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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 2 - ComplexSex (Sex-limited experimental evolution of natural and novel sex chromosomes: the role of sex in shaping complex traits)

Teaser

Summary

The origin and evolution of sexual reproduction and sex differences represents one of the major unsolved problems in evolutionary biology. The standard model for sex chromosome evolution assumes that sexually antagonistic loci (genes with opposite fitness effects in males and female) accumulated near a novel sex determining locus, leading to suppression of recombination and eventual degeneration of the non-recombining chromosome (e.g. Y or W). Although much progress had been made both via theory and empirical research, recent data suggest that sex chromosome evolution may be more complex than previously thought. The concept of sexual antagonism has become essential to our understanding of sex chromosome evolution. Sexual antagonism occurs when there is a positive intersexual genetic correlation in trait expression but opposite fitness effects of the trait(s) in males and females (it is also known as intralocus sexual conflict when the trait is the same in both sexes). Although it has long been considered likely that the differentiation of new sex chromosomes via cessation of recombination is because of selection on sexually antagonistic loci, the direct evidence that sexual antagonism is the driving force is surprisingly slim. In addition to the link between sexual antagonism and sex chromosome evolution, sex chromosomes are known to be important in shaping the genetic architecture of complex traits. Finally, although most theoretical models of sexual antagonism deal with single or very few loci, most of the empirical data comes from quantitative traits. This project therefore aims to fill in the gaps in our knowledge about how the interacting effects of sex-linked genetic variation and sex-specific selection shape the genetic architecture of complex traits. A better understanding in this area can help us explain how and why sex differences evolve, which is important for a wide range of questions, including sex-specific adaptation to e.g. climate change, sex differences in disease prevalence and severity, and population divergence and speciation.
Main objectives:
1. To recreate in the lab three key points in the evolution of sex chromosomes: establishment of a new sex chromosome (WP4), between-population divergence of sex chromosomes (WP2), and within-population adaptation in a sex chromosome (WP1).
2. To test the hypothesis that sexually antagonistic loci are a key component in the above stages in sex chromosome evolution
3. To test theoretical predictions about the relationship between individual sexually antagonistic loci and trait-level evidence for sexual antagonism
These objectives are addressed by five work packages: female-limited X-chromosome evolution in Drosophila melanogaster, X-Y coevolution in Drosophila melanogaster, quantitative genetics of fitness in the hermaphrodite flatworm Macrostomum lignano, experimental evolution of a novel sex chromosome in Macrostomum lignano, and modelling of sexual antagonism in hermaphrodites and sex chromosome evolution.

Work performed

WP1) Female-limited X-chromosome evolution: For this part of the project it was planned that pooled sequencing of RNA from the heads of flies (to measure gene expression) and DNA (to measure allele frequency changes across populations) would be completed, as well as fitness assays and sequencing of individual genotypes. Extraction of RNA from heads for sequencing has been carried out but took longer than expected, so the other parts of this work package were delayed. Analysis of the RNAseq data is currently underway. The first attempt at DNA extraction for the pooled DNA sequencing was unsuccessful, but good quality DNA was extracted on the second try using a different extraction protocol. These samples have now been submitted for sequencing. In addition, more phenotypic assays have been carried out, and it has become clear that the FM balancer chromosome used as part of the experimental evolution protocol has had a larger effect than anticipated. This has led us to plan to do additional analysis of the effect of adaptation to the FM. We have also determined that most of the adaptation to the FM balancer is through male fitness effects, so this means that we have a combination of different sex-specific selection pressures on the X chromosome and autosomes between the FLX and CFM treatments. This unanticipated result is interesting in that it gives us new predictions for how these effects will change G- and B-matrices between treatments. A large quantitative genetics study addressing this question will be carried out in 2019. Two manuscripts (based on results in Katrine Lund-Hansen\'s PhD thesis) are currently being prepared for submission; one presenting the phenotypic results of the experimental evolution and one the results of the pooled RNAseq analysis of whole flies.
WP2) X-Y coevolution: For this part of the project it was planned that the experimental evolution portion of the experiment would be completed, DNA sequenced to look for changes as a result of adaptation to the presence of a novel Y chromosome, and results published by this point. Experimental evolution was completed as planned and samples obtained, but we have decided to carry out RNAseq of males with mis-matched sex chromosomes instead of DNA sequencing of the evolved populations. This decision has been taken after the development of a model to validate our speculation that sexually antagonistic effects can be responsible for the observed increase in male fitness in males with mis-matched sex chromosomes (see also WP5 below). The model confirmed our proposed explanation as being biologically plausible, but suggested that most of the effect will be due to incomplete selective sweeps at relatively few loci. This sort of signature would be very difficult to detect in the pooled DNA data, so RNAseq to identify the possible mechanisms behind the increase in male fitness was deemed more likely to provide relevant insights. Samples for the RNAseq analysis are currently being produced, and a manuscript of the phenotypic results and model is currently in preparation.
WP3) Quantitative genetics of fitness in a hermaphrodite: For this part of the project it was planned that all data collection would be completed and in the process of being published. This work package has progressed according to plan, and the manuscript (based on a chapter from Anna NordÃ©n\'s PhD thesis) is currently in preparation for submission.
WP4) Neo-sex chromosome evolution: For this part of the project it was planned that experimental evolution should be completed and population-level phenotypic assays carried out, as well as pooled RNAseq data obtained. This part of the project has progressed as expected. We confirmed that the experimental evolution protocol has been successful and measured several phenotypes, and RNAseq data has been obtained and is currently being analyzed. Additional phenotypic assays measuring the plastic response to food restriction and mating behaviour are currently under

Final results

Based on the results to date, I anticipate that the main general insight gained from the project will be how valuable experimental evolution can be in testing theories of sex chromosome evolution. The majority of work on sex chromosome evolution is currently comparative in nature, e.g. using genomics to compare species of different relatedness. This approach has been very successful in demonstrating how much more variation there is in sex chromosome evolution than was anticipated. However a weakness of this approach is that it is impossible to disentangle cause and effect from stochastic changes. In a recently submitted manuscript from a previous project, I was able to show how experimental evolution managed to recapture on a microevolutionary scale, macroevolutionary effects on the evolution of sexual dimorphism, constraints arising from dosage compensation, and mitonuclear interactions. Since RNAseq and DNAseq data collection and analysis is still underway, it\'s difficult to say at this point exactly what patterns we will find this time, but I think it\'s clear that experimental evolution has the potential to provide results beyond the current state of the art.

Apart from an increased understanding of sex chromosome evolution at various scales, the contribution of coevolution of the sex chromosomes to population divergence will be important to our understanding of speciation and hybridisation, and may provide a new dimension to Haldane\'s rule (the fact that among hybrids, it is usually the hemizygous sex that is sterile or inviable). Similarly, an understanding of the stability of the G- and B-matrices and how they are shaped by sex-specific selection on different parts of the genome will help us to better understand the genotype-phenotype map.