Researchers have reconstructed a genome 10 times as old as any retrieved so far and now say DNA should be recoverable from animals that lived 1 million years ago. This would greatly extend biologists' ability to understand the evolutionary past.
The genome was that of a horse from about 700,000 years ago in what is now the Yukon Territory in Canada, and its reconstruction has already led to new insights. The researchers who sequenced it then analysed DNA from a less ancient horse, one that lived 43,000 years ago, as well as five contemporary horse breeds and a donkey. They concluded that the genus that gave rise to modern horses, zebras and donkeys - Equus - arose about 4 million years ago, twice as far back as had been thought.
Before this work, the oldest genome that had been recovered was that of a Denisovan human who lived 70,000 years ago. The new finding, if accepted, would extend by tenfold the reach of palaeogenomics, the study of ancient genomes reconstructed from fossil bones. Within the past few decades this young science has become a powerful complement to palaeontology, the study of fossils, as a way of reconstructing evolutionary history.
"I think the field has now in many respects matured," said Svante Paabo of the Max Planck Institute for Evolutionary Anthropology, who solved many of the early problems and went on to reconstruct the genome of Neanderthals and more recently of the Denisovan human. "It is clear that with frozen material one can go far back in time, approaching a million years," he said, but the challenge now is to retrieve very ancient genomes from temperate zones, where important fossil bones are more plentiful.
The horse DNA was extracted from a hind toe bone found in the Thistle Creek region of the Yukon's Klondike gold mines. It owes its remarkable longevity to the bone having been buried in permafrost, which kept the DNA both very cold and very dry.
The researchers who discovered the bone, Duane Froese of the University of Alberta and Eske Willerslev, an expert on ancient DNA at the University of Copenhagen, first estimated its date from the layers of volcanic ash where it was found.
To help establish that the DNA from the horse bone was really 700,000 years old, Willerslev and Ludovic Orlando, a colleague at the University of Copenhagen, started an ambitious project to analyse the genomes of many other members of the horse evolutionary tree. These include the horse that lived 43,000 years ago, before horses were domesticated; a Przewalski's horse, a species thought to represent the last living wild horse population; five domestic horse breeds (Arabian, Icelandic, Norwegian fjord, Standardbred and Thoroughbred); and the donkey.
Orlando said the range of genetic variation in the Thistle Creek bone lay outside that of all the other horses, showing it could not have been contaminated by modern horse DNA. Also, the DNA in the bone was much more fragmented than that of late Ice Age horse bones from the same region, indicating it was older. The geological evidence for the bone's age is "very secure", Orlando said.
In a report published on Wednesday in Nature, he and colleagues say they have identified 29 regions in the genome of domestic horses where the DNA shows statistical evidence of selection, meaning variant genes in these regions were favoured as horses became domesticated.
Another finding is that the Przewalski's horse shows no signs of having interbred with domestic horses. Since the horse is threatened in the wild, this gives added reason for protecting it.