PhD defence Philip Francis Thomsen – University of Copenhagen

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05 October 2012

PhD defence Philip Francis Thomsen


Monitoring Biodiversity using Environmental DNA

Time and place

Thursday 18 October 2012 at 9:15 in the Auditorium at The Geological Museum

The Natural History Museum of Denmark

Øster Voldgade 5-7, 1350 Copenhagen K


Professor Eske Willerslev, Natural History Museum of Denmark

Assessment committee

  • Professor Gitte Petersen, Natural History Museum of Denmark
  • Professor Pierre Taberlet, Univ. Joseph Fourier, Grenoble, France
  • Professor Mike Bruford, University of Cardiff, UK.


Most organisms will expel DNA in the surroundings that can be picked up in environmental samples. Within the last decade, the search and analyses of such Environmental DNA (eDNA) has developed to become a multidisciplinary research field. Recent advances in DNA sequencing technology have revolutionized this field opining new frontiers in ecology, evolution and environmental sciences. It has also become a powerful tool for field biologists providing new and efficient means for monitoring biodiversity.

This thesis focuses on the use of eDNA in monitoring of biodiversity in different settings. In freshwater, a diversity of rare animals – representing amphibians, fish, mammals, insects and crustaceans – are detected and quantified based on eDNA obtained from 15 ml water samples of lakes, ponds and streams. Furthermore, entire faunas of amphibians and fish are detected by next-generation sequencing of eDNA from pond water.

Application of the method in a marine setting shows that eDNA obtained from ½ l seawater samples can account for both marine fish and whale species. In both freshwater and seawater, eDNA seems to degrade beyond detectable levels within days or weeks.

In the terrestrial habitat, insect DNA is retrieved from thousands of years old permafrost-preserved macrofossils and temperate soil sediments. Furthermore, dried beetle specimens yield DNA after nearly 200 years in museum collections. Finally, examining DNA extracted from leeches collected in tropical rainforests reveals that this can account for biodiversity of terrestrial mammals, on which they have been feeding, and uncover poorly known, cryptic and threatened species. Mammalian DNA in leech guts is shown to persist for at least 4 months post feeding.