700,000-Year-Old Horse's DNA Sequenced

700,000-Year-Old Horse's DNA Sequenced

While studying the ancient stallion's DNA, the team see found that the Przewalski’s horse (seen here) diverged from the line that became domestic horses about 50,000 years ago.

Photo: Photos.com

When it comes to mapping equine genomes, researchers’ test horses seem to be getting older: In 2007 it was a 3-year-old gray Thoroughbred marecalled Twilight from New York. In 2012 it was 18-year-old Sugar, a Quarter Horse mare from Texas.

Now in 2013 it’s Thistle Creek, a Middle Pleistocene stallion from the Yukon permafrost near the eastern Alaskan border. He’s roughly 700,000 years old. That makes Thistle Creek—named for the excavation site where his leg bone fragment was discovered—the oldest equine to have its DNA fully sequenced.

And actually, Thistle Creek’s DNA is the oldest DNA of any species to be fully sequenced. The second oldest? 110,000-year-old polar bear DNA.

Ludovic Orlando, PhD, HDR, associate professor in the Centre for GeoGenetics Paleomix Group at the University of Copenhagen's Natural History Museum of Denmark, led an international team of 56 scientists listed as co-authors of the groundbreaking study.

Sequencing such old equid DNA was like "working a jigsaw puzzle," Orlando said, as millenniums of damage resulted in sequences no longer being on the same place on the genome map as the modern horse. Still, with patience and dedication, the team worked out the 2.4-billion-piece puzzle.

"We've been working on the technology to be able to do this for the past three years, and we realized that we just weren't pushing the right buttons to fully use the tools we have that would allow us to succeed in mapping such an ancient genome," Orlando said.

Orlando's "buttons" included what is known as "third generation sequencing," a novel technique that allows researchers to sequences genes "on the fly," he said, without having to go through the delicate and possibly inaccurate process of trying to amplify damaged DNA. "We expected this to drastically improve our sensitivity, and we were right," Orlando said.

While this finding is exciting for genome scientists throughout the world, it’s also particularly interesting for equine research. By sequencing this one horse, Orlando and colleagues have been able to compare data with that of domestic horses—including Twilight and Sugar—of varying breeds as well as the partial sequencing of a 43,000-year-old horse. By looking at the number of mutations occurring over the years in these horses, the scientists were able to calculate—with surprising confidence—approximate dates of the history of the horse.

Notably, the common ancestor of the horse, donkey, and zebra roamed modern-day North America four million years ago, according to the research team. That’s about twice as long ago as paleontologists had thought, Orlando said. They could also see that the Przewalski’s horse diverged from the line that became domestic horses about 50,000 years ago. They even detected numerous changes in horse population at different times throughout prehistory, specifically due to severe climate changes.

"We were amazed to discover that there were three major periods of expansion in the horse population, which were always followed right after by a drastic decline in the demographic of the horse," said Orlando. "The most recent was around 25,000 years ago. That trend stopped at the start of a warm climactic period that we are still experiencing today, so the horses did not get enough resources to keep on expanding." The other two periods occurred 200,000 and 1.2 billion years ago, he added.

Thistle Creek was probably around 14.2 to 15 hands, or about the size of a modern-day Arabian or Icelandic horse, Orlando said. Between 50,000 and 700,000 years ago the horse evolved to become smaller. Domestication and breeding programs then led the horse to its now wide range of sizes, he said.

By contrast, the common ancestor of all modern equids was probably what paleontologists identified as not even a member of the Equus genus at all, Orlando said. This genus no longer exists, but its lines led to the horse, donkey, and zebra, he said.

Orlando's research also confirms what scientists have declared for years: The equid originated in the Americas but was then driven to extinction about 12,000 years ago. Horses returned to the Americas on European ships after Christopher Columbus' famous 1492 journey, he said.

“This research opens up hundreds of doors and possibilities of working with DNA samples that until now have been considered too old,” Orlando concluded.

The study, "Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse," will appear in an upcoming issue of Nature

About the Author

Christa Lesté-Lasserre, MA

Christa Lesté-Lasserre is a freelance writer based in France. A native of Dallas, Texas, Lesté-Lasserre grew up riding Quarter Horses, Appaloosas, and Shetland Ponies. She holds a master’s degree in English, specializing in creative writing, from the University of Mississippi in Oxford and earned a bachelor's in journalism and creative writing with a minor in sciences from Baylor University in Waco, Texas. She currently keeps her two Trakehners at home near Paris. Follow Lesté-Lasserre on Twitter @christalestelas.

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