The state of nature
This book is naturalistic in its treatment of society. As a woman in London, Madelene's life quickly spirals into panic and alcoholism. But, when she is in tune with her animal self, living as an animal in nature with an animal for a spouse, she feels free and happy. The moral and political philosophy of the novel also points to naturalism, especially in Erasmus's character, who is both an ape and a theologian.
Absurdity and meaninglessness
This novel's plot is post-modern in many regards. One of the clearest signs of the author's philosophy is the absurdity of the plot. By making random, unfathomable claims in the story that the reader cannot suspend their disbelief to enjoy, the author brings attention to meaning itself. Because the reader is constantly asking, "What does this all mean?" the novel is existential in flavor. In the plot, Erasmus details his own personal philosophy about religion and meaning. The plot itself is absurdist because it seems to celebrate bestiality.
Humans are animals
Everyone in the story has some sort of relationship with animals. Adam is a zoologist, meaning that he studies animals for a living, but that doesn't necessarily mean that he is in tune with his own self as an animal. In fact, he seems stiff and uncoordinated next to Erasmus. The captain is a criminal who kidnaps animals as if they are below him, but when Erasmus is freed, the captain cannot contain him again.
Only Madelene arrives at the thematic answer to this question. She does not view Erasmus's species as an important distinction—after all, both are just apes. One is a human ape, and the other is a non-human ape with human-like abilities. So, she finds they are compatible. In other words, she identifies as an ape, because humans are animals too.