Understanding how genomic variation translates into adaptive phenotypic divergence is central to evolutionary biology, particularly in systems experiencing ecological speciation with ongoing gene flow. Periwinkle Littorina saxatilis is a model for studying this process, with distinct crab and wave ecotypes that coexist on small spatial scales in different microhabitats and differ in shell morphology, behavior, and genomic architecture. Several chromosomal inversions have been linked to ecotypic divergence and shell traits, but their functional effects on gene expression and gene regulation remain poorly understood. This project aims to investigate how chromosomal inversions influence gene expression and regulatory networks underlying adaptive divergence in L. saxatilis. We will analyze RNA-sequencing data from mantle and foot tissues collected from a large common-garden experiment comprising over 200 genotyped and phenotyped individuals, including pure ecotypes and hybrids (already sent to SciLifeLabs). Pilot analyses based on a subset of samples reveal extensive differential gene expression between ecotypes, enrichment of differentially expressed genes within specific inversions, distinct gene coexpression modules associated with ecotype and hybrid status, and unexpected sex-specific expression patterns despite the absence of sex chromosomes. The full analysis will involve RNA-seq processing (bioinformatics such as alignment, filtering, etc), differential expression modeling, weighted gene coexpression network analysis, permutation-based enrichment tests across 22 known inversions, and integration with existing QTL data reanalyzed using a newly available reference genome. These analyses are computationally demanding due to the size of the dataset, the complexity of the statistical models, and the extensive resampling required for robust inference. By integrating gene expression, regulatory network structure, inversion genotypes, and phenotypic data, this project will improve the genotype–phenotype map in a classic system of local adaptation. The results will advance our understanding of how regulatory evolution and structural genomic variation contribute to rapid adaptive divergence in natural populations facing environmental change. My main supervisor is Professor Erica Leder, Department of marine sciences, University of Gothenburg.