It seems that the answer to this question is linked with the "alternative" version of events that Pi gives to Mr. Chiba and Mr. Okamoto in Chapter 99 of the tale, who are obviously unconvinced by the version that Pi gives them and us as readers. Trying to come up with a different story, Pi gives a much more realistic account of what supposedly happened, with each of the animals clearly represented by a character. Thus it is that the zebra is replaced by a sailor, the hyena by the cook, and the orangutang by his mother. Interestingly, the only animal that is absent is Richard Parker, the tiger, which suggests that allegorically Richard Parker in the "first" tale represents Pi himself. The second tale charts the way in which Pi was forced to kill the Cook and how he ate human flesh to sustain himself:
I stabbed him in the throat, next to the Adam's apple. He dropped like a stone. And died. He didn't say anything. He had no last words. He only coughed up blood. A knife has a horrible dynamic power; once in motion, it's hard to stop. I stabbed him repeatedly. His blood soothed my chapped hands. His heart was a struggle--all those tubes that connected it. I managed to get it out. it tasted delicious, far better than turtle. I ate his liver. I cut off great pieces of his flesh.
Note how Pi is forced to become savage himself to survive. He later comments that the sailor was an evil man, but that worse was the way in which he met "evil" in Pi too. By allegorically creating Richard Parker to represent this untamed savagery in his original story, Pi symbolically indicates his own descent into savagery in his grim battle for survival.