The Genetics of Adaptation in Arabidopsis species

As environmental change accelerates in the Anthropocene, a central challenge in evolutionary biology is understanding how populations respond to novel and rapidly changing conditions. Adaptation underpins whether species can persist and diverge under increasingly variable selective pressures. While adaptive potential is often inferred from phenotypic change or standing genetic variation, it remains unclear what determines the evolutionary “fuel” that enables sustained response. Using Arabidopsis species as model systems, this thesis examines the genetic basis of adaptation and how variation is generated and structured across biological scales, from life-history traits to gene expression and genomic interactions, with a particular focus on how genetic architecture shapes the pace and predictability of evolutionary change. The first study shows that variation in heat-induced secondary dormancy in Arabidopsis thaliana - an ecologically critical life-history trait - reflects local adaptation to climatic gradients and mediates population persistence under environmental uncertainty. In the second study, analyses of gene expression in natural populations of Arabidopsis lyrata reveal that although heritable expression variation is widespread, the amount of non-additive variance is substantial and shaped by past selection and genomic features. Adaptive potential at the molecular scale is therefore limited not by a lack of variation, but by functional and selective constraints. Finally, analyses of Arabidopsis lyrata hybrid populations in the third study demonstrate that genetic background can reshape the components of genetic variance. As hybrid outcomes are often shaped by context-dependent epistasis, the role of admixture in adaptation depends on the type of epistasis and how genetic variance components are reorganised within the genetic architecture. Together, this thesis conceptualises adaptive potential as an emergent population-level property arising from interactions among ecological traits, genetic architecture, molecular regulation, and environmental context. Adaptive potential depends not on the amount of variation present, but on its structure, heritability, and exposure to selection across evolutionary timescales.