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Early Horse Domestication Features Revealed in Ancient Sequences

Horses in Kazakhstan

NEW YORK (GenomeWeb) – In their ongoing effort to understand the history of horse domestication and horse relationships with human populations, University of Copenhagen researchers have generated ancient horse genomes that appear to represent early stages of the horse domestication process.

University of Copenhagen researcher Ludovic Orlando described the 14 new horses genomes at a session on evolutionary and non-human genomics at the Biology of Genomes meeting at the Cold Spring Harbor Laboratory last week. The ancient samples — sequenced to between twofold and fivefold coverage, on average — were collected at sites in the Kazak Altai region, eastern Mongolia, and western Kazakhstan and ranged in age from 2,300 to 4,000 years old.

"This corresponds to roughly the first half or first two-thirds of the domestication times," Orlando told GenomeWeb.

In a study published in the Proceedings of the National Academy of Sciences in 2014, he and his colleagues sequenced ancient horse samples stretching back as far as 43,000 years that pre-dated horse domestication events — detecting a now extinct horse population that contributed relatively little to the genetics of present-day horses.

For their latest analysis, the researchers considered far younger samples that they suspected might coincide more closely with the timing of domestication.

Eleven of the 14 horses belonged to the same generation and were collected from the same location in the Kazak-Altai region: a 2,300 year-old burial site where the steeds were sacrificed as part of a funeral ritual for a deceased Scythian prince. The Scythians, a nomadic, horse-riding Iranian aboriginal group, lived in the Pontic-Caspian steppe region as recently as around 1000 BCE.

"This is the first time, to my knowledge, in ancient DNA that we have 11 individuals … that were from the same generation," Orlando said.

Another sequenced sample from western Kazakhstan is believed to be about 4,000 years old, he explained, while two other horse samples from eastern Mongolia were dated at around 2,400 years old.

Beyond the phenotypic information that be reconstructed from ancient horse genotypes — from their likely color patterns to clues to their gait — the genomic data is an important resource for starting to tease apart the selection events that coincided with different stages of horse domestication.

For example, the new sequence data suggests that neither the very low Y diversity nor increased mutational load that have been documented in contemporary domestic horses were present during early stages of the domestication process.

Having access to sequence data from horses believed to existed midway through the domestication process also provides a window into the genes that were subject to selection in the earliest stages of horse domestication compared to those showing signals of selection later on in the domestication process, Orlando explained.

"That way you can [track] the temporal dynamics as to human preferences: maybe we were interested, in the beginning, by domesticating or taming the horses for behavioral traits and then later on, maybe improving their speed or whatever else," he said.

The team's scans for positive selection in the new genome sequences revealed potential selection signals at genes believed to influence cognition, skeletal modifications, and metabolism, for example. But selection on these genes was not necessarily uniform across the time frame considered, Orlando noted.

Whereas genetic changes predicted to impact the spine and other skeletal features were widespread, the researchers uncovered some apparent metabolic and dementia-related signals seemed to be limited to the earlier stages domestication.

"This is very descriptive for the moment, but it's a series of candidates that we will further refine in the future," Orland said, noting that follow-up work will be needed to more carefully trace the aspects of horse biology that have undergone changes during and after the animals' domestication.

The team plans to expand its collection of ancient horse genomes in the future, Orlando said, having recently secured funding for more global studies of horse genomics, epigenomics, and microbiomes.