At first glance, the meerkats on the island sleeping on trees seem to be a clear example of Somewhere, a Mammalogist Is Crying, because those animals actually live in burrows. But from an evolutionary standpoint, it makes perfect sense: Imagine a bunch of meerkats by some means arriving on the island. Those who show their normal behavior of creating burrows quickly get devoured by the island, and only a few, showing the abnormal behavior of climbing on trees, survive. Those are the ancestors of the current meerkat population Pi encounters. That's how natural selection works! ( Of course, the point is moot if Pi just made everything up.)
Also do note Pi being raised by someone who clearly understood biology and in the book his atheist biology teacher. If he did make it up, then that was more than likely on purpose.
Pi's second story accounts for all the characters and events that happened in the first story, except for one: the island. Except, it does. If you choose to believe the second story, then what happened is that Pi found one of the other survivors' teeth in the boat, probably the cook's.
The carnivorous island Pi finds himself on sort of resembles a dead body from afar in the film. The roots from the trees could represent human veins, and the meerkats could represent maggots.
Actually in the film, the island resembles the famous image of the sleeping Buddha, a representation often replicated in illustration and sculpture. What it suggests of the connection between the Buddha and the carnivorous nature of the island is up for debate. Do note that image mostly came about from the time the Buddha knew he was dying, and simply took that position while sleeping in order to die peacefully.
Given the above, one possible interpretation is that the island represents suicide. Pi, having given in to despair, finds the idea of giving up and dying increasingly attractive, represented by the idea of staying on the island and giving up on ever being rescued. Finding the tooth could represent him coming to his senses and regaining his will to survive.
Another implication of the second story is that Pi was forced to cannibalize his mother - in the book it is only her head the cook threw overboard, and in the animal version Richard Parker eats part of Orange Juice's body after the hyena kills her. If the island is meant to represent a dead body, it was likely his mother's body.
Except Pi was never forced to cannibalize his mother - the cook throws her head into his lap, after which it sinks, and then a little later the cook pushes the rest of her body overboard, with the implication that he, the cook, had eaten part of her first. Richard Parker is never explicitly stated to have eaten Orange Juice - Pi only observes him eating the hyena.
A still different interpretation is that while the first story ends with a big climatic story that takes faith to believe in, the second story ends with "Solitude set in. I turned to God. I survived" which is basically what he calls dry yeastless factuality.
The boat thrashed for hours, Pi screamed for a long time, and even looked under the tarp for supplies, but never saw Richard Parker, a full-grown tiger there. There was even a hyena under the tarp as well that apparently didn't get into a fight with Richard Parker beforehand.
Take into account the alternate story, it makes sense. The only time Richard Parker manifests (aka Pi's savage side) is when the hyena has gone too far and killed Pi's mother/Orange Juice. Up to that point, Pi kept his humanity. It was the hyena/cook that pushed him to unleash his inner tiger, and Richard Parker actually starts existing.
In the film, at least, Pi mentions that the hyena is acting strangely because of the drugs in its system. Perhaps Richard Parker was still too heavily sedated to be aggressive or noticeable.