​Paleontologists Solve the Mystery of Darwin’s 'Strangest Animals Ever'

While visiting Uruguay in the 1830s, Charles Darwin came across the fossilized remains of Toxodon, a giant hoofed creature, which he called "one of the strangest animals ever discovered."

"In size it equalled an elephant or megatherium," he wrote in The Voyage of the Beagle, "but the structure of its teeth, as Mr. Owen states, proves indisputably that it was intimately related to the Gnawers, the order which, at the present day, includes most of the smallest quadrupeds."

In other words, Darwin was surprised by the odd clash between Toxodon's enormous size and its rodent-like teeth, which he had only observed in smaller animals. In the text, he goes on to describe several other seemingly out-of-place features spanning several zoological families.

"How wonderfully are the different Orders, at the present time so well separated, blended together in different points of the structure of the Toxodon!" Darwin marveled.

Darwin's enchantment with the specimen is understandable. Toxodonts looked like evolutionary Frankensteins, with hippo-like heads, rhino-like bodies, and an elephantine frame. Moreover, it wasn't the only South American ungulate (or hoofed animal) endowed with such an exotic body plan—others include Macrauchenia, a humpless camel with a snout reminiscent of the muppet Gonzo's nose.

The origins of these giant South American ungulates, which went extinct roughly 15,000 years ago, has been hotly debated ever since Darwin first introduced them to the scientific community some 180 years ago. Some scientists argue that they are clearly cousins to Afrotherian animals, like elephants and aardvarks, while others claim that they are more closely related to the Perissodactyla group, which includes horses, rhinos, and tapirs.

Now, a team of researchers led by molecular evolutionary biologist Ian Barnes may have finally cracked this longstanding evolutionary puzzle, and they did so with proteomics, a technique that is poised to greatly extend the reach of paleontology.

"With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time," wrote the authors in a new study about their research, published today in Nature.

When Barnes and his colleagues first attempted to unravel the mysterious lineages of these giant ungulates, they focused on DNA analysis of surviving fossils. But as the team discovered, South America's lush, humid environments are much better at producing vibrant ecosystems than they are at preserving them. DNA degrades quickly under such saturated conditions, leaving very little genetic information to parse.

Proteins, however, can have a much longer shelf life, so Barnes's team switched gears from genetic analysis to proteomic analysis. The researchers focused on the structural protein collagen, which can survive in animal bones for about a million years in a wide variety of environmental conditions.

Complex proteins like collagen are built when genetic processes string amino acids together to form very specific molecular structures. By cross-referencing the collagen extracts of 48 fossils from two ungulate species, Toxodon platensis and Macrauchenia patachonica, the team was able to zero in on these trademark amino acid chains, and accordingly, the genetic drivers that created them.

"People have been successful in retrieving collagen sequences from specimens dating up to 4 million years old, and this is just the start," said proteomics specialist Matthew Collins in a statement. "On theoretical grounds, with material recovered from permafrost conditions, we might be able to reach back 10 million years."

The team's results revealed that toxodonts and macraucheniids belong to an ancient mammalian group known as the condylarths. Though both animals sported elephant-like features, it turns out that they are much more closely related to horses and other perissodactyls than elephants.

After almost two centuries of paleontological gridlock, it appears that these evolutionary weirdos, which astonished even a seasoned observer like Darwin, have finally found their taxonomical home. What's more, Barnes and his colleagues have proved that proteomic analysis can solve longstanding mysteries about the extraordinary origins of Earth's lost creatures.