Genetic analyses from ancient DNA
Open accessAbstract
About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.
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aDNA damage results in C-to-T and G-to-A substitutions.
“This therefore results in a pattern of C-to-T substitutions. When a double-stranded library preparation is used, these substitutions can occur on the opposite strand thus resulting in G-to-A substitutions due to base complementarity.”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [1]
aDNA is typically fragmented due to post-mortem enzymatic processes.
“much of the DNA will typically have been degraded (i.e. fragmented) due to post-mortem enzymatic processes.”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [1]
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Percentages, sums and reported differences re-computed from the paper’s own numbers.
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Carbon-based archiving: current progress and future prospects of DNA-based data storage.
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Moreno-Mayar, J. V., Korneliussen, T. S., Dalal, J., Renaud, G., Albrechtsen, A., Nielsen, R., & Malaspinas, A.-S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz660 · Cited by 21 · see citing works
Ancient DNA Extracted from Danish Aurochs (Bos Primigenius): Genetic Diversity and Preservation
Gravlund, P., Aaris-Sørensen, K., Hofreiter, M., Meyer, M., Bollback, J. P., & Noe-Nygaard, N. (2012) · Annals of Anatomy - Anatomischer Anzeiger · doi:10.1016/j.aanat.2011.10.011 · Cited by 19 · see citing works
Self-citation<tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings
Rubin, J., van Waaij, J., Kraft, L., Sirén, J., Sackett, P. W., & Renaud, G. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf170 · Cited by 1 · see citing works
“The most characteristic hallmark of aDNA, however, re-sults from the hydrolytic cleavage of amino groups from certain nucleobases resulting from long-term exposure to moisture and is known as deamination [ 1 , 4 , 5 ].”
- Authors
- Pääbo, S., Poinar, H., Serre, D., Jaenicke-Després, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L., & Hofreiter, M.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- ORCID
- Venue
- Annual Review of Genetics
- Publisher
- Annual Reviews
- Published
- 2004-12-01
- Volume
- 38
- Issue
- 1
- Pages
- 645-679
- ISSN
- 0066-4197 (ISSN-L)
- 1545-2948
- OpenAlex
- W2101294025
- Cited by
- 1,333
- References
- 176
- Citations by year
- 2026: 34 · 2025: 51 · 2024: 38 · 2023: 39 · 2022: 46 · 2021: 56 · 2020: 57 · 2019: 60 · 2018: 116 · 2017: 60 · 2016: 84 · 2015: 73 · 2014: 77 · 2013: 72 · 2012: 64
- FWCI
- 4.71
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Annual Review of Genetics (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Social Sciences › Arts and Humanities › Archeology › Paleopathology and ancient diseases
- Keywords
- ancient DNA, museum specimens, archaeological finds, fossils, quagga
- MeSH terms
- Animals, Animals, Domestic, Archaeology, Behavior, Cloning, Molecular, Deamination, Diet, DNA, DNA Damage, DNA, Mitochondrial, Fossils, Humans, Mummies, Phylogeny, Hominidae, Sequence Analysis, DNA, Geologic Sediments
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