Elucidating the molecular architecture of adaptation via evolve and resequence experiments

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Abstract
The evolve and resequence (E&R) approach is a powerful paradigm for understanding the molecular basis of adaptation. Several E&R systems exist, ranging from in vitro RNA and DNA molecules to microorganisms evolving from an isogenic clone and sexual eukaryotes harbouring standing variation. E&R experiments are producing different results in the different systems. Can observed differences be reconciled with evolutionary theoretical models? The systems differ in: population size, level of standing variation, initial variance in fitness and level of genetic exchange. We argue that when these differences between systems are taken into account many of the apparent differences can be explained. Nevertheless, enigmas remain. Why do ploidy changes and/or large duplications and deletions seem to be more important in asexual microorganisms and sexual eukaryotes? At what point do sexually reproducing organisms need newly arising mutations? In sexually reproducing organisms, does allele frequency change often plateau before fixation? How much can macroscopic epistasis help us to understand evolution in microorganisms, and what is the role of epistasis in sexually reproducing organisms?

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