DNA typing has tracked down the "relationships" of numerous fossils. It's failed with a group of fossil ungulates in South America.
We now know, though, that they're related to horses. How? Protein sequencing. DNA doesn't survive well unless the animal's fossilized in a cold environment. Collagen? Survives much better. And the scientists who developed the technique think they can sequence samples that are 20 million years old in colder places.
It might be useful for learning more about evolution - or just finding out cool stuff.