Before 1984 the quagga's relationships rested on skins, skulls and paintings, and it was widely treated as a distinct species. Work led by Russell Higuchi in Allan Wilson's laboratory extracted short mitochondrial sequences from dried muscle attached to a museum skin, establishing that usable DNA could survive in preserved specimens and founding the field of ancient DNA.
The sequences grouped the quagga inside the plains zebra, Equus quagga, rather than as a separate branch. Estimated divergence was on the order of a few hundred thousand years, consistent with a recently differentiated southern population rather than an old lineage. The animal is now normally written as Equus quagga quagga.
That finding underpins the Quagga Project in South Africa, which selectively breeds plains zebras for reduced striping. The result is a phenotypic approximation. It recreates a coat pattern, not the extinct population's full genetic makeup, and describing such animals as revived quaggas overstates what selective breeding can do.