animals

Genome of 700,000-year-old horse sequenced

U. SOUTHAMPTON (UK) — Scientists have set a new world record, sequencing the oldest genome to date from a prehistoric creature.

Researchers sequenced and analyzed short pieces of DNA molecules preserved in bone-remnants from a horse kept frozen in the permafrost of Yukon, Canada, for the last 700,000 years.

By tracking the genomic changes that transformed prehistoric wild horses into domestic breeds, the researchers have revealed the genetic make-up of modern horses in unprecedented detail.


The results also bring a happy end to a long discussion about the so-called Przewalski’s horse from the Mongolian steppes. This horse population was discovered by the Western world in the second-half of the nineteenth century and rapidly became threatened. It almost became extinct in the wild by the 1970s, but has survived until now following massive conservation efforts. (Credit: RayMorris1/Flickr)

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Jacobo Weinstock, archaeologist at the University of Southampton, took part in the original expedition to Yukon in 2003, when the horse bone was recovered and has been involved in the project since.

He extracted DNA and sequenced part of the specimen’s genome as an independent replication of the results obtained by a team from the Natural History Museum of Denmark at the University of Copenhagen.

“Extracting and sequencing DNA from ancient organisms is not straightforward; contamination with extraneous DNA is always a potential problem,” Weinstock says.

“Therefore, an independent replication of the results in a different laboratory is essential to validate the results, especially in the case of exceptional specimens such as the horse from Yukon. The perfect match between both sequences, in addition to the phylogenetic position of the ancient horse outside the diversity of any horse ever sequenced, provided clear evidence that the data was real.”

DNA molecules can survive in fossils well after an organism dies. Not as whole chromosomes, but as short pieces that can be assembled back together, like a puzzle. Sometimes enough molecules survive so that the full genome sequence of extinct species can be resurrected.

Over recent years the full genome sequence of a few ancient humans and archaic hominins has been characterized, but none have dated back to before 70,000 years ago.

However, Ludovic Orlando and Eske Willerslev from the Centre for GeoGenetics have achieved a new DNA-record. In collaboration with other colleagues, they were able to track major genomic changes of the horse lineage over the last 700,000 years of evolution.

Their findings are published in the journal Nature.

“The results of the studies and the applied techniques open up new doors for the exploration of prehistoric living creatures,” Willerslev says. “Now with genomics and proteomics, we can reach ten times further back in time compared to before.

“New knowledge about the horse’s evolutionary history has been added—a history which is considered as a classical example in evolutionary biology and a topic which is taught in high schools and universities.”

By comparing the genome in the 700,000-year-old horse with the genome of a 43,000-year-old horse, six present day horses, and a donkey, the researchers could estimate how fast mutations accumulate through time and calibrate a genome-wide mutation rate. This revealed that the last common ancestor of all modern equids lived about 4 to 4.5 million years ago.

Therefore, the evolutionary radiation underlying the origin of horses, donkeys, and zebras reaches back in time twice as long as previously thought. Additionally, this new clock revealed multiple episodes of severe demographic fluctuation in horse history, in phase with major climatic changes such as the Last Glacial Maximum, some 20,000 years ago.

The world’s only wild horse

The results also bring a happy end to a long discussion about the so-called Przewalski’s horse from the Mongolian steppes. This horse population was discovered by the Western world in the second-half of the nineteenth century and rapidly became threatened. It almost became extinct in the wild by the 1970s, but has survived until now following massive conservation efforts.

The evolutionary origin of this horse, which shows striking physical differences compared to domesticated horses, as well as an extra-pair of chromosomes, remained a mystery.

The researchers have now revealed that the Przewalski’s horse population became isolated from the lineage, leading to present day domesticated horses, about 50,000 years ago. As the scientists could detect similar levels of genetic diversity within the Przewalski’s horse genome than in the genomes of several domestic breeds, this suggests that the Przewalski’s horses are likely genetically viable and therefore worthy of conservation efforts.

Researchers from Denmark, China, Canada, US, Switzerland, UK, Norway, France, Sweden, and Saudi Arabia and contributed to the study with financial support from the Danish National Research Foundation.

Source: University of Southampton

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