Using Experimental Evolution to Study Temporal Responses of the Genome to Selection. Julien F. Ayroles1,2, Lawrence G. Harshman3, Jennifer Grenier2, Andrew G. Clark2. 1) OEB, Harvard, Cambridge, MA; 2) MBG, Cornell, Ithaca, NY; 3) School of Biological Sciences, Univ. of Nebraska, Lincoln, NE.

   For nearly a century, experimental evolution has been a favorite tool of biologists seeking to test evolutionary models. By coupling this approach with DNA sequencing, we can obtain a detailed view of the dynamics of evolutionary change. For example, how acccurately does the Wright-Fisher model capture the true variability in evolutionary trajectories of neutral alleles? How similar are the trajectories of selected alleles across replicates? To address these questions, we used a bulk segregant analysis to describe standing genetic variation associated with starvation resistance in a base population. Using next generation sequencing of DNA pools drawn from these starvation selection experiments, we quantified allele frequency dynamics over 15 generations for every segregating nucleotide in the genome in 4 selected and 4 control lines. We observed a strong phenotypic response associated with changes in allele frequency at hundreds of loci. Here, we present a novel analytical framework using methods borrowed from signal processing theory that enables the description not only of changes in allele frequency at individual loci, but also the covariance of allele frequency dynamics across linked sites. From the covariance matrix of allele frequency changes we assembled genetic networks for the selection response, highlighting the importance of non-additive effects in shaping evolutionary trajectories. Our analysis yields a fit to quantitative models for the temporal dynamics of genome-wide allele frequency changes across discrete generations, and the observed over-dispersion compared to Wright-Fisher provides an improved null model for assessment of the impact of selection on the genome.