RNA plasticity emerges as an evolutionary response to fluctuating environments

Phenotypic plasticity refers to the ability of a single genotype to produce multiple distinct phenotypes. Using the computationally tractable genotype-phenotype (GP) map of RNA secondary structures, we model RNA phenotypic plasticity using the Boltzmann distribution of secondary structures for each genotype. Through evolutionary simulations that involve periodic environmental switching on the GP map, we reveal that RNA phenotypes can adapt to these fluctuations towards an optimal plasticity. The optimal phenotypes exhibit dominant near-equal Boltzmann probabilities of distinct structures, each representing the fittest structure for each alternating environment. Our findings demonstrate that phenotypic plasticity, a widespread biological phenomenon, is a fundamental evolutionary response to changing environments for RNA secondary structure. We also find naturally evolved functional RNAs that exhibit optimal plasticity unlikely to arise by neutral drift alone, suggesting functional relevance in fluctuating environments.