Ancient DNA points to a much simpler family tree for horses, say researchers

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An artists impression of Hippidion, from W.B. Scott’s 1913 book, A History of Land Mammals in the Western Hemisphere. Image: Robert Bruce Horsfall

The analysis of ancient horse DNA has cast fresh light on the tumultuous evolutionary journey of the horse, uncovering important information on the origins of important extinct species in the Americas.

The work by an international team of researchers indicates that the equid family trees needs to be dramatically simplified.

It reveals that an important extinct South America species is more closely related to the modern-day horse than first believed, and that another species thought to have migrated from Eurasia to North America was, in fact, a line that arose in the Americas.

The rich fossil record of horses has made them a classic example of evolutionary processes.

However, while the overall picture of equid evolution is well known, the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, from 3 million years ago until much more recent times, around 10,000 years ago.

“Nowhere is the later evolution of horses more problematic than in the Americas, where more than 50 species of Pleistocene equids have been named, most of them during the 19th and early 20th centuries,” the study team wrote in the open-access journal, PLOS Biology.

“While recent paleontological studies suggest that this number should be drastically revised, no consensus has been reached about the number of valid species or their phylogenetic relationships.”

The evidence from their analysis backs a dramatic reduction in the number of species.

“There is no consensus on the number of equid species or even the number of lineages that existed in these continents.”

Similarly, the origin of the endemic South American genus Hippidion is unresolved, nor is it clear where the “stilt-legged” horses of North America lie in the horse family tree.

In order to learn more about them, the study team analyzed mitochondrial DNA segments extracted from fossil horse remains from different locations in North America, South America and Eurasia. They ranged in age from around 53,000 years ago to historical times.

The provenance of bone samples extracted and sequenced for this study. Image: Weinstock et al. https://doi.org/10.1371/journal.pbio.0030241

Oxford University researcher Jaco Weinstock and his colleagues found that, in contrast to current models based on body shape and a recent genetic study, Hippidion was genetically close to the caballine (true) horses, with origins considerably more recent than the currently accepted date of around 10 million years ago.

Therefore, Hippidion should not be seen as a descendant from the Miocene pliohippines, they said. Instead, its origins appear to be much more recent, around 3 million years ago.

Their work also showed that stilt-legged horses, commonly regarded as Eurasian migrants related to the hemionid asses of Asia, were, in fact, an endemic North American lineage.

Interestingly, specimens of this horse from both north (Alaska/Yukon) and south (Wyoming/Nevada) of the Pleistocene ice sheets clearly belong to the same taxon.

The large geographic distribution of this species raises the possibility that other Late Pleistocene New World stilt legged horses currently described as different species, for example, E. francisci, E. tau, E. quinni, E. cf. hemionus, E. (Asinus) cf. kiang, and others with similar limb proportions, may represent the same taxon.

They said the origins of this horse probably lie south of the Pleistocene ice sheets. While it made it to eastern Beringia (unglaciated Alaska/Yukon), the stilt-legged horses apparently failed to disperse through the Bering land bridge into what is now northeast Siberia.

Populations in eastern Beringia disappeared around 31,000 years ago, but persisted south of the ice sheets until at least 13,000 years ago, close to the date of the other megafaunal extinctions.

The authors noted that size has been used as one of the main criteria for defining many species of Pleistocene equids.

“The body size of the Late Pleistocene North American caballines we sampled did exhibit marked regional variability,” they said. For example, horses in Alberta were larger than their eastern Beringian and Wyoming counterparts.

“The DNA evidence strongly suggests, however, that all of these large and small North American caballine samples belong to a single species.

The presence of a caballine species of different body size widely distributed north and south of the Pleistocene ice sheets raises the tantalizing possibility that, despite the many taxa named on body size and shape, most or even all North American caballines were members of the same species.

Indeed, both caballine and stilt-legged lineages may each have comprised single, wide-ranging species, they said.

A single species?

The researchers reported another significant discovery, with evidence suggesting that all caballine horses from western Europe to eastern Beringia — including the domestic horse — may have been a single species with a vast range across the northern hemisphere continents.

There was probably a high degree of mobility and adaptability in this species, they said.

The caballines appeared to group into two major clades, one broadly distributed from central Europe to North America north and south of the ice. The second clade seems to have been restricted to North America.

“If present in the Old World at all, it probably disappeared there before horse domestication took place, (around 5000 years ago), as all domestic horses — only some of which are shown in the tree — cluster within clade A.”

“Thus, our results indicate that only two lineages — a caballine and a stilt-legged — may have been present in North America during the Late Pleistocene, each comprising perhaps only a single species with temporal and regional variation in body size and morphology.

“This model would greatly simplify the systematics of North American Pleistocene horses and could open the way to the analysis of morphological variation in terms of adaptation to different environments.”

The study of this variation should dramatically improve our understanding of the biogeography, evolution, and extinction of horses in this continent, they said.

The study team comprised Weinstock, Eske Willerslev, Andrei Sher, Wenfei Tong, Simon Y.W Ho, Dan Rubenstein, John Storer, James Burns, Larry Martin, Claudio Bravi, Alfredo Prieto, Duane Froese, Eric Scott, Lai Xulong and Alan Cooper, from a range of institutions.

Weinstock J, Willerslev E, Sher A, Tong W, Ho SY, Rubenstein D, et al. (2005) Evolution, Systematics, and Phylogeography of Pleistocene Horses in the New World: A Molecular Perspective. PLoS Biol 3(8): e241. https://doi.org/10.1371/journal.pbio.0030241

The study, published under a Creative Commons License, can be read here

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