This always was, and is, the natural order: Women want serial monogamy. She wants the highest-value man she can get, all to herself, until a better man wants her. Men want polygyny. He wants to collect as many high-value women that desire him, and will follow him, as he can.
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It's effective population size, not population size. I think the Bronze Age collapse decreased this, but that's not a genetic bottleneck.
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The Y chromosome is small; it's not likely that men with particularly effective Ychrs took over. Some subpopulations of men took over, and their Ychrs dominate as a result. The genomes of the other men are still around, except in their paternal lines.
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It doesn't even have to be particularly violent to work: found a dynasty, one where your sons, and your sons' sons, have 4 kids while everyone else has <2, and 500 years later your Y chromosome is dominant. It's happened in living memory multiple times.
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