Transcriptomic analysis of diverse organisms reveals the rareness of genetic assimilation in environmental adaptations

Genetic assimilation is the evolutionary process by which an environmentally induced phenotype becomes genetically encoded and constitutive. Genetic assimilation has been proposed as the concluding step in the plasticity-first model of environmental adaptation and has been observed in multiple species, but its prevalence has not been systematically investigated. By analyzing transcriptomic data collected upon reciprocal transplant, we address this question in the experimental evolution, domestication, or natural evolution of a bacterial, a fungal, a plant, and four animal species. We find that genetic assimilation of environment-induced gene expression is the exception rather than the rule and that substantially more genes retain than lose their expression plasticity upon organismal adaptations to new environments. The probability of genetic assimilation varies among genes and decreases with the number of transcription factors controlling the gene and the expression level of the gene, supporting the hypothesis that genetic assimilation results primarily from passive losses of gene regulations that are not mutationally robust. Therefore, at the level of gene expression, our findings argue against the purported importance of genetic assimilation to environmental adaptation.