Paleogenomics—the study of ancient genomes reconstructed from fossil bones—got a huge boost this week when a multinational team of scientists announced they had been able to determine the genetic code of a horse that roamed Canada’s Yukon Territory 7,000 centuries ago. Their work shatters by nearly 10 times the record for the oldest complete genome ever sequenced, and suggests that the new techniques and computing they used may eventually allow genetic mapping for fossils up to 1 million years old. In addition to lending greater insight into the evolution of one of history’s most studied mammals, the discovery suggests exciting possibilities for deciphering the genetic codes of other ancient mammals, including mastodons, mammoths, bison and perhaps even early human ancestors.
The 5-inch (12.5-centimeter) hind-toe bone fragment that the team used to decipher the ancient horse’s genetic code was unearthed in the Thistle Creek region of the Yukon’s Klondike gold mines. Because the fossil bone was preserved in permafrost, the horse’s DNA remained very cold and very dry, which slowed the disintegration process that usually begins immediately after death. The scientists’ task was made more difficult, however, by the fact that much of the fossil was contaminated by more current bacteria: For every 200 DNA molecules sequenced, only one was actually from the horse.
As part of their work, published in the journal Nature this week,the researchers working with the Yukon horse fossil also analyzed DNA from a less ancient horse (from 43,000 years ago); a Przewalski’s horse, thought to be the last surviving wild horse breed; five domestic horse breeds (Arabian, Icelandic, Norwegian fjord, Standardbred and Thoroughbred); and a donkey named Willy, a resident of the Copenhagen Zoo. Their findings allowed them to estimate that the 700,000-year-old horse was around the size of a modern-day Arabian–larger than once thought, but lacking the size and strength genes of horses that are now bred for racing. Interestingly, the scientists concluded that the most recent common ancestor of horses, zebras and donkeys, a genus known as Equus, lived some 4 million years ago, twice as far back as had previously been thought.
As a byproduct of their study of the ancient horse’s DNA, the researchers assembled the first complete genome of the donkey, the horse’s ever humble cousin. As for Przewalski’s horse, the scientists found that it shows no genetic signs of having interbred with domestic horses (as had been suggested by some). Their conclusion–that the breed is truly the last surviving wild horse–adds greater weight and urgency to the need for its conservation. Once considered extinct in the wild, Przewalski’s horse was reintroduced to the Mongolian steppes in 1985, and can be found today in limited numbers in Mongolia and China.
The most exciting implications of the scientists’ work may be the sheer chronological scope it appears to lend to potential future DNA analysis. Before this week’s findings, the oldest animal fossil to be genetically mapped was that of an ancient Neanderthal relative called the Denisovans, found in a Siberian cave and dating to around 75,000 years ago. Eske Willerslev of the University of Copenhagen, one of the lead authors of the Thistle Creek horse study, referred to his and his colleagues’ work as “breaking the time barrier.”
Other specialists in sequencing ancient genomes caution that the work done in Canada probably won’t help much with the decoding of ancient human DNA. In fact, much of the earliest human development occurred in Africa, where the hot climate makes DNA disintegrate far more quickly and completely than in colder regions. Yet Edward Rubin, who heads the U.S. Department of Energy’s Joint Genome Institute and did not take part in the Yukon horse study, is more optimistic, suggesting to Wired that the Earth’s warming climate and thawing permafrost may yet reveal “other samples that reside in friendly environments out there that could push back what we know about the origin of species.”