Imagine an elephant that is significantly larger, heavier and has longer tusks. This is the Colombian mammoth, an imposing animal that roamed much of North America in the last Ice Age.
When it comes to the mammoth pedigree, it has long been believed that the Colombian mammoth evolved earlier than the smaller, shaglier woolly mammoth. With DNA more than a million years old – the oldest ever extracted from a fossil – researchers have turned that assumption on its head: they found that the Colombian mammoth was actually a mix of the woolly mammoth and one before it unrecognized is mammoth line.
These results were published on Wednesday in the journal Nature.
Mammoths are depicted in many cave paintings, reflecting their importance as a food source, skin, and bones during the Pleistocene. During the last Ice Age, people living in what is now the United States would have mostly encountered the Colombian mammoth, said Love Dalen, a paleogeneticist at the Center for Paleogenetics in Stockholm. “It’s an iconic species from the last ice age,” he said.
Fossilized remains of mammoths, especially those preserved down to the smallest detail, can shed light on how these animals lived and died. However, analyzing the genetic code of an ancient creature – by recovering its DNA and reassembling it into a genome – opens up huge new research opportunities, said David Díez-del-Molino, another paleogeneticist at the Center for Paleogenetics. “You can trace the origin of the species.”
A research team, including Dr. Dalen and Dr. Díez-del-Molino recently set out to do just that with three mammoth molars unearthed in northeast Siberia.
These teeth are old – roughly 700,000 years, 1.1 million years, and 1.2 million years – and they’re also impressive to look at, said Dr. Dalen. “They’re the size of a carton of milk.”
The researchers first extracted some material from the inside of each tooth with a small dental drill. They then used chemicals and enzymes followed by a washing protocol to isolate the DNA in the resulting tooth powder.
Most of the DNA they extracted consisted of sequences that were only a few tens of base pairs long. This is to be expected because the passage of time for DNA molecules is difficult. Bacteria and enzymes chop up DNA after an organism dies, and water and cosmic rays continue to break down even after a sample is buried in permafrost.
Patricia Pecnerova, evolutionary biologist at the University of Copenhagen and researcher on the team, said millions of base pairs will soon be degraded. “The DNA is very fragmented,” she said.
Before everything can be digitally put back together, however, each sample must be decontaminated, said Tom van der Valk, another team member and bioinformatician at the Science for Life Laboratory in Stockholm. That’s because DNA from plants, bacteria, and humans can sneak into fossils very well, he said. “Much of our data does not come from the mammoth.”
To sort out interloping DNA, the team compared the sequences with the genetic code of an African elephant, a close relative of mammoths. They threw away everything that didn’t go together. In addition, they threw out sequences that corresponded to the human genome.
After removing the non-mammoth DNA, the team left between 49 million and 3.7 billion base pairs in each of their three samples. (The mammoth genome is roughly 3.2 billion base pairs, which is slightly larger than the human genome.) The researchers compared their data a second time with the DNA of African elephants, which enabled them to put all of their DNA fragments in the correct order.
That mammoth DNA shattered the record for the oldest DNA ever sequenced, previously held by a horse specimen about 700,000 years old, said Morten E. Allentoft, an evolutionary biologist at Curtin University in Perth, Australia who was not involved in the research. “It is the oldest DNA ever authentically identified,” he said.
When the researchers looked at the three genomes they had reconstructed, the oldest was noticed. “The genome looked weird,” said Dr. Dalen. “I think it’s likely that this is a different species.”
That was a shock: Researchers have long believed that there was only one line of mammoths in Siberia that gave rise to woolly and Colombian mammoths. This discovery suggests that a previously undiscovered mammoth line also existed.
“It’s a big surprise,” said Dr. Dalen. “From paleontology it is completely unexpected that there would be a second line.”
Next, the team compared the three genomes to the genetics of the Colombian mammoth, which was common in much of North America 12,000 years ago. The aim was to determine how, if any, these two species were related.
They found compelling evidence that the woolly mammoth and this new unknown line crossed to form the Colombian mammoth, a hybrid species.
Nobody knows where and how long this new mammoth line thrived, said Dr. van der Valk. “It would be absolutely amazing if we could get a few more samples of this line.”
There is also the possibility of reconstructing increasingly older DNA, said Dr. Dalen. We’re not going to recreate Jurassic Park, he said, but theoretical models suggest that DNA could survive for up to a few million years. “I don’t think we’re still at the limit.”