In a comparison between replicate sexual and asexual populations of Saccharomyces cerevisiae, sexual reproduction increases fitness by reducing clonal interference and alters the type of mutations that get fixed by natural selection. Explaining the prevalence of sexual reproduction despite its costly nature is a famously long-standing question in evolutionary biology. Theory and some experimental studies suggest various mechanisms responsible, such as a reduction in clonal interference or the ability to reduce hitchhiking of deleterious mutations. Using the experimental evolution of Saccharomyces cerevisiae as a model system, Michael Desai and colleagues compared the sequence-level dynamics of adaptation in sexual and asexual populations. They find that sexual reproduction increases fitness by reducing clonal interference between beneficial mutations and alters the type of mutations that are fixed by natural selection. The net effect is that that sex speeds adaptation and allows natural selection to more efficiently sort beneficial from deleterious mutations. Sex and recombination are pervasive throughout nature despite their substantial costs1. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology2,3. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation4. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher–Muller effect)5,6 or by separating them from deleterious load (the ruby in the rubbish effect)7,8. Previous experiments confirm that sex can increase the rate of adaptation9,10,11,12,13,14,15,16,17, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.