Increased fitness in nutrient-limited environments is associated with amplification of specific permease genes.

(A) Fitness increases for clones recovered from each selection are typically >10%. Haploid (1N) and diploid (2N) ancestral strains were also tested in ammonium-limited chemostats but did not show fitness differences. (Amm : ammonium, Arg : arginine, Gln : glutamine, Pro : proline, Glu : glutamate, Urea : urea, Alla : allantoin, Anc : ancestor). (B) DNA copy number was estimated using aCGH. Each black point represents a measurement from a unique probe on the microarray from analysis of population DNA samples. We detected CNVs containing genes with clear connections to nitrogen import at high frequencies in populations (red lines) and clones (blue lines). Retrotransposon (Ty) sequences were frequently found at the boundary regions of CNVs.