Lineage-specific effects of structural variants on thermal tolerance in a marine snail

Structural variants (SVs) represent a significant but poorly understood source of genetic variation that contributes to phenotypic diversity and local adaptation. Investigating the molecular mechanisms by which SVs influence thermal tolerance across different geographical populations is crucial for understanding the adaptive potential of species in the context of global climate change. In the present study, we examined the contribution of SVs to lineage divergence and thermal tolerance in the intertidal snail Littorina brevicula . Selection signature analysis identified inversions and deletions putatively under selection between the northern and southern lineages of the snail. Putative selected SVs were located within genes involved in core biological processes and heat-stress responses, suggesting their potential roles in driving lineage divergence and thermal adaptation. Integrating with experimental validation, we identified a deletion upstream of Innexin unc-9 that reduces thermal tolerance by suppressing heat-induced expression of Innexin unc-9 . Importantly, this regulatory effect occurs only in the northern lineage, leading to region-specific selection on the deletion that further drives genetic differentiation between the two lineages. Our study provides a framework for understanding thermal adaptation mediated by SVs and highlights the need to consider lineage-specific effects of SVs.