Periodic Reporting for period 4 - No Sex No Conflict (Evolutionary Consequences of Arrested Genomic Conflict in Asexual Species)
Período documentado: 2024-10-01 hasta 2025-09-30
Genomic conflict arises when different genetic elements within the same organism pursue competing evolutionary interests. Such conflicts are a pervasive but often hidden force shaping genome architecture, gene regulation, development, and evolutionary innovation. They can generate maladaptation and impose constraints on phenotypic optimization, and they are increasingly recognized as contributors to human disease, including infertility, cancer, and developmental disorders. Despite their importance, genomic conflicts are difficult to quantify in natural animal populations because they are deeply embedded in the biology of sexual reproduction, where opposing selective pressures between males and females, between chromosomes, and between selfish genetic elements are tightly intertwined.
This project was built on the insight that asexual reproduction offers a powerful natural experiment to disentangle these effects. When species transition from sexual to asexual reproduction, all genetic elements are transmitted together through clonal inheritance, males are no longer produced, and most major sources of intra- and inter-genomic conflict are abruptly halted. Comparing sexual species to their independently derived asexual relatives therefore allows direct inference of how strongly sexual reproduction and genomic conflict shape phenotypes, gene expression, and genome structure.
The stick insect genus Timema provides an exceptional system for such comparisons. Asexuality has evolved repeatedly and independently within this genus, producing multiple sexual–asexual species pairs spanning tens of millions of years of evolution. The overarching goal of the project was to use these repeated transitions to asexuality to reconstruct the evolutionary consequences of arrested genomic conflict. Specifically, the project aimed to determine how sexual antagonism shapes gene expression across development, how sex chromosome regulation evolves when selection is relaxed, how centromeres and meiotic mechanisms respond to altered conflict regimes, and how genomic parasites such as transposable elements behave when their evolutionary interests are no longer opposed by sexual reproduction.
Together, these objectives allowed a systematic and integrative assessment of how deeply genomic conflict is embedded in animal genomes and how its removal reshapes genome evolution.
This project was built on the insight that asexual reproduction offers a powerful natural experiment to disentangle these effects. When species transition from sexual to asexual reproduction, all genetic elements are transmitted together through clonal inheritance, males are no longer produced, and most major sources of intra- and inter-genomic conflict are abruptly halted. Comparing sexual species to their independently derived asexual relatives therefore allows direct inference of how strongly sexual reproduction and genomic conflict shape phenotypes, gene expression, and genome structure.
The stick insect genus Timema provides an exceptional system for such comparisons. Asexuality has evolved repeatedly and independently within this genus, producing multiple sexual–asexual species pairs spanning tens of millions of years of evolution. The overarching goal of the project was to use these repeated transitions to asexuality to reconstruct the evolutionary consequences of arrested genomic conflict. Specifically, the project aimed to determine how sexual antagonism shapes gene expression across development, how sex chromosome regulation evolves when selection is relaxed, how centromeres and meiotic mechanisms respond to altered conflict regimes, and how genomic parasites such as transposable elements behave when their evolutionary interests are no longer opposed by sexual reproduction.
Together, these objectives allowed a systematic and integrative assessment of how deeply genomic conflict is embedded in animal genomes and how its removal reshapes genome evolution.
Over the lifetime of the project, all major objectives described in the Description of the Action were achieved. The work combined genome sequencing, transcriptomics, cytology, comparative genomics, and theory-driven evolutionary analyses, resulting in a uniquely comprehensive resource for studying genomic conflict in animals.
A major initial effort focused on building the genomic and experimental foundation required for all subsequent analyses. Chromosome-level genome assemblies were generated for the large majority of focal species, complemented by whole-genome alignments across all ten Timema species and the identification of approximately 12,000 one-to-one orthologous genes. In parallel, an extensive RNA-seq dataset was assembled, covering multiple tissues, developmental stages, sexes, and reproductive modes. These resources enabled direct and robust comparisons between sexual and asexual lineages at unprecedented resolution. In addition, new molecular tools were developed, including custom antibodies against key centromere and kinetochore proteins, allowing detailed cytological and chromatin-based analyses of chromosome behavior.
Using these resources, the project first addressed how sexual antagonism is expressed and resolved across development. By tracking sex-biased gene expression from early juvenile stages to adulthood, it revealed that sexual dimorphism in gene expression emerges much earlier than previously appreciated, particularly in developing gonads. Comparisons with asexual sister species showed that most sexual antagonism over gene expression is efficiently resolved in sexual species, with only a restricted set of genes retaining signatures of unresolved conflict.
The project then examined the fate of sex chromosome regulation under relaxed selection. By combining developmental transcriptomics with cytological analyses, it produced the first complete picture of dosage compensation and meiotic sex chromosome inactivation in a hemimetabolous insect. Contrary to long-standing theoretical expectations, both mechanisms were found to be remarkably stable in asexual lineages that no longer experience selection on males.
One of the most striking outcomes of the project emerged from work on centromere evolution. While developing tools to study centromere drive, the project uncovered a previously unknown form of chromosome organization and meiosis in Timema. These insects possess chromosomes that are functionally monocentric yet display hallmarks of holocentricity. This discovery revealed an unanticipated degree of flexibility in centromere organization and established Timema as a new model for studying chromosome evolution. Ongoing comparative analyses of centromere sequences in sexual and asexual species are now providing the first empirical tests of centromere-drive theory across repeated, independent transitions in reproductive mode.
Finally, the project investigated how transposable elements and other repetitive sequences evolve when genomic conflict is reduced. Long-read genome assemblies and improved annotation pipelines allowed reconstruction of transposable element turnover across the Timema phylogeny.
Overall, the work performed not only fulfilled but substantially exceeded the original aims of the project. The remaining effort at the end of the action concerns the synthesis and writing of two very large comparative genomics papers that integrate these results across work packages and are expected to have particularly broad impact.
A major initial effort focused on building the genomic and experimental foundation required for all subsequent analyses. Chromosome-level genome assemblies were generated for the large majority of focal species, complemented by whole-genome alignments across all ten Timema species and the identification of approximately 12,000 one-to-one orthologous genes. In parallel, an extensive RNA-seq dataset was assembled, covering multiple tissues, developmental stages, sexes, and reproductive modes. These resources enabled direct and robust comparisons between sexual and asexual lineages at unprecedented resolution. In addition, new molecular tools were developed, including custom antibodies against key centromere and kinetochore proteins, allowing detailed cytological and chromatin-based analyses of chromosome behavior.
Using these resources, the project first addressed how sexual antagonism is expressed and resolved across development. By tracking sex-biased gene expression from early juvenile stages to adulthood, it revealed that sexual dimorphism in gene expression emerges much earlier than previously appreciated, particularly in developing gonads. Comparisons with asexual sister species showed that most sexual antagonism over gene expression is efficiently resolved in sexual species, with only a restricted set of genes retaining signatures of unresolved conflict.
The project then examined the fate of sex chromosome regulation under relaxed selection. By combining developmental transcriptomics with cytological analyses, it produced the first complete picture of dosage compensation and meiotic sex chromosome inactivation in a hemimetabolous insect. Contrary to long-standing theoretical expectations, both mechanisms were found to be remarkably stable in asexual lineages that no longer experience selection on males.
One of the most striking outcomes of the project emerged from work on centromere evolution. While developing tools to study centromere drive, the project uncovered a previously unknown form of chromosome organization and meiosis in Timema. These insects possess chromosomes that are functionally monocentric yet display hallmarks of holocentricity. This discovery revealed an unanticipated degree of flexibility in centromere organization and established Timema as a new model for studying chromosome evolution. Ongoing comparative analyses of centromere sequences in sexual and asexual species are now providing the first empirical tests of centromere-drive theory across repeated, independent transitions in reproductive mode.
Finally, the project investigated how transposable elements and other repetitive sequences evolve when genomic conflict is reduced. Long-read genome assemblies and improved annotation pipelines allowed reconstruction of transposable element turnover across the Timema phylogeny.
Overall, the work performed not only fulfilled but substantially exceeded the original aims of the project. The remaining effort at the end of the action concerns the synthesis and writing of two very large comparative genomics papers that integrate these results across work packages and are expected to have particularly broad impact.
This project advances the state of the art in several fundamental ways. It provides the first direct, comparative quantification of genomic conflict using replicated transitions to asexuality in animals. It overturns the assumption that key sex chromosome regulatory mechanisms rapidly decay under relaxed selection, instead revealing their surprising evolutionary stability. It uncovers an entirely new form of centromere organization and meiosis, demonstrating that chromosome architecture is far more flexible than previously recognized. Finally, it delivers the first comparative tests of centromere-drive and repeat evolution theories in a natural, phylogenetically replicated framework.
Taken together, the project demonstrates that sexual reproduction leaves deep and lasting imprints on genome structure and regulation, many of which persist even when selection is relaxed. By showing how asexuality exposes, modifies, or freezes these processes, the project establishes transitions in reproductive mode as a powerful lens through which to study genome evolution. The datasets, tools, and conceptual advances generated by this work will continue to inform research on genomic conflict, chromosome biology, and reproductive evolution well beyond the lifetime of the grant.
Taken together, the project demonstrates that sexual reproduction leaves deep and lasting imprints on genome structure and regulation, many of which persist even when selection is relaxed. By showing how asexuality exposes, modifies, or freezes these processes, the project establishes transitions in reproductive mode as a powerful lens through which to study genome evolution. The datasets, tools, and conceptual advances generated by this work will continue to inform research on genomic conflict, chromosome biology, and reproductive evolution well beyond the lifetime of the grant.