Dynamics of copy number variation in evolving populations

The goal of this study was to understand the dynamics with which copy number variants (CNVs) are generated and selected in evolving populations of yeast. We used long-term nutrient limitation in chemostats to address this question. During nitrogen limitation, CNVs form at the GAP1 locus (duplications in glutamine and deletions in urea-limited chemostats). We used a fluorescent reporter, integrated into the genome near GAP1, to track the generation and selection of GAP1 CNVs in real time. We observed GAP1 duplications and deletions, which we confirmed by sequencing whole populations and isolated clones from generation 150 and generation 250. We used a barcode-lineage tracking method to further dissect the CNV dynamics we observe, and to begin understanding the extent of clonal interference between distinct CNV lineages.