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Oldest Ever Genome Sequenced from Horse Bone

06/26/2013
Sarah C.P. Williams

The genome obtained from a 700,000 year old bone helps tell the story of horse evolution, diversification, and domestication. Learn more...


Using a combination of sequencing techniques, researchers have pieced together the entire genome of an ancient horse from DNA found in a 700,000 year old bone fragment. This genome—the oldest ever to be fully sequenced—not only provides information on horse evolution, but also sheds light on how biomolecules age over hundreds of millennia.

Late Pleistocene Horse skull, Equus lambei, from the Klondike region, Yukon. Source: D.G. Froese




By outward appearances, the bone uncovered from the frozen ground of Canada’s Yukon Territory in 2003 didn’t reveal much about the animal it came from. Scientists could tell, though, that the 15 centimeter specimen was from the leg of a horse that lived about 700,000 years ago. And an initial mass spectrometry analysis of the bone revealed a plethora of intact molecules, including those not commonly found at high levels in bone.

“What was encouraging, and the reason why we started to look at the genome, was that we found proteins beyond collagen,” said Ludovic Orlando of the Natural History Museum of Denmark and the University of Copenhagen, first author of a paper published today in the journal Nature describing the work. “That suggested that there could be other molecules surviving, including DNA.”

Orlando and colleagues tweaked established protocols to maximize the information they could get out of the ancient sample; they were then able to isolate enough DNA to sequence the entire genome of the horse.

By comparing the new genome to a previously sequenced sample from 43,000 years ago, as well as the genomes of 5 modern-day domestic horse breeds, wild Przewalski’s horses, and donkeys, the team could determine when certain genes appeared or changed.

“We actually discovered that a full range of ‘–omics’ approaches, including proteomics and genomics, could be used as a sort of methodological tool to characterize the deep evolutionary past,” said Orlando.

Traits that evolved early in horses include the immune system and the ability to smell. Surprisingly, the compact muscular structure of today’s horses evolved significantly later, likely appearing around 200,000 years ago, says Eske Willerslev of the University of Copenhagen, also an author of the new work

The data also helped answer a long-standing question as to whether Przewalski’s horses, a species native to Mongolia, have ever interbred with domesticated horses.

“It is truly wild. It’s a hundred percent wild. There is no domestic genetics present in that horse,” said Willerslev. “We estimate the divergence time between the Przewalski’s horse and the domestic horse to be about 50,000 years ago.”

The team plans to continue analyzing the genome to learn more about the ancient horse's biology and appearance as well as to determine how particular genes from modern horses have evolved. But their research also paves the way toward developing better techniques to recover genetic material from ancient samples. According to Orlando, it’s not unreasonable to expect that older fossils will soon yield genomes.

“In a similar environment, we could actually beat the million year time period,” he said. “It suggests to me that half a million years is something totally realistic for even temperate environments.”

References

1. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, et al. (2013) Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature online June 26, 2013.

Keywords:  fossil genome