The oldest full genome sequence, recovered from ancient horse bone, pushes back equine origins by 2 million years.
The humble horse has provided the oldest full genome sequence of any species — from a specimen more than half a million years old, found frozen in the permafrost of the Canadian Arctic. The finding, published in Nature today1, pushes back the known origins of the equine lineage by about 2 million years, and yields a variety of evolutionary insights.
The sequence was extracted from a foot bone of a horse that lived between 780,000 and 560,000 years ago. By sequencing the animal’s genome, along with those of a 43,000-year-old horse, five modern domestic horse breeds, a wild Przewalski’s horse and a donkey, researchers were able to trace the evolutionary history of the horse family in unprecedented detail. They estimate that the ancient ancestor of the modern Equus genus, which includes horses, donkeys and zebras, branched off from other animal lineages about 4 million years ago — twice as long ago as scientists had previously thought.
“We have beaten the time barrier,” says evolutionary biologist Ludovic Orlando of the University of Copenhagen, who led the work with colleague Eske Willerslev. Noting that the oldest DNA sequenced before this came from a polar bear between 110,000 and 130,000 years old2, Orlando says: “All of a sudden, you have access to many more extinct species than you could have ever dreamed of sequencing before.”
The team was able to sequence such old DNA partly because of the freezing ground temperatures in the area where the bone was found, which would have slowed the rate of DNA decay.
But the researchers were also successful because they had perfected techniques for extracting and preparing the DNA to preserve its quality for sequencing. They targeted tissue within the fossil which has high DNA content, such as collagen. They also combined DNA sequencing techniques to get maximum DNA coverage — using routine next-generation sequencing with single-molecule sequencing in which a machine directly reads the DNA without the need to amplify it up which can lose some DNA sequences.
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