During natural selection it acts on a phenotype, but the genetic basis of the phenotype that gives a reproductive advantage will become more common in a population of a specific genotype. Over time, this process can result in populations that have an increased rate of mutations. In other words, natural selection is an important process by which evolution takes place within a population of organisms.
Reference: http://www.globalchange.umich.edu/globalchange1/current/lectures/selection/selection.html
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