One must be very careful using studies of mitochondrial DNA to make conclusions about the natural history of animals. The DNA is inherited matrilinearly. It does not follow the entire genetic legacy of an organism.
However, it can point to the possibility that our understanding of taxonomy is incorrect, and these studies have pointed to multiple cryptic species in what we once thought was only a single one. Gray foxes and black-backed jackals have deep divergences in mitochondrial DNA lineages in populations that are not contiguous, which suggests that there are more species than the single one currently recognized.
Of course, these findings do require more study to figure out if these divergences are reflected in the nuclear DNA. But these studies are just the beginning.
Recently, I came across this paper from PLoS ONE that was published 2017. It looked the mitochondrial DNA of the jaguarundi, a neotropical cat that is most closely related to the cougar. It does range into the United States, but it hasn’t been seen here in decades.
This species has been a bit of problem for molecular biologists, because it is been quite difficult to figure out subspecies. There is little correlation between mitochondrial DNA sequences and morphology, which has made classifying them quite difficult.
But the authors discovered a rather unusual discovery. Using calculations of mutation rate, they found that the two main clades of jaguarundi diverged 3.2 million years ago. The same metric found that jaguarundis and cougars diverged 3.9 million years ago, and the divergence between the two clades of jaguarundi happened earlier than the divergence between lions and common leopards and the divergence between the tiger and the snow leopard.
This discovery does suggest that there at least two species of jaguarundi, which are morphologically indistinguishable. Of course, the authors make it clear that more evidence from nuclear DNA needs to be included in the analysis, but the discovery does suggest that our classification of the jaguarundi as a single species may be faulty.