Modeling the impact of unequal recombination on multigene family copy number variation in apomictic lineages

Copy number variation in multigene families composed of tandemly arrayed repeat units is shaped in part by recombination events such as unequal homologous chromosome exchange (HCE) and sister chromatid exchange (SCE). To explore the relative contribution of intrachromosomal and interchromosomal recombination to multigene family copy number dynamics in apomictic organisms, we conducted computational simulations using empirically determined parameters obtained by measuring recombination rate in the 45S rDNA of mutation accumulation lines of Daphnia obtusa. Our simulations showed that copy number variance across generations was greater when the rate of SCE exceeded that of HCE. This pattern was partially driven by the higher frequency of recombination events associated with SCE, even if HCE offset sizes were larger. These results highlight the distinct roles of recombination modes in shaping the copy number of multigene families arranged in tandem arrays.