Mammoth molars yield the oldest DNA ever sequenced

Researchers sequenced DNA from two mammoths that lived more than 1 million years ago, including a steppe mammoth (illustrated here), the direct ancestor to woolly mammoths.

Beth Zaiken/Centre for Palaeogenetics

A genetic analysis of long-extinct Siberian mammoths has nearly doubled the record for the oldest DNA yet sequenced. The genetic material, from a creature that roamed frozen lands some 1.2 million years ago, pushes the study of ancient DNA closer to its theoretical limit—and reveals a new lineage of mammoth.

“I love this paper,” says Ludovic Orlando, a paleogeneticist at Paul Sabatier University whose team previously held the record for oldest DNA sequenced, from a 750,000-year-old horse. “I have been waiting since 2013 [for] our world record for the oldest genome to be broken.”

Genetic material breaks down relatively quickly in most environments. The oldest DNA sequenced from humans in Africa dates to about 15,000 years ago; in Europe, scientists have sequenced DNA from a Neanderthal that lived some 120,000 years ago. But the DNA of living things buried in permafrost can persist for much, much longer, as the deep freeze slows chemical degradation.

In the 1970s, Russian paleontologist Andrei Sher discovered a trove of frozen remains at several sites in northeastern Siberia, including a trio of mammoths. Based on the orientation of magnetic materials in the surrounding rocks and the types of rodents found buried alongside them, the researchers estimated that the mammoths had lived about 1.2 million, 1 million, and 700,000 years ago.

The researchers behind the new study drilled out tiny samples from the molar of each mammoth—about a pinch of salt’s worth—and attempted to extract DNA. The ravages of time had degraded the DNA into many billions of short, fragmented sequences. “The more puzzle pieces you have, the harder it is to reconstruct the whole puzzle,” says co-author Tom van der Valk, an evolutionary geneticist at Uppsala University.

To put those pieces together, researchers used the previously sequenced genomes of elephants and of much younger mammoth remains as a reference. It was a bit like “looking at the picture on the puzzle box,” says Love Dalén, an evolutionary geneticist at the Centre for Palaeogenetics in Stockholm and study co-author. When the researchers plotted the relationships between the older mammoths and the elephants and estimated how long it would have taken for their genes to diverge, the dates matched those provided by the earlier methods.

The youngest mammoth, at about 700,000 years old, is one of the oldest known woolly mammoths, cold-weather specialists that ranged across the Northern Hemisphere for hundreds of thousands of years. Most died out about 10,500 years ago when the climate warmed at the end of the last ice age (though a small population persisted north of the Bering Strait until about 4000 years ago).

The second mammoth, dated to about 1 million years old, was a steppe mammoth, the direct ancestor to woolly mammoths, the researchers report today in Nature. The third and oldest specimen, at about 1.2 million years old, belongs to a previously unknown lineage, which the researchers named Krestovka after a village near where it was found. By linking several of this mammoth’s genes to known traits, they learned it already possessed many of the extreme cold adaptations of the later woolly mammoths, including thick fur and ample fat deposits. The researchers also discovered that North America’s Columbian mammoths, which went extinct about 13,000 years ago, shared about half their genes with the new lineage and the other half with woolly mammoths. The researchers suspect the Krestovka mammoth entered North America about 1.5 million years ago, then hybridized with woolly mammoths about 1 million years later to produce the continent’s distinct subspecies.

Some scientists had doubted whether it was even possible to sequence DNA that was more than 1 million years old. “These [specimens] push back pretty substantially what we’d come to think of as the oldest possible ancient DNA,” says co-author and evolutionary biologist Beth Shapiro of the University of California, Santa Cruz. Theoretically, it’s possible to sequence DNA that’s as old as the permafrost itself, or about 2.6 million years, Dalén and van der Valk say.  

“It’s an exciting study revealing [that DNA can survive] beyond what many in the field would have predicted being the upper limit just a decade ago,” says geneticist and ancient DNA expert Eske Willerslev of the University of Cambridge, who wasn’t involved with the study.

Vincent Lynch, an evolutionary developmental biologist at the University at Buffalo, says the new study adds considerably to what scientists know about mammoths, including the origins of the Columbian mammoths. Yet the mammoths’ eventual fate should serve as a warning to our own species, he adds. “They were an extremely common, widespread population that went extinct very quickly … because of climate change. There’s got to be a lesson for us in that.”

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