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The oldest-ever DNA discovery reveals a new type of ancient animal

Scientists extracted a 1.2 million-year-old DNA sample out of Russian permafrost.

Finding new branches on the family tree is complicated when it comes to ancient woolly mammoths. You can't exactly send a spit sample to 23andMe.

However, thanks to a new discovery made in Russia's permafrost, researchers uncovered a previously unknown woolly mammoth relative. This mammoth is now known as the Krestovka mammoth.

The new finding is more than just the discovery of a long-lost family member: In one of three tusk samples discovered, scientists extracted the oldest DNA sample ever found. It's estimated to be 1.2 million years old.

Why it matters — For researchers, this new discovery helps answer the question of just how far back can you trace ancient DNA before it degrades and is lost to history.

Because this DNA dates up to 1.2 million years old, the researchers speculate they might even find DNA up to 2.6 million years old in the future.

The research was published Wednesday in the journal Nature.

"The samples are a thousand times older than Viking remains, and even pre-date the existence of humans and Neanderthals."

Here's the background — Paleoarchaeologists and paleogeneticists study some of the Earth's oldest creatures, which means they're locked in a race against time when it comes to DNA degradation.

If not properly preserved, for example in icy permafrost, DNA will degrade over the years. This means there may be insufficient genetic information to properly sequence some of Earth's oldest fossils. Dinosaur DNA, for example, is typically lost to time.

Researchers found these three mammoth molars buried under permafrost in Siberia.

Before this study, the oldest DNA sequenced to date was discovered in 2013 and belonged to an ancient horse dating back to (a now quaint) 560,000 to 780,000 years ago.

In a statement about the research, senior author and professor of evolutionary genetics at the Centre for Palaeogenetics, Love Dalén, puts just how old this DNA is into perspective.

"This DNA is incredibly old. The samples are a thousand times older than Viking remains, and even pre-date the existence of humans and Neanderthals," Dalén said.

Among this oldest DNA sample, the researchers also uncovered two other mammoth tusks that dated back to over 1 million years and roughly 700,000 years respectively.

Unlike ancient human molars, the molars of ancient mammoths were a site to behold.van der Valk et al. / Nature

What they did — To analyze these three mammoth molars, the researchers used a couple of different methods.

  • They isolated short fragments of DNA that would have been best preserved by permafrost
  • Used a method called "biostratigraphy" to cross-reference these faunal remains with faunal remains at sites with more absolute age data
  • They used DNA dating from the mitochondrion (famously, the powerhouse of the cell) to estimate the specimen's antiquity
  • They compared the ancient mammoth genomes to that of modern-day Asian and African elephants to understand with different environmental adaptations might have evolved

With all this data combined, researchers were able to build a new, rough sketch of the mammoth's family tree.

What they discovered — One major discovery the team made was that the oldest specimen (nicknamed "Krestovka" for the site it was discovered at) represented a previously unknown lineage of mammoth.

"This came as a complete surprise to us," said Tom van der Valk, the study's lead author and a postdoctoral researcher at the Swedish Museum of Natural history.

"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. We can’t say for sure yet, but we think these may represent two different species."

This new mammoth discovery also changes what scientists thought they knew about a subset of mammoths called the Columbian mammoth who roamed North America after the Ice Age. Instead of being pure woolly mammoth, researchers now speculate that the Columbian mammoth may actually be a hybrid of woolly and Krestovka lineage. (Critically, woolly mammoths are just one species of mammoth, despite being the most well known)

The ancient woolly steppe mammoth roaming Siberia.van der Valk et al.

Through their analysis, the researchers also discovered genetic adaptations associated with life in the Arctic (such as fat deposits, hair growth, and thermoregulation) were already present in the million-year-old mammoth — long before woolly mammoths came on the scene.

What's next — Researchers still don't know much about this time in ancient history, but they are encouraged by these results. The study suggests the cut-off point for viable DNA analysis may be even further back than originally thought.

“One of the big questions now is how far back in time we can go," Anders Götherström, a professor in molecular archaeology and joint research leader at the Centre for Palaeogenetics, said in a statement.

"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."

Abstract: Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale, the oldest genomic data recovered so far are from a horse specimen dated to 780– 560 thousand years ago. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
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