Science

Mammoth Genomes Shatter Record for Oldest DNA Sequences


Scientists have recovered DNA from mammoth fossils found in Siberian permafrost that are more than a million years old. This DNA—the oldest genomic evidence recovered to date—illuminates the evolutionary history of woolly mammoths and Columbian mammoths. It also raises the prospect of recovering DNA from other organisms this ancient—including extinct members of the human family.

Ever since the recovery of two short DNA sequences from a recently extinct zebra subspecies known as the quagga in 1984, researchers have been working to get ever larger amounts of DNA from ever older remains. Advances in ancient DNA extraction and sequencing methods eventually brought to light genomes of creatures from deeper time, including cave bears and Neandertals. In 2013, investigators announced that they had retrieved DNA from a 700,000-year-old horse fossil—by far the oldest genomic data ever obtained. But as astonishingly old as that genetic material was, some experts predicted that sequenceable DNA should survive more than a million years in fossils preserved in frozen environments.

The new findings, published today in Nature, bear that prediction out. Tom van der Valk and Love Dalén of the Center for Paleogenetics in Stockholm and their colleagues obtained DNA from molar teeth belonging to three mammoths from different time periods. Mammoth species can be distinguished on the basis of dental characteristics. One tooth, discovered in deposits thought to be around 700,000 years old, looked like that of an early woolly mammoth, Mammuthus primigenius. The other two teeth—one dated to around one million years ago and the other to 1.2 million years ago or more—resembled molars of the steppe mammoth, Mammuthus trogontherii.

The genetic material extracted from the teeth was highly degraded, having fragmented into lots of tiny pieces over the millennia. To reassemble the pieces and help filter out any DNA from microbes or other contaminants, the researchers used the genomes of modern-day elephants as guides, much as someone solving a jigsaw puzzle might refer to the image on the box. In all they recovered billions of DNA base pairs from the youngest fossil (the woolly mammoth)—about 70 to 80 percent of the genome. They got hundreds of millions of base pairs constituting around 25 to 30 percent of the genome of the second oldest mammoth. The oldest fossil yielded the least DNA, but the team still sequenced around 60 million base pairs from it—enough to provide insights into mammoth evolution.

The fossil record of mammoths indicates that they arose around five million years ago in Africa and spread across much of the world, evolving into number of species and enduring for millions of years before going extinct just a few thousand years ago. Comparing the new genomic data to genomes of younger mammoths, the researchers confirmed their expectation that the woolly mammoth evolved from the steppe mammoth, and they showed that it gradually acquired its adaptations to the extreme cold of ice age Siberia.

The results also revealed surprises about another branch of the mammoth family tree. The oldest mammoth the team sampled turned out to belong to a previously unknown lineage that was ancestral to the mammoths that colonized North America 1.5 million years ago during the early Pleistocene epoch and gave rise to the Columbian mammoth that inhabited temperate regions of North and Central America. The Columbian mammoth may have been the product of interbreeding between woolly mammoths and members of the lineage to which the researchers’ oldest fossil specimen belonged, they suggest.

Outside experts say the work represents a significant advance in ancient DNA research. “It’s an exciting study revealing DNA survival beyond what many in the field would have predicted being the upper limit just a decade ago,” remarks Eske Willerslev of the University of Copenhagen, whose team recovered the 700,000-year-old horse genome in 2013. He and his colleagues were among the researchers who calculated that DNA more than a million years old could survive in permafrost conditions. “Now this has been proven,” he says. 

“This is a very exciting study, not only because it pushes back the age of the oldest DNA yet recovered, but because the DNA that the team obtained from these very ancient mammoths provides important insights into early mammoth populations and into the origins of later mammoths both in Europe and the Americas,” says Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

Mammoths are not the only creatures of interest from this time period. Dalén, van der Valk and their colleagues note that many modern-day mammal and bird species got their start in the Early and Middle Pleistocene. At a press teleconference on February 16, Dalén said that the team is starting projects looking into some of these species, including horses, musk ox and various rodents.

Can scientists expect to recover DNA from similarly ancient human ancestors? The human fossil record spans up to seven million years. The oldest human DNA comes from remains dated to 430,000 years ago. “We know that environmental conditions matter a lot for the preservation of DNA. The extraordinary preservation of these mammoth specimens is likely thanks to the fact that they have been ‘on-ice’—frozen in Northern Siberia since the death of these mammoths,” says Kelso, who has studied a number of ancient human genomes. “The ancient humans that have been discovered so far are not found in such ideal conditions, and our view back into the human past is unfortunately therefore still limited.”

But all hope is not lost. “Every year there are new innovations in methods,” Dalén said at the press teleconference. “Maybe a number of years in the future the methods will be there to recover DNA from human nonpermafrost specimens that are getting close to a million years old.” Alternatively, he added, “it is quite possible that in the future someone will find human remains frozen in permafrost of that age.”


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