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Anthropological Applications of Ancient DNA: Problems and Prospects

  • Connie J. Mulligan (a1)
Abstract

The analysis of DNA extracted from archaeological specimens to address anthropological questions is becoming increasingly common. Despite widespread interest in ancient DNA (aDNA), the difficulties inherent in aDNA analysis are not generally appreciated by researchers outside of the field. The majority of samples subjected to aDNA analysis often fail to produce results, and successful analysis is typically limited to specimens that exhibit excellent preservation. Contamination of samples with exogenous DNA is an ongoing problem and requires careful design of research strategies to limit and identify all DNA contaminants. Overall, aDNA analysis is a highly specialized and technical field that requires extensive training and can be quite expensive. Thus, each aDNA study should be carefully planned with significant input from archaeologists, physical anthropologists, linguists, and related researchers and should focus on well-preserved samples that are likely to produce a clear answer to a question that is not amenable to nongenetic analysis. In this manuscript, I explain the problems and prospects of various anthropological applications of aDNA technology. I present a series of previously published studies, which are of general anthropological interest, to illustrate the strengths and weaknesses of aDNA methods in each case. I also provide a checklist of questions to evaluate the utility of archaeological remains for aDNA analysis and to provide guidelines when designing an aDNA study.

El análisis del ADN extraido de muestras arqueológicas para investigar preguntas antropológicas es cada vez más comùn. A pesar del amplio interés, las dificultades inherentes al análisis del ADN antiguo (ADNa) no son generalmente apreciadas por investigadores ajenos a esta especialidad. Típicamente, la mayoría de las muestras sujetas al análisis de ADNa fallan en producir resultados, y los análisis exitosos son limitados generalmente a muestras que exhiben una preservación excelente. La contaminación de las muestras con ADN exógeno es un problema recurrente y necesita un diseño experimental cuidadoso. El campo del análisis del ADN antiguo es muy especializado y técnico, requiere un amplio entrenamiento técnico y puede ser bastante costoso. Así, cada estudio de ADNa debe ser planeado cuidadosamente con un aporte significativo de arqueólogos, antropólogos físicos, lingüistas e investigadores relacionados al tema de trabajo. A su vez, se debe enfocar en un número pequeño de muestras bien preservadas que produzcan una respuesta clara para una pregunta que no puede ser contestada con un estudio no-genético. En este manuscrito, explico los problemas y las perspectivas de varias aplicaciones antropológicas de la tecnología de ADNa. Presento una lista de estudios previamente publicados de interés antropológico general para ilustrar los puntos fuertes y las debilidades de los métodos de ADNa en cada caso. Proporciono también una lista de preguntas para evaluar la conveniencia de un estudio propuesto de ADNa y que pude ser usada como guía en el diseño de un estudio de ADNa.

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Allard, M. W., Young, D., and Huyen, Y 1995 Detecting Dinosaur DNA. Science 268(5214): 1192; author reply 1194.
Austin, Jeremy J., Ross, Andrew J., Smith, Andrew B., Fortey, Richard A., and Thomas, Richard H. 1997 Problems of Reproducibility—Does Geologically Ancient DNA Survive in Amber-preserved Insects? Proceedings of the Royal Society of London. Series B, Biological Sciences 264(1381):46774.
Barnes, I., Matheus, P., Shapiro, B., Jensen, D., and Cooper, A. 2002 Dynamics of Pleistocene Population Extinctions in Beringian Brown Bears. Science 295(5563):22672270.
Basler, Christopher F., Reid, Ann H., Dybing, Jody K., Janczewski, Thomas A., Fanning, Thomas G., Zheng, Hongyong, Salvatore, Mirella, Perdue, Michael L., Swayne, David E., Garcia-Sastre, Adolfo, Palese, Peter, and Taubenberger, Jeffrey K. 2001 Sequence of the 1918 Pandemic Influenza Virus Nonstructural Gene (NS) Segment and Characterization of Recombinant Viruses Bearing the 1918 NS Genes. Proceedings of the National Academy of Sciences of the United States of America 98:27462751.
Birky, C. William Jr. 1995 Uniparental Inheritance of Mitochondrial and Chloroplast Genes: Mechanisms and Evolution. Proceedings of the National Academy of Sciences of the United States of America 92:1133111338.
Bradley, Daniel G., MacHugh, David E., Cunningham, Patrick, and Loftus, Ronan T. 1996 Mitochondrial Diversity and the Origins of African and European Cattle. Proceedings of the National Academy of Science USA 93:51315135.
Burger, Joachim, Hummel, Susanne, Pfeiffer, Ina, and Herrmann, Berndt 2000 Palaeogenetic Analysis of (Pre)historic Artifacts and its Significance for Anthropology. Anthroplogischer Anzeiger 58:6976.
Carlyle, Shawn W., Parr, Ryan L., Geoffrey Hayes, M., and O’Rourke, Dennis H. 2000 Context of Maternal Lineages in the Greater South west. American Journal of Physical Anthropology 113:85101.
Chikhi, Lounes, Bruford, Michael W., and Beaumont, Mark A. 2001 Estimation of Admixture Proportions: A Likelihood-based Approach Using Markov Chain Monte Carlo. Genetics 158:13471362.
Chikhi, Lounes, Nichols, Richard A., Barbujani, Guido, and Beaumont, Mark A. 2002 Y Genetic Data Support the Neolithic Demic Diffusion Model. Proceedings of the National Academy of Sciences of the United States of America 99:1100811013.
Cooper, Alan, and Poinar, Hendrik N. 2000 Ancient DNA: Do It Right or Not At All. Science 289(5482): 1139.
Cunha, Eugenia, Fily, Marie-Laure, Clisson, Isabelle, Santos, Ana L., Silva, Ana M., Umbelino, Claudia, Cesar, Paulo, Corte-Real, Artur, Crubezy, Eric, and Ludes, Bertrand 2000 Children at the Convent: Comparing Historical Data, Morphology and DNA Extracted from Ancient Tissues for Sex Diagnosis at Santa Clara-a-Velha (Coimbra, Portugal). Journal of Archaeological Science 27:949952.
Donoghue, Helen D., Spigelman, Mark, Greenblatt, Charles L., Lev-Maor, Galit, Bar-Gal, Gila K., Matheson, Carney, Vernon, Kim, Nerlich, Andreas G., and Zink, Albert R. 2004 Tuberculosis: From Prehistory to Robert Koch, as Revealed by Ancient DNA. The Lancet Infectious Diseases 4(9):584592.
Drancourt, Michel, and Raoult, Didier 2002 Molecular Insights into the History of Plague. Microbes and Infection 4(1): 105109.
Faerman, Marina, Bar-Gal, Gila K., Filon, Dvora, Greenblatt, Charles L., Stager, Lawrence, Oppenheim, Ariella, and Smith, Patricia 1998 Determining the Sex of Infanticide Victims from the Late Roman Era Through Ancient DNA Analysis. Journal of Archaeological Science 25:861865.
Faerman, Marina, Filon, Dvora, Kahila, Gila, Greenblatt, Charles L., Smith, Patricia, and Oppenheim, Ariella 1995 Sex Identification of Archaeological Human Remains Based on Amplification of the X and Y Amelogenin Alleles. Gene 167(1–2):327332.
Gerstenberger, Julia, Hummel, Susanne, Schultes, Tobias, Hack, Bern-hard, and Herrmann, Bernd 1999 Reconstruction of a Historical Genealogy by Means of STR Analysis and Y-haplotyping of Ancient DNA. European Journal of Human Genetics 7(4):469477.
Gilbert, M. Thomas P., Cuccui, Jon, White, William, Lynnerup, Niels, Titball, Richard W., Cooper, Alan, and Prentice, Michael B. 2004 Absence of Yersinia pesfi’s-specific DNA in Human Teeth from Five European Excavations of Putative Plague Victims. Microbiology 150(Pt 2):341354.
González-Oliver, Angélica, Márquez-Morfin, Lourdes, Jiménez, José C., and Torre-Bianco, Alfonso 2001 Founding Amerindian Mitochondrial DNA Lineages in Ancient Maya from Xcaret, Quintana Roo. American Journal of Physical Anthropology 116(3):230235.
Handt, Oliva, Hoss, Matthias, Krings, Matthias, and Paabo, Svante 1994 Ancient DNA: Methodological Challenges. Experientia 50(6):524529.
Handt, Oliva, Krings, Matthias, Ward, Ryk H., and Paabo, Svante 1996 The Retrieval of Ancient Human DNA sequences. American Journal of Human Genetics 59(2):368376.
Hedges, S. B., and Schweitzer, M. H. 1995 Detecting Dinosaur DNA. Science 268(5214): 11911192; author reply 1194.
Hofreiter, Michael, Poinar, Hendrik N., Geoffrey Spaulding, W., Bauer, Karin, Martin, Paul S., Possnert, Goran, and Paabo, Svante 2000 A Molecular Analysis of Ground Sloth Diet through the Last Glaciation. Molecular Ecology 9(12):19751984.
Jackson, Paul J., Hugh-Jones, Martin E., Adair, Debra M., Green, Gertrude, Hill, Karen K., Kuske, Cheryl R., Grinberg, Lev M., Abramova, Faina A., and Keim, Paul 1998 PCR Analysis of Tissue Samples from the 1979 Sverdlovsk Anthrax Victims: The Presence of Multiple Bacillus anthracis Strains in Different Victims. Proceedings of the National Academy of Sciences of the United States of America 95:12241229.
Jaenicke-Despres, Viviane, Buckler, Ed S., Smith, Bruce D., Gilbert, M. Thomas P., Cooper, Alan, Doebley, John, and Paabo, Svante 2003 Early Allelic Selection in Maize as Revealed by Ancient DNA. Science 302(5648):12061208.
Jones, Martin 2003 Ancient DNA in Pre-Columbian Archaeology: A Review. Journal of Archaeological Science 30:629635.
Kaestle, Frederika A., and Smith, David Glenn 2001 Ancient Mitochondrial DNA Evidence for Prehistoric Population Movement: The Numic Expansion. American Journal of Physical Anthropology 115(1):112.
Kaestle, Frederika A. 2000 Report on DNA Analysis of the Remains of “Kennewick Man” from Columbia Park, Washington. Electronic document, http://www.cr.nps.gov/aad/kennewick/kaestle.htm, accessed January 26, 2006.
Kaestle, Frederika A. and Ann Horsburgh, K. 2002 Ancient DNA in Anthropology: Methods, Applications, and Ethics. Yearbook of Physical Anthropology 45:92130.
Kelman, Lori M., and Kelman, Zvi 1999 The Use of Ancient DNA in Paleontological Studies. Journal of Vertebrate Paleontology 19:820.
Kemp, Brian M., and Smith, David Glenn 2005 Use of Bleach to Eliminate Contaminating DNA from the Surface of Bones and Teeth. Electronic document, Forensic Science International, accessed Feb 2, 2005.
Keyser-Tracqui, Christine, Crubezy, Eric, and Ludes, Bertrand 2003 Nuclear and Mitochondrial DNA Analysis of a 2,000-Year-Old Necropolis in the Egyin Gol Valley of Mongolia. American Journal of Human Genetics 73(2):247260.
Kimura, Birgitta, Brandt, Steven A., Hardy, Bruce L., and Hauswirth, William W. 2001 Analysis of DNA from Ethnoarchaeological Stone Scrapers. Journal of Archaeological Science 28:4553.
Kolman, Connie J. 1999 Molecular Anthropology: Progress and Perspectives on Ancient DNA Technology. In Genomic Diversity: Applications in Human Population Genetics, edited by S. S. Papiha, R. Deka and R. Chakraborty, pp. 183200. Kluwer Academic/Plenum Publishers, New York.
Kolman, Connie J., Centurion-Lara, Arturo, Lukehart, Sheila A., Owsley, Douglas W., and Tuross, Noreen 1999 Identification of Treponema pallidum Subspecies pallidum in a 200-Year-Old Skeletal Specimen. Journal of Infectious Diseases 180(6):20602063.
Kolman, Connie J., and Tuross, Noreen 2000 Ancient DNA Analysis of Human Populations. American Journal of Physical Anthropology 111(1):523.
Krings, Matthias, Capelli, Cristian, Tschentscher, Frank, Geisert, Helga, Meyer, Sonja, Haeseler, Arndt von, Grosss-chmidt, Karl, Possnert, Goran, Paunovic, Maja, and Paabo, Svante 2000 A View of Neandertal Genetic Diversity. Nature Genetics 26(2): 144146.
Krings, Matthias, Geisert, Helga, Schmitz, Ralf W., Krainitzki, Heike, and Paabo, Svante 1999 DNA Sequence of the Mitochondrial Hypervariable Region II from the Neandertal Type Specimen. Proceedings of the National Academy of Sciences of the United States of America 96(10):55815585.
Krings, Matthias, Stone, Anne, Schmitz, Ralf W., Krainitzki, Heike, Stoneking, Mark, and Paabo, Svante 1997 Neandertal DNA Sequences and the Origin of Modern Humans. Cell 90(1): 1930.
Lalueza-Fox, Carles, Sampietro, Maria L., Caramelli, David, Puder, Yvonne, Lari, Martina, Calafell, Francesc, Martinez-Maza, Cayetana, Bastir, Markus, Fortea, Javier, Rasilla, Marco de la, Bertranpetit, Jaume, and Rosas, Antonio 2005 Neandertal Evolutionary Genetics: Mitochondrial DNA Data from the Iberian Peninsula. Molecular Biology and Evolution 22(4):10771081.
Lalueza, Carles, Perez-Perez, Alejandro, Prats, Eva, Cornudella, Lluis, and Turbon, Daniel 1997 Lack of Founding Amerindian Mitochondrial DNA Lineages in Extinct Aborigines from Tierra del Fuego-Patagonia. Human Molecular Genetics 6(1):416.
Leonard, Jennifer A., Wayne, Robert K., Wheeler, Jane, Valadez, Raul, Guillen, Sonia, and Vila, Carles 2002 Ancient DNA Evidence for Old World Origin of New World Dogs. Science 298(5598): 16131616.
Malhi, Ripan S., Breece, Katherine E., Shook, Beth A., Kaestle, Frederika A., Chatters, James, Hackenberger, Steven, and Smith, David G. 2004 Patterns of mtDNA Diversity in Northwestern North America. Human Biology 76(1):3354.
Matsuoka, Yoshihiro, Vigouroux, Yves, Goodman, Major M., Jesus, Sanchez G, Buckler, Edward, and Doebley, John 2002 A Single Domestication for Maize Shown by Multi-locus Microsatellite Genotyping. Proceedings of the National Academy of Sciences of the United States of America 99(9):60806084.
Mawk, E. J., Hyman, M., and Rowe, M. W. 2002 Re-examination of Ancient DNA in Texas Rock Paintings. Journal of Archaeological Science 29:301306.
Merriwether, D. Andrew, Reed, David M., and Ferrell, Robert E. 1997 Ancient and Contemporary Mitochondrial DNA Variation in the Maya In Bones of the Maya. Studies of Ancient Skeletons, pp. 208217. Smithsonian Institution Press, Washington, D. C.
Merriwether, D. A., Rothhammer, F., and Ferrell, R. E. 1994 Genetic Variation in the New World: Ancient Teeth, Bone, and Tissue as Sources of DNA. Experientia 50(6):592601.
Merriwether, D. Andrew, Cabana, Gabriela S., and Reed, David R. 2000 Kennewick Man Ancient DNA Analysis: Final Report Submitted to the Department of the Interior, National Park Service. Electronic document, http://www.cr.nps.gov/aad/kennewick/merriwether_cabana.htm, accessed January 26, 2006.
Monsalve, M. V., Cardenas, F., Guhl, F., Delaney, A. D., and Devine, D. V. 1996 Phylogenetic Analysis of mtDNA Lineages in South American Mummies. Annals of Human Genetics 60 (Pt 4):293303.
Mulligan, Connie J. 2005 Isolation and Analysis of DNA from Archaeological, Clinical, and Natural History Specimens. Methods in Enzymology 395:87103.
Mullis, Kary B., and Faloona, F. A. 1987 Specific Synthesis of DNA in vitro via a Polymerase-Catalyzed Chain Reaction. Methods in Enzymology 155:335350.
Newman, Margaret E., Parboosingh, Jillian S., Bridge, Peter J., and Ceri, Howard 2002 Identification of Archaeological Animal Bone by PCR/DNA Analysis. Journal of Archaeological Science 29:7784.
O’Rourke, Dennis H., Carlyle, Shawn W., and Parr, Ryan L. 1996 Ancient DNA: Methods, Progress, and Perspectives. American Journal of Human Biology 8:557571.
Ovchinnikov, Igor V, Gotherstrom, Anders, Romanova, Galina P., Kharitonov, Vitaliy M., Liden, Kerstin, and Goodwin, William 2000 Molecular Analysis of Neanderthal DNA from the Northern Caucasus. Nature 404(6777):490493.
Paabo, Svante, Gifford, John A., and Wilson, Allan C. 1988 Mitochondrial DNA Sequences from a 7000-Year Old Brain. Nucleic Acids Research 16(20):97759787.
Paabo, Svante, Poinar, Hendrik, Serre, David, Jaenicke-Despres, Viviane, Hebler, Juliane, Rohland, Nadin, Kuch, Melanie, Johannes, Krause, Vigilant, Linda, and Hofreiter, Michael 2004 Genetic Analyses from Ancient DNA. Annual Review of Genetics 38:645679.
Parr, Ryan L., Carlyle, Shawn W., and O’Rourke, Dennis H. 1996 Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake Wetlands. American Journal of Physical Anthropology 99(4):507518.
Piperno, D. R., and Flannery, K. V. 2001 The Earliest Archaeological Maize (Zea mays L.) from Highland Mexico: New Accelerator Mass Spectrometry Dates and Their Implications. Proceedings of the National Academy of Sciences of the United States of America 98:21012103.
Poinar, Hendrik N., Hofreiter, Michael, Geoffrey Spaulding, W., Martin, Paul S., Artur Stankiewicz, B., Bland, Helen, Evershed, Richard P., Possnert, Goran, and Paabo, Svante 1998 Molecular Coproscopy: Dung and Diet of the Extinct Ground Sloth Nothrotheriops shastensis . Science 281(5375):402406.
Poinar, Hendrik N., Hoss, Matthias, Bada, Jeffrey L., and Paabo, Svante 1996 Amino Acid Racemization and the Preservation of Ancient DNA. Science 272(5263):864866.
Poinar, Hendrik N., Kuch, Melanie, Sobolik, Kristin D., Barnes, Ian, Stankiewicz, Artur B., Kuder, Tomasz, Geofferey Spaulding, W., Bryant, Vaughn M., Cooper, Alan, and Paabo, Svante 2001 A Molecular Analysis of Dietary Diversity for Three Archaic Native Americans. Proceedings of the National Academy of Sciences of the United States of America 98(8):43171322.
Reese, R. L., Hyman, M., Rowe, M. W., Derr, J. N., and Davis, S. K. 1996 Ancient DNA from Texas Pictographs. Journal of Archaeological Science 23:269277.
Richards, M. B., Sykes, B. C., and Hedges, R. E. M. 1995 Authenticating DNA Extracted from Ancient Skeletal Remains. Journal of Archaeological Science 22:291299.
Salo, Wilmar L., Aufderheide, Arthur C., Buikstra, Jane, and Holcomb, Todd A. 1994 Identification of Mycobacterium tuberculosis DNA in a Pre-Columbian Peruvian Mummy. Proceedings of the National Academy of Sciences of the United States of America 91(6):20912094.
Schmitz, Ralf W., Serre, David, Bonani, Georges, Feine, Susanne, Hillgruber, Felix, Krainitzki, Heike, Paabo, Svante, and Smith, Fred H. 2002 The Neandertal Type Site Revisited: Interdisciplinary Investigations of Skeletal Remains from the Neander Valley, Germany. Proceedings of the National Academy of Sciences of the United States of America 99:1334213347.
Schultes, Tobias, Hummel, Susanne, and Herrmann, Bernd 1999 Amplification of Y-chromosomal STRs from Ancient Skeletal Material. Human Genetics 104(2): 164166.
Serre, David, Langaney, Andre, Chech, Mario, Teschler-Nicola, Maria, Paunovic, Maja, Mennecier, Philippe, Hofreiter, Michael, Possnert, Goran, and Paabo, Svante 2004 No Evidence of Neandertal mtDNA Contribution to Early Modern Humans. PLoS (Public Library of Science) Biology 2(3):E57.
Shanks, Orin C, Bonnichsen, Robson, Vella, Anthony T., and Ream, Walt 2001 Recovery of Protein and DNA Trapped in Stone Tool Microcracks. Journal of Archaeological Science 28:965972.
Shanks, Orin C, Hodges, Larry, Tilley, Lucas, Kornfeld, Marcel, Larson, Mary L., and Ream, Walt 2005 DNA from Ancient Stone Tools and Bones Excavated at Bugas-Holding, Wyoming. Journal of Archaeological Science 32:2738.
Smith, David Glenn, Mahli, Ripan S., Eshleman, Jason A., and Kaestle, Frederika A. 2000 Report on DNA Analysis of the Remains of “Kennewick Man” from Columbia Park, Washington. Electronic document, http://www.cr.nps.gov/aad/kennewick/smith.htm, accessed January 26,2006.
Stone, Anne C., and Stoneking, Mark 1993 Ancient DNA from a Pre-Columbian Amerindian Population. American Journal of Physical Anthropology 92(4):463471.
Stone, Anne C. 1996 Genetic and Mortuary Analyses of a Prehistoric Native American Community. Pennslvania State University, University Park.
Stone, Anne C., and Stoneking, Mark 1999 Analysis of Ancient DNA from a Prehistoric Amerindian Cemetery. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 354(1379):153159.
Tuross, Noreen, and Kolman, Connie J. 2000 Potential for DNA Testing of the Human Remains from Columbia Park, Kennewick, Washington. Electronic document, http://www.cr.nps.gov/aad/kennewick/tuross_kolman.htm, accessed January 26, 2006.
Wang, Rong-Lin, Stec, Adrian, Hey, Jody, Lukens, Lewis, and Doebley, John 1999 The Limits of Selection during Maize Domestication. Nature 398(6724):236239.
Whitt, Sherry R., Wilson, Larissa M., Tenaillon, Maud I., Gaut, Brandon S., and Buckler, Edward S. IV 2002 Genetic Diversity and Selection in the Maize Starch Pathway. Proceedings of the National Academy of Sciences of the United States of America 99:1295912962.
Willerslev, Eske, Hansen, Anders J., Binladen, Jonas, Brand, Tina B., Gilbert, M. Thomas P., Shapiro, Beth, Bunce, Michael, Wiuf, Carsten, Gilichinsky, David A., and Cooper, Alan 2003 Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments. Science 300(5620):791795.
Woodward, Scott R., Weyand, Nathan J., and Bunnell, Mark 1994 DNA Sequence from Cretaceous Period Bone Fragments. Science 266(5188):12291232.
Yang, Dongya Y., Woiderski, Joshua R., and Driver, Jonathan C. 2005 DNA Analysis of Archaeological Rabbit Remains from the American Southwest. Journal of Archaeological Science 32:567578.
Zischler, H., Hoss, M., Handt, O., von Haeseler, A., van der Kuyl, A. C., Goudsmit, J. and Paabo, S. 1995 Detecting Dinosaur DNA. Science 268(5214): 11921193; author reply 1194.
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