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Empirical explorations of fungal fitness landscapes

Final Report Summary - FITNESS LANDSCAPES (Empirical explorations of fungal fitness landscapes)

The aim of the research project was to experimentally test predictions from theoretical models on adaptation. These models are central to the field of evolutionary biology. Most notably, the geometric model developed by RA Fisher in the 1930s is often used to describe and aim to predict the trajectory and outcome of evolutionary processes such as evolution by natural selection. However, this model has never been tested experimentally. In this project, we developed specific and testable predictions on epistasis (interactions) between beneficial mutations, see Figure 1 (in attached document).
To test the predictions, we developed techniques and tools to generate de novo beneficial mutations in the experimental system Aspergillus nidulans. We managed to collect over 650 beneficial mutants in either a simple or a complex nutrient environment. Through sexual crosses, these were combined in one background in pairs of two in order to quantify the pattern of epistasis, as measured by the deviation from expected additivity of the fitness effects of these mutations. By measuring the mycelium growth rate of wild-type, single mutants and double mutants, we quantified the amount of epistasis between these beneficial mutations. We found wide-spread epistasis among beneficial mutations, both positive and negative, although most (40 out of 43) epistatic effects were found to be negative. We found significant statistical support (linear regression) for a negative relationship between the effect size of single mutations. We find the same qualitative result when expressing epistasis relative to the effect size of the single mutations (Figure 2 in attached document).

In conclusion, our results support the predictions by Fishers geometric model, that there is more epistasis between beneficial mutations of large effect than between mutations of small effect. These results have implications for the outcome of evolutionary trajectories, since it has been shown that epistasis greatly affects the number accessible paths accessible by evolution through the successive fixation of beneficial mutations. We will follow up on this work by expanding the number of environments used to collect beneficial mutations as well as the inclusion of higher order combinations of beneficial mutations.

Transfer of knowledge:
Dr Schoustra implemented an approach of experimental evolution with filamentous fungi into the laboratory at Wageningen University which was not being used at the time he arrived. He was involved in several workshops, most notably in Groningen and Cologne, on this topic. He provided guidance to others, setting up experimental evolution with fungi (PhD candidates J Zhang and C Valero-Jimenez). Further, he communicated his experience on research in Zambia to others in Wageningen, which has led to novel collaborations (e.g. between the food science department in Wageningen and Zambia).
Moreover, I have assisted others to cement contacts with Zambian researchers. Dr Rob Nout had retired, I have talked with his successor Eddy Smid and his colleague Anita Linnemann about several projects. For the teaching, I have been a guest lecturer in several courses with a large contingent of students from Africa (and China). The courses were (1) Genetic Analysis, Concepts and Tools and (2) Quantitative Genetics. I managed to place the course material in a context that aligned with the background of the African students and the students felt more part of the group. I have given special invited seminars in Groningen (University of Groningen) and in Roscoff (Station Biologique of the CNRS). Finally, I have prepared new proposals in collaboration with the University of Zambia, working with the successor of Dr Chitundu Kasase, Dr John Shindano. One proposal was submitted to CORDIS KP7 (Marie Curie IOF) and has been funded, the project will start beginning of 2014. Two proposals, that apart from the University of Zambia also included the Zambian Tropical Diseases Research Institute of Dr Ray Handema, where he moved after leaving the Zambian National Institute of Scientific and Industrial Research. These proposals have been submitted to the Netherlands government funding body NWO-WOTRO (budget asked for EUR 750,000) and a pre-proposal to the Wageningen based funding body INREF (budget to be asked for EUR 1,200,000).