Abstract
Classical mutational theories centered on single nucleotide polymorphisms suggest that outcrossing enhances the purging of deleterious mutations by promoting recombination. However, larger structural variants, such as insertions, deletions, and inversions, can suppress recombination and create linkage blocks. In this study, using experimental evolution in C. elegans lines and whole-genome sequencing, we show that outcrossing populations struggle to purge structural mutations and instead retain mutations small and large as single nucleotide polymorphisms become trapped within larger structural variants. Supporting this, our population genetic simulations showed that structural variants accumulate more readily under higher outcrossing rates. These findings contradict classical population genetic expectations, showing that outcrossing can hinder the removal of structural mutations and complicate mutation purging by trapping small variants within larger mutations. Together, our results challenge the prevailing view that sex uniformly promotes genomic resilience and reveals a previously underappreciated constraint on mutation purging.