Crossover is believed to initiate at specific sites called hotspots, by combinational-repair mechanism in which the initiating hotspot is replaced by a copy of its homologue. Boulton et al. studied through simulation the effect of this mechanism, and observed in their model that active hotspot alleles are rapidly replaced by inactive alleles. This is paradoxical because active hotspots alleles do not disappear in natural systems. We give a theoretical analysis of this model, which confirms their experimental result, and we argue that they failed to take properly into account the benefits of recombination, because of the optimality of their initial population. On the other hand, we show that even with an initial population of low fitness the model does not sustain the active hotspot alleles. Those results suggest that at least one model is wrong, either the one for the recombination of chromosomes, or the one for the diffusion of the hotspot alleles: we suggest another model for the diffusion of hotspots alleles.
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