While the HMS Beagle stopped at the port of St. Julian in Patagonia, Charles Darwin collected some bone fragments that he tentatively identified as belonging to "some large animal, I fancy a Mastodon." But when the leg bone and bits of spine got back to England, later study revealed that the animal was a different creature altogether, one that resembled a huge camel or a llama with a long neck and a droopy, tapir-like nose. Anatomist Richard Owen named it Macrauchenia patachonica.

On his trip, Darwin also discovered Toxodon platensis, which had the body of a heavy rhinoceros, the face of a hippo and the teeth of a rodent. These strange animals from the Pleistocene were fascinating, but until recently, no one could figure out exactly where to place them in the mammalian family tree, reports Jo Marchant for Nature News. They were ungulates — part of the large group of hoofed animals that contains horses, pigs, deer and hippos. But were they more like African elephants and aardvarks or like South American armadillos and sloths? Even more recent methods of constructing animal family trees using DNA couldn’t help: the bones didn’t have enough DNA to analyze.

But, a research team realized, the bones did have bundles of structured protein—collagen, which is found in skin, tendons and holding together muscle tissue. A detailed analysis of the collagen scraped from the bones of these ancient ungulates provided the answer. Marchant writes:

The team first built a collagen family tree, which laid out the collagen sequences of different mammals on the basis of their familial relationships. The researchers had to extract and sequence collagen from tapirs, hippos and aardvarks to build up their picture. With that in hand, they sequenced collagen from four ungulate specimens from two different museums in Argentina — two Toxodon specimens around 12,000 years old and twoMacrauchenia that could not be carbon-dated — and compared the ancient proteins against their tree.

Both huge animals belong to the same group as horses, tapirs and rhinoceros, called Perissodactyla. The llama-like Macrauchenia and the rhino-like Toxodon now have a taxonomic home. The researchers published their findings in Nature.

The team’s sucess might not be the only one enabled by analysis of ancient proteins. Today’s tools are better than ever at pulling bits of protein from old samples and measuring them. Marchant writes:

Proteins could also be useful for studying extinct species that lived more recently in hotter environments where DNA studies are difficult: what [bioarcheologist Matthew Collins of the University of York, UK] describes as “weird and wonderful” animals around during the late Pleistocene, from the dwarf elephants and enormous rodents of the Indonesian island of Flores to Australia’s giant lizards and kangaroos.

For figuring out the lineages of recently extinct animals, Collins says that ancient protein analysis "could really rock the boat."