Towards a unified model of aneuploid karyotype dynamics

Aneuploidies—whole-chromosome copy number imbalances arising from nondisjunction—underlie numerous congenital and somatic disorders, but unlike many other disease-causing variants, they can revert back to euploidy through subsequent errors of the same type. The extent to which this inherent plasticity impacts the stability and persistence of aneuploid karyotypes in populations remains poorly understood, a gap in knowledge that continues to limit our understanding of aneuploidy-driven disease incidence, penetrance, and progression. To assess how reversion shapes aneuploid population dynamics, we developed a budding yeast system to systematically measure the rates at which aneuploidies arise and revert and quantify the relative fitness differences between these karyotypic states. We integrated these data into a computational framework encompassing the broad physiological range of aneuploid karyotype dynamics captured in our experiments. The resulting models reveal that canonical reversion ( i.e. , subsequent secondary nondisjunction) occurs rarely, conferring a negligible effect on the population dynamics of most chromosomal aneuploidies. However, our models also identified that the reversion dynamics of some chromosomes—those displaying extremely high apparent rates of reversion—were more consistent with a coupled mutational process involving a transient aneuploid state. Whole-genome sequencing and live-cell microscopy demonstrates that this mechanism is facilitated by unresolved intermolecular linkages that disrupt chromosome segregation, leading to chromosome breakage and recombination-mediated repair over subsequent cell divisions. Collectively, this work advances a model of aneuploid population genetics and expands our perspective of the diverse, and chromosome-specific, mutational mechanisms shaping genome architecture.