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The Gene Regulatory Landscape of Local Adaptation

Local adaptation is a key driver of ecological specialization. Despite its importance, the evolution of gene regulatory divergence among locally-adapted populations is poorly understood. Here, we evaluate allele-specific gene expression responses for locally-adapted coastal and inland accessions of the plant Mimulus guttatus in a field reciprocal transplant experiment. We found 18% of transcripts were characterized by habitat-specific differential expression, a pattern consistent with the minimization of fitness trade-offs through expression plasticity. Cis-regulatory variation was pervasive, affecting 92% of differentially expressed genes. Chromosomal inversions were enriched for genes with expression divergence between ecotypes in a habitat-dependent manner, and gene expression heterosis was prevalent across habitats. These results provide multiple new insights into the evolution of transcriptome-wide gene regulatory divergence and plasticity among locally adapted populations.