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Evolutionary genetics

The genesis of paleogenetics

Nature Reviews Genetics volume 26, page 297 (2025)Cite this article

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Evolutionary genetics is a historical science that has typically relied on inferring the past through modern day genomes. These historical processes could be studied more directly by sequencing ‘ancient DNA’ (from historical or preserved specimens), but for a long time it was unclear whether this DNA was too degraded to work with. In the November 1984 issue of Nature, a team of scientists from the University of California Berkeley were among the first to report the retrieval of ancient DNA sequences from a historical specimen, a 140-year-old quagga stored at the Museum of Natural History in Mainz, Germany. Quagga were a species of zebra — with zebra-like stripes towards the front but more horse-like features towards the rear — that were endemic to South Africa and went extinct circa 1883 because of overhunting.

To sequence the ancient quagga DNA, the authors first cloned it all into phage vectors, which enabled them to screen for mitochondrial DNA (mtDNA) based on hybridization with radioactively labelled mtDNA from the related extant zebra. The authors targeted mtDNA because, in contrast to nuclear DNA, it has a higher copy number in cells and therefore was thought more likely to be recovered. Indeed, Sanger sequencing was successful on 229 bp of the ancient quagga mtDNA, which differed at only 12 locations from the related region in zebra mtDNA and mostly by synonymous mutations and transitions, suggesting a close genetic relationship. With this new information, the authors dated the mtDNA divergence times between the quagga and zebra to 3–4 million years and between their common ancestor (odd-toed ungulates) and cow (even-toed ungulates) to 55–60 million years. Their investigation raised further questions as to the phylogenetic position of the quagga, which have since been addressed using additional mtDNA and genome-wide markers from more zebra species.

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References

Original article

  • Higuchi, R. et al. DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282–284 (1984)

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Related article

  • Schmeck, H. M. Jr. Scientists clone bits of genes taken from extinct animal. The New York Times (5 June 1984)

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Authors and Affiliations

  1. Department of Human Genetics & Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA

    Maanasa Raghavan

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  1. Maanasa Raghavan
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Correspondence to Maanasa Raghavan.

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The author declares no competing interests.

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Raghavan, M. The genesis of paleogenetics. Nat Rev Genet 26, 297 (2025). https://doi.org/10.1038/s41576-025-00835-0

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