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Straight from the horse's toe: the world's oldest genome

Scientists have reconstructed the genome of a horse that lived some 700,000 years ago, mapping out the evolutionary history of the modern horse.

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The data from the ancient horse, coupled with the data collected from the younger horse and modern samples, now suggest that Equus lineage, which includes all living horses, zebras, and donkeys, evolved from a common ancestor that galloped across the intermittently frozen grasslands some 4 million years ago – about twice as long ago as was previously believed.

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“This means that our horse evolutionary record stretches back 700,000 years,” Beth Shapiro, one of the senior authors on the paper and an associate professor at the University of California, Santa Cruz, told the Monitor.

The amalgamated data also helps to tell a narrative of natural selection that created the domestic horse, Dr. Shapiro said. Scientists looked at genetic variants known as single nucleotide polymorphisms in the horse’s DNA to investigate which variants had been selected throughout the horse’s evolutionary trajectory, identifying some 29 regions in the domestic horse’s genome where variants were favored over time. The Mongolian horse, called Przewalski's horse, is now believed to be the last surviving wild horse, after being isolated from the domestic horse's lineage some 50,000 years ago.

And the new data have contributed to scientists’ understanding of the population booms and busts that have dotted and complicated the horse’s evolutionary trajectory, said Shapiro. “We can now ask how large-scale geological changes affected the diversity of horses,” she said.

Scientists now believe that horses have undergone some three cycles of population peaks and valleys over about 2 million years, with the most recent high point during a glacier-covered period some 25,000 years ago, at the end of the last ice age. Cold periods provided sufficient grasslands for horses, while warm spells created forests that sent the horse population plunging, the scientists said.

But perhaps the most stunning part of the discovery is the very discovery itself: the fact that scientists were able to reach so far backward in the animal kingdom’s evolutionary path and then piece together a rough tale of where the domestic horse came from, and how it did so.

The challenge for scientists now lies in recovering DNA from bones found in warmer and wetter zones, where the DNA is often so mangled that it is beyond the investigative limits of current sequencing technology, Shapiro said. To extract that DNA, if any is left at all, scientists will need currently unavailable technology to put together complete genomes from the tiniest fragments of decomposed DNA.

“It’s not that all of a sudden we’re going to be able to get DNA out of any bone,” said Shapiro. “To do so, we will have to be able to capture the smallest fragments of DNA, and in most cases there won’t be any DNA left in a bone that’s 700,000 years old.”

The field of paleogenetics has been in rapid acceleration in recent years, especially in studies of human bones. The previous oldest genome was sequenced from DNA extracted from the pinky of a 70,000-year-old girl found in Siberia’s Denisova Cave.

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