This project investigates how epigenetic modifications interact with genetic variation to shape genome evolution in natural populations.
Genetic information is encoded in DNA and passed from one generation to the next. In addition, gene activity can be regulated by reversible chemical modifications, known as epigenetic changes. One of the most important of these is DNA methylation. These modifications allow organisms to respond to environmental and developmental signals, but their role in long-term evolutionary processes remains unclear.
The central aim of this project was to understand how epigenetic variation contributes to genome evolution, and how it interacts with genetic and structural variation across different biological levels. Rather than acting independently, these processes may be closely linked, but this has been difficult to study due to technical limitations.
To address this, the project focused on three main aspects.
First, we investigated how epigenetic variation arises and is structured across individuals and species. While the original aim was to establish detailed temporal trajectories, the project instead generated comparative datasets across natural populations. These revealed patterns of early-stage epigenetic variation and provided insight into how such variation is distributed across genomes.
Second, we examined how epigenetic variation interacts with genetic and structural variation. Using long-read sequencing approaches, we generated high-resolution datasets that capture both DNA sequence and epigenetic modifications. This allowed us to show that epigenetic variation frequently co-occurs with structural genomic features, including regions influenced by mobile DNA. In particular, we identified pronounced differences between female and male genomes in otherwise highly similar regions, suggesting that transposable elements play an important role in shaping these patterns.
Third, we investigated how these processes influence population structure, introgression, and species divergence. By combining population genomic data with epigenetic information, we showed that genomic regions affected by structural and epigenetic variation contribute to differentiation between populations and may be involved in adaptive processes.
Overall, the project demonstrates that epigenetic modification, structural variation, and genetic diversity are strongly interconnected. These findings challenge the common view that these processes can be studied independently and instead highlight the need for integrated approaches to understand genome evolution.
The project is relevant for society because epigenetic regulation plays a key role in how organisms respond to environmental change, including climate change, stress, and disease. Understanding how epigenetic and genetic processes interact improves our ability to interpret biological responses to changing environments and contributes to research in areas such as ageing and disease biology.
Although this project focuses on bird species, their epigenetic mechanisms are comparable to those in humans. The insights gained therefore contribute to a broader understanding of how epigenetic processes shape genome function and evolution across organisms.
