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Ancient Genome Analysis Links Early Horse Domestication to Botai Region

NEW YORK (GenomeWeb) – An ancient genome sequence analysis suggests early horse domestication took place in a region north of what is now Kazakhstan that was inhabited by the Botai culture.

As they reported in Science today, researchers from the Natural History Museum of Denmark, the University of Toulouse, and elsewhere sequenced dozens of ancient horses from the Botai and Eurasia. When they compared the ancient sequences with one another and with modern horse genomes, they saw signs that horse domestication in the Botai produced ancestors to Przewalski's horse — a feral Central Asian horse species long regarded as the lone remaining wild horse species.

"We thought there was one last wild species, and we're only just now aware that all wild horses went extinct," co-author Sandra Olsen, an archeology and zoology researcher affiliated with the University of Kansas and King Saud University, said in a statement.

Even so, the team noted that most modern-day domestic horses have very little Botai-related ancestry, pointing to possible introgression from another wild horse population or the presence of a second domestication in another part of the world.

The Botai culture is known to have developed a horse-centric and settlement-focused lifestyle following transition from an earlier hunter-gatherer lifestyle, the team explained, prompting a deeper analysis of this region when trying to untangle horse domestication.

Along with enhanced levels of nitrogen and sodium, which appeared to be concentrated in corrals where horses were penned, presence of horse milk residues have been found on ancient pottery in the region.

"The final smoking gun was finding residues of mares' milk in the pottery," Olsen said, noting that "[i]t's commonplace today in Mongolia and Kazakhstan to milk horses — when it's fermented it has considerable nutritional value and is very high in vitamins."

For the current study, the researchers sequenced ancient DNA from 20 Botai horses and 22 Eurasian horses going back roughly 5,000 years, including 31 stallions and 11 mares. They analyzed the genome sequences, which ranged from 1.1- to 9.3-fold average coverage, alongside published sequences for three wild horses dated at 5,100 to nearly 43,000 years old, six modern Przewalski's horses, one 19th century Przewalski's horse, and 100 ancient or contemporary domesticated horse representatives.

The team's phylogenetic analysis revealed a cluster containing Przewalski's horses, ancient Botai horses, and ancient, domesticated horses from Kazakhstan that were sequenced previously. A distinct cluster contained domesticated horses from other parts of the world.

"What's interesting is that we have two different domestication events from slightly different species, or separate sub-species," Olsen said.

Despite the separation between the Botai cluster and other domestic horses, the researchers saw signs of intermittent Botai-related introgression into horses in Central Asia, Iran, Turkey, and western Europe between roughly 1,100 and more than 3,300 years ago.

By comparing bone measurements for hundreds of ancient and modern horses — and digging into the sequences for genes related to traits such as coat spotting — the team began reconstructing physical features of early domestic horses in the Botai and beyond. It also got a look at sequences that appear to have been subject to positive selection during this early domestication process.

"Early domestication most likely followed the 'prey pathway' whereby a hunting relationship was intensified until reaching concern for future progeny through husbandry, exploitation of milk, and harnessing," the authors noted. "Other horses, however, were the main source of domestic stock over the last [approximately] 4,000 years or more."