Evolution and plasticity of gene expression in Tribolium castaneum exposed to a stressful environment

Understanding how populations genetically adapt to environmental stress is a central question in evolutionary biology, especially in the context of rapid anthropogenic climate change. This thesis investigates the genetic and transcriptional basis of adaptation in Tribolium castaneum, a model beetle species, using data from a long-term experimental evolution study under heat-dry (HD) stress. Starting from published RNA-seq datasets and genomic variant calls from generations 1 and 22, the study integrates Genome-Wide Association Studies (GWAS), differential gene expression (DE) analyses, and gene selection metrics to dissect the polygenic response to environmental selection. Eight GWAS were conducted using linear mixed models (EMMAX) to account for relatedness among individuals, revealing few variants significantly associated with fitness due to its highly polygenic nature, but hundreds of SNPs associated with environmental contrast (CT vs HD) already in generation 1, increasing to over 1,600 in generation 22. DE analysis identified over 5,000 plastic genes in generation 1 and 2,300 in generation 22. In addition, in generation 22, 731 evolved genes were identified, subdivided into three categories: genes that were non‐plastic in both generations, genes that were plastic in generation 1 but lost plasticity by generation 22, and genes that were non‐plastic in generation 1 yet became plastic only by generation 22. Covariance between gene expression and fitness revealed shifting selection pressures over time. Permutation tests highlighted significantly higher selection intensity in specific categories of differentially expressed genes. By combining genotypic association, transcriptomic divergence, and fitness-related metrics, this thesis offers a comprehensive view of the molecular mechanisms driving polygenic adaptation in a model system, providing valuable insights into the evolutionary dynamics of gene regulation under climatic stress.