Congrats to Martina Weiss for the successful defence of her PhD thesis entitled “Investigating patterns and processes underlying cryptic diversity and small-scale population structure in hololimnic freshwater species”. The project was part of the “GeneStream” project funded by the Kurt Eberhard Bode Foundation.
Foto: Florian Leese, Martina Weiss und Steffen Pauls.
Congrats to Jan Macher for successfully defending his PhD thesis on the “Development, testing and application of DNA-based methods to study freshwater invertebrate biodiversity under stress”.
Examiner were Prof. Dr. Ralph Tollrian (Ruhr University of Bochum, Prof. Dr. Jens Boenigk and Prof. Dr. Florian Leese. Chair of the committee was Prof. Dr. Daniel Hering.Photo: PhD committee and candidate. F.r.t.l.: Daniel Hering, Jens Boenigk, Florian Leese, Jan Macher, Ralph Tollrian
Congrats to Vasco for his highly successful defense of his PhD thesis entitled “Development of DNA metabarcoding methods for stream ecosystem assessment”.
The PhD committee consisted of the following examiners: Prof. Dr. Jens Boenigk, Prof. Dr. Simon Creer (University of Bangor, UK) and Florian Leese. Chair of the committe was Prof. Dr. Peter Haase.
Photo: PhD thesis committee of Vasco Elbrecht. F.r.t.l.: Peter Haase, Florian Leese, Vasco Elbrecht, Simon Creer, Jens Boenigk
In a just-released article in the journal Methods in Ecology and Evolution, we investigate the potential of DNA metabarcoding of freshwater macroinvertebrates for the assessment of stream health. With the “DNA metabarcoding” method hundreds of specimen in a sample can be identified, often up to species level. The assessment results of the morphology and DNA based methods were very similar with both methods, while DNA metabarcoding detected more taxa on species level. However, metabarcoding has also shortcomings, for example, the method failed to detect ~ 30% of the taxa identified by morphology. This work is an important step into validation and improvement of the metabarcoding method, and it highlights it’s potential for more rapid and accurate routine monitoring of freshwater streams.
Picture 1: Vasco Elbrecht, Edith Vamos and Florian Leese (from left to right), in cooperation with Kristian Meissner and Jukka Aroviita from the Finnish Environment institute, analysed 18 monitoring samples from Finnish streams.
Additionally, our R package PrimerMiner was featured on the cover page of the journal Methods in Ecology and Evolution.
Picture 2: The cover picture in Methods in Ecology and Evolution shows a macroinverterte sample which is homogenised using liquid nitrogen and a mortar, in order to extract the DNA from the sample.
If you’re interested please join a discussion on the state and future of the oceans on Monday 15th of May at Unperfekthaus Essen.
We’re happy to welcome Darina Siposova from the Slovak Academy of Sciences to our group. Darina has been awarded a DBU stipendship and joins our GBOL project on metabarcoding / eDNA anayses of rivers. Furthermore, Darina studies the population genetic structure of aquatic beetles in the high Tatra as part of her PhD thesis.
Foto: Darina Siposova
… during the international conference of “Polar Educators International” in Italy, or actually they met. For the scientific input Jana Dömel was invited to lead a workshop on genetic analyses.
During the scientific year 2016*17 Seas and Oceans the aim of the project “MEERwert. Polare Biodiversität.” (The value of the sea. Polar biodiversity.; www.meer-wert.info) is to introduce schools and anyone else who is interested to genetic methods that help us to discover the biological variety of the polar regions. In addition to the already freely available “Extraction box”, that includes all material needed for a DNA extraction of e.g. fish fingers, we designed further worksheets to present at the workshop. (The Extraction box will be send to you on request. Contact: email@example.com)
During the conference teachers, but also scientists worked on two working sheet that introduce the basics for DNA analyses and were asked to improve the exercises from a didactical perspective. To start, fish sequences are compared to a database to find out species names. Subsequently, phylogenetic trees are reconstructed to solve the origin and relationships between fish of the so called „cod“ fishes.
We got very positive feedback, which confirmed that our project is of great educational interest.
Yesterday, a new publication by Vasco und Florian entitled “Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment“has been published in Frontiers in Environmental Science (Link). In the study we demonstrate problems with several of the currently available metabarcoding primers and tested four newly developed COI primers targeting aquatic macroinvertebrates. Our analyses show that the new primers (BF/BR) are highly suitable and amplify very equally the analysed taxa. Most importantly, however, our study shows how important careful design and validation of primers for a certain region, habitat or target taxon group is. With growing data bases there is still much potential for future improvement.