A tree of life for every Pokemon that is based on a real organism. Contains Plantae, Fungi, and all of Animalia. Each Pokemon is shown in the group of the organism it represents. So that means it is not following any of the lore that says that mew is the ancestor to all Pokemon, or that Arceus created the rest. Arceus looks like a horse, so it's counted as a horse, not a god. This is going mostly off of Bulbapedia's description of what they're supposed to be. Keep in mind that I've only taken Botany, Icthyology, Invertebrate zoology, and Marine Mammal zoology, so all the rest are based off of wikipedia's description of relatedness and such.
Also, Paras and Parasect are on here twice, one for the insect that is the basis, and one for the fungus that is taking over them. I couldn't think of any others that were clearly two different creatures in one, so that's the only example of that.
Also, I'm working on another one with all the Pokemon based on non-living or non-real things, like ghosts and dragons, so that will be up shortly as well.
It's a really large file, so I had to decrease the quality a bit. Also, I'm not quite sure how you guys will be able to view it and navigate around to see it all, but if it doesn't seem to work, you can just download it and you should be able to view it from ms paint or whatever.
Let me know what you think!
Edited to include a couple I missed, as well as the gen 6 Pokemon revealed so far.
Xerneas sprite by TomTheZombie
Froakie sprite by BaconBoy914
Fennekin sprire by Kevfin
Chespin sprite by DancesofShadows
Updated with the Tympole line, which I had forgotten, moved the eeveelutions around a bit, and moved Charmander and Charmeleon to the Mythologidae. Also moved the blobs to protista.
Check out the other one here: [link]