Behind the shadow play: Shedding light on the population genetics of partially clonal organisms through clone age distributions

Abstract

Partial clonality is widespread in natural populations; however, the distributions of clone ages under different rates of clonality and their effects on genetic diversity remain unexplored. To fill this gap, we simulated partially clonal populations over 10,000 generations across a range of clonality and mutation rates. Using a forward-in-time individual-based model, we evaluated genetic and genotypic indices alongside measures of clone age distribution to examine how different clonality rates influence clone age distributions, and how these distributions impact population structure and genetic diversity over time. Our results reveal two distinct trajectories: (i) at low to moderate rates of clonality evolution is driven by sharp and predictable patterns of rapid clone turnovers, resulting in predominantly young clones which relative abundances well align with genotypic indices ; (ii) at extreme rates of clonality, demographic stochasticity generates very variable clone age distributions which mirror the high variance of mean and variance of FIS that summarize gene reshuffling between individuals. Interestingly, a portion of the variability of these indices can be explained by differences in clone age distribution that occur by chance. Our results, therefore, complement previous theoretical studies on the population genetics of partial clonality by providing biological insights into how clonal turnover dynamics shape the temporal evolution and variability of highly clonal populations. These results have practical implications for inferring evolutionary trajectories and managing partially clonal species.