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Genome of Horse Buried 700,000 Years Is Recovered Genome of Horse Buried 700,000 Years Is Recovered
(about 4 hours later)
Researchers have reconstructed an ancient genome that is 10 times as old as any retrieved so far, and now say that DNA should be recoverable from animals that lived one million years ago. This would greatly extend biologists’ ability to understand the evolutionary past. Researchers have reconstructed an ancient genome that is 10 times as old as any retrieved so far, and they now say that DNA should be recoverable from animals that lived one million years ago. This would greatly extend biologists’ ability to understand the evolutionary past.
The genome was that of a horse that lived some 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 analyzed DNA from a less ancient horse, one that lived 43,000 years ago, as well as five contemporary horse breeds and a donkey named Willy that resides in the Copenhagen zoo. They concluded that the genus that gave rise to modern horses, zebras and donkeys — Equus — arose about four million years ago, twice as far back as had been thought. The genome was that of a horse that lived 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 analyzed DNA from a less ancient horse, one that lived 43,000 years ago, as well as five contemporary horse breeds and a donkey named Willy that resides in the Copenhagen Zoo. They concluded that the genus that gave rise to modern horses, zebras and donkeys — Equus — arose about four 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 paleogenomics, the study of ancient genomes reconstructed from fossil bones. Within the last few decades this young science has become a powerful complement to paleontology, the study of fossils, as a way of reconstructing evolutionary history.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 paleogenomics, the study of ancient genomes reconstructed from fossil bones. Within the last few decades this young science has become a powerful complement to paleontology, 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 the temperate zones, where important fossil bones are more plentiful.“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 the 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 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. They also conducted tests that showed that the horse bone, despite its age, was likely to contain DNA, even though the chemical starts to degrade as soon as an animal dies. 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. They also conducted tests that showed that the horse bone, despite its age, was likely to contain DNA, even though the chemical starts to degrade as soon as an animal dies.
To help establish that the DNA from the horse bone was really 700,000 years old, Dr. Willerslev and Ludovic Orlando, a colleague at the University of Copenhagen, started an ambitious project to analyze 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 horse, a species thought to represent the last living wild horse population; five domestic horse breeds (Arabian, Icelandic, Norwegian fjord, Standardbred and Thoroughbred); and Willy the donkey. To help establish that the DNA from the horse bone was really 700,000 years old, Dr. Willerslev and Ludovic Orlando, a colleague at the University of Copenhagen, started an ambitious project to analyze 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 Willy the donkey.
Dr. 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,” Dr. Orlando said. With this and other data he is confident that the Thistle Creek horse and its genome are indeed 700,000 years old.Dr. 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,” Dr. Orlando said. With this and other data he is confident that the Thistle Creek horse and its genome are indeed 700,000 years old.
In a report published in the journal Nature on Wednesday, he and colleagues say that they have identified 29 regions in the genome of domestic horses where the DNA shows statistical evidence of selection, meaning that variant genes in these regions were favored as horses became domesticated. But each of the regions is some 200,000 DNA units in length and contains many genes, so the researchers do not yet know which of these genes was the target of selection, Dr. Orlando said. In a report published in the journal Nature on Wednesday, he and colleagues say that they have identified 29 regions in the genome of domestic horses where the DNA shows statistical evidence of selection, meaning that variant genes in these regions were favored as horses became domesticated. But each of the regions is about 200,000 DNA units in length and contains many genes, so the researchers do not yet know which of these genes was the target of selection, Dr. Orlando said.
Another finding from the new collection of horse genome data is that the Przewalski horse shows no signs of having interbred with domestic horses, as some researchers had assumed was likely. Since the horse is threatened in the wild, this gives added reason for protecting it. Another finding from the new collection of horse genome data is that the Przewalski’s horse shows no signs of having interbred with domestic horses, as some researchers had assumed was likely. Since the horse is threatened in the wild, this gives added reason for protecting it.
The rich genomic data on the horse family tree has enabled the Danish team to make statistical estimates of the size of the horse population through the ages. In the last two million years, horses have gone through three cycles of a population increase followed by a crash. The most recent peak was during the last glacial maximum, a cold period 25,000 years ago that preceded the end of the last ice age.The rich genomic data on the horse family tree has enabled the Danish team to make statistical estimates of the size of the horse population through the ages. In the last two million years, horses have gone through three cycles of a population increase followed by a crash. The most recent peak was during the last glacial maximum, a cold period 25,000 years ago that preceded the end of the last ice age.
The reason seems to be that during cold periods there are extensive grasslands, but these revert to forest during warmer times. “When it’s fairly cold it’s good to be a horse, but when it’s warm it’s pretty bad,” Dr. Willerslev said at news conference in Helsinki, Finland, on Tuesday.The reason seems to be that during cold periods there are extensive grasslands, but these revert to forest during warmer times. “When it’s fairly cold it’s good to be a horse, but when it’s warm it’s pretty bad,” Dr. Willerslev said at news conference in Helsinki, Finland, on Tuesday.
The most distant ancestor of the horse, Eohippus, was a cat-size animal that lived in forests 50 million years ago. Its descendants learned to feed on grass, but life in the open plains required larger size and speed to escape predators. The Thistle Creek horse, a male, would have been of modern size.The most distant ancestor of the horse, Eohippus, was a cat-size animal that lived in forests 50 million years ago. Its descendants learned to feed on grass, but life in the open plains required larger size and speed to escape predators. The Thistle Creek horse, a male, would have been of modern size.
Bruce MacFadden, an expert on fossil horses at the University of Florida, said the Danish team’s findings were reasonable in light of the fossil data. “It’s always wonderful when the fossil and molecular evidence coincide,” he said. But the influence of climate on horse demography is more complicated that the genomic data suggests, he said. Bruce MacFadden, an expert on fossil horses at the University of Florida, said the Danish team’s findings were reasonable in light of the fossil data. “It’s always wonderful when the fossil and molecular evidence coincide,” he said. But the influence of climate on horse demography is more complicated than the genomic data suggests, he said.
The horse’s genome consists of 2.7 billion units of DNA. The DNA extracted from the Thistle Creek bone was fragmented into minute pieces some 25 to 75 DNA units in length. The Danish team calculates that pieces only 25 units long could survive for a million years, which they see as the theoretical limit for reconstructing ancient genomes. The horse’s genome consists of 2.7 billion units of DNA. The DNA extracted from the Thistle Creek bone was fragmented into minute pieces about 25 to 75 DNA units in length. The Danish team calculates that pieces only 25 units long could survive for a million years, which they see as the theoretical limit for reconstructing ancient genomes.