Gene Regulatory Divergence Between Locally Adapted Ecotypes in Their Native Habitats

Local adaptation is a key driver of ecological specialization and the formation ofnew species. Despite its importance, the evolution of gene regulatory divergenceamong locally adapted populations is poorly understood, especially how that divergencemanifests in nature. Here, we evaluate gene expression divergence and allele‐specific gene expression responses for locally adapted coastal perennial and inlandannual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocaltransplant experiment. Overall, 6765 (73%) of surveyed genes were differentiallyexpressed between coastal and inland habitats, while 7213 (77%) were differentiallyexpressed between the coastal perennial and inland annual accessions. Cis‐regulatoryvariation was pervasive, affecting 79% (5532) of differentially expressed genes.We detected trans effects for 52% (3611) of differentially expressed genes. Expressionplasticity of alleles across habitats (G × E interactions) appears to be relativelycommon (affecting 18% of transcripts) and could minimize fitness trade‐offs at locithat contribute to local adaptation. We also found evidence that at least one chromosomalinversion may act as supergene by holding together haplotypes of differentiallyexpressed genes, but this pattern depends on habitat context. Our resultshighlight multiple key patterns regarding the relationship between gene expressionand the evolution of locally adapted populations.