Million-year-old mammoth genome breaks record for oldest ancient DNA

The million year old genome is here. Mammoth teeth preserved in the eastern Siberian permafrost produced the oldest ancient DNA recorded, pushing the technology near – but perhaps not beyond – the boundaries.

Genomic DNA extracted from a trio of tooth samples unearthed in the 1970s has identified a new species of mammoth that gave rise to a later North American species. The findings were published in Nature on February 17¹.

“I love the newspaper. I have been waiting for the paper for eight years now, ”said Ludovic Orlando, an ancient DNA specialist at the Center for Anthropobiology and Genomics in Toulouse, France, who led a 2013 effort that gave the previous oldest order . ancient DNA – a genome of a horse bone from 560,000 to 780,000 years². “I’m glad I lost this record because it was a heavy record,” he says.

Researchers have suspected that ancient DNA could survive for more than one million years if the correct sample could be found. Once an organism dies, the chromosomes break down into pieces that become shorter over time. Eventually, the DNA strands become so small that, even if they can be extracted, they lose their information content.

Orlando’s team found that fragments of only 25 DNA letters in their horse bones, from the Canadian Yukon Territory, could still be interpreted. They estimate that millions of years old remnants stored in the constant cold of permafrost – which slows down DNA fragmentation – must also contain DNA fragments of that length. “My only doubt: does such an example exist?” See Orlando.

Decadal dream

Love Dalén, an evolutionist geneticist from the Swedish Museum of Natural History (SMNH) in Stockholm, has been working on the idea of ​​tracking down many ancient mammoth remains since he encountered a collection of them in 2007. The monsters his team set up, one of an early woolly mammoth (Mammuthus primigenius) and two awarded to a forerunner known as steppe mammoths (Mammuthus trogontherii), was excavated by the Russian paleontologist Andrei Sher.

Dalén had hoped that DNA from the samples could capture the evolution of woolly mammoths and other species in action, but he was skeptical due to previous bad experiences with much younger remains found in permafrost. ‘It’s not as if everything in the permafrost always works. The vast majority of samples have crap DNA, ”he says.

And indeed, two of the three giant molars from Sher’s excavations, which are made of sediments more than a million years old, contain so little DNA that Dalén says he would have thrown them away if they were younger.

But thanks to advances in sequential technology and bioinformatics, his team has managed to retrieve 49 million base pairs of nuclear DNA from the oldest sample, found near a town called Krestovka, and 884 million base pairs from another tooth, called Adycha. Analysis of the DNA suggested that the Krestovka sample was 1.65 million years old, and the Adycha sample about 1.3 million (see ‘Ancient genomes’). The third sample, a 600,000-year-old woolly tooth named Chukochya, produced nearly 3.7 billion base pairs of DNA, more than the length of its 3.1 billion base pair genome.

From their shape, the two oldest teeth looked like they belonged to steppe moths, a European species that researchers say are dated woolly mammoths and Columbian mammoths (Mammuthus columbi), a North American species. But their genomes painted a more complicated picture. The Adycha specimen was part of the genus that gave rise to woolly mammoths, but the Krestovka specimen was clearly not.

Dalén’s team has found that it belongs to a whole new generation. “We can not say that it is a different species, but it certainly looks like that,” he says. Although the Krestovka monster originated in Russia, he suspects that the lineage was isolated from other steppe mammoths in North America. The team found that Columbian mammoths trace half of their ancestry to the Krestovka mammoth line, and the other half to woolly mammoths. Dalén estimates that the two generations mixed more than 420,000 years ago.

The idea that new species can form by mixing – and not just splitting from a single parent species – is gaining ground among evolutionary biologists. But this is the first evidence for ‘hybrid speciation’ of ancient DNA, Orlando says. “It’s amazing.”

Hendrik Poinar, an ancient DNA specialist at McMaster University in Hamilton, Canada, says different mammoth species probably hybridized regularly when glacier expansion brought them together. His team found evidence that later woolly and mammoth mammoths sometimes stepped in.

The future of ancient DNA

Although researchers have long been expecting a million-year-old genome, it is important to exceed this threshold, says Viviane Slon, a paleogeneticist at Tel Aviv University in Israel. “There’s a difference between what we think is possible and actually showing it.”

Tom van der Valk, a bioinformatics scientist at Uppsala University in Sweden who led the giant dental work with evolutionary biologists Patrícia Pečnerová and David Díez-del-Molino at the SMNH, hopes it will encourage other laboratories. “It’s a symbolic barrier that I hope can inspire and motivate other groups that have ideas about right depth order.”

By exceeding the million-year-long threshold, ancient DNA researchers may have access to the early history of large and small mammals, says Dalén. Many old permafrost samples of musk oxen, elk and lemmings are now on his laboratory’s radar.

The giant DNA does not represent the oldest biomolecular information from the fossil record. In 2016, researchers reported protein sequences of 3.8 million-year-old ostrich eggshells from Tanzania³, and in 2019 another team will decode proteins from a 1.77 million year old rhino tooth from Georgia⁴. Protein sequences tend to be much less informative about the origin of an organism than DNA. But protein molecules are much harder, so researchers can use them to gain insights from very old fossils found in places without permafrost. The ostrich and rhino specimens both come from archeological sites known for hominin remains.

The chances of millions-old remains of ancient human relatives being found in the permafrost are very low, researchers say. But Dalén thinks that the right environment, like a deep cave, can produce such ancient monsters. Early Neanderthal remains from a Spanish cave dated 430,000 years ago represent the oldest DNA of an ancient human family member discovered so far.⁵. “It’s a dream to find a hominin in the ideal context for conservation like permafrost,” says Slon.

Regarding the probable age limit of ancient DNA, Dalén says it is easy to determine: “2.6 million years. This is the limit of the permafrost. Before that it was too hot. ”