Evolutionary Regulatory Genomics

Research Focus

When organisms encounter new or shifting environments, their survival and reproductive success depend on the evolution of regulatory processes that enable them to tolerate unfamiliar and often extreme conditions, such as temperature stress. Our research seeks to uncover the gene regulatory mechanisms that allow insects, including agricultural pests and disease vectors, to outcompete competitors and successfully colonize new environments. We investigate how genetic and epigenetic mechanisms shape physiology and fertility under stress, as well as how gene regulatory processes contribute to major evolutionary innovations, such as the diversification of reproductive traits and the transition from solitary to social behaviour. Our research aims to reveal how the evolution of these mechanisms underpins functional diversity and enables species to persist in a rapidly changing world. To this end, we integrate experimental and computational approaches that allow us to analyze regulatory processes across molecular and organismal scales.

Methods and Approaches

Computational. We integrate genomic, transcriptomic, and epigenomic data to characterize regulatory variation, reconstruct network dynamics, and develop quantitative models of gene regulation. Statistical inference and machine-learning methods are employed to provide deeper insight into regulatory patterns and environmental responsiveness.

Experimental. We mainly work with the genetically tractable Drosophila genus to study regulatory variation in vivo, making use of state-of-the-art genome editing techniques in combination with phenotypic, physiological, and fertility assays. This integrated analytical and functional framework enables us to connect regulatory changes to their effects on development, stress tolerance, and population-level diversity, providing a mechanistic understanding of how organisms maintain function in fluctuating and changing environments.

Selected Publications

Yılmaz VM, Bao Z, Grath S: Navigating the Cold: Integrative Transcriptome Sequencing Approach Reveals Ionoregulatory and Whole-Body Responses to Cold Acclimation in Drosophila ananassae. Genome Biology and Evolution, 17(5):evaf077. https://doi.org/10.1093/gbe/evaf077

Taprogge M, Grath S (2024): Modelling suggests Wolbachia-induced cytoplasmic incompatibility in oak gall wasps with cyclical parthenogenesis. Journal of Evolutionary Biology, 37(8):926-934. https://doi.org/10.1093/jeb/voae077

Hoedjes KM, Grath S, Posnien N, Ritchie MG, Schlötterer C, Abbott JK, Almudi I, Coronado-Zamora M, Durmaz Mitchell E, Flatt T, Fricke C, Glaser-Schmitt A, González J, Holman L, Kankare M, Lenhart B, Orengo DJ, Snook RR, Yılmaz VM, Leeban Y (2024): From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Molecular Ecology, e17382.https://doi.org/10.1111/mec.17382

Yılmaz VM, Ramnarine TJS, Königer A, Mussgnug S, Grath S (2023): Tropical super flies: Integrating Cas9 into Drosophila ananassae and its phenotypic effects. Journal of Insect Physiology, 147:104516. https://doi.org/10.1016/j.jinsphys.2023.104516

Ramnarine TJS, Grath S, Parsch J (2022): Natural variation in the transcriptional response of Drosophila melanogaster to oxidative stress. G3 Genes|Genomes|Genetics, 12(1), jkab366. https://doi.org/10.1093/g3journal/jkab366

Job Opportunities

We are currently looking for PhD students that are interested in working with us on a newly funded project on the evolution of gene regulatory mechanisms underlying the evolution of eusociality in wild bees. The project is part of the priority programme "Genomic Basis of Evolutionary Innovations (GEvol)" (SPP 2349) funded by the German Science Foundation (DFG).

For more information, please contact Sonja Grath.