Reconstructing past environments using ancient environmental DNA (eDNA) in the Paleo Environmental Genomics Group

Led by Mikkel Winther Pedersen, the Paleo Environmental Genomics Group (PEGG) focus is to use shotgun sequenced ancient DNA and DNA metabarcoding. The aim is to reconstruct past environments in order to address scientific questions concerning the interaction between past humans – environments – climatic changes and their effect on species distribution, speciation, evolution, population structure and community compositions.

Mikkel W. Pedersen and others in the field collecting samples.

Research focus

We operate across a range of research fields including geology, archaeology, biology and geography where we extract and analyse ancient DNA data to answer questions about the past. The different projects currently cover 5 different continents, Africa, North America, South America, Europe and Asia, and includes reconstruction of past environments, speciation, and human activities.

“Being part of developing this new research field – it is important to constantly explore and evolve the boundaries of the method – while still addressing important scientific question. We are therefore constantly working on improving and expanding its possibilities in both the laboratory and computational”, says Mikkel Winther Pedersen, group leader.

Key publications

Zampirolo, G., Ruter, A., Živaljević, I., Penezić, K., Thomsen, P. F., Orton, D., Kašanin Grubin, M., Antić, N., & Pedersen, M. W. (2025). Ancient DNA reconstruction of late holocene ecosystems within the Carpathian basin from paleo-meanders and archaeological deposits. Scientific Reports 16(4301).

Ngoepe, N., Mwaiko, S., Kishe, M. A., Wienhues, G., Temoltzin-Loranca, Y., King, L., Courtney Mustaphi, C., Grosjean, M., Tinner, W., Matthews, B., Vogel, H., Heiri, O., Jemmi, E., Lürig, M., Pedersen, M. W., Seehausen, O., & Muschick, M. (2025). Fossil evidence for trait diversification in an adaptive radiation. Scientific Reports 15(38824).

Holman, L. E., Bohmann, K., Craig, O. E., Orton, D., Pedersen, M. W., Olsen, M. T., Thurstan, R. H., & Scourse, J. (2025). Shifting seas: understanding deep-time human impacts on marine ecosystems. Philosophical Transactions of the Royal Society B, 380(1930), 20240026.

Lindahl, A., Epp, L. S., Boessenkool, S., Pedersen, M. W., Brace, S., Heintzman, P. D., Dalén, L., & Díez del Molino, D. (2025). Palaeogenomic inference of biodiversity dynamics across Quaternary timescales. Nature Reviews Biodiversity.

Zampirolo, G., McCarthy, M. L., Živaljević, I., Penezić, K., Vuković, S., Mladenović, T., Marković, D., Marković, N., Radmanović, D., Orton, D., Olsen, M. T., & Pedersen, M. W. (2025). Continuous mitochondrial diversity of Danube sturgeon species over millennia: insights from ancient DNA. Philosophical Transactions of the Royal Society B, 380(1930).

Holman, L., Zampirolo, G., Gyllencreutz, R., Scourse, J., Frøslev, T., Carøe, C., Gopalakrishnan, S., Pedersen, M. W., & Bohmann, K. (2025). Navigating past oceans: comparing metabarcoding and metagenomics of marine ancient sediment environmental DNA. Molecular Ecology Resources, e14086.

Full list of publications by Mikkel Winther Pedersen.