A new NGS milestone: The million-year-old genome

The million-year-old genome is no longer the stuff of science fiction.

Researchers in February announced the oldest-yet sequenced genome, eclipsing the previous record for the oldest genomic data recovered.

The DNA were lifted from teeth belonging to 2 mammoths found in Russia. The findings, announced in Nature, were based on 49 million base pairs of nuclear DNA from one tooth and 884 million base pairs from the other.

Those DNA, researchers say, illustrate the evolutionary history of woolly mammoths and Columbian mammoths and may have identified a new species.

Recovery of the tooth DNA builds on sequencing efforts that first began in 1984, when 2 short DNA sequences were recovered from a recently extinct southern African animal called the quagga. Since then, ancient DNA extraction has delved deeper into time. In 2013, researchers pulled DNA from a 700,000-year-old horse fossil, which raised the question—if the conditions were right, just how long could DNA survive?

In the new findings, Tom van der Valk and Love Dalén of the Center for Paleogenetics in Stockholm, along with colleagues, obtained DNA from molars belonging to 3 mammoths from different periods. One tooth dated to around 1 million years ago and the other to 1.2 million years ago or more; they both resembled molars of the steppe mammoth, Mammuthus trogontherii. A third tooth, discovered in deposits believed to be around 700,000 years old, looked like that of an early woolly mammoth, Mammuthus primigenius.

The genetic material pulled from the teeth was highly degraded—it had fallen into oodles of tiny pieces over the millennia. Researchers reassembled the pieces and filtered out any renegade DNA that might have snuck in over the years by using modern-day elephant genomes as guides.

According to fossil evidence, mammoths developed about 5 million years ago in Africa and spread across much of the world. Along the way they evolved into the steppe mammoth, which gave birth to the wooly mammoth, which adapted to Siberia’s harsh conditions. Mammoths went extinct just a few thousand years ago. Research from this study suggests that the oldest mammoth sequenced from this batch was the ancestor to mammoths that lived in North America some 1.5 million years ago and eventually inhabited warmer areas of North America, migrating as far south as Central America.

Key to the ability to recover the DNA was the fact that they had been preserved in ice—the animals were apparently frozen from almost the moment they died until the remnants were recovered. Could similarly old DNA be sequenced for ancient humans? The oldest human remains tend to be found in warmer areas, where DNA preservation is not ideal.

“This is—by a wide margin—the oldest DNA ever recovered,” said Dalén at a press conference. “Maybe a number of years in the future, the methods will be there to recover DNA from human non-permafrost specimens that are getting close to a million years old. The other alternative would be to find a Homo Erectus in the permafrost. No such finds have been done to date, but it is quite possible that someone will find human remains in the permafrost of this age. In that case, it would be more-or-less equally easy to get genomic DNA from these [hominin specimens] as it was for us to get DNA from the mammoths."

Study co-author Tom van der Valk told Nature in an interview that his lab would be investigating permafrost-found samples of musk oxen, moose, and lemmings in the future.

“The chances of finding million-year-old remains of ancient human relatives in the permafrost are very low,” the Nature interview added. “But Dalén thinks that the right environment, such as a deep cave, could yield samples that old. Early Neanderthal remains from a Spanish cave dated to 430,000 years ago represent the oldest DNA from an ancient human relative discovered so far.”

One thing is for sure: ancient DNA recovered from permafrost will never be more than 2.6 million years old. Why? Before that, the climate was too warm for permafrost.