Aquinas refutes the idea that animals have subsistent (continues after death) souls, and as it turns out, also refutes the idea that sensation requires some immaterial component that dualists often used to prove that humans have a subsistent soul (ST I, Q. 75, Art. 3):

“Plato, however, drew a distinction between intellect and sense; yet he referred both to an incorporeal principle, maintaining that sensing, just as understanding, belongs to the soul as such. From this it follows that even the souls of brute animals are subsistent. But Aristotle held that of the operations of the soul, understanding alone is performed without a corporeal organ. On the other hand, sensation and the consequent operations of the sensitive soul are evidently accompanied with change in the body; thus in the act of vision, the pupil of the eye is affected by a reflection of color: and so with the other senses. Hence it is clear that the sensitive soul has no “per se” operation of its own, and that every operation of the sensitive soul belongs to the composite. Wherefore we conclude that as the souls of brute animals have no “per se” operations they are not subsistent. For the operation of anything follows the mode of its being.”

Modern philosophers, particularly those of the Cartesian sort, seem to have this obsession with qualia as a means of proving that there is a soul. Aquinas, on the other hand, thought the only relevant faculty that required a subsistent soul was the intellect and the will. In a way then, Aquinas can be said to side with the materialists on this issue with some qualification. Alfred Freddesso affirms this exact point in his article entitled, “Oh My Soul, There’s Animals and Animals:”

Second, and this is exceedingly strange from a Thomistic perspective, the main contemporary arguments against one or another form of materialism have to do almost exclusively with sensing and feeling and not with intellective understanding or willing. In part, this is the legacy of Cartesianism. What I mean is that quite a few materialists share in common with their dualist opponents Descartes’ assumption that any sort of interior psychological life, be it sentient or intellective, must have an immaterial immediate subject.

I see absolutely no problem with explaining sensation, whether human or animal, without appealing to some immaterial soul that persists after death. The neural corollaries of qualia is sufficient to explain the sensation, and the individual substance is sufficient to explain the private experience of that sensation. Aquinas’ alternative conception of matter (as opposed to the modern conception) is superior in many ways and it is the rejection of this conception that leads to this problem in the first place. Let’s all be hylemorphic dualists and be done with it.