016. Glutamine deamidation: An indicator of antiquity, or preservational quality? Rapid Communications in Mass Spectrometry 30(2):251–255.Google Scholar

Schweitzer, M. H., Zheng, W. X., Organ, C. L., Avci, R., Suo, Z. Y., Freimark, L. M., Lebleu, V. S., Duncan, M. B., Heiden, M. G. V., Neveu, J. M., Lane, W. S., Cottrell, J. S., Horner, J. R., Cantley, L. C., Kalluri, R., and Asara, J. M. 2009. Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324(5927):626–631.Google Scholar

Shevchenko, A., Yang, Y. M., Knaust, A., Thomas, H., Jiang, H. E., Lu, E. G., Wang, C. S., and Shevchenko, A. 2014. Proteomics identifies the composition and manufacturing recipe of the 2500-year-old sourdough bread from Subeixi cemetery in China. Journal of Proteomics 105:363–371.Google Scholar

Shewry, P. R., Kirkman, M. A., Burgess, S. R., Festenstein, G. N., and Miflin, B. J. 1982. A comparison of the protein and amino acid composition of old and recent barley grain. The New Phytologist 90(3):455–466.Google Scholar

Smith, P. R. and Wilson, M. T. 1992. Blood residues on ancient tool surfaces: A cautionary note. Journal of Archaeological Science 19(3):237–241.Google Scholar

Solazzo, C., Clerens, S., Plowman, J. E., Wilson, J., Peacock, E. E., and Dyer, J. M. 2015. Application of redox proteomics to the study of oxidative degradation products in archaeological wool. Journal of Cultural Heritage 16:896–903.Google Scholar

Solazzo, C., Dyer, J. M., Clerens, S., Plowman, J., Peacock, E. E., and Collins, M. J. 2013a. Proteomic evaluation of the biodegradation of wool fabrics in experimental burials. International Biodeterioration and Biodegradation 80:48–59.Google Scholar

Solazzo, C., Dyer, J. M., Deb-Choudhury, S., Clerens, S., and Wyeth, P. 2012. Proteomic profiling of the photo-oxidation of silk fibroin: Implications for historic tin-weighted silk. Photochemistry and Photobiology 88(5):1217–1226.Google Scholar

Solazzo, C., Fitzhugh, W. W., Rolando, C., and Tokarski, C. 2008. Identification of protein remains in archaeological potsherds by proteomics. Analytical Chemistry 80(12):4590–4597.CrossRefGoogle ScholarPubMed

Solazzo, C., Heald, S., Ballard, M. W., Ashford, D. A., Depriest, P. T., Koestler, R. J., and Collins, M. J. 2011. Proteomics and Coast Salish blankets: A tale of shaggy dogs? Antiquity 85(330):1418–1432.Google Scholar

Solazzo, C., Wadsley, M., Dyer, J. M., Clerens, S., Collins, M. J., and Plowman, J. 2013b. Characterisation of novel α-keratin peptide markers for species identification in keratinous tissues using mass spectrometry. Rapid Communications in Mass Spectrometry 27(23):2685–2698.Google Scholar

Solazzo, C., Wadsley, M., Dyer, J. M., Clerens, S., Collins, M. J., and Plowman, J. 2014. Modeling deamidation in sheep α-keratin peptides and application to archeological wool textiles. Analytical Chemistry 86(1):567–575.Google Scholar

Steele, T. E. 2015. The contributions of animal bones from archaeological sites: The past and future of zooarchaeology. Journal of Archaeological Science 56:168–176.Google Scholar

Stewart, J. R. M., Allen, R. B., Jones, A. K. G., Kendall, T., Penkman, K. E. H., Demarchi, B., O’connor, T., and Collins, M. J. 2013. ZooMS: Making eggshell visible in the archaeological record. Journal of Archaeological Science 40(4):1797–1804.Google Scholar

Stewart, J. R. M., Allen, R. B., Jones, A. K. G., Kendall, T., Penkman, K. E. H., Demarchi, B., O’Connor, T., and Collins, M. J. 2014. Walking on eggshells: A study of egg use in Anglo-Scandinavian York based on eggshell identification using ZooMS. International Journal of Osteoarchaeology 24(3):247–255.Google Scholar

Sykes, N., 2014. Beastly Questions: Animal Answers to Archaeological Issues. London: Bloomsbury Academic.Google Scholar

Terwilliger, T. C. and Clarke, S. 1981. Methylation of membrane proteins in human erythrocytes. Identification and characterization of polypeptides methylated in lysed cells. The Journal of Biological Chemistry 256(6):3067–3076.Google Scholar

Tokarski, C., Martin, E., Rolando, C., and Cren-Olive, C. 2006. Identification of proteins in renaissance paintings by proteomics. Analytical Chemistry 78(5):1494–1502.Google Scholar

Towe, K. M. 1972. Collagen-like structures in Ordovician graptolite periderm. Nature 237:443–445.Google Scholar

Tran, T. N. N., Aboudharam, G., Gardeisen, A., Davoust, B., Bocquet-Appel, J. P., Flaudrops, C., Belghazi, M., Raoult, D., and Drancourt, M. 2011. Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling. PLoS One 6(2):e17319.Google Scholar

Tuross, N., Barnes, I., and Potts, R. 1996. Protein identification of blood residues on experimental stone tools. Journal of Archaeological Science 23(2):289–296.Google Scholar

Toniolo, L., D’amato, A., Saccenti, R., Gulotta, D., and Righetti, P. G. 2012. The Silk Road, Marco Polo, a Bible and its proteome: A detective story. Journal of Proteomics 75(11):3365–3373.Google Scholar

Vaiglova, P., Bogaard, A., Collins, M., Cavanagh, W., Mee, C., Renard, J., Lamb, A., Gardeisen, A., and Fraser, R. 2014. An integrated stable isotope study of plants and animals from Kouphovouno, southern Greece: A new look at Neolithic farming. Journal of Archaeological Science 42:201–215.Google Scholar

Vanden Berghe, I. 2012. Towards an early warning system for oxidative degradation of protein fibres in historical tapestries by means of calibrated amino acid analysis. Journal of Archaeological Science 39(5):1349–1359.Google Scholar

Van Der Sluis, L. G., Hollund, H. I., Buckley, M., De Louw, P. G. B., Rijsdijk, K. F., and Kars, H. 2014. Combining histology, stable isotope analysis and ZooMS collagen fingerprinting to investigate the taphonomic history and dietary behaviour of extinct giant tortoises from the Mare aux Songes deposit on Mauritius. Palaeogeography, Palaeoclimatology, Palaeoecology 416:80–91.Google Scholar

van Der Werf, I. D., Calvano, C. D., Palmisano, F., and Sabbatini, L. 2012. A simple protocol for Matrix Assisted Laser Desorption Ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis of lipids and proteins in single microsamples of paintings. Analytica Chimica Acta 718:1–10.Google Scholar

van Doorn, N. L. 2014. Zooarchaeology by Mass Spectrometry (ZooMS). In: Encyclopedia of Global Archaeology, pp. 7998–8000. New York: Springer.Google Scholar

van Doorn, N. L., Wilson, J., Hollund, H., Soressi, M., and Collins, M. J. 2012. Site-specific deamidation of glutamine: A new marker of bone collagen deterioration. Rapid Communications in Mass Spectrometry 26:2319–2327.Google Scholar

von Holstein, I. C. C., Ashby, S. P., van Doorn, N. L., Sachs, S. M., Buckley, M., Meiri, M., Barnes, I., Brundle, A., and Collins, M. J. 2014. Searching for Scandinavians in pre-Viking Scotland: Molecular fingerprinting of Early Medieval combs. Journal of Archaeological Science 41:1–6.Google Scholar

Wadsworth, C. and Buckley, M. 2014. Proteome degradation in fossils: Investigating the longevity of protein survival in ancient bone. Rapid Communications in Mass Spectrometry 28(6):605–615.Google Scholar

Wang, S.-Y., Cappellini, E., and Zhang, H.-Y. 2012. Why collagens best survived in fossils? Clues from amino acid thermal stability. Biochemical and Biophysical Research Communications 422(1):5–7.Google Scholar

Warinner, C., Hendy, J., Speller, C., Cappellini, E., Fischer, R., Trachsel, C., Arneborg, J., Lynnerup, N., Craig, O. E., Swallow, D. M., Fotakis, A., Christensen, R. J., Olsen, J. V., Liebert, A., Montalva, N., Fiddyment, S., Charlton, S., Mackie, M., Canci, A., Bouwman, A., Ruhli, F., Gilbert, M. T. P., and Collins, M. J. 2014a. Direct evidence of milk consumption from ancient human dental calculus. Scientific Reports 4:7104.Google Scholar

Warinner, C., Rodrigues, J. F. M., Vyas, R., Trachsel, C., Shved, N., Grossmann, J., Radini, A., Hancock, Y., Tito, R. Y., Fiddyment, S., Speller, C., Hendy, J., Charlton, S., Luder, H. U., Salazar-Garcia, D. C., Eppler, E., Seiler, R., Hansen, L. H., Castruita, J. a. S., Barkow-Oesterreicher, S., Teoh, K. Y., Kelstrup, C. D., Olsen, J. V., Nanni, P., Kawai, T., Willerslev, E., Von Mering, C., Lewis, C. M., Collins, M. J., Gilbert, M. T. P., Ruhli, F., and Cappellini, E. 2014b. Pathogens and host immunity in the ancient human oral cavity. Nature Genetics 46(4):336–344.Google Scholar

Welker, F., Collins, M. J., Thomas, J. A., Wadsley, M., Brace, S., Cappellini, E., Turvey, S. T., Reguero, M., Gelfo, J. N., Kramarz, A., Burger, J., Thomas-Oates, J., Ashford, D. A., Ashton, P. D., Rowsell, K., Porter, D. M., Kessler, B., Fischer, R., Baessmann, C., Kaspar, S., Olsen, J. V., Kiley, P., Elliott, J. A., Kelstrup, C. D., Mullin, V., Hofreiter, M., Willerslev, E., Hublin, J. J., Orlando, L., Barnes, I., and Macphee, R. D. E. 2015a. Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates. Nature 522(7554):81–84.Google Scholar

Welker, F., Soressi, M., Rendu, W., Hublin, J. J., and Collins, M. 2015b. Using ZooMS to identify fragmentary bone from the Late Middle/Early Upper Palaeolithic sequence of Les Cottés, France. Journal of Archaeological Science 54:279–286.Google Scholar

Whiteaker, J. R., Zhao, L., Zhang, H. Y., Feng, L. C., Piening, B. D., Anderson, L., and Paulovich, A. G. 2007. Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Analytical Biochemistry 362(1):44–54.Google Scholar

Wilson, A. S., Brown, E. L., Villa, C., Lynnerup, N., Healey, A., Ceruti, M. C., Reinhard, J., Previgliano, C. H., Araoz, F. A., Diez, J. G., and Taylor, T. 2013. Archaeological, radiological, and biological evidence offer insight into Inca child sacrifice. Proceedings of the National Academy of Sciences of the United States of America 110(33):13322–13327.Google Scholar

Wilson, J., van Doorn, N. L., and Collins, M. J. 2012. Assessing the extent of bone degradation using glutamine deamidation in collagen. Analytical Chemistry 84(21):9041–9048.Google Scholar

Yamashita, M. and Fenn, J. B. 1984. Electrospray ion source. Another variation on the free-jet theme. The Journal of Physical Chemistry 88(20):4451–4459.Google Scholar

Yan, H. T., An, J. J., Zhou, T., Xia, Y., and Rong, B. 2014. Identification of proteinaceous binding media for the polychrome terracotta army of Emperor Qin Shihuang by MALDI-TOF-MS. Chinese Science Bulletin = Kexue tongbao 59(21):2574–2581.Google Scholar

Yang, Y. M., Shevchenko, A., Knaust, A., Abuduresule, I., Li, W. Y., Hu, X. J., Wang, C. S., and Shevchenko, A. 2014. Proteomics evidence for kefir dairy in Early Bronze Age China. Journal of Archaeological Science 45:178–186.Google Scholar

Zhu, Z. Y., Chen, H. F., Li, L., Gong, D. C., Gao, X., Yang, J. C., Zhao, X. C., and Ji, K. Z. 2014. Biomass spectrometry identification of the fibre material in the pall imprint excavated from Grave M1, Peng-state Cemetery, Shanxi, China. Archaeometry 56(4):681–688.Google Scholar

Aichholz, R. and Lorbeer, E. 2000. Investigation of combwax of honeybees with high-temperature gas chromatography and high–temperature gas chromatography-chemical ionization mass spectrometry II. High-temperature gas chromatography-chemical ionization mass spectrometry. Journal of Chromatography A 883:75–88.Google Scholar

Aillaud, S. 2001. Field and laboratory studies of diagenetic reactions affecting lipid residues absorbed in unglazed archaeological pottery vessels. Doctoral thesis, University of Bristol, UK.Google Scholar

Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., Malaspinas, A.-S., Margaryan, A., Higham, T., Chivall, D., Lynnerup, N., Harvig, L., Baron, J., Della Casa, P., Dąbrowski, P., Duffy, P. R., Ebel, A. V., Epimakhov, A., Frei, K., Furmanek, M., Gralak, T., Gromov, A., Gronkiewicz, S., Grupe, G., Hajdu, T., Jarysz, R., Khartanovich, V., Khokhlov, A., Kiss, V., Kolář, J., Kriiska, A., Lasak, I., Longhi, C., McGlynn, G., Merkevicius, A., Merkyte, I., Metspalu, M., Mkrtchyan, R., Moiseyev, V., Paja, L., Pálfi, G., Pokutta, D., Pospieszny, L., Price, T. D. Saag, L., Sablin, M., Shishlina, N., Smrčka, V., Soenov, V. I., Szeverényi, V., Tóth, G., Trifanova, S. V., Varul, L., Vicze, M., Yepiskoposyan, L., Zhitenev, V., Orlando, L., Sicheritz-Pontén, T., Brunak, S., Nielsen, R., Kristiansen, K. and Willerslev, E. 2015. Population genomics of Bronze Age Eurasia. Nature 522:167–172.Google Scholar

Asperger, A., Engewald, W. and Fabian, G. 1999. Analytical characterization of natural waxes employing pyrolysis-gas chromatography-mass spectrometry. Journal of Analytical and Applied Pyrolysis 50:103–115.Google Scholar

Barnard, H., Shoemaker, L., Rider, M., Craig, O. E., Parr, R. E., Sutton, M. Q. and II Yohe, R. M. 2007. Introduction to the analysis of protein residues in archaeological ceramics. In: `Barnard, H. and `Eerkens, J. (eds.) Theory and Practice of Archaeological Residue Analysis. BAR International Series 1650, pp. 216–231. Oxford: Archaeopress.Google Scholar

Barton, H. and Matthews, P. J. 2006. Taphonomy. In `Torrence, R. and `Barton, H. (eds.) Ancient Starch Research. California: Left Coast Press.Google Scholar

Beja-Pereira, A., Luikart, G., England, P. R., Bradley, D. G. Jann, O.C., Bertorelle, G., Chamberlain, A. T., Nunes, T. P., Metodiev, S., Ferrand, N. and Erhardt, G. 2003. Gene-culture coevolution between cattle milk protein genes and human lactase genes. Nature Genetics 35(4):311–313.Google Scholar

Beverly, M. B., Kay, P. T. and Voorhees, K. J. 1995. Principal component analysis of the pyrolysis-mass spectra from African, Africanized hybrid, and European beeswax. Journal of Analytical and Applied Pyrolysis 34:251–263.Google Scholar

Boyd, M., Surette, C. and Nicholson, B. A. 2006. Archaeobotanical evidence of prehistoric maize (Zea mays) consumption at the northern edge of the Great Plains. Journal of Archaeological Science 33(8):1129–1140.Google Scholar

Boyd, M., Varney, T., Surette, C. and Surrette, J. 2008. Reassessing the northern limit of maize consumption in North America: Stable isotope, plant microfossil, and trace element content of carbonised food residue. Journal of Archaeological Science 35:2545–2556.Google Scholar

Buckley, S. A., Stott, A. W. and Evershed, R. P. 1999. Studies of organic residues from ancient Egyptian mummies using high temperature gas chromatography mass spectrometry and sequential thermal desorption gas chromatography mass spectrometry and pyrolysis gas chromatography mass spectrometry. Analyst 124(4):443–452.Google Scholar

Buckley, S., Usai, D., Jakob, T., Radini, A. and Hardy, K. 2014. Dental calculus reveals unique insights into food items, cooking and plant processing in prehistoric Central Sudan. PLoS One 9 :e100808.Google Scholar

Buonasera, T. 2007. Investigating the presence of ancient absorbed organic residues in ground stone using GC-MS and other analytical techniques: A residue study of several prehistoric milling tools from central California. Journal of Archaeological Science 34:1279–1390.Google Scholar

Cattaneo, C., Gelsthorpe, K., Phillips, P. and Sokol, R. J. 1993. Blood residues on stone tools — indoor and outdoor experiments. World Archaeology 25(1):29–43.Google Scholar