Ancient DNA helps clarify the origins of two extinct New World horse species

The Patagonian Hippidion horse genus and North American stilt-legged horses have found a new place on the evolutionary tree, according to a new article in the open access journal PLoS Biology. In the paper, Jaco Weinstock, Alan Cooper, and colleagues use ancient DNA to argue that the Hippidion genus is younger than previously thought and that American stilt-legged horses were American endemics, not Asian emigres. Their analysis has also whittled down the taxonomy of North American species to just two. “I think the biggest issue is that we showed the apparent lack of species diversity in North American horses in the Late Pleistocene – as horses are a poster child of evolution,” says Cooper.

To explore the origins of the horses, the authors examined mitochondrial DNA (mtDNA) extracted from fossilized horse bones. Mitochondria, which have their own genome, contain a stretch of sequence that’s useful for inferring evolutionary relationships: though the region undergoes high mutation rates, the patterns of mutations remain stable over thousands of generations. The mtDNA analysis of the South and North American horses provided evidence that stilt-legged horses, the Hippidion genus, and caballine, or true horses, all arose from a common lineage.

The authors showed that the Hippidion genus is only 3 million years old, a much more recent date than previously believed. “South American horses were thought to stem from a very old lineage of fossil forms in North America,” Cooper says. “And instead, our data show that they probably diverged and moved into South America around three million years ago, during the great biotic interchange that occurred when the Panama Isthmus was established.”

And while morphological similarities between American stilt-legged horses and certain Eurasian caballines (a group that includes both the domestic horse and the nearly extinct Przewalskii horse of Mongolia) suggest that the stilt-legged horses once trekked across the Bering Strait, the new PLoS Biology study shows that the American and Eurasian horses’ genomes are too distinct for this theory. “We found that the stilt-legged horse in North America was in fact a home-grown endemic, and had just converged morphologically, probably due to shared environments,” Cooper explains.

The study also suggests that all the North American caballines–traditionally classified as multiple species based on their diverse size–belong to the same species. Thus, only two horse lineages lived in North America during the Late Pleistocene, the stilt-legged horses and the caballines. Though the different horses in each species “varied in size and shape quite a bit” regionally and temporally, Cooper explains, “we see no genetic evidence that these are different species.”

If true, the study’s new model could provide a tool for exploring how environmental adaptations give rise to morphological variation.