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For over 30 years a central question in molecular evolution has been whether natural selection plays a substantial role in evolution at the DNA sequence level^,. Evidence has accumulated over the last decade that adaptive evolution does occur at the protein level^,, but it has remained unclear how prevalent adaptive evolution is. Here we present a simple method by which the number of adaptive substitutions can be estimated and apply it to data from Drosophila simulans and D. yakuba. We estimate that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species.