There are actual genetics? hmm... I need to be a little more selective with which animals I slaughter then...
oh yes. I did some tests on this with rabbits.
I embarked with 10 bunnies. male and female. then i checked their traits and ended up terminating one, keeping 9. these 9 were unique enough for me to trace their genes via skin and eye-color.
what I found was that they impregnate eachother regardless of location. (through grates, doors, pens, walls...) (i didn't try across z-levels but I assume it's the same) but that's been researched before me and confirmed so it's old news ... but what was news to me was that Female specimen 5 was impregnated by male specimen 4, even though he was on the other side of the map and she had male specimen 2 right next to her. They were placed in the same pen because I wanted their offspring.
This means that, save for having only 1 male (and avoiding interference from wildlife and merchants) there is no way to control who mates with who.
A tiny, skinny, good-for-nothing male can instantly inseminate every single female in the herd regardless of his location and in spite of your best attempts to breed good meat-yielding livestock.
I imagine the best way to go about it is this:
Kill all weak males at birth.
Place all weak females in a special pasture, butcher them as they reach adulthood.
Only keep strong animals.