The changed eye color of the apes is a side-effect of the ALZ 111, 112, & 113 virus. What's also interesting is the manufactured virus meant to originally to "cure" Alzheimer's by repairing/enhancing certain areas of the brain in the films somewhat hinted what would happen. In the first film when a scientist tried the ALZ 111 on his ailing father the father was "cured" for 5 years before the illness returned tenfold. Now consider the stronger strain (113) was released by accident to the human population by the first film's ending. By the 3rd film, it seems more likely it wasn't merely a mutation...but a natural end result. The critical error was not just the scientists assuming animals & humans "evolved" in the first place...they also assumed God's unique design of DNA & Genetics was transferrable.