Charles Darwin’s Mystery Animal: Solved! By Dan Franck email@example.com | Jun 29, 2017 11:24 PM EDT We can imagine how it was: Charles Darwin, a young, energetic (and probably seasick) naturalist, looking down at a table and staring at the mysterious bones. The Beagle was anchored in Port St. Julia in Argentina. All he had in front of him was a leg bone and a few fractured parts of a spine. What in the world? Was it a camel? An antelope? A cow? "Some large animal," he later wrote, "I fancy a mastodon." Certainly, when Richard Owen, the greatest anatomist in world, saw it the answer would emerge. No such luck. He had no idea either. As fossil hunters discovered more bones, mostly from the southeastern regions of South America, some idea of the animal's morphology developed. It had long legs and quite a snout. Its nostrils were near the top of its head. Could it be a relative of an elephant? It was the size of a llama and it was from South America, so taxonomists gave it a genus name that meant long llama. But that head with the elongated snout made it look more like an anteater. It's been a long time since Darwin scratched his chin in front of the bones in 1834, but scientists have finally determined the phylogenetic affinities of Macrauchenia patachonica. A worldwide team of scientists say it is most closely related to a horse, maybe a Przewalski's house, or better, the genus Hippidion, a large-faced horse that went extinct about 10,000 years ago. Even so, Macrauchenia, and its sister taxon Toxodon, split off from the lineage of horses over 66 million years ago and evolved independently in South America. In a paper in Nature Communications, an international team of scientist performed the tricky task of recovering and purifying mitochondrial DNA from the bones of M. patachonica from museums all over the world. This was not an easy task as the bone were from temperature but often warm areas and these were fossils from a species that most likely went extinct 15,000 years ago. But the researchers found the mDNA. Pieces of it anyway. They isolated over 13,000 base pairs. They amplified it enough to read the pieces. Then they used some very clever statistical processes to reconstruct mDNA sequences. This is a real innovation that may allow other scientists to discern DNA sequences from random fragments. From that point, it was a matter of reconstructing a phylogenetic tree, something that is never easy but which evolutionary biologists have gotten good at. The fully reconstructed phylogeny shows that Macrauchenia and Toxodon are relatives of the horse and zebra, but different enough to be placed in their own taxonomic order. They once roamed the forests and grasslands of what is today Uruguay, Argentina, Chile, and Bolivia. For reasons unknown, they died out about 15,000 years ago. Only bones remained, bones that left the world's best anatomist and the world's premier biologist scratching their heads in wonder.