Ancient DNA

by

Michael Hofreiter

• LAST REVIEWED: 13 January 2014
• LAST MODIFIED: 13 January 2014
• DOI: 10.1093/obo/9780199941728-0036

Introduction

It is generally accepted that research on ancient deoxyribonucleic acid (DNA) started in 1984, with the publication of the seminal paper Higuchi, et al. 1984 (cited under Historically Important Publications), on DNA sequences obtained from a skin sample of the quagga, an extinct population of the plains zebra (Equus quagga). Strictly speaking, “ancient DNA” does not represent a research field, but rather a technical approach: the analysis of damaged and fragmented DNA from samples that have been exposed to the environment for a certain amount of time. There are no clear parameters indicating from which age onward DNA should be referred to as ancient DNA. Although Higuchi, et al. 1984 (cited under Historically Important Publications) is typically viewed as marking the beginning of research on ancient DNA, the term ancient DNA is used more restrictively in the early 21st century and is applied only to DNA obtained from archaeological and paleontological specimens. As such, the study of ancient DNA is differentiated from forensic DNA analyses dealing with samples up to a few decades old and also from the analysis of museum specimens that can be as old as approximately two hundred years and that were alive prior to collection (such as the quagga specimens). While there is no strict age limit as to when a sample can be considered ancient DNA, and although the challenges and problems in ancient DNA research (i.e., small amounts of damaged and fragmented DNA, in combination with often high background contamination from bacterial DNA) are similar to those of forensic or museum specimen DNA, in order to restrict the scope of this article, except for a few classical papers, the works cited are limited to “true” ancient DNA publications and therefore mostly do not include publications that deal with forensic or museum specimen DNA. Owing to its very nature (i.e., the amplification and analysis of minute amounts of fragmented and damaged DNA), research on ancient DNA is prone to false-positive results. This problem hit the field especially during the early application of polymerase chain reaction (PCR) amplification, when researchers did not have any knowledge of how easily results could be affected by amplification of contaminating modern DNA. For this reason, there are a considerable number of studies that have later been shown to be based on flawed results. These studies (with one exception) are not included here, but some studies that have shed light on what can go wrong in ancient DNA analyses are listed. Studies using ancient DNA have provided insights into many areas of research. In phylogenetic studies these insights are mostly restricted to the extinct species investigated and its close relatives. Other research areas, such as studies on DNA damage in ancient DNA, are restricted to the field of ancient DNA itself. However, there are also research areas in ancient DNA that have more general understandings. Thus, ancient DNA studies not only resulted in the discovery of a new extinct human taxon, the Denisovans, but also gave evidence for gene flow from archaic human populations, such as the Denisovans and Neanderthals, into the modern human gene pool, radically changing the generally accepted scenario for modern human evolution. Ancient DNA analyses have also been key in advancing our understanding of more recent human history, for example, by disproving the long accepted theory that Clovis people were the first Americans. Other important general insights come from animal population studies, in which ancient DNA analyses showed that populations are genetically much more dynamic units than what was assumed based on studies using modern DNA alone, and from studies using ancient sediment DNA, which have contributed to a greater knowledge of past environments.

General Overviews

There are a number of review articles on ancient DNA, but, owing to the broad scope of the field, many of these deal with specific topics within the field. However, there are several wide-ranging articles and some that attempt to cover the research field in its breadth. General, more recent overviews are provided in Hofreiter, et al. 2001 and Pääbo, et al. 2004, whereas Pääbo, et al. 1989 and Brown and Brown 1992 offer early overviews. The other publications listed here deal with more specific aspects. Thus, Stoneking and Krause 2011 discusses both modern and ancient human genomes. Ho and Shapiro 2011 presents an overview of methods for analyzing ancient population genetics data, and Palmer, et al. 2012 gives a comprehensive overview of the work done with plant ancient DNA. Maybe more surprising, there is no comprehensive book on the topic. Therefore, this bibliography is almost entirely based on scientific journal papers, which also reflects the rapid developments of the field, especially in the early 21st century. However, the edited volume Shapiro and Hofreiter 2012 covers the technical aspects of the field, including case studies for a number of the methodologies covered.

• Brown, T. A., and K. A. Brown. 1992. Ancient DNA and the archaeologist. Antiquity 66:10–23.

  An early guide for the use of ancient DNA analyses with archaeological samples.

• Hofreiter, M., D. Serre, H. N. Poinar, M. Kuch, and S. Pääbo. 2001. Ancient DNA. Nature Reviews Genetics 2.5: 353–359.

  DOI: 10.1038/35072071

  A comprehensive overview of the field at the time.

• Ho, S. Y. W., and B. Shapiro. 2011. Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources 11.3: 423–434.

  DOI: 10.1111/j.1755-0998.2011.02988.x

  This article describes Bayesian skyline-plot methods for DNA sequence analyses, including heterochronous (originating from different points in time) sequence datasets, in a comprehensive and, at the same time, accessible way.

• Pääbo, S., H. Poinar, D. Serre, et al. 2004. Genetic analyses from ancient DNA. Annual Review of Genetics 38:645–679.

  DOI: 10.1146/annurev.genet.37.110801.143214

  An update and substantial extension of Hofreiter, et al. 2001, representing probably still the most comprehensive overview of the field.

• Pääbo, S., G. Russell, R. G. Higuchi, and A. C. Wilson. 1989. Ancient DNA and the polymerase chain reaction–the emerging field of molecular archaeology. Journal of Biological Chemistry 264.17: 9709–9712.

  An early overview of the emerging field, published soon after the first studies applying polymerase chain reaction (PCR) amplification to ancient DNA.

• Palmer, S. A, O. Smith, and R. G. Allaby. 2012. The blossoming of plant archaeogenetics. In Special issue: Ancient DNA. Edited by Michael Hofreiter. Annals of Anatomy 194.1: 146–156.

  DOI: 10.1016/j.aanat.2011.03.012

  A review of ancient DNA analyses using plant specimens. The article is especially noteworthy, as it includes a complete literature list on plant ancient DNA studies published through the end of 2010.

• Shapiro, B., and M. Hofreiter, eds. 2012. Ancient DNA: Methods and protocols. Methods in Molecular Biology. New York: Humana.

  DOI: 10.1007/978-1-61779-516-9

  This edited volume summarizes the state of the art with regard to ancient DNA methodology, from DNA extraction to sequence dataset analyses.

• Stoneking, M., and J. Krause. 2011. Learning about human population history from ancient and modern genomes. Nature Reviews Genetics 12.9: 603–614.

  DOI: 10.1038/nrg3029

  A review on the use of human genome sequences for inferring human evolution, including the analysis of ancient human DNA sequences and genomes.