Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.
Keywords: Assay for Transposase-Accessible Chromatin using sequencing (ATACseq); ChIPseq; RNAseq; allele specific expression; chromatin; evolution; expression quantitative trait loci (eQTL); gene expression; gene regulation; genotype–phenotype map.