Fowler intends this book to be read without any background knowledge of the plot, which means that Fern is only revealed to be a chimp about a quarter of the way into the book. This forces the reader to consider the similarities between chimps and humans, the assumptions we make about kinship, and what really makes a family.

Although Rosemary never knows exactly what her father's goals were in the study of her and Fern, this allows for a broader thematic consideration for the novel. He may have been studying nature vs. nurture: how does the environment we are raised in have an effect on who we become? What does it mean, not only that Fern was raised in a human family, but that Rosemary was raised with a chimpanzee sister? In addition, what does it mean for Rosemary and Lowell to have grown up with the kind of intellectual surveillance of the study? How has that affected them both in their adult lives?

An important aspect of the novel is the trauma of Fern's removal from the family, and the effects that has on Rosemary, Lowell, and both of their parents. In juxtaposing the present with the past, Fowler is able to show the ways that each person has changed in the face of the loss, and how they have been able to process or not process that loss.

The theme of communication is present not only in the content of the novel but also in the structure. Through the structuring of the novel out of chronological order, using flashbacks, and following the avoidant logic of the unreliable narrator, the reader is shown the breakdown of communication that Rosemary faced after the loss of Fern. It is emphasized that Rosemary was a very big talker/storyteller when she was younger, until Fern was taken away and she withdrew inside herself. The theme of communication also extends to the ways Rosemary and Fern were able to learn to communicate with each other. Fern was able to learn rudimentary sign language, but a lot of the time she allowed Rosemary to speak for her. In Rosemary's processing of the past, she wonders if her father was in fact studying her ability to learn to communicate with a chimp and not the other way around.

One of the social themes of the novel is the effects of scientific study on animals (and humans). In the present-day portion of the novel, Rosemary's brother Lowell is an animal rights activist who illegally frees animals that are being studied, and is on the run from the police. His trajectory as a character, from a child who lived with and loved a chimp as his sister, and had that sister taken away and never spoken about, to a radical activist fighting against animal studies, shows the impact of his relationship with Fern, and the trauma of his loss of her. His radicalism, juxtaposed against the family's past, forces the reader to consider the ways we devalue, disrespect, and hurt animals, and to confront our justifications for that harm. If connection is possible, why do we choose exploitation?