Van Trigt, LF; (2013) Experimental Evolution of Fission Yeast Genomes in Response to Repeated Environmental Changes. Doctoral thesis (PhD), UCL (University College London).

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Abstract

Evolutionary biology has mainly relied on comparative studies. Supported by the advances in genomics, several groups are now using microorganisms for experimental evolution studies to directly observe the evolution process and its genetic basis. To understand how cells adapt to an environmental stress, I developed experimental evolution assays during which fission yeast populations were repeatedly exposed to short heat-shocks, followed immediately by ideal growth conditions. Samples were frozen after each selection cycle for subsequent phenotypic and genotypic analyses. In total, I performed 10 independent such experiments for up to 150 selection cycles, including a control experiment with mock-treated samples. In all experiments, except for the mock-treated control, cells acquired a markedly increased survival to heat and other stresses within only 10-20 selection cycles, while during later cycles there was a more subtle but continuous increase in stress resistance. Surprisingly, all populations, including the mock-treated control, also evolved a more rapid re-initiation of exponential growth following heat shock and a more efficient use of the growth medium, reflected by higher biomass in stationary phase. These rapid adaptations seem to be based on DNA variations as the new phenotypes are stable. The cellular phenotypes and global regulation of gene expression of the evolved strains were determined using stress assays and DNA microarrays. Genomes of 96 strains at selected time points over the course of the evolution experiments were sequenced. We analyzed what genetic changes in regulatory and coding regions occurred in the different independent experiments, with the ultimate goal of uncovering the specific changes that are causing the striking alteration in phenotype. In collaboration with Dr. Ville Mustonen, we determined dynamic allele frequency trajectories that had swept through each population. Genetic variation among the parental cells seems to underlie the rapid initial adaptation of new phenotypes. This analysis led to the discovery of a common haplotype consisting of 9 mutations, which is likely associated with the more rapid recovery of growth after heat shock.

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