In my combo-campaign I had two mutant bosses and one animal boss. The people was also divided the same way (so it was 2/3 mutants and 1/3 animals).
I also created some backstory that a smaller Ark that before they had the chance to develop their community they met a small stray group of animals (I wanted to have around 200 "people" living in the ark, the normal start amount). The campaign started a couple of years after this meeting so the two groups had a chance to teach the other group their roles and talents. I limit the old animals to only play the animal roles, the other two age group can choose anything. The animal boss is also the alpha of the biggest animal group (dogs in my campaign). There are only a few rabbits in the Ark (what happen to the rabbits after GA is described in Die, Meateater, Die). The big animal groups (apes, rats) have their alfas but are under the boss alfa.
Socially the mutants think of themselves as superior and don't care of the ranks that the animals have. I should also mention that I have something called social status* in my campaign. This is the only thing that the mutants care about. The animals are divided. Some animals think it was a bad idea to live together with the mutants and want to find where the rest of the animals (they have heard that at least one big group of animals have an all-animal ark.
* The Elder (5)
* Boss (4)
* Seer, Chronicler (3)
* All other (2)
* Scavengers & Workers (NPCs with no role) (1)
* Slaves (0)
The difference is a modifier when you manipulate (I use a negative modifier as a bonus to the other side). This modifier applies only when you manipulate within your own social group (i..e your Ark) and not for people you meet out in the zone. It can also apply to another ark if that ark has a similar culture and have some sort of relations with your ark.
The main difference here is that the animals can't manipulate (and that is actually tough to not being able to do that). Sure they can dominate, but dominating a mutant or a human is basically only a variant of Intimidate, since the mutants can't dominate back, they can only defend against the domination (with Sense Emotion). This setup will create a society where the animals become secondary citizens. This was also the case in the original game (the original from the 80s) so I wanted my world to slowly grow inte the same thing.
“Thanks for noticin' me.” - Eeyore