In the September 2016 Unearthed Arcana The Ranger, Revised, it says:
Your companion uses your proficiency bonus rather than its own.
The ape, for example, has a +5 bonus to Athletics and +3 to Perception. When the ape becomes a ranger's companion, does the ranger's proficiency bonus compound with these bonuses or replace them? That is, are these bonuses considered the ape's "proficiency bonus"?
It also says:
Your animal companion gains proficiency in two skills of your choice.
Is the ape considered already proficient with Athletics and Perception?