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We recently reported evidence for widespread adaptive evolution of gene expression in budding yeast (1). One component of our analysis was the demonstration that genes we predicted (based on gene expression data) to have undergone positive selection showed reduced heterozygosity compared with a control set, suggesting the action of recent selective sweeps. Jensen and Rando (2) propose that this result is because of “a failure to consider the demographic history of these strains.” However, this claim is not supported either by theory or empirical evidence. The simulation presented by Jensen and Rando (2) simply illustrates a phenomenon that has been well known for decades: population bottlenecks …

Reply to Jensen and Rando: Population size change does not account for widespread gene expression adaptation in yeast