Functional Environmental Genomics

Influence of anthropogenic substances on the germ cell mutation rate​

Institution: Senckenberg Society for Nature Research

Mutagenicity tests in ecotoxicology are currently carried out with prokaryotes or unicellular eukaryotes or infer a mutagenic effect from phenotypic changes. In view of the largely different mutation and repair mechanisms, a transfer to multicellular eukaryotes (including humans) is questionable and so far untested. The development of a new method makes it possible to measure the influence of substances on the mutation rate at reasonable expense. Genome-wide screening promises a much higher sensitivity in mutagenicity assessment than conventional tests. The aim is to test a new dimension of ecotoxicological assessment of anthropogenic substances and possibly establish it within the framework of ISO.


  • Prof. Dr. Markus Pfenninger (PI)
  • Dr. Halina Binde-Doria (TBG-Postdoc)
  • Jun.-Prof. Dr. Ann-Marie Waldvogel (affiliated)


We are using NGS techniques to build reference genomes of non-model organisms, re-sequence individuals and/or population pools. In addition, RNA-seq is used depending on the scientific question.
Other corecompetences include: environmental association studies and ecological and evolutionary experiments. The data are usually analysed in a population genomics framework with state-of-the-art methods. 


A multigenerational approach can detect early Cd pollution in Chironomus riparius
Halina Binde Doria, Markus Pfenninger
Chemosphere, August 2020

A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera)
Hanno Schmidt, Sören Lukas Hellmann, Ann-Marie Waldvogel, Barbara Feldmeyer, Thomas Hankeln, Markus Pfenninger: 
G3-Genes Genomes Genetics, February 2020

Temperature-dependence of spontaneous mutation rates
AM Waldvogel, M Pfenninger
Genome Research, gr. 275168.120

Measuring mutagenicity in ecotoxicology: A case study of Cd exposure in Chironomus riparius
HB Doria, AM Waldvogel, M Pfenninger
Environmental Pollution 272, 116004

Spontaneous rate of clonal mutations in Daphnia galeata
M Pfenninger, H Binde-Doria, J Nickel, A Thielsch, K Schwenk, …

Contributions to other PROJECT AREAS WITHIN TBG

De novo Genome Assembly of the Raccoon Dog (Nyctereutes procyonoides)
LJ Chueca, J Kochmann, T Schell, C Greve, A Janke, M Pfenninger, …
Frontiers in genetics 12, 559

Whole-genome re-sequencing data to infer historical demography and speciation processes in land snails: the study of two Candidula sister species
LJ Chueca, T Schell, M Pfenninger
Phil. Trans. R. Soc. B 376 (doi/10.1098/rstb.2020.0156)

Little parallelism in genomic signatures of local adaptation in two sympatric, cryptic sister species
J Hartke, AM Waldvogel, PP Sprenger, T Schmitt, F Menzel, M Pfenninger, …
Journal of Evolutionary Biology

Precise estimation of genome size from NGS data
M Pfenninger, P Schönnenbeck, T Schell

A chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs
B Mishra, B Ulaszewski, J Meger, M Pfenninger, DK Gupta, S Wötzel, …

tbg-a new file format for genomic data
P Schönnenbeck, T Schell, S Gerber, M Pfenninger

Climate change genomics calls for standardized data reporting
AM Waldvogel, D Schreiber, M Pfenninger, B Feldmeyer
Frontiers in Ecology and Evolution 8, 242

Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome
JH Nickel, T Schell, T Holtzem, A Thielsch, SR Dennis, B Schlick-Steiner, …

De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)
LJ Chueca, T Schell, M Pfenninger

Genomic divergence landscape in recurrently hybridizing Chironomus sister taxa suggests stable steady state between mutual gene flow and isolation
D Schreiber, M Pfenninger
Evolution Letters


Climate change genomics calls for standardized data reporting
AM Waldvogel, D Schreiber, M Pfenninger, B Feldmeyer
Frontiers in Ecology and Evolution 8, 242

Range-wide patterns of human-mediated hybridisation in European wildcats
A Tiesmeyer, L Ramos, JM Lucas, K Steyer, PC Alves, C Astaras, M Brix, …
Conservation Genetics 21 (2), 247-260

Combining environmental DNA and species distribution modeling to evaluate reintroduction success of a freshwater fish
M Riaz, M Kuemmerlen, C Wittwer, B Cocchiararo, I Khaliq, M Pfenninger, …
Ecological Applications 30 (2), e02034

Hybrid genome assembly of a neotropical mutualistic ant
J Hartke, T Schell, E Jongepier, H Schmidt, PP Sprenger, J Paule, …
Genome biology and evolution 11 (8), 2306-2311

Environmental DNA time series in ecology
M Balint, M Pfenninger, HP Grossart, P Taberlet, M Vellend, MA Leibold, …
Trends in Ecology & Evolution 33 (12), 945-957

The genomic footprint of climate adaptation in Chironomus riparius
AM Waldvogel, A Wieser, T Schell, S Patel, H Schmidt, T Hankeln, …
Molecular ecology 27 (6), 1439-1456