Data from: Gene regulatory divergence between locally adapted ecotypes in their native habitats

Local adaptation is a key driver of ecological specialization and the
formation of new species. Despite its importance, the evolution of gene
regulatory divergence among locally-adapted populations is poorly
understood, especially how that divergence manifests in nature. Here, we
evaluate gene expression divergence and allele-specific gene expression
responses for locally-adapted coastal perennial and inland annual
accessions of the yellow monkeyflower, Mimulus guttatus, in a field
reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes
were differentially expressed between coastal and inland habitats, while
7213 (77%) were differentially expressed between the coastal perennial and
inland annual accessions. Cis-regulatory variation was pervasive,
affecting 79% (5532) of differentially expressed genes. We detected trans
effects for 52% (3611) of differentially expressed genes. Expression
plasticity of alleles across habitats (GxE interactions) appears to be
relatively common (affecting 18% of transcripts) and could minimize
fitness trade-offs at loci that contribute to local adaptation. We also
found evidence that at least one chromosomal inversion may act as
supergene by holding together haplotypes of differentially expressed
genes, but this pattern depends on habitat context. Our results highlight
multiple key patterns regarding the relationship between gene expression
and the evolution of locally adapted populations.