First of all saying that “feminine words tend to derive from masculine words, and masculine is generally the “default” gender,” is most likely a false assumption that is not for discussion here.

What about animals?
The majority of animal names are generic terms that are used for both male and female, and if the sex remains unspecified then you use elle or il according to the grammatical gender used for the generic term. For example:

• J’ai vu un rhinoceros, il était gros.
• J’ai vu une girafe, elle était grande.

Sometimes, of course, we need to specify the sex of the animal, then we say, for example, une souris mâle or une souris femelle and use the pronouns accordingly. As we can see in this article where il is used once it has been established that this specific giraffe was a male:

Il est mort de vieillesse au milieu de son troupeau de femelles et de ses derniers petits.

Some animals have different names to designate the male and the female, such as:

• La chèvre (elle) is the female of le bouc (il).
• Le cochon (il) is the male and la truie (elle) is the female.

On this page you will find a list with some animal names and the associate grammatical gender.

In addition to Laure’s excellent answer, note that the agreement stays with the feminine in cases like:

Les souris mâles sont plus agressives que les femelles.

Une panthère mâle est cachée dans la forêt.

but:

Chez les souris, les mâles sont plus agressifs.