Periodic Reporting for period 1 - CONstrainCONverge (Constrained convergence: does pleiotropy constrain convergent alpine adaptation?)
Berichtszeitraum: 2022-09-01 bis 2024-08-31
The CONstrainCONverge project aims to explore how constraints due to availability of shared genetic variation and pleiotropy (a single gene affecting multiple traits) influences adaptive evolution, specifically focusing on alpine adaptation in Arabidopsis. The project seeks to unravel how and mainly why repeatedly used genetic ‘hotspots’ are involved in the adaptation to alpine environments. The broader objective is to deepen the understanding of evolutionary processes in natural settings, contributing to more comprehensive knowledge in evolutionary biology.
The project operates in four main work packages (WPs):
WP1 focuses on genome-wide inference of convergent selection, successfully identifying polygenic adaptations to alpine environments. The identification of ‘hotspot’ genes provides the foundation for further work, highlighting the significance of both regulatory and coding changes in adaptation.
WP2 involves transcription network analysis to estimate pleiotropic constraints. Initial findings suggest that genes with a wide range of network connectivity play key roles in adaptation, possibly with more connected genes being essential for adaptation to more extreme environments, with more analysis to come.
WP3 assesses pleiotropic constraints based on genomic position and has demonstrated that adaptive alleles are often shared across species, enhancing the understanding of the genetic basis of convergent evolution.
WP4 is the most challenging and focuses on the fitness effects and pleiotropy of hotspot genes in their natural alpine settings. Initially planned transgenic experiments were changed into a natural crossing design. Early results give indication about functions of hotspot genes, with further testing planned to validate their fitness impacts.
The project has alignment with the European Green Deal’s focus on biodiversity and ecological resilience, by improving our understanding of how and why species use certain genes to adapt to extreme environments.
The impact of CONstrainCONverge extends beyond academic contributions, including significant advances in the researcher’s career development and the establishment of a collaborative network across Europe. The project’s outcomes are expected to contribute to empirical research of adaptation in evolutionary biology, perhaps offering practical insights into managing biodiversity in a changing world.
The project operates in four main work packages (WPs):
WP1 focuses on genome-wide inference of convergent selection, successfully identifying polygenic adaptations to alpine environments. The identification of ‘hotspot’ genes provides the foundation for further work, highlighting the significance of both regulatory and coding changes in adaptation.
WP2 involves transcription network analysis to estimate pleiotropic constraints. Initial findings suggest that genes with a wide range of network connectivity play key roles in adaptation, possibly with more connected genes being essential for adaptation to more extreme environments, with more analysis to come.
WP3 assesses pleiotropic constraints based on genomic position and has demonstrated that adaptive alleles are often shared across species, enhancing the understanding of the genetic basis of convergent evolution.
WP4 is the most challenging and focuses on the fitness effects and pleiotropy of hotspot genes in their natural alpine settings. Initially planned transgenic experiments were changed into a natural crossing design. Early results give indication about functions of hotspot genes, with further testing planned to validate their fitness impacts.
The project has alignment with the European Green Deal’s focus on biodiversity and ecological resilience, by improving our understanding of how and why species use certain genes to adapt to extreme environments.
The impact of CONstrainCONverge extends beyond academic contributions, including significant advances in the researcher’s career development and the establishment of a collaborative network across Europe. The project’s outcomes are expected to contribute to empirical research of adaptation in evolutionary biology, perhaps offering practical insights into managing biodiversity in a changing world.
The CONstrainCONverge project has made significant technical and scientific progress across its four main work packages (WPs), with outcomes in understanding the genetic mechanisms behind adaptive evolution.
WP1: The genome-wide analysis of convergent selection was completed, revealing that alpine adaptation in Arabidopsis is polygenic and partly repeatable across species. A list of repeatedly used ‘hotspot’ genes was established, serving as the basis for further work in other WPs. The discussion of the results was published in Trends in Ecology and Evolution, offering a detailed exploration of the genetic basis of convergence in natural systems.
WP2: Transcriptomic data was processed using tools like DESeq2 and WGCNA. The analysis revealed that adaptive genes exhibit variable levels of pleiotropy, with some acting as peripheral genes while others are highly connected "hub" genes within transcription networks. This suggests that more connected genes may play a key role in adapting to challenging environments. Part of the findings are under review for publication in PLOS Genetics, with data analysis ongoing to refine the understanding of these pleiotropic networks.
WP3: This WP focused on modeling the origins and positions of adaptive alleles in hotspot genes. I found that adaptive alleles are shared across species, sometimes even across species boundaries. Both regulatory and coding changes were found to contribute to repeated adaptation, and the proportion of these changes varies according to the gene's functional type (e.g. transcription factors vs. structural proteins). This work is complete, and the results will be combined with WP2 for publication.
WP4: This WP aimed to functionally assess the fitness impacts and pleiotropy of selected hotspot genes. A shift occurred in the experimental design, moving from transgenic approaches to natural crossings of alpine and foothill alleles to avoid potential genetic incompatibilities. Using this approach, naturally contrasting lines were generated for key genes, such as PAP1 (anthocyanin synthesis), FAR5 (fatty acid reductase), and MAP18 (pollen tube elongation). Initial experiments showed that the alpine allele of PAP1 is responsible for pink flower pigmentation, and the FAR5 gene alters suberin composition. However, fitness effects of these alleles have not yet been conclusively determined, and further experiments are planned for the 2025 growing season.
Overall Scientific Outcomes
The technical work accomplished in CONstrainCONverge has deepened the understanding of how pleiotropy shapes adaptive evolution, particularly in challenging alpine environments. The identification of pleiotropic constraints and convergent genetic mechanisms provides insights into how organisms repeatedly adapt to environmental pressures. The use of both genomic and transcriptomic data, along with the innovative shift to natural variability in fitness experiments, underscores the project's contribution to evolutionary genetics.
WP1: The genome-wide analysis of convergent selection was completed, revealing that alpine adaptation in Arabidopsis is polygenic and partly repeatable across species. A list of repeatedly used ‘hotspot’ genes was established, serving as the basis for further work in other WPs. The discussion of the results was published in Trends in Ecology and Evolution, offering a detailed exploration of the genetic basis of convergence in natural systems.
WP2: Transcriptomic data was processed using tools like DESeq2 and WGCNA. The analysis revealed that adaptive genes exhibit variable levels of pleiotropy, with some acting as peripheral genes while others are highly connected "hub" genes within transcription networks. This suggests that more connected genes may play a key role in adapting to challenging environments. Part of the findings are under review for publication in PLOS Genetics, with data analysis ongoing to refine the understanding of these pleiotropic networks.
WP3: This WP focused on modeling the origins and positions of adaptive alleles in hotspot genes. I found that adaptive alleles are shared across species, sometimes even across species boundaries. Both regulatory and coding changes were found to contribute to repeated adaptation, and the proportion of these changes varies according to the gene's functional type (e.g. transcription factors vs. structural proteins). This work is complete, and the results will be combined with WP2 for publication.
WP4: This WP aimed to functionally assess the fitness impacts and pleiotropy of selected hotspot genes. A shift occurred in the experimental design, moving from transgenic approaches to natural crossings of alpine and foothill alleles to avoid potential genetic incompatibilities. Using this approach, naturally contrasting lines were generated for key genes, such as PAP1 (anthocyanin synthesis), FAR5 (fatty acid reductase), and MAP18 (pollen tube elongation). Initial experiments showed that the alpine allele of PAP1 is responsible for pink flower pigmentation, and the FAR5 gene alters suberin composition. However, fitness effects of these alleles have not yet been conclusively determined, and further experiments are planned for the 2025 growing season.
Overall Scientific Outcomes
The technical work accomplished in CONstrainCONverge has deepened the understanding of how pleiotropy shapes adaptive evolution, particularly in challenging alpine environments. The identification of pleiotropic constraints and convergent genetic mechanisms provides insights into how organisms repeatedly adapt to environmental pressures. The use of both genomic and transcriptomic data, along with the innovative shift to natural variability in fitness experiments, underscores the project's contribution to evolutionary genetics.
The CONstrainCONverge project identified key genes involved in alpine adaptation, revealing the polygenic nature of this process and the varying pleiotropy of adaptive genes. Key results include the discovery of variable pleiotropic constraints and the role of both regulatory and coding changes in repeated adaptation. To continue, additional fitness experiments will be crucial, especially for validating gene-environment anf gene-fitness interactions. No immediate commercialization or IPR needs are foreseen, but international collaborations will continue to enhance the project's scientific impact.