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Ancient Horse Genome Analysis Documents Domestication History, Diversity Dips

NEW YORK (GenomeWeb) – Results from a large analysis of ancient horse genomes across Eurasia suggests traits such as speed have been under selection relatively recently in horse domestication, leaving an outsized stamp on modern-day domestic horse genomes.

"Some of those traits that we are most familiar with are only a modern invention, and in the last few hundred years, we have actually impacted the horse genome a lot more than in the previous 4,000 years of domestication," senior and corresponding author Ludovic Orlando, a molecular anthropology researcher affiliated with the University of Toulouse and the University of Copenhagen's Lundbeck Foundation GeoGenetics Center, said in a statement. 

As they reported online yesterday in Cell, Orlando and colleagues from dozens of centers around the world brought together new and available genome sequences or genome-wide genotyping data for nearly 300 ancient horse samples from sites in Europe, East Asia, the Middle East, and the UK, representing some 42,000 years of horse history.

Based on the genetic profiles present in the ancient horse set, together with sequences from modern domestic horses, the researchers identified two previously unappreciated, extinct horse lineages in Europe and Asia, centered in Iberia and Siberia roughly 5,000 years ago.

"We found two lineages of horses at the far ends of Eurasia that are not related to what we call the domestic horse today, nor to the Przewalski's horse," Orlando said, explaining that the newly identified horse branches "are a sort of horse equivalent of what Neanderthals are to modern humans."

Even so, the team's results suggest that the newly detected horse lineages contributed relatively little ancestry to present-day domestic horses. Rather, the results revealed pronounced genetic ancestry from a horse lineage related to horses in Persia, which became prominent via migrations through Europe and Asia after Arab raids in the Mediterranean region in the 7th to 9th century.

Within the last 200 years or so, though, the researchers estimated that modern breeding methods have led to a more than 16 percent decline in domestic horse genetic diversity, as measured by individual heterozygosity, paralleled with a rise in mutational loads.

Horse domestication, which appears to have started more than 5,000 years ago, has dramatically influenced human history, the team explained. With the help of horses, humans not only expanded their agricultural exploits, for example, but also became capable of moving more quickly into new regions, interacting with new populations to share everything from language, culture, and commerce to disease and conflict.

To get a better idea of how those human processes have been reflected in the horse genome, the researchers generated new genome sequences for 87 ancient horses — sequenced to average depths of onefold to more than ninefold coverage — which they analyzed in conjunction with 42 available ancient horse genomes and genome-wide data for another 149 ancient horses from dozens of sites in northern Europe, western Europe, eastern Europe, the Middle East, and East Asia.

"Our goal was to understand how humans and their activities transformed the horse throughout history to fit their purposes — and how these changes in biology influenced human history," Orlando said.

Most of those samples covered the last 6,000 years or so, though more than a dozen were older, the team noted. Six belonged to the other equine species, and 27 appeared to be mules based on their genetic features.

Among other findings, the genome sequence data paralleled known historical events and changes in the way horses were managed, the researchers reported, while offering a clearer look at equine relationships, population structure, and genetic diversity.

In particular, the authors concluded that genetic diversity has been more acutely impacted by selective breeding in recent history — particularly the last 200 years — than in the thousands of years that preceded it, making it difficult to discern the full suite of ancestry that was once present in horses without digging into DNA from ancient, extinct horses. 

"Our findings show that the past is a lot more diverse than we thought it was and that it cannot be imagined or inferred through modern-day variation," Orlando said. "But ancient DNA tells us a lot about today as well, because it teaches us about the consequences of some shifts in breeding practices."