Skip to main content

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
Cancel
×
×
Home
  • Home
Chapter
  • Print publication year: 2006
  • Online publication date: June 2012

Chapter 8 - Ancient DNA and its Application to the Reconstruction of Human Evolution and History

Export citation
Summary

Introduction

The use of ancient nucleic acids to infer population history and phylogeny is now entering its third decade, with the initial demonstration of the possibility and utility of the approach pioneered by Higuchi et al. (1984) on museum specimens of the extinct quagga, and by Pääbo (1985) on preserved soft tissue from Egyptian mummies. Now uniformly termed ancient DNA (aDNA) studies, the approach has exploded in the past decade to encompass studies of modern human origins, regional history and dynamics of prehistoric human populations, as well as phylogenetic studies of nonhuman organisms. A full review of this vast and rapidly growing literature is beyond the scope of this chapter, and interested readers are directed to several excellent and recent reviews of the field from a variety of disciplinary perspectives (e.g. Wayne et al., 1999; O'Rourke et al., 2000a; Hofreiter et al., 2001a; Kaestle and Horsburgh, 2002, Pääbo et al., 2004, Cipollaro et al., 2005).

The study of contemporary patterns of human genetic variation has proven a powerful approach to inferring human population history and evolution, although such approaches are bound by assumptions of evolutionary rates in the markers under study, effective population sizes over time, rates of population movement, levels of admixture, etc. The use of aDNA analyses in conjunction with such modern genetic studies affords a temporal perspective on human genetic variation that is, to some degree, independent of model assumptions.

Recommend this book

Email your librarian or administrator to recommend adding this book to your organisation's collection.

Anthropological Genetics
  • Online ISBN: 9781139167222
  • Book DOI: https://doi.org/10.1017/CBO9781139167222
Please enter your name
Please enter a valid email address
Who would you like to send this to *

CAPTCHA *

Skip to the audio challenge
×
References
Adachi, N., Umetsu, K., Takigawa, W. and Sakaue, K. (2004). Phylogenetic analysis of the human ancient mitochondrial DNA. J. Archaeol. Sci., 31, 1339–48
Anderson, S., Bankier, A., Arrell, B., Bruijn, M., Coulson, A., Drouin, J., Eperon, I., Nierlich, D., Roe, B., Sanger, F., Schreier, P., Smith, A., Staden, R. and Young, I. (1981). Sequence and organization of the human mitochondrial genome. Nature, 290, 457–65
Arriaza, B. T., Salo, W., Auferheide, A. C. and Holcomb, T. A. (1995). Pre-Columbian tuberculosis in Northern Chile – molecular and skeletal evidence. Amer. J. Phys. Anthropol., 98, 37–45
Barnes, I., Matheus, P., Shapiro, B., Jensen, D. and Cooper, A. (2002). Dynamics of Pleistocene population extinctions in Beringian brown bears. Science, 295, 2267–70
Basler, C. F., Reid, A. H., Dybing, J. K., Janczewski, T. A., Fanning, T. G., Zheng, H., Salvatore, M., Perdue, M. L., Swayne, D. E., García-Sastre, A., Palese, P. and Taubenberger, J. K. (2001). Sequence of the 1918 pandemic influenza virus nonstructural gene (SN) segment and characterization of recombinant viruses bearing the 1918 NS genes. PNAS, 98, 2746–51
Batista dos Santos, S. E., Rodrigues, J. D., Ribeiro-Dos-Santos, A. K. C. and Zago, M. A. (1999). Differential contribution of indigenous men and women to the formation of an urban population in the Amazon Region as revealed by mtDNA and Y-DNA. Amer. J. Phys. Anthrop., 109, 175–80
Bosch, E., Calafell, F., Rosser, Z. H., Norby, S., Lynnerup, N., Hurles, M. E. and Jobling, M. A. (2003). High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis. Hum. Genet., 112, 353–63
Bouwman, A. S. and Brown, T. A. (2005). The limits of biomolecular paleopathology: ancient DNA cannot be used to study venereal syphilis. J. Archaeol. Sci., 32, 703–13
Caramelli, D., Lalueza-Fox, C., Vernesi, C., Lari, M., Casoli, A., Mallegni, F., Chiarelli, B., Dupanloup, I., Bertranpetit, J., Barbujani, G. and Bertorelle, G. (2003). Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. PNAS, 100, 6593–97
Cipollaro, M., Galderisi, U. and DiBernardo, G. (2005). Ancient DNA as a multidisciplinary experience. J. Cell Physiol., 202, 315–22
Coltrain, J. B., Hayes, M. G. and O'Rourke, D. H. (2004). Sealing, whaling and caribou: the skeletal isotope chemistry of Eastern Arctic foragers. J. Arch. Sci., 31, 39–57
Coltrain, J. B., Hayes, M. G. and O'Rourke, D. H. (2006). A radiometric evaluation of Hrdlicka's Aleutian replacement hypothesis: population continuity and morphological change. Current Anthropology, in press.
Cooper, A. and Poinar, H. (2000). Ancient DNA: do it right or not at all. Science, 289, 1139.
Di Bernardo, G., Del Gaudio, S., Cammarota, M., Galderisi, U., Cascino, A. and Cipollaro, M. (2002). Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains. Nucleic Acids Res., 30, e16.
Donoghue, H. D., Spigelman, M., Zias, J., Gernaey-Child, A. M. and Minnikin, D. E. (1998). Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old. Let. Appl. Microbiol., 27, 265–9
Drancourt, M., Aboudharam, G., Signoli, M., Dutour, O. and Raoult, D. (1998). Detection of 400-year old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia. Proc. Natl. Acad. Sci., USA, 95, 12637–40
Eshleman, J. A. and Smith, D. G. (2001). Use of DNase to eliminate contamination in ancient DNA analysis. Electrophoresis, 22, 4316–19
Gilbert, M. T. P., Willerslev, E., Hansen, A. J., Barnes, I., Rudbeck, L., Lynnerup, N. and Cooper, A. (2003). Distribution patterns of postmortem damage in human mitochondrial DNA. Amer. J. Hum. Genet., 72, 32–47
Gilbert, M. T. P., Wilson, A. S., Bunce, M., Hansen, A. J., Willerslev, E., Shapiro, B., Higham, T. F. G., Richards, M. P., O'Connell, T. C., Tobin, D. J., Janaway, R. C. and Cooper, A. (2004a). Ancient mitochondrial DNA from hair. Curr. Biol., 14, R463–R464.
Gilbert, M. T. P., Cuccui, J., White, W., Lynnerup, N., Titball, R. W.et al. (2004b). Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims, Microbiol. Sgm., 150, 341–54
Gilbert, M. T. P., Rudbeck, L., Willerslev, E., Hansen, A. J., Smith, C., Penkman, K. E. H., Prangenberg, K., Nielsen-Marsh, C. M., Jans, M. E., Arthur, P., Lynnerup, N., Turner-Walker, G., Biddle, M., Kjølbye-Biddle, B. and Collins, M. J. (2005). Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera, Italy. J. Archaeol. Sci., 32, 785–93
Guhl, F., Jaramillo, C., Valleho, G. A., Yockteng, R., Cárdenas-Arroyo, F.et al. (1999). Isolation of Trypanosoma cruzi DNA in 4,000-year-old mummified human tissue from Northern Chile. Amer. J. Phys. Anthrop., 108, 401–07
Gutiérrez, G., Sánchez, D. and Marín, A. (2002). A reanalysis of the ancient mitochondrial DNA sequences recovered from Neandertal bones. Mol. Biol. Evol., 19, 1359–66
Handt, O., Höss, M., Krings, M. and Pääbo, S. (1994a). Ancient DNA: methodological challenges. Experientia, 50, 524–9
Handt, O., Richards, M., Trommsdorff, M., Kilger, C., Simanainen, J.et al. (1994b). Molecular genetic analyses of the Tyrolean ice man. Science, 264, 1175–8
Hänni, C., Brousseau, T., Laudet, V. and Stehelin, D. (1995). Isoproponaol precipitation removes PCR inhibitors from ancient bone extracts. Nucleic Acid Res., 23, 881–2
Hansen, A., Willerslev, E., Wiuf, C., Mourier, T. and Arctander, P. (2001). Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol., 18, 262–5
Hawkes, J., Hunley, K., Lee, S. H. and Wolpoff, M. (2000). Population bottlenecks and Pleistocene human evolution. Mol. Biol. Evol., 17, 2–22
Hayes, M. G. (2002). Paleogenetic Assessments of Human Migration and Population Replacement in North American Arctic Prehistory. Ph.D. Dissertation, University of Utah.
Hayes, M. G, Coltrain, J. B.and, D. H. (2006). Genetic signature of human population replacement coincident with paleoclimatic change in the North American Arctic. Submitted.
Higuchi, R., Bowman, B., Freiberger, M., Ryder, O. A. and Wilson, A. C. (1984). DNA sequences from the quagga, an extinct member of the horse family. Nature, 312, 282–4
Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M. and Pääbo, S. (2001a). Ancient DNA. Nature Rev. Genet., 2, 353–9
Hofreiter, M., Jaenicke, V., Serre, D., Haeseler, A. and Pääbo, S. (2001b). DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res., 29, 4793–9
Höss, M., Jaruga, P., Zastawny, T., Dizdaroglu, M. and Pääbo, S. (1996). DNA damage and DNA sequence retrieval from ancient tissue. Nucleic Acids Res., 24, 1304–7
Hrdlicka, A. (1945). The Aleutian and Commander Islands and Their Inhabitants. The Wistar Institute of Anatomy and Biology, Philadelphia.
Kaestle, F. A. and Horsburgh, K. A. (2002). Ancient DNA in anthropology: methods, applications and ethics. Yrbk Phys. Anthrop, 45, 92–130
Karanth, K. P., Delefosse, T., Rakotosamimanana, B., Parsons, T. J. and Yoder, A. D. (2005). Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates. PNAS, 102, 5090–5
Kiesslich, J., Radacher, M., Neuhuber, F., Meyer, H. J. and Zeller, K. W. (2002). On the use of nitrocellulose memberanes for dialysis-mediated purification of ancient DNA from human bone and teeth extracts. Ancient Biomol., 4, 79–87
Kolman, C. J., Centurion-Lara, A., Lukehart, S. A., Owsley, D. A. and Tuross, N. (1999). Identification of Treponema pallidum subspecies pallidum in a 200-year-old skeletal specimen. J. Infect. Dis., 180, 2060–3
Krings, M., Stone, A., Schmitz, R. W., Krainitzki, H, Stoneking, M. and Pääbo, S. (1997). Neandertal DNA sequences and the origin of modern humans. Cell, 90, 19–30
Krings, M., Geisert, H., Schmitz, R. W., Krainitzki, H. and Pääbo, S. (1999). DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. PNAS, 96, 5581–5
Krings, M., Capelli, C., Tschentscher, F., Geisert, H., Meyer, S.et al. (2000). A view of Neandertal genetic diversity. Nat. Genet., 26, 144–6
Lalueza-Fox, C., Sampietro, M. L., Caramelli, D., Puder, Y., Lari, M., Calafell, F., Martínez-Maza, C., Bastir, M., Fortea, J., Rasilla, M., Bertranpetit, J. and Rosas, A. (2005). Neandertal evolutionary genetics: mitochondrial DNA data from the Iberian peninsula. Mol. Biol. Evol., 22, 1077–81
Lambert, D. M., Ritchie, P. A., Miller, C. D., Holland, B., Drummond, A. J. and Baroni, C. (2002) Rates of evolution in ancient DNA from Adelie penguins. Science, 295, 2270–3
Lau, A., Wyuatt, M., Glassner, B., Samson, L. and Ellenberger, T. (2000). Molecular basis for discrimination between normal and damaged bases by the human alkyladenine glycosylase, AAG. PNAS, 97, 13575–8
Leonard, J. A., Wayne, R. K. and Cooper, A. (2000). Population genetics of Ice Age brown bears. Proc. Natl. Acad. Sci., USA, 97, 1651–4
Longo, M. C., Berninger, M. S. and Hartley, J. L. (1990). Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene, 93, 125–8
Matisoo-Smith, E., Roberts, R. M., Allen, J. S., Irwin, G. J., Penny, D. and Lambert, D. M. (1997). Patterns of human colonization in Polynesia revealed by mitochondrial DNA from the Polynesian rat. PNAS, 95, 15145–50
McCartney, A. P. (1984). Prehistory of the Aleutian Region. In Handbook of North American Indians, Vol. 5 The Arctic, ed. Damas, D.. Washington, DC: Smithsonian Institution, p. 119–35.
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, 1099–1102
Nordborg, M. (1998). On the probability of Neanderthal ancestry. Amer. J. Hum. Genet., 63, 1237–40
O'Rourke, D. H., Hayes, M. G. and Carlyle, S. W. (2000a). Ancient DNA studies in physical anthropology. Ann. Rev. Anthropology, 29, 217–42
O'Rourke, D. H., Hayes, M. G. and Carlyle, S. W. (2000b). Spatial and temporal stability of mtDNA haplogroup frequencies in Native North America. Hum. Biol., 72, 15–34
O'Rourke, D. H., M. G. Hayes and S. W. Carlyle (2005). The consent process and aDNA research: contrasting approaches in North America. In Biological Anthropology and Ethics, ed. Turner, T. R.. SUNY Press, Albany, pp. 231–40.
Ovchinnikov, I. V., Götherström, G., Romanova, G. P., Kharitonov, V. M., Lidén, K. and Goodwin, W. (2000). Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature, 404, 490–3
Pääbo, S. (1985). Preservation of DNA in ancient Egyptian mummies. J. Archaeol. Sci., 12, 411–17
Pääbo, S. (1989). Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. PNAS, 86, 1939–43
Pääbo, S., Poinar, H., Serre, D., Jaenicke-Després, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L. and Hofreiter, M. (2004). Genetic analyses from ancient DNA. Ann. Rev. Genet., 38, 645–79
Paxinos, E. E., James, H. F., Olson, S. L., Ballou, J. D., Leonard, J. A. and Fleischer, R. C. (2002). Prehistoric decline of genetic diversity in the Nene. Science, 296, 1827.
Poinar, H., Hofreiter, M., Spaulding, G., Martin, P., Stankiewicz, A., Bland, H., Evershed, R., Possnert, G. and Pääbo, S. (1998). Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science, 281, 402–6
Pusch, C., Giddings, I. and Scholz, M. (1998). Repair of degraded duplex DNA from prehistoric samples using Escherichia coli, DNA polymerase I and T4 DNA ligase. Nucleic Acids Res., 26, 857–9
Pruvost, M. and Geigl, E.-M. (2004). Real-time quantitative PCR to assess the authenticity of ancient DNA amplification. J. Archaeol. Sci., 31, 1191–7
Pruvost, M., Grange, T. and Geigl, E.-M. (2005). Minimizing DNA contamination by using UNG-coupled quantitative real-time PCR on degraded DNA samples: application to Ancient DNA studies. BioTechniques, 38, 569–75
Raoult, D., Aboudharam, G., Crubezy, E., Larrouy, G., Ludes, B. and Drancourt, M. (2000). Molecular identification by ‘suicide PCR’ of Yersinia pestis as the agent of Medieval Black Death. PNAS, 97, 12800–3
Reid, A. H., Fanning, T. G., Hultin, J. V. and Taubenberger, J. K. (1999). Origin and evolution of the 1918 ‘Spanish’ influenza virus hemagglutinin gene. PNAS, 96, 1651–6
Relethford, J. H. (2001). Absence of regional affinities of Neandertal DNA with living humans does not reject multiregional evolution. Amer. J. Phys. Anthrop., 115, 95–8
Rightmire, G. P. (2001). Patterns of hominid evolution and dispersal in the Middle Pleistocene. Quaternary Int., 75, 77–84
Ritchie, P. A., Millar, C. D., Gibb, G. C., Baroni, C. and Lambert, D. M. (2004). Ancient DNA enables timing of the Pleistocene origin and Holocene expansion of two Adelie penquin lineages in Antarctica. Mol. Biol. Evol., 21, 240–8
Rubicz, R., Schurr, T. G., Babb, P. L. and Crawford, M. H. (2003). Mitochondrial DNA variation and the origins of the Aleuts. Hum. Biol., 75, 809–35
Salo, W. L., Aufderheide, A. C., Buikstra, J. and Holcomb, T. A. (1994). Identification of Mycobacterium tuberculosis DNA in a Pre-Columbian Peruvian mummy. PNAS, 91, 2091–4
Savolainen, P., Leitner, T., Wilton, A. N., Matisoo-Smith, and Lundeberg, J. (2004). A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc. Natl. Acad. Sci., USA, 101, 12387–90
Schmitz, R. W., Serre, D., Bonani, G., Feine, S., Hillgruber, F.et al. (2002). The Neandertal sype site revisited: Interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. PNAS, 99, 13342–7
Serre, D., Langaney, A., Chech, M., Teschler-Nicola, M., Paunovic, M., Mennecier, P., Hofreiter, M., Possnert, G. and Pääbo, S. (2004). No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biology, 2, 313–17
Smith, S. E., Hayes, M. G., Coltrain, J. B. and O'Rourke, D. H. (2006). Inferring population continuity versus replacement with aDNA: a cautionary tale in the Aleutians. Amer. J. Phys. Anthrop., 129(S42), 167.
Spigelman, M. and Lemma, E. (1993). The use of the polymerase chain reaction to detect Mycobacterium tuberculosis in ancient skeletons. Int. J. Osteoarch., 3, 137–43
Stone, A. and Stoneking, M. (1998). mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. Amer. J. Hum. Genet., 62, 1153–70
Wall, J. (2000). Detecting ancient admixture in humans using sequence polymorphism data. Genetics, 154, 1271–9
Wayne, R. K., Leonard, J. A. and Cooper, A. (1999). Full of sound and fury: the recent story of ancient DNA. Ann. Rev. Ecol. Syst., 30, 457–77
Yang, D. Y., Cannon, A. and Saunders, S. R. (2004). DNA species identification of archaeological salmon bone from the Pacific Northwest Coast of North America. J. Archaeol. Sci., 31, 619–31
Yang, D. Y. and Watt, K. (2005). Contamination controls when preparing archaeological remains for ancient DNA analysis. J. Archaeol. Sci., 32, 331–6
Yang, D. Y., Woiderski, J. R. and Driver, J. C. (2005). DNA analysis of archaeological rabbit remains from the American Southwest. J. Archaeol. Sci., 32, 567–78
Yoder, A. D., B. Rakotosamimanana and T. J. Parsons (1999). Ancient DNA in subfossil lemurs: methodological chanllenges and their solutions. In New Directions in Lemur Studies, eds. Rakotosamimanana, B., et al. New York: Kluwer Academic/Plenum Press.
Zink, A. R., Grabner, W., Reischl, U., Wolf, H. and Nerlich, A. G. (2003). Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt. Epidemiol. Infect., 130, 239–49
Zlojutro, M., Rubicz, R., Devor, E. J., Spitsyn, V. A., Makarov, S. V., Wilson, K. and Crawford, M. H. (2006). Genetic structure of the Aleuts and circumpolar populations based on mitochondrial DNA sequences: a synthesis. Amer. J. Phys. Anthrop., 129, 446–64
Cancel
Confirm
×