Ancient horse DNA yields world’s oldest genome sequence

Delila James | @@delilalaw| June 27, 2013

Ancient horse DNA yields world’s oldest genome sequence

A new DNA experiment leads to the oldest genome sequence in history.

An international team of scientists has sequenced the genome of a 735,000 year old horse, making it the oldest genome ever deciphered. The achievement is providing new answers to questions about the evolution of the Equus genus, which includes all modern horses, donkeys, and zebras. The oldest previous DNA sequences came from a polar bear that lived between 110,000 and 130,000 years ago. The team’s findings are detailed in the June 26 issue of the journal Nature.

The researchers extracted DNA from a fossilized leg bone of an ancient horse that once roamed what is now Canada’s Yukon Territory. After pulverizing a bone fragment and subjecting it to high throughput, next-generation gene sequencing, the scientists were able to tease out 70 percent of the animal’s complete genome. That was enough to reveal some important secrets about both the individual creature and the evolutionary history of the horse. Because the bone was kept in virtual cold storage by being buried in permafrost, the remains of its ancient DNA were better preserved than in most fossil specimens, according to researchers.

Before the team could unravel the ancient horse’s genome, they had the painstaking task of sifting through the 12 billion gene sequences to separate out the DNA patterns belonging to the horse and those that came from contaminating organisms, such as bacteria. Once that was accomplished, the team worked with biologists from around the globe to compare the ancient equine genes with the genes of a 43,000-year old horse, a modern donkey, five modern-day domestic horse breeds. and one Przwalski’s horse. The Przwalski’s horse, native to Mongolia, is a contemporary horse believed to be the last example of a genuinely wild horse species.

The genetic comparisons yielded a wealth of new information about horse evolution. Importantly, the researchers discovered that the Equus genus first evolved some four million years ago–about twice as long ago as most scientists previously thought. They also learned that horse populations fluctuated in size repeatedly over the past two million years, mostly in response to extreme climatic changes. The new data also suggests that genes regulating the immune system and sense of smell were very important for horses’ survival over time.

The team’s findings also resolved an ongoing debate about whether the Przwalski’s horse is truly wild or an offshoot of a domestic breed. Named after a Russian colonel who discovered them while on an 1881 expedition in Mongolia, these horses became extinct in the wild until reintroduced there in the 1990s by a captive breeding program. While some scientists believed these short, stocky beasts to be a separate wild horse species (Equus ferus przwalski), others considered them a type of feral animal derived from domestic horses, such as the ponies of Chincoteague Island or the wild Mustang of the American west.

Through DNA comparisons, the team was able to conclude that the Przwalski’s horse split off from the lineage that led to modern horses sometime between 38,000 and 72,000 years ago and was a truly wild species. According to the study, the Przwalski’s horse never interbred with domestic breeds, making it 100 percent wild. Interestingly, Przwalski horses have retained greater genetic diversity than the domestic breeds studied by the research team. According to study co-author Ludovic Orlando, an evolutionary biologist at the University of Copenhagen, this bodes well for conservation efforts and means there is a good chance of saving that horse population.

Because their initial read of the ancient horse genome is just a first step, more study will be needed to glean information about the animal’s appearance, according to co-author Eske Willersley, a geneticist with the Natural History Museum of Denmark. The team was able to determine that their specimen was male and about the size of a modern-day Arabian horse.

Although some aspects of ancient DNA research have been controversial, the field is now generally regarded as reliable and methodologically sound. A number of recent studies have demonstrated the potential of these archaic samples to reveal evolutionary patterns and the genetic relationships between extinct and contemporary organisms. New techniques have allowed scientists to decode the genome of the extinct Homo neanderthalensis and confirm a once-controversial theory that Neanderthals and modern humans actually interbred.

Ground-breaking genetic research has also shed light on other ancient human populations. For example, one study was able to identify Denisova man as a distinct hominin group that shared a common ancestor with the Neanderthal but was different from both Neanderthals and modern humans. Another looked at the genome of a 4000-year old human from Greenland and gleaned new information about an extinct people, including that the population had little or no genetic contribution from Europeans.

Commenting to BBC News on the broader significance of sequencing the oldest genome yet, Willersley said, “Pushing back the time barrier is important because it has implications for our evolutionary understanding of anything from hominins to other animals, because we can look further back in time than people have done previously.”

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