Adaptive evolution of a rock-paper-scissors sequence along a direct line of descent

Non-transitivity - commonly illustrated by the rock-paper-scissors game - is purported to be common in evolution despite a lack of examples of non-transitive interactions arising along a single line of descent. We identify a non-transitive evolutionary sequence in the context of yeast experimental evolution in which a 1,000-generation evolved clone loses in direct competition with its ancestor. We show that non-transitivity arises due to the combined effects of adaptation mediated by the evolving nuclear genome combined with the stepwise deterioration of an intracellular virus. We show that multilevel selection is widespread: nearly half of all populations fix adaptive mutations in both the nuclear and viral genomes, and clonal interference and genetic hitchhiking occur at both levels. Surprisingly, viral mutations do not increase the fitness of their host. Instead, the evolutionary success of evolved viral variants results from their selective advantage over viral competitors within the context of individual cells. Overall, our results show that widespread multilevel selection is capable of producing complex evolutionary dynamics - including non-transitivity - under simple laboratory conditions.