There are lots of animals in the anime - when they show "underwater" scenes, in addition to fish Pokemon, they show actual schools of fish swimming along too, for example.
Also, in the Pokedex of both games and the anime, there are tons of references to real-world animals. Raichu and Gastly's entries both infamously refer to "Indian elephants" for some reason.
These are both FireRed entries:
Raichu - Its electric charges can reach even 100,000 volts. Careless contact can cause even an Indian elephant to faint.
Gastly - A being that exists as a thin gas. It can topple an Indian elephant by enveloping the prey in two seconds.
And not to mention, the species listed in the Pokedex frequently refer to real-world animals too, like "Charmander, the Lizard Pokemon", "Squirtle the Young Turtle Pokemon", and so on, so animals must exist in addition to Pokemon, otherwise entries like "lizard Pokemon" mean nothing to them. So humans still belong to the animal kingdom, since it does exist.
The most troubling, to me, is that a lot of Ghost Pokemon entries in the Pokedex clearly state that some Pokemon used to be human. Like Yamask, who are spirits of people that are now holding their own faces. Or Phantumps, who are all just tree stumps possessed by dead human children.
So yeah, I have no clue what Pokemon actually are, they just range from "kind of like real animals but not really" to "sentient inanimate objects" and "actual dead people that other people now catch and force to battle", but in terms of "where do humans come from", since animals do exist in the Pokemon world as a separate kind of creatures, then humans still evolved from animals.
I think that's what you're asking, at least, sorry if I misunderstood. :P
