This was the product of months of data collecting and 16million generations of simulated Pokémon evolution.
The results are surprisingly realistic! Pokémon life seems to have begun in the water, with terrestriality evolving later. The psychic pokemon evolved from the birds. The missing link between the grass types and the normal types is Venusaur. Nidoking and Nidoqueen are sister groups and should probably be lumped into the same species. Etc, etc.
The best part: The paper was PUBLISHED in a peer reviewed [humor] journal! And PROFESSOR OAK IS THE CO-AUTHOR! Published in the Annals of Improbable Research, vol 18, nov 4, p15-17. "A Phylogeny and Evolutionary History of the Pokémon." by Matan Shelomi, Andrew Richards, Ivana Li, Yukinari Okido.
See the tree below: