"Mutation" refers to special effects and abilities that the Alien Units can gain or use via the Overmind Player's Mutation cards.
There are two kinds of Mutation cards: Forced Mutation cards, and Ultimate Mutation cards. The Overmind Player starts the game with a deck of 20 Forced Mutation cards. The Ultimate Mutation cards can be gained as upgrades.
Forced Mutation cards can be played at any time for the effect described by the card. Many of the cards also have a more powerful version of its effect, the "Supreme Mutation" option, which can be gained by discarding another Mutation card when playing the Forced Mutation card for its "Supreme Mutation" effect.