Y chromosome introgression between deeply divergent primate species

Hybridization and introgression are widespread in nature, with important implications for adaptation and speciation. Since heterogametic hybrids often have lower fitness than homogametic individuals, a phenomenon known as Haldane’s rule, loci inherited strictly through the heterogametic sex rarely introgress. We focus on the Y-chromosomal history of guenons, African primates that hybridized extensively in the past. Although our inferences suggest that Haldane’s rule generally applies, we uncover a Y chromosome introgression event between two species ca. six million years after their initial divergence. Using simulations, we show that selection likely drove the introgressing Y chromosome to fixation from a low initial frequency. We identify non-synonymous substitutions on the novel Y chromosome as candidate targets of selection, and explore meiotic drive as an alternative mechanism. Our results provide a rare example of Y chromosome introgression, showing that the ability to produce fertile heterogametic hybrids likely persisted for six million years in guenons.