Expression plasticity biases the propensity for and direction of genetic expression divergence
Evolutionary theory and empirical studies suggest that environmentally induced plasticity may facilitate adaptation to novel environments. To test this prediction, we first asked whether genes with significant ancestral expression plasticity were more likely to show genetic divergence in expression. To compare expression changes upon colonization of low-predation environments by high-predation fish to those present after generations of adaptation to low-predation environments, we examined the extent of overlap in gene sets differentially expressed between high-predation fish reared with and without predators and high- versus low-predation fish reared in a shared, predator-free environment. In both drainages, the DE genes with significant ancestral plasticity were more likely to show significant population divergence than expected by chance (Aripo: 264 transcripts, 95% CI for differences in conditional probability of significant divergence for plastic genes compared to conditional probability of divergence for non-plastic genes: [0.125, 0.150]; Quare: 409 transcripts, 95% CI: [0.211,0.239]), supporting an association between plastic responses and genetic divergence.
We next asked whether the directions of expression plasticity and genetic divergence were associated. We did so for those genes with both significant ancestral plasticity and population differences, as well as the larger set of all transcripts with significant population differences (i.e. including those without significant expression plasticity). We performed the second, more conservative comparison because we reasoned that even subthreshold expression plasticity could influence the direction of adaptive divergence. Within both drainages, we found a signature of non-adaptive plasticity associated with genetic expression divergence. Approximately 84% of DE genes exhibited population and rearing expression changes in non-concordant directions in the Aripo drainage (95% CI for difference in probability of same versus opposite expression direction: [-0.564,-0.499]), and 68% of DE genes exhibiting non-concordant expression in the Quare drainage (95% CI: [-0.520,-0.456]) (Fig. 3). Patterns were consistent in both drainages when we considered the larger set of all genes with significant population expression differences (Aripo: 80% of genes with non-concordant expression, 95% CI: [-0.811,-0.752]; Quare: 66% of genes with non-concordant expression, 95% CI: [-0.803,-0.733]).