Genome evolution in hybrid Formica aquilonia × F. polyctena ants

Hybridization is frequent in the wild but it is unclear at which timescale may admixture events lead to predictable outcomes. We show that selection led to correlated sorting of genetic variation in less than 50 generations in three hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.