Prof. Dr.

Michael T. Monaghan

Research Group Leader
+49 (0)30 64181 684

Müggelseedamm 301, 12587 Berlin / Königin-Luise-Str. 2-4 Gartenhaus, 14195 Berlin


molecular ecology, evolution, biodiversity, phylogeny / rivers, streams, lakes



at Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, Institute of Biology


since 2018  Professor of Biology, Freie Universität Berlin

2016  Visiting Professor, Duke-NUS Medical School, Singapore

since 2015  Guest Professor, Ehime University, Matsuyama

since 2008  Senior Scientist and Research Group Leader, IGB

2003-08  Research Fellow, Imperial College and Natural History Museum, London

2002  Dr. sc. nat. ETH Zürich

1998-2002  Doctoral student, Swiss Federal Institute of Aquatic Science and Technology (Eawag)

1998  M.S. Biology, Idaho State University

1995  B.S. Natural Resources Management, The Ohio State University

Recent Publications

Kuhl et al. (2024)
The haplotype-resolved Prymnesium parvum (type B) microalga genome reveals the genetic basis of its fish-killing toxins
Current Biology 10.1016/j.cub.2024.06.033

Kohler et al. (in press)
Unpredicted ecosystem response to compound human impacts in a European river
Scientific Reports

Thomé et al. (2024)
Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum
Molecular Phylogenetics and Evolution 197:108103

Warter et al. (2024)
Environmental DNA, hydrochemistry and stable water isotopes as integrative tracers of urban ecohydrology
Water Research 250:121065

Thomé et al. (2023)
Single-cell genomics reveals new Rozellid lineages and supports their sister relationship to Microsporidia.
Biology Letters 19:20230398

Theissinger et al. (2023)
How genomics can help biodiversity conservation
Trends in Genetics 39:545-559

Sukhodolov et al. (2023)
Interactions between diurnal winds and floodplain mosaics control the insect boundary layer in a river corridor
Aquatic Sciences 85:109.

Strassert & Monaghan (2022)
Phylogenomic insights into the early diversification of fungi
Current Biology 32:3628-3635.e3.

Premke et al. (2022)
Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes
Environmental Pollution 308:119627.   

Sire et al. (2022)
Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species
Communications Biology 5:57.

Maasri et al. (2022)
A global agenda for advancing freshwater biodiversity research
Ecology Letters 25:255-263.

Formenti et al. (2022)
The era of reference genomes in conservation genomics
Trends in Ecology and Evolution 37:197-202.

Welti et al. (2022)
Temperature drives variation in flying insect biomass across a German malaise trap network
Insect Conservation and Diversity 15:168-180.

Heeger et al. (2021)
Evidence for lignocellulose-decomposing enzymes in the genome and transcriptome of the aquatic hyphomycete Clavariopsis aquatica
Journal of Fungi 7:854.

Beng et al. (2021)
Temporal dynamics of freshwater planktonic parasites inferred using a DNA metabarcoding time-series
Parasitology 148:1602-1611.

Rutschmann et al. (2021)
Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae)
Mitochondrial DNA Part B: Resources 6:2969-2971

Hoffmann et al. (2021)
PriSeT: Efficient de novo primer discovery
Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics Article No.: 2, pp. 1-12.

Rodriguez-Ezpeleta et al. (2021)
Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA
Molecular Ecology 30:4601-4605.

Bracamonte et al. (2021)
Encapsulation of Anguillicola crassus reduces the abundance of adult parasite stages in the European eel (Anguilla anguilla)
Journal of Fish Diseases 44:771-782.

van Rees et al. (2021)
Safeguarding freshwater life beyond 2020: recommendations for the new Global Biodiversity Framework from the European experience
Conservation Letters 14:e12771

Jähnig et al. (2021)
Revisiting global trends in freshwater insect biodiversity
WIREs Water 8:e1506.

Link to complete list


Freie Universität Berlin

Institute of Biology (Faculty of Biology, Chemistry, Pharmacy)

  • 23204 Data Science in Biology (ABV)
  • 23306 Experimental and Theoretical Evolutionary Ecology
  • 23308 Biotic Interactions in a Changing World
  • Project (10 LP)
  • Research Project (15 LP)
  • Master's Project / Thesis

Institute of Computer Science (Faculty of Mathematics and Computer Science)

  • 23779 Biodiversity and Evolution
  • 23780 Environmental Genomics
  • 23781 Evolutionary Bioinformatics and NGS Applications (Seminar)
  • Research Internship (10 LP)
  • Master's Project / Thesis


  • Introduction to R / RStudio
  • Reviewing Scientific Papers
  • Preparing an Academic Job Application

Share page