How I would implement species traits would be 1 would be free, but anymore after that (Full max of three) the others would require you to make a disadvantage for the species per extra trait.

Example:
Trait 1 - Can live flourishingly in frozen temperatures

Trait 1 - increased melee damage due to claws
Trait 2 - Can live flourishingly in frozen temperatures
Trait 3 - Can not live in dry environments at all