I would also really like a real family tree.
For now I have a naming scheme that works really well for me for animals with one alpha male:
Put the generation of the animal in front of their name, and name the stud bock something so you always recognize it.
For example: I buy a few female and one male pronghorn antelopes. I put "1" in front of their names. Then, when they have offspring I put "2" in front of their names. As soon as the first female pronghorn with a 2 in front of her name becomes an adult, I know that I have to switch out the male to prevent incest. The new male gets called "2 something", and all of his offspring "3 name". And so on. That makes breeding way easier imo because I immediately know where there's risk of incest.
Renaming a bunch of animals is actually pretty easy in the all animals in the zoo list because you can press the tab key to apply the name you're currently renaming and switch to the next animal. I made a makro key on my keyboard that types tab, arrow left, a number, space