Periodic Reporting for period 4 - DECAF (Deciphering adaptive footprints of epiC evolution on different timescales)
Reporting period: 2024-07-01 to 2026-01-31
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.
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.
This project explored how changes to DNA that do not alter the genetic code itself known as epigenetic modifications contribute to evolution. These changes help organisms respond to their environment, but their role in long-term evolutionary processes has remained unclear.
To address this, the project combined fieldwork, laboratory experiments, and large-scale data analysis.
A key part of the project was the study of wild bird populations in Northern Germany. By expanding an existing field site, we were able to collect around 1,000 samples from blue tits and great tits over multiple breeding seasons. These were complemented by additional samples from other bird populations.
Using these samples, we developed new laboratory methods to analyse epigenetic patterns alongside genetic information. This allowed us to investigate how epigenetic changes are distributed across individuals and populations, and how they relate to differences in DNA sequence.
We also applied advanced DNA sequencing technologies that provide a much more detailed view of genomes than previously possible. These data revealed unexpected patterns, including differences between female and male genomes in regions that were previously thought to be very similar. Our results suggest that mobile DNA elements play an important role in shaping these patterns, linking epigenetic processes with genome structure.
In addition, we studied how genetic and epigenetic variation differ between populations and in hybrid individuals. This work showed that regions of the genome affected by these processes are often involved in population differentiation and may contribute to adaptation.
Overall, the project demonstrates that genetic variation, epigenetic modification, and genome structure are closely interconnected. Rather than acting independently, these processes jointly shape how genomes evolve over time.
The results have been shared through scientific publications, preprints, and conference presentations. The large datasets generated in this project, particularly from advanced sequencing technologies, will continue to support future research. These include studies on how genomes change over time and how organisms adapt to rapidly changing environments.
Beyond basic research, the findings are relevant for understanding how living organisms respond to environmental stress, including climate change, and have broader implications for fields such as ageing and disease biology.
To address this, the project combined fieldwork, laboratory experiments, and large-scale data analysis.
A key part of the project was the study of wild bird populations in Northern Germany. By expanding an existing field site, we were able to collect around 1,000 samples from blue tits and great tits over multiple breeding seasons. These were complemented by additional samples from other bird populations.
Using these samples, we developed new laboratory methods to analyse epigenetic patterns alongside genetic information. This allowed us to investigate how epigenetic changes are distributed across individuals and populations, and how they relate to differences in DNA sequence.
We also applied advanced DNA sequencing technologies that provide a much more detailed view of genomes than previously possible. These data revealed unexpected patterns, including differences between female and male genomes in regions that were previously thought to be very similar. Our results suggest that mobile DNA elements play an important role in shaping these patterns, linking epigenetic processes with genome structure.
In addition, we studied how genetic and epigenetic variation differ between populations and in hybrid individuals. This work showed that regions of the genome affected by these processes are often involved in population differentiation and may contribute to adaptation.
Overall, the project demonstrates that genetic variation, epigenetic modification, and genome structure are closely interconnected. Rather than acting independently, these processes jointly shape how genomes evolve over time.
The results have been shared through scientific publications, preprints, and conference presentations. The large datasets generated in this project, particularly from advanced sequencing technologies, will continue to support future research. These include studies on how genomes change over time and how organisms adapt to rapidly changing environments.
Beyond basic research, the findings are relevant for understanding how living organisms respond to environmental stress, including climate change, and have broader implications for fields such as ageing and disease biology.
This project has advanced our understanding of evolution by showing that genetic and epigenetic processes cannot be studied separately, but are closely interconnected. Traditionally, evolutionary research has focused mainly on changes in DNA sequence. Our work demonstrates that additional layers, such as epigenetic modifications and structural features of the genome, play an important role in shaping how genomes evolve.
A key advance of the project is the ability to analyse genetic and epigenetic information together at high resolution using modern sequencing technologies. This allowed us to uncover patterns that were previously difficult to detect. In particular, we identified genomic regions where different types of variation - genetic, epigenetic, and structural - coincide and interact.
One important finding is that differences between female and male genomes can arise in regions that were previously considered very similar. These differences are likely linked to mobile DNA elements and highlight a new mechanism by which genome structure and regulation evolve.
The project also provided new insights into how populations diverge and how hybridisation contributes to evolutionary change. By analysing natural populations and hybrid individuals, we showed that regions affected by these combined processes are often involved in population differentiation and may contribute to adaptation.
Together, these findings go beyond the current state of the art by moving from a simplified view of evolution - based mainly on DNA sequence changes - to a more integrated perspective that includes multiple interacting layers of genome biology.
Looking forward, the datasets and methods developed in this project will enable further research on how genomes evolve in response to environmental change. In particular, they provide a foundation for studying how genetic and epigenetic variation jointly contribute to adaptation, with potential implications for understanding processes such as ageing, disease, and responses to climate change.
A key advance of the project is the ability to analyse genetic and epigenetic information together at high resolution using modern sequencing technologies. This allowed us to uncover patterns that were previously difficult to detect. In particular, we identified genomic regions where different types of variation - genetic, epigenetic, and structural - coincide and interact.
One important finding is that differences between female and male genomes can arise in regions that were previously considered very similar. These differences are likely linked to mobile DNA elements and highlight a new mechanism by which genome structure and regulation evolve.
The project also provided new insights into how populations diverge and how hybridisation contributes to evolutionary change. By analysing natural populations and hybrid individuals, we showed that regions affected by these combined processes are often involved in population differentiation and may contribute to adaptation.
Together, these findings go beyond the current state of the art by moving from a simplified view of evolution - based mainly on DNA sequence changes - to a more integrated perspective that includes multiple interacting layers of genome biology.
Looking forward, the datasets and methods developed in this project will enable further research on how genomes evolve in response to environmental change. In particular, they provide a foundation for studying how genetic and epigenetic variation jointly contribute to adaptation, with potential implications for understanding processes such as ageing, disease, and responses to climate change.