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Palaeogenomic inference of biodiversity dynamics across Quaternary timescales

Nature Reviews Biodiversity volume 1, pages 233–247 (2025)Cite this article

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Abstract

Biodiversity is essential for the resilience and stability of life, yet it is highly dynamic and has continuously evolved throughout Earth’s history. The biodiversity concept encompasses three hierarchical levels of equal importance to fundamental ecological processes: diversity at the ecosystem, species and genetic levels. The current biodiversity crisis calls for an urgent need to understand the causes and consequences of widespread diversity losses at all three levels. Breakthroughs in palaeogenomics have increased the ecological and temporal scales on which we can use genomic information to study past biodiversity, reaching as far back as the Early Pleistocene. In this Review, we explore the possibilities and limitations of using palaeogenomics for studying all aspects of biodiversity. We explore how incorporating palaeogenomics into biodiversity research can provide clues about ecosystem composition, trophic interactions, species distributions, adaptation, evolution and extinction through time, in response to natural processes and as a consequence of human impact. We report how palaeogenomics can be applied to address a wide range of topics across all three hierarchical levels of biodiversity, and we show how advances within the field are making palaeogenomics an invaluable tool for understanding past and present declines in biodiversity, and in helping to predict future losses.

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Fig. 1: Temperature trends and key biodiversity events from the Quaternary accessible using palaeogenomics.
Fig. 2: Palaeogenomic insights across the biodiversity hierarchy.
Fig. 3: Simplified overview of common ancient DNA methods for investigating biodiversity.
Fig. 4: Challenges of studying ecosystem biodiversity with ancient DNA.
Fig. 5: Ancient environmental DNA records of human disturbance in sediment cores from Lake Ljøgottjern, Norway.
Fig. 6: Ancient DNA reveals genetic turnover in the collared lemming during the Late Quaternary.

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Acknowledgements

S. Boessenkool acknowledges support from the Research Council of Norway (grant 314464). The authors thank S. Nylin and K. Norén, as well as the students in course BL7075 at Stockholm University for providing feedback on earlier versions of the manuscript.

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Authors and Affiliations

  1. Centre for Palaeogenetics, Stockholm, Sweden

    Amanda Lindahl, Peter D. Heintzman, Love Dalén & David Díez del Molino

  2. Department of Zoology, Stockholm University, Stockholm, Sweden

    Amanda Lindahl, Love Dalén & David Díez del Molino

  3. Department of Biology, University of Konstanz, Konstanz, Germany

    Laura S. Epp

  4. Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway

    Sanne Boessenkool

  5. Centre for Ancient Environmental Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark

    Mikkel Winther Pedersen

  6. Natural History Museum, London, UK

    Selina Brace

  7. Department of Geological Sciences, Stockholm University, Stockholm, Sweden

    Peter D. Heintzman

  8. Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden

    Love Dalén & David Díez del Molino

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  1. Amanda Lindahl
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  2. Laura S. Epp
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  3. Sanne Boessenkool
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Contributions

L.D., A.L., D.D.d.M. and P.D.H. conceived the review and A.L. wrote the first draft. All authors contributed to discussion of the content, conceptualized the figures, substantially reviewed and edited the manuscript before submission, and approved the final manuscript.

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Correspondence to Amanda Lindahl or David Díez del Molino.

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Nature Reviews Biodiversity thanks Tyler Murchie and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

Convention on Biological Diversity: http://www.cbd.int/

Earth BioGenome Project: https://www.earthbiogenome.org/

The Intergovernmental Panel on Climate Change: https://www.ipcc.ch/

Glossary

Baits

Baits or probes for target enrichment are made of short biotinylated single-stranded DNA or RNA molecules that bind to DNA fragments from specific genomic regions, which are then separated from the remaining non-target DNA molecules.

Bulk bone

A collection of morphologically unidentifiable bone fragments collected from a single stratigraphic layer in a cave, for example.

Endogenous DNA

The fraction of DNA in a sample that derives from the organism(s) under study.

Exogenous DNA

The fraction of DNA in a sample that derives from organisms other than the one(s) under study; this can be introduced by the environment in which the sample is preserved, during handling of the sample, or by laboratory preparations.

Glacial periods

Intervals of time characterized by cold temperatures, the formation of extensive continental ice sheets and reduced sea levels.

Glacial refugia

Geographical areas with warmer climates that provide suitable living conditions for warm-adapted species during glacial periods.

Interglacial periods

Intervals of time between glacial periods characterized by warm temperatures, retreated ice sheets and sea levels comparable to those of today.

Palaeogenomics

The genome-wide analysis of DNA from ancient organisms.

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Lindahl, A., Epp, L.S., Boessenkool, S. et al. Palaeogenomic inference of biodiversity dynamics across Quaternary timescales. Nat. Rev. Biodivers. 1, 233–247 (2025). https://doi.org/10.1038/s44358-025-00033-0

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