Scientists Extract and Sequence Million-Year-Old Mammoth DNA

A team of 22 researchers from nine countries – led by the Centre for Palaeogenetics (CPG) – has sequenced ancient DNA from the remains of three different mammoth species excavated in the Siberian permafrost. This is the oldest DNA to have been sequenced in the history of science. The study findings are published in the journal Nature.¹

A mammoth of a task

The high-throughput technologies of modern genomics are enabling scientists to make new discoveries about the past. Since the "genomic era" an increasing number of research groups have focused on sequencing ancient DNA, or "aDNA" – DNA that has been isolated from ancient specimens. Until now, the oldest DNA sequenced was horse DNA, dating back to 780,000–560,000 years ago.²

Sequencing ancient remains is no easy task, said Tom van der Valk, postdoctoral researcher at the CPG: "The DNA is often highly degraded – meaning it is fragmented into tiny pieces. It can be somewhat challenging to figure out which of the fragments belong to the species of interest, and which pieces belong to microbial specimens, for example."

Van der Valk is the lead author of a new study in which scientists have successfully analyzed the genomes of three ancient mammoths. The DNA, extracted from fossilized molars excavated in Siberia, is estimated to be 1.2 million-years-old.

"This is – by a wide margin – the oldest DNA that has ever been recovered and sequenced," said Love Dalén, professor of evolutionary genetics at the Centre for Palaeogenetics in Stockholm, and senior author of the study.

In addition to setting a new bar for the study of aDNA, the study reveals novel insights into the adaptation of mammoths.

A step back in mammoth history

Fans of the film series Ice Age may have a vision of mammoths as being gigantic creatures, but the woolly mammoth (Mammuthus primigenius) is actually believed to have been a similar size to African elephants.

Mammoths are estimated to have first appeared in Africa ~ 5 million years ago. During the Pleistocene epoch – also known as the Ice Age – mammoths underwent evolution, resulting in different species, such as the southern mammoth (Mammuthus meridionalis), the steppe mammoth (Mammuthus trogontheri) and eventually the Columbian (Mammathus columbi) and woolly mammoths.

"Our main aim [of the study] was to recover genomes from before and after the origin of the woolly mammoth," said van der Valk.

The molars of the three ancient mammoths analyzed in the study had been buried for 0.7–1.2 million years in the Siberian permafrost prior to their excavation in the 1970s.

The oldest mammoth sample – which the team refer to as the Krestovka mammoth – was morphologically similar to the steppe mammoth. The age of the second sample, known as "Adycha" was lesser known, but its morphology suggested it dated between 1–1.2 million years. The third and youngest mammoth specimen, "Chukochya" was morphologically similar to an early form of the woolly mammoth and was estimated to data back 0.–-0.8 million years.

Outlining their methods in the paper, the authors write: "We extracted DNA from the three molars using methods designed to recover highly degraded DNA fragments, converted the extracts into libraries and sequenced these."

A surprise finding

The team found that the Krestovka mammoth belonged to an unknown genetic lineage of mammoth, which was unexpected considering its morphological similarities to the steppe mammoth.

Van der Valk said: "This came as a complete surprise to us. All previous studies have indicated that there was only one species of mammoth in Siberia at that point in time, called the steppe mammoth. But our DNA analyses now show that there were two different genetic lineages, which we here refer to as the Adycha mammoth and the Krestovka mammoth." He added that whilst the team cannot be certain, they think their finding represents two different species.

The Adycha mammoth genome was compared to those of the earliest known woolly mammoths, in addition to woolly mammoth genomes that are a few thousand years old. Through this comparison, the scientists were able to explore the adaptations that the mammoths underwent to live in cold environments. “To be able to trace genetic changes across a speciation event is unique. Our analyses show that most cold adaptations were present already in the ancestor of the woolly mammoth, and we find no evidence that natural selection was faster during the speciation process,” said co-lead author David Díez-del-Molino in a press release.

The researchers believe the study offers a promising new avenue for further research and poses the question: How far back in time can we go?

"We haven’t reached the limit yet. An educated guess would be that we could recover DNA that is two million years old, and possibly go even as far back as 2.6 million. Before that, there was no permafrost where ancient DNA could have been preserved,” Anders Götherström, a professor in molecular archaeology and joint research leader at the CPG, said in a press release.

References:

1.      van der Valk T, Pečnerová P, Díez-del-Molino, et al. Million-year-old DNA sheds light on the genomic history of mammoths. Nature. 2021. doi:10.1038/s41586-021-03224-9.

2.      Orlando L, Ginolhac A, Zhang G, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 2013;499(7456):74-78. doi:10.1038/nature12323.