Abstract

Environmental conditions shape phenotype and fitness, influencing which mutations rise in frequency, the maintenance of genetic diversity, and evolutionary outcomes. When the combined impact of two environments deviates from expectations based on their individual effects, this is known as an environment-by-environment interaction. While the terms “gene-by-gene interaction” and “gene-by-environment interaction” are widely recognized, “environment-by-environment interaction” is a term used less often. In this study, we find that environment-by-environment interactions are a meaningful driver of phenotypes, and moreover, that they differ across genotypes (suggestive of environment-by-environment-by-genotype interactions). To support this conclusion, we analyzed a large dataset of approximately 1,000 mutant yeast strains with varying degrees of resistance to different antifungal drugs. Our findings reveal that the effectiveness of a drug combination, relative to single drugs, often differs across drug-resistant mutants. Even mutants that differ by only a single nucleotide change can have dramatically different drug × drug interactions. Understanding how environment-by-environment interactions change across genotypes is crucial not only for modeling the evolution of pathogenic microbes but also for understanding the sources of phenotypic variance within populations. While the significance of environment-by-environment-by-genotype interactions has been overlooked in evolutionary and population genetics, these fields and others stand to benefit from understanding how these interactions shape the complex behavior of living systems.