Beyond single-trait GxE: higher-order environmental interactions and clonal diversity govern trait relationships in yeast

Predicting organismal responses to complex ecological change requires understanding how multiple environmental stressors (E) and genetic background (G) interact on phenotypic variation (P). Here, we investigate how temperature (ET) and salinity (ES) shape growth (PG) and flocculation (PF) in multiple strains of the fission yeast, Schizosaccharomyces pombe. We find that environmental interactions are critical, with the effect of temperature on flocculation being inverted by changes in salinity (P[~]ExE). Multi-stress reaction norms are genotype-dependent (P[~]GxExE), revealing that evolution can adopt diverse strategies to deal with ExE interactions. We further show that the covariation between traits (PxP) is itself a plastic and evolvable feature. The relationship between growth and flocculation changed from negative to positive or completely uncoupled, depending on the specific GxExE context. This context-dependent covariation suggests that clonal variability and stochastic processes modulate phenotypic outcomes beyond deterministic genotypic effects. Our findings demonstrate that higher-order interactions govern not only individual traits but also their interrelationships, highlighting the necessity of integrating GxExE effects and phenotypic covariation into models of adaptation.