There are three skill trees to upgrade in Far Cry 3, each corresponding to a different set of tattoos that will appear on your arm as you acquire more skills. It's all got something to do with "becoming a warrior," in some mystic sense, as you fight to prove yourself to a tribe led by lead pirate Vaas's sexy sister, Citra.
You'll interact with the world and go about confrontations slightly differently depending on what skills you choose. The Heron path focuses on long range and mobility, with skills that let you reload without breaking away from your scope, sprint longer, and take out enemies from above their heads.
The Shark has skills like first aid and up-close stealth kills, as well as those that aid in defense, and the Spider focuses on stealth and survival; sliding at the end of a long sprint, archery, etc.