Searching for intralocus sexual conflicts in the three-spined stickleback (Gasterosteus aculeatus) genome

Differences between sexes in trait fitness optima can generate intralocus sexual conflicts that have the potential to maintain genetic diversity through balancing selection. However, these differences are unlikely to be associated with strong selective coefficients and are challenging to detect. Additionally, recent studies have highlighted that duplications on sexual chromosomes can create artifactual signals of intralocus sexual conflicts. Thus, testing the relationship between intralocus sexual conflicts and balancing selection requires stringent filtering of duplicated regions, and dedicated methods to detect loci with low levels of intersex differentiation. In this study, we investigated intralocus sexual conflicts in the three-spined stickleback using whole-genome sequencing (mean coverage = 12×) of 50 females and 49 males from an anadromous population in the St. Lawrence River, Québec, Canada. After stringent filtering of duplications from the sex chromosomes, we compared three methods to detect intralocus sexual conflicts. We found only two genomic regions under potential intralocus sexual conflict that also showed signals of balancing selection. Overall, our results suggest that most intralocus sexual conflicts do not drive long-term balancing selection and are most likely transient.