Pairwise and higher order genetic interactions during the evolution of a tRNA

A central question in genetics and evolution is the extent to which mutations have outcomes that change depending on the genetic context in which they occur1–3. Pairwise interactions between mutations have been systematically mapped within4–18 and between19 genes, and contribute substantially to phenotypic variation amongst individuals20. However, the extent to which genetic interactions themselves are stable or dynamic across genotypes is unclear21,22. Here we quantify >45,000 genetic interactions between the same 87 pairs of mutations across >500 closely related genotypes of a yeast tRNA. Strikingly, all pairs of mutations interacted in at least 9% of genetic backgrounds and all pairs switched from interacting positively to interacting negatively in different genotypes (FDR<0.1). Higher order interactions are also abundant and dynamic across genotypes. The epistasis in this molecule means that all individual mutations switch from detrimental to beneficial in even closely-related genotypes. As a consequence, accurate genetic prediction requires mutation effects to be measured across different genetic backgrounds and the use of higher order epistatic terms.