Multiple chromosomal inversions modulate continuous local adaptation along a steep thermal cline

Chromosomal inversions are often implicated in divergence between distinct ecotypes, but their role in maintaining continuous adaptive divergence in complex traits remains poorly understood. Using quantitative and population genetics, transcriptomics, and artificial selection experiments, we demonstrate how inversions enable clinal adaptive divergence along a steep environmental gradient despite extensive gene flow in a widely distributed marine fish. We show that three inversions are associated with multiple adaptive traits and harbor the strongest signatures of divergent selection in the genome, implying a crucial adaptive role. These inversions exhibit contrasting selection signatures across latitudes, suggesting that they control distinct aspects of the same complex traits and facilitate adaptation in a modular way to different environmental pressures despite gene flow.