The mode and repeatability of thermal adaptation in gene expression in the seed beetle Callosobruchus maculatus

Transcriptional plasticity can maintain organismal homeostasis but its potential to buffer negative effects from climate change remains contentious and may rely on genetic adaptation. Theory predicts two general outcomes: genetic reinforcement, where adaptive plasticity is enhanced by genetic adaptation; or genetic compensation, where genetic adaptation reverses maladaptive plasticity. Here, we explored the prevalence, repeatability, and molecular basis of compensation and reinforcement of gene expression responses to temperature using experimental evolution in the beetle pest, Callosobruchus maculatus. We evolved lines from three genetic backgrounds under hot or cold conditions and compared them to ancestral lines after 80-135 generations. Cold adaptation was dominated by genetic compensation, revealing a highly repeatable mode of adaptation across backgrounds, however, the underlying genes and their biological functions were largely idiosyncratic. In contrast, heat adaptation showed a less consistent mode, combining compensation and reinforcement, but greater repeatability at the level of genes and their functions. Network analysis identified many heat reinforcement genes as hubs and strongly temperature dependent, suggestive of roles in orchestrated adaptive thermal plasticity, potentially explaining their high repeatability. Genomic analyses identified repeatable allele frequency changes at both hot and cold compensation and reinforcement genes during experimental evolution. However, these were not causally linked to changes in expression levels, suggesting trans-regulation. There was also no broader correspondence between the level of repeatability of sequence and expression evolution across gene categories. Our findings suggest that the predictability of evolution under climate change might critically depend on the thermal range and the level of the genotype-phenotype map that is studied.