Sexual reproduction is ancient and ubiquitous despite its obvious disadvantages1. Theory predicts that the reassortment of alleles that results from sex is necessary for natural selection to act effectively on individual loci; therefore, a purely clonal organism should rapidly accumulate deleterious mutations and go extinct2–4. Nevertheless, many asexual species have existed for longer than theory predicts is possible5–7, such as the Amazon molly (Poecilia formosa), a clonally reproducing fish arising from a single hybridization event more than 100,000 years ago8–10. Here we show that although the Amazon molly has accumulated mutations faster than its sexual progenitor species, this has not led to functional mutational decay, defying theoretical expectations. Instead, gene conversion facilitates both adaptive and purifying selection by generating new clonal lineages in which previous mutations are either reverted or fixed, and by resolving hybrid incompatibilities between the ancestral haplotypes. The transition to clonality altered chromatin structure, but the asexual haplotypes of the Amazon molly nonetheless maintain the divergent mutational landscapes of their progenitor species. Together, these results provide new insights into long-standing questions about the trade-offs involved in asexual reproduction.
