For 180 years researchers have puzzled over the beasts that Charles Darwin called the “strangest animals ever discovered”. The so-called “native ungulates” of South America.

The fossils Darwin examined did not seem to fit neatly into the mammalian family tree. The animals, which became extinct about 10,000 years ago, varied widely. One looked like a rodent crossed with a hippo and a rhino, another looked a bit like a camel but with a short, elephant like trunk.

Now, new research shows that the animals were not relatives of African mammals such as the elephant, as some had suspected, but instead had ties to known North and South American species like horses.

The researchers from the University of York, the American Natural History Museum and the American Museum of Natural History made the discovery by using fossil protein sequences, which can hold their integrity for 10 times longer than DNA.

“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. 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,” said Ross MacPhee in a statement.

McPhee is one of the authors of a paper appearing in the journal Nature, and a curator in the American Museum of Natural History’s Department of Mammalogy.

Ian Barns, research leader at the Natural History Museum in London and another of the papers authors reports that the team initially hoped to use a DNA analysis.

“Although the bones of these animals had been studied for over 180 years, no clear picture of their origins had been reached. Our analyses began by investigating ancient DNA to try to resolve the problem,” said Barnes.

The team soon realized that the ancient DNA had degraded too much in the wet, warm conditions in South America. Instead, they switched to analyzing collagen. Collagen is a structural protein that occurs in all animal bones. Unlike DNA it can survive for more than a million years under most environmental conditions.

The amino acids that make up the protein have a chemical structure which is dictated by specific coding sequences in the DNA. So, by studying the composition of the proteins, the researchers can effectively read the DNA sequences without an actual DNA sample.

“People have been successful in retrieving collagen sequences from specimens dating up to 4 million years old, and this is just the start. On theoretical grounds, with material recovered from permafrost conditions, we might be able to reach back 10 million years,” said University of York professor Matthew Collins, whose lab did the sequencing work.

In total, the researchers analyzed samples from 48 fossils of Toxodon platensis and Macrauchenia patachonica, the very animals which had puzzled Darwin.

“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. This opens the way for various other applications in paleontology and paleoanthropology, which we are currently exploring,” said lead author Frido Welker, a Ph.D. student at the Max Planck Institute for Evolutionary Anthropology and the University of York.

The researchers were able to conclusively show that perissodactyls, the group that includes horses, rhinos, and tapirs represented the closest living relatives of the pre-historic, South American animals.

The research validates the view of many paleontologists that the ungulates came from North America about 60 million years ago, likely just after the mass extinction that killed the dinosaurs.

However, because the ungulates large and varied group it is not immediately clear that they all had the same lineage.

“This is a definite possibility and we are now working with our South American colleagues to sample fossils that might settle once and for all where these magnificent beasts came from,” said McPhee.