Researchers have sequenced the oldest known DNA in the world. Using material from the sub-eras of the early and middle Pleistocene, ancient DNA analysis shatters the record of the world’s oldest sequenced DNA. It comes from mammoth remains discovered in Siberian permafrost and proves that, under the right conditions, ancient DNA can survive more than a million years.
But the analysis of that ancient DNA depends on whether researchers also have the right technology. Fortunately, an international team led by researchers from the Center for Palaeogenetics in Stockholm, Sweden, had advanced sequencing technology and bioinformatics. A Nature news report for the new paper says the researchers have pushed current technology almost to the limit to enable the extraction of ancient DNA strands from mammoth teeth preserved in the Siberian permafrost. Senior author of the Nature study, Love Dalén, a professor of evolutionary genetics at the Center for Palaeogenetics, notes that the scientific team has been lucky, saying:
“It’s not that everything found in permafrost always works. The vast majority of samples have worthless DNA. ”
How the Ancient Mammoth broke DNA records
The discovery is truly astonishing, because after an organism dies, its chromosomes gradually get smaller and smaller, and in most cases extremely old strands of DNA have become so small that they have lost all of their informational content. But a new article published in the magazine Nature shows that the team managed to obtain 49 million base pairs of nuclear DNA from a 1.65 million year old tooth found near a village called Krestovka (the tooth is also called Krestovka). They also extracted 884 million base pairs of ancient DNA from a 1.3-million-year-old tooth they call Adycha and 3.7 billion base pairs of DNA from a 600,000-year-old woolly mammoth tooth they named Chukochya. The three mammoth remains were discovered in the 1970s and are part of the collection of the Russian Academy of Sciences in Moscow.
I like Dalén and co-lead author Patrícia Pečnerová with a giant tusk on Wrangel Island. (Credit: Gleb Danilov)
The Nature news report explains that the ancient mammoth DNA study has not uncovered the oldest biomolecular information from the fossil record – that is, the sequence of proteins in 2016 from 3.8 million-year-old ostrich eggshells from Tanzania. In second place is a protein sequence from a 1.77 million year old rhinoceros tooth from Georgia, which was analyzed in 2019. Although protein is stronger and can survive in extremely old fossils from places without permafrost, it is not as useful as DNA to researchers who want to study the origin of an organism.
That’s just one of the reasons the new mammoth DNA study is so important – it contains genetic information that wasn’t available in the older protein samples.
A second reason the study is making headlines is that it records ancient DNA from a genome of a 560,000 to 780,000 year-old horse leg bone found in Canada’s Yukon Territory for the oldest ancient DNA sequence. Putting the age of the mammoth samples into context, Dalén said:
“This DNA is incredibly old. The monsters are a thousand times older than Viking remains and predate the existence of humans even Neanderthals
The first example of hybrid speciation in ancient DNA
The new study has also increased researchers’ ability to track the evolutionary process of speciation – the formation of new and different species. A Nature The press release states that this process generally takes place “at periods that are believed to be beyond the boundaries of DNA research.”
A woolly mammoth tusk discovered in a creek bed on Wrangel Island in 2017. (Credit: Love Dalén)
Nevertheless, the scientists’ study of the mammoth DNA suggests that not one, but two different mammoth lines lived in the region of what is now Eastern Siberia during the early Pleistocene. Adycha and Chukochya are believed to be members of a species that spawned the woolly mammoth, but Krestovka appears to be from an unknown and possibly entirely new mammoth line. Tom van der Valk, the study’s lead author and a bioinformatician at Uppsala University in Sweden, explains the researchers’ shock at this discovery:
“This came as a complete surprise to us. All previous studies have shown that there was only one mammoth species in Siberia at the time, called the steppe mammoth. But our DNA analyzes now show that there were two different genetic lines, which we here call the Adycha mammoth and the Krestovka mammoth. We can’t say for sure yet, but we think these two could represent different species. ”
In their study, the researchers suggest that the Krestovka genome may have diverged from the other mammoths between 2.66 and 1.78 million years ago. They also believe this mammoth line was “ the ancestor of the first mammoths to colonize North America. ” It appears that the North American Colombian mammoths ( Mammuthus columbi ) can trace half of their ancestors to woolly mammoths and the other half to the previously unrecognized Krestovka mammoth line.
The Nature news report states that this means the new study has also provided the first evidence for ‘hybrid speciation’ – a new species created by mixing – found in ancient DNA. Study co-lead author Patrícia Pečnerová, an evolutionary biologist at the Swedish Museum of Natural History, says the team believes that “ the Colombian mammoth, one of North America’s most iconic Ice Age species, evolved through a hybridization that happened roughly. 420 thousand years ago. ”
How far back can researchers go?
Finally, the ancient mammoth DNA study inspired Dalén to analyze more permafrost animal samples that are over a million years old. Next on his list? Musk oxen, moose and lemmings. But the evolutionary genetics professor knows there is an age limit he will not be able to exceed when analyzing the ancient DNA – 2.6 million years – “That’s the permafrost limit. It was too hot for that, ”he says.
Tusk of a woolly mammoth emerging from the permafrost on centrally located Wrangel Island, in northeastern Siberia. (Credit: Love Dalén)
Top image: The image represents a reconstruction of the steppe mammoth that preceded the woolly mammoth, based on the genetic knowledge we now have of the Adycha mammoth. Source: Beth Zaiken / Center for Palaeogenetics
By Alicia McDermott