Cladistic classification has some important implications for domestic animals. Because we classify taxa according to descent from a common ancestor, it is useful to place most domestic animals within the species of their wild ancestor. Generally, domestic forms are classed as a subspecies, so one will often see Canis lupus familiaris for the domestic dog and Equus ferus caballus for the horse.
I have noticed a strong resistance to classifying the domestic cat as a subspecies of the Lybica wild cat, but this resistance makes very little sense. We know that domestic cats come from a Near Eastern population of this cat, and domestic cats are not morphologically or behavioral that distinct from it.
But there are cases in which it is certainly appropriate to give domestic animals their own species designation.
The gayal or mithun, a domestic bovine that is found in South Asia. It has been given its own scientific name (Bos frontalis). but it has been claimed that is nothing more than domestic form of gaur (Bos gaurus). The wild gaur is the largest species of cattle, but the gayal is quite a bit smaller. It is quite common for domesticated forms to be smaller than their wild ancestors, so this smaller size should be expected if the gayal is a domesticated gaur.
However, whole genome sequencing of the gayal has revealed that is a hybrid between male gaur and female domestic cattle. It is thus a hybrid species that exists only in a domesticated form.
Because it has this hybrid ancestry, it rightly deserves its own species status. This species does not exist in the wild, but because it is a mixture of two distinct ones, it makes sense to place the gayal into Bos frontalis.
Another good place where it makes sense to have the domestic and wild forms as separate species is in the case of wild and domestic Bactrian camels. The Bactrian camels, which are known for their two humps, are found in Central Asia.
A small population of wild Bactrian camels lives in parts of China and Mongolia. Traditionally, these camels were classified as a subspecies of the domestic Bactrian camel, which is much more widespread. It was believed that the wild ones were nothing more than feral domestic animals. They might have been a relict population that never became domesticated, but the truth is we didn’t really know until quite recently exactly what they were.
Various DNA analysis suggest a divergence between wild and domestic Bactrian camels that has been estimated have happened 700,000 to 1.1 million years ago. These findings mean that the wild Bactrian camels are a distinct species. They are not ancestral to the domestic ones, and they are not a relict population of conspecific Bactrians that never became domesticated.
So the domestic Bactrian camel is called Camelus bactrianus, while the wild one is called Camelus ferus.
It is in camelids that species designations get a bit tricky, because the literature has come up with quite contradictory phylogenetic trees for the evolution of South American camels. The most well-known South American camel is the llama, and the llama is usually regarded as a domestic form of the guanaco. Indeed, about the only thing the literature seems to agree upon is that the llama and the guanaco are closely related. However, I have seen papers that place the other two species, the alapaca and the vicuña, as being sister species or place the vicuña as being closely related to the llama.
I remain agnostic on how to classify the South American camelids until these questions are examined using a broader section of nuclear DNA. These four species all can hybridize and produce fertile offspring, and it is not exactly clear if they truly deserve to have two genera or not.
It may be that these four species as currently listed are deserving from a cladistic classification perspective, but it could be that some of these species are better classified as subspecies of one of the wild forms.
As it stands right now, I am holding out for more information before I will drop my two cents.
So when the domestic form is found to be a hybrid between two species, it is useful to classify the domestic form as a distinct species. When the domestic form is found to be highly genetically divergent from the extant wild form, it is also useful, and when we just don’t know yet, keep them as separate species until we have better answers.
We know what the wild ancestor of most of our domestic animals is, so we should be placing them within their wild ancestor’s species, if we are to adhere to cladistic classification.
But there are these curve-balls out there, and sometimes, it really does make sense to have a domestic animal as its own distinct species.