Ancient DNA Recovered from Caves

New techniques are allowing scientists to extract ancient DNA from cave soil. But is it really as old as claimed?

DNA has a lifetime. It decays. That’s why researchers do not consider it likely that dinosaur DNA will ever be recovered sufficient to make “Jurassic Park” a reality. Now that DNA is being recovered from cave soil where early humans lived—without the need for bones—will the evolutionary dates drive the interpretation, or will known decay rates lead scientists to reconsider their assumptions about how old it is? We examine recent news reports for clues.

“This work represents an enormous scientific breakthrough.”

DNA of extinct humans found in caves (BBC News). This article describes an “enormous scientific breakthrough”: the recovery of “DNA of extinct humans …. from sediments in caves – even in the absence of skeletal remains.” Researchers from the Max Planck Institute recovered soil from seven sites in Belgium, Croatia, France, Russia and Spain. The article says that components of sediments are known to bind DNA; “Even sediment samples that had been stored at room temperature for years yielded DNA,” they found. Among samples of DNA from “extinct species such as the woolly mammoth, woolly rhinoceros, cave bear and cave hyena,” they found bits of Neanderthal and Denisovan mitochondrial DNA where no skeletal remains were known. They think it will even be possible to recover nuclear DNA (from the nucleus). Nothing is said about the longevity of DNA in these environments.

Mud DNA means we can detect ancient humans even without fossils (New Scientist). Michael LePage calls it “an astonishing new way to study our early human ancestors” to find DNA in cave soil. “Just about any sample of soil or water is full of DNA from all kinds of organisms,” he mentions, providing some examples of detection in recent studies. But how long can the DNA last? “In sediments buried in cool caves and in permafrost, this environmental DNA can survive for up to 700,000 years,” LePage says, but is that from DNA decay rates, or from evolutionary assumptions about the sample ages? Eske Willerslev, who found mammoth DNA, has doubts about the dating method:

What could be an issue, says Willerslev, is establishing exactly how old ancient hominin DNA is. “Cave sediments are often highly disturbed,” he says, which makes it hard to accurately date them.

Ancient-human genomes plucked from cave dirt (Nature News). “For the first time, researchers have identified DNA of human relatives without the need to find their bones, opening new window into the past,” Ewen Callaway writes. “…The DNA is exceedingly rare in the soil compared with that from plants, animals, fungi and microbes,” he notes, and researchers have to be very careful to avoid contamination from their own DNA. While scientists are excited about this new way to probe ancient environments, it’s not clear how old the samples are. Callaway explains,

Determining when these individuals lived is tricky. DNA attached to dirt can be picked up by water, then seep through the soil of archaeological sites and end up in a geological layer containing much older material — potentially confounding efforts to date it. So the researchers tried to demonstrate that the DNA they recovered hadn’t been displaced into older layers. In Siberia’s Chagyrskaya Cave, the researchers found abundant animal DNA in geological layers that contained animal bones and stone tools and none in older layers that lacked any sign of human or animal presence. That means it’s likely that hominin DNA didn’t move through layers either, they suggest.

But Robin Allaby, an evolutionary geneticist at the University of Warwick in Coventry, UK, isn’t convinced. He thinks that the large amount of DNA recovered from some sites is evidence that lots of different material might have mixed and settled in a particular layer. “You can identify the hominins, but dating them becomes a bit of an issue,” he says.

In short, none of the articles mentions the decay rate of DNA. If it was difficult to recover DNA from bones, how much more from soil exposed to water, dessication, oxygen and disruption by micro-organisms over the decades? Complex molecules do not last forever. Even in isolation, they are subject to thermal perturbations that break bonds. That’s why molecular machines in the cell invest a lot of time and energy repairing DNA. In 2012, Nature announced that the half-life of DNA is 521 years. After 1.5 million years, fragments would be so broken up, they would be unreadable.

After cell death, enzymes start to break down the bonds between the nucleotides that form the backbone of DNA, and micro-organisms speed the decay. In the long run, however, reactions with water are thought to be responsible for most bond degradation. Groundwater is almost ubiquitous, so DNA in buried bone samples should, in theory, degrade at a set rate.

To think that DNA is going to remain intact and discernible for up to half a million years seems contrary to empirical evidence. One can’t just say, “the DNA must be that old, because according to evolution, that’s when these hominins lived.” That would be circular reasoning, using Darwinian assumptions to drive the interpretation. But since reassigning the dates down to reasonable upper limits of a few thousand years would run afoul of evolution, scientists resist that interpretation. They either ignore it or make new assumptions to keep evolutionary dating from being falsified.

Now consider that dinosaur DNA has been reported. Bob Enyart provides links to peer-reviewed papers reporting recovery of dinosaur DNA.

Cave+Man=Caveman (yours truly, 1989)