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First of all, given that we only have a limited sample of the Y-chromosome space, I don't think we can conclude that no native Y-chromosomes actually survived. That aside, it's easy to get selection for specific Y chromosomes without extermination, for example if you have a ruling caste whose males are favored (e.g. by primogeniture) or through preferential mating by lineage. See: the prevalence of the (presumed) Chingisid chromosome here: https://doi.org/10.1086%2F367774



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