Macrauchenia patachonica lived during the last ice age. It resembled a bulky camel without a hump, with a long neck like that of a llama and a short trunk for a nose.
The long neck would enable the herbivore to reach leaves on plants and bushes across what is now South America and the open landscapes of Patagonia.
"It was a fairly bulky quadruped, probably not very fleet of foot," said Ross MacPhee, study co-author and curator at the American Museum of Natural History. "Its outstanding feature, however, was its nose. We have no soft tissue fossils, so we don't know whether the nose was developed into an actual trunk, like an elephant's, or was something more like a big fleshy appendage, resembling the tapir's proboscis. It would not have looked very much like anything alive today."
The nasal opening is right between the eye sockets, rather than just above the teeth.
Legendary British scientist Darwin found the first fossil of this creature, as well as those of other extinct animals that fall under the "South American native ungulates" category, in 1834. The fossils were given to Richard Owen, a British paleontologist, to study. Neither Owen or Darwin could clarify the Macrauchenia's combination of features to a modern-day counterpart or a distinct mammal lineage. But they had only a few limb bones and vertebrae to study.
The ungulates group itself is puzzling to researchers because some of them seem elephant-like, while others are more like aardvarks and moles. Owen even used an old name for the llama to come up with the genus Macrauchenia.
"What we knew for quite some time is that there is a large number of species that are put into this group, and many of them looked quite peculiar," said Michi Hofreiter, lead author of the new study and paleogenomics expert at the University of Potsdam. "They are all extinct, and we do not even know if they represent a single group or belong to different phylogenetic groups."
A previous study tried to place Macrauchenia on the tree of life by using ancient collagen. The new study, led by MacPhee and Hofreiter, built on the 2015 collagen study by extracting mitochondrial DNA from a fossil found in South America. The researchers also used a new approach to recovering Macrauchenia's genome, even without a modern analog.
"I'm pleased to see that our ancient protein results for Macrauchenia are verified using this advancement in ancient DNA alignments of a deeply diverged mammal without close modern relatives," said Frido Welker, author of the 2015 collagen study. "Overcoming the absence of a close relative while achieving a near-complete mitochondrial genome is impressive."
Before these studies using protein and DNA, arguments for where the animal belonged were derived from bone morphology, leading to a variety of possibilities.
Macrauchenia now belongs to a sister group of Perissodactyla, which includes horses, rhinos and tapirs. The two groups split about 66 million years ago, around the time a mass extinction occurred when an asteroid struck the Earth.
"We now have found a place in the tree of life for this group, so we can now also better explain how the peculiarities of these animals evolved," Hofreiter said. "And we lost a pretty old branch on the mammalian tree of life when the last member of this group went extinct."
The new study "finally settles who it is closely related to," MacPhee added. "Finally settles that its lineage had already diverged from that of modern perissodactyls as early as the close of the age of dinosaurs."
Next, the researchers want to solve the mystery of what Darwin dubbed "the strangest animal ever discovered": Toxodon. This giant animal is thought to have looked something like a fur-covered rhinoceros, with the head of a hippopotamus .
They tried to extract Toxodon DNA from fossil samples for this study, but it wasn't possible, as is often the case with fossils found in temperate climates rather than cold ones. However, solving the riddle of Macrauchenia has given them hope.
They will also use these techniques to look at fossils of ancient sloths, armadillos, anteaters and their extinct relatives, MacPhee said. The benefit of ancient proteins like collagen is that they contain genetic information and break down slowly.
Without having to rely on close living relatives of ancient, extinct creatures, researchers can use the latest technology to push their fields forward.
"We will eventually be able to recover complete genomes from many kinds of fossil species," MacPhee said. "Then, we can start comparing genes from different species and make inferences about functional differences in gene products. This will have a profound effect on the study of evolution, because it will be fully empirical, not inferential."
Filling in the gaps that these strange creatures left behind also answers basic questions about the history of our planet.
"The vast majority of all species that ever lived on Earth are now extinct," Hofreiter said. "So if we want to understand the history of life on Earth, we also need to study the extinct species."