Testing new hypotheses on the evolution  of sex-related chromosomes
The sex chromosomes of plants and animals often contain large non-recombining regions due to a stepwise cessation of recombination generating “evolutionary strata” of genetic differentiation. The reasons for the extension of recombination suppression beyond sex-determining genes remain unclear. Sexual antagonism, involving the linkage to sex-determining genes of alleles beneficial in only one sex, is the prevailing hypothesis, as this explanation is both theoretically plausible and attractive. However, decades of research have unearthed little evidence to support this hypothesis. Furthermore, I have shown that chromosomes involved in sexual compatibility in systems lacking male and female functions can nevertheless display a stepwise suppression of recombination beyond mating-compatibility genes. Thus, evolutionary strata can evolve without sexual antagonism. Alternative hypotheses, such as neutral rearrangements, epigenetic changes associated with transposable elements and the sheltering of deleterious alleles accumulating near non-recombining regions, must thus be seriously considered. I propose to use a synergic combination of different approaches and biological systems to refine and test these hypotheses, to broaden the theory of sex-related chromosome evolution, and, more generally, of the evolution of supergenes (linked allelic combinations). I will use mathematical modeling to test hypothesis plausibility and generate predictions. I will use comparative and population genomic approaches to test predictions, and an innovative experimental evolution approach with functional manipulations to assess the ability of the proposed mechanisms to generate strata. The EvolSexChrom project will challenge the current theory, opening up new avenues of research and potentially creating a paradigm shift in the dynamic research field focusing on the evolution of sex-related chromosomes and other supergenes, relevant to diverse traits and organisms.