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Ancient DNA

Key Points

  • DNA-sequence information can, in principle, be retrieved from archaeological and palaeontological remains that are less than 100,000 years old.

  • In most circumstances, only multicopy DNA, such as mitochondrial DNA (mtDNA) and chloroplast DNA, can be retrieved.

  • Extensive control experiments are necessary to ensure that results are not caused by contamination with modern or recent DNA.

  • Human remains are particularly difficult to work with because human DNA is almost ubiquitously present on old specimens and laboratory equipment.

  • Owing to the technical difficulties, not all published results in the field are reliable.

  • Using the techniques for ancient DNA retrieval, zoological and botanical museum collections from the past two centuries are important repositories of molecular genetic information.

  • The biological relationships and history of many Ice Age animals have been clarified using ancient DNA.

  • The mtDNA of Neanderthals has been shown not to be present among contemporary humans.

  • Coprolites represent a source of genetic information about animals and their diet that is often more reliable than bones from the same time period.

  • Cold environments are particularly conducive to DNA preservation.

  • Population studies of extinct animals, plants and Neanderthals are becoming possible.

Abstract

DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied.

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Figure 1: DNA damage shown or likely to affect ancient DNA.
Figure 2: Alignment of eight mitochondrial DNA clones sequenced from a single amplification from a 26,000-year-old cave-bear bone.
Figure 3: Some extinct organisms from which DNA sequences have been determined.
Figure 4: Schematic phylogenetic tree.
Figure 5: 20,000-year-old ground sloth coprolite.

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Acknowledgements

We thank Qin Zhan-Xiang for providing the cave bear samples; and the Max Planck Society, the Deutsche Forschungsgemeinschaft and the Bundesministerium für Bildung und Forschung for financial support.

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DATABASE LINKS

gas chromatography and mass spectrometry

Miocene

Pleistocene

quagga

marsupial wolf

sabre-toothed cat

moa

mammoth

cave bear

blue antelope

giant ground sloths

mastodon

Steller's sea cow

Neanderthal

bandicoots

Myotragus balearicus

Glossary

COPROLITES

Faecal material from humans and animals found at archaeological excavations.

HYDANTOINS

Oxidation products of the pyrimidine bases (cytosine and thymine).

PLEISTOCENE

The geological time period from two million to 10,000 years ago.

RACEMIZATION

The change in the three-dimensional structure of amino acids from one form to a mirror image over time.

PYROLYSIS GC/MS

An analysis in which macromolecules are decomposed by heat, and the products analysed by gas chromatography followed by mass spectrometry.

MICROSATELLITES

A class of repetitive DNA that is made up of repeats that are 2–8 nucleotides in length. They can be highly polymorphic and are frequently used as molecular markers in population genetics studies.

COMPETITIVE AND REAL-TIME QUANTITATIVE PCR

A PCR analysis in which the approximate number of molecules that initiate the reaction is measured either by competition with a template of known concentration or by accumulation of product throughout the PCR.

DIAGENESIS

All physical, chemical and biological changes undergone by any material from the time of its initial deposition in the environment.

CRETACEOUS

The geological time period from 144 to 65 million years ago.

DIACHRONICAL

A continuous process over time rather than a process at one time point (synchronical).

PERMAFROST

A layer below the surface soil that never thaws in subarctic regions.

NEANDERTHAL

A hominid form, morphologically distinct from contemporary humans, that existed until 30,000 years ago in Europe and western Asia.

COALESCENCE

The joining of genetic lineages to common ancestors when they are traced backwards in time.

SCATS

Faecal material left behind by animals.

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Hofreiter, M., Serre, D., Poinar, H. et al. Ancient DNA. Nat Rev Genet 2, 353–359 (2001). https://doi.org/10.1038/35072071

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