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Well i had a villgar that had breeding skill and the box was not checked. Belive me, i saw him do it!

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I once had an original villager with just a tiny chunk of breeding skill. She was a master scientist, and her prefrences were set to "science", but every time I'd get on the game, I'd hear smooch while I was still on the loading screen! By the time the screen was up she'd be toting a baby. I grew to hate her...

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It might have been a male that was responsible (yes, I know, they are always responsible! )

When a villager has breeding as a preference, they will look for the Alpha Male or Female of the appropriate gender to mate with. The Original villagers are often first on the list and therefore will be "chosen."