Scientists solved the evolutionary mystery behind the creatures Charles Darwin called the "strangest animals ever discovered." 

The findings showed South America's "native ungulates," which became extinct 10,000 years ago, are related to mammals such as horses instead of African elephants, as researchers previously believed, the American Museum of Natural History reported. The findings are based on protein sequences, which allowed the scientists to see 10 times farther into the past than they could through DNA analysis alone.

"Fitting South American ungulates to the mammalian family tree has always been a major challenge for paleontologists, because anatomically they were these weird mosaics, exhibiting features found in a huge variety of quite unrelated species living all over the place," said Ross MacPhee, one of the paper's authors and a curator in the American Museum of Natural History's Department of Mammalogy. "This is what puzzled Darwin and his collaborator Richard Owen so much in the early 19th century. With all of these conflicting signals, they couldn't say whether these ungulates were related to giant rodents, or elephants, or camels - or what have you."

Since DNA quickly degrades, the researchers switched to analyzing collagen, which can be found in the animal bones and can survive for millions of years. The chemical structure of the amino acids found that make up proteins in this collagen can tell a detailed story of the past. The team analyzed material from 48 fossils of Toxodon platensis and Macrauchenia patachonica.

"By selecting only the very best preserved bone specimens and with various improvements in proteomic analysis, we were able to obtain roughly 90 percent of the collagen sequence for both species," said lead author Frido Welker, a Ph.D. student at the Max Planck Institute for Evolutionary Anthropology and the University of York. "This opens the way for various other applications in paleontology and paleoanthropology, which we are currently exploring."

The findings revealed the closest living relatives of these species were perissodactyls, which is a group that included horses and rhinos. This suggests the ancestor of the South American ungulates came from North America about 60 million years ago.

The findings were published in a recent edition of the journal Nature.