PhD defence by Christina Islas Lynggaard

Assessment committee
Professor Hugo de Boer, University of Oslo
Professor Sebastien Calvignac-Spencer, Robert Koch-Institut Berlin
Assoc. professor Tobias Frøslev, UCPH

Kristine Bohmann
Tom Gilbert

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Thesis title: Using amplicon sequencing to study nested biodiversity

Thesis short abstract:
We live on a highly biodiverse planet. Traditional methods to study biodiversity rely on direct visual observation, in the case of macroorganisms, and on isolation and plate cultivation in the case of bacteria. Taxonomic expertise on each of these groups is needed and having to identify a great number of organisms can be time-consuming. Historically, the amplification of genetic barcodes by polymerase chain reaction (PCR) improved the way we study biodiversity and accelerated the rate at which these studies were made. Nevertheless, this method relied on Sanger sequencing and it was still costly and time-consuming if needing to work with taxonomically complex samples.

DNA metabarcoding (also known as amplicon sequencing) has been an important new milestone for biodiversity studies. This method, still relying on PCR, uses uniquely 5’ tagged primers to amplify DNA from target taxa. The advantage of this method is parallel sequencing of thousands of samples at a time. This molecular tool has improved the characterisation of biological networks and therefore our understanding of biodiversity. It is now possible to not only obtain information of what we see in the sample, but also about the biodiversity of what is surrounding these samples and the microorganisms within them.

In this thesis, I explore the use of amplicon sequencing to study different levels of biodiversity: the taxonomic content of highly diverse samples such as bulk arthropod samples, the vertebrates which these arthropods have been in contact with and the bacteria found in the crop of blood feeding leeches.