Are epistatic interactions more prevailing and significant for short-term evolution than previously thought?

Hakemuksen tiivistelmä

Understanding how species adapt to rapid environmental change is critical for conserving biodiversity. Current models emphasize simple additive effects of individual genes, but this overlooks epistasis – interactions where the effect of one gene depends on others. While such interactions are known to shape long-term evolution, their role in short-term adaptation remains poorly understood. My project challenges the additive view by showing that strong gene-gene interactions across multiple chromosomes are more common and influential than recognized. Using and extending my method Linkage Disequilibrium Network Analysis (LDna), I will detect genome-wide signatures of epistatic selection that traditional approaches miss. Combined with powerful simulation software developed in-house, this framework will allow me to distinguish genuine epistasis from simpler forms of adaptation and reveal when complex haplotype groups arise and persist. Preliminary results in flounder and stickleback demonstrate striking patterns: individuals fall into two distinct multi-chromosomal haplotype groups associated with freshwater or marine adaptation, with no viable recombinants. This suggests that genome-wide epistatic incompatibilities can strongly shape adaptation, maintaining “pre-packaged” genetic solutions to environmental change. I will test three hypotheses: (1) multi-locus haplotypes are widespread but under-detected, (2) their origin requires both local adaptation and periods of geographic separation, and (3) genetic signatures of epistasis can be reliably separated from parallel adaptation. By uncovering hidden layers of genetic interaction, this project will reshape evolutionary theory and provide practical tools for detecting epistasis in genomic data. The results will improve our ability to predict resilience to environmental change, informing conservation and management of biodiversity.