Recent demography drives changes in linked selection across the maize genome
The interaction between genetic drift and selection in shaping genetic diversity is not fully understood. In particular, a population’s propensity to drift is typically summarized by its long-term effective population size (Ne ), but rapidly changing population demographics may complicate this relationship. To better understand how changing demography impacts selection, we investigated linked selection in the genomes of 23 domesticated maize and 13 wild maize (teosinte) individuals. We show that maize went through a domestication bottleneck with a population size of approximately 5% that of teosinte before it experienced rapid expansion post-domestication. We observe that hard sweeps on genic mutations are not the primary force driving maize evolution. As expected, a reduced population size during domestication decreased the efficiency of purifying selection to purge deleterious alleles from maize, but rapid expansion after domestication has since increased the efficiency of purifying selection to levels exceeding those seen in teosinte. This final observation demonstrates that rapid demographic change can have wide-ranging impacts on diversity that conflict with would-be expectations based on long-term Ne.