Epistasis substantially impacts evolution, in particular the rate of adaptation. We generated combinations of beneficial mutations that arose in a lineage during rapid adaptation of a bacterium whose growth depended upon a newly-introduced metabolic pathway. The proportional selective benefit for three of the four loci consistently decreased when introduced upon more fit backgrounds. These three alleles all reduced morphological defects caused by expression of the foreign pathway. A simple theoretical model segregating the apparent contribution of individual alleles to benefits and costs effectively predicted the interactions between them. These results provide the first evidence that patterns of epistasis may differ for within- and between-gene interactions during adaptation, and that diminishing returns epistasis contributes to the consistent observation of decelerating fitness gains during adaptation.
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