New Technique Could Demystify Ancient Human DNA

An artist's depiction of a Neanderthal family. (Image credit: NASA/JPL-Caltech)

This story was updated on Wednesday, Jan. 29 at 11:00 a.m. E.T.

The DNA of a Neanderthal found in a Siberian cave has been sequenced, thanks to a new technique that weeded out contamination from modern humans.

The method, described today (Jan. 27) in the journal Proceedings of the National Academy of Sciences, seems to work on very contaminated samples, as well as on incredibly ancient remains. These benefits could help scientists finally analyze some of the most intriguing archaic human fossils, which have thus far been inaccessible because of contamination from modern DNA, said study co-author Pontus Skoglund, a paleogenomics researcher at Uppsala University in Sweden.

Archaeologists excavated some of the most tantalizing fossils of ancient humans, such as Neanderthal bones, decades or even centuries ago. However, while handling the bones, archaeologists often contaminated the archaic DNA sequences with their modern genetic material. [Top 10 Mysteries of the First Humans]

"We can't really blame them for this," Skoglund told LiveScience. "Many of the fossils were excavated before people knew DNA existed." (DNA was discovered in the late 1800s and its information-encoding potential was only understood decades later.)

Without a surefire way to distinguish contamination from ancient DNA, many of the most fascinating fossils have kept their genetic secrets hidden.

Predictable degradation

The new method takes advantage of the fact that DNA degrades in a predictable way over time. One of the nucleotides, or building blocks of DNA, cytosine (C), tends to convert to other nucleotides, either thymine (T) or uracil (U). This process occurs most frequently at the ends of DNA, where the genetic molecule is likeliest to be in a single-stranded form, Skoglund said.

The new method tracks all the C's, T's and U's in DNA snippets from a fossil, and compares them to a reference sequence from the modern human genome. 

Based on the differences between the fossil DNA and the modern genome, and knowing how the DNA nucleotides convert over time, the team can estimate a sample's degradation level, and in turn, its age. If the DNA is too young, then the model throws it out.

To test the method, the team analyzed genetic material from a roughly 40,000-year-old Neanderthal found in Okladnikov Cave in Siberia. The ancient Neanderthal's mitochondrial genome, or DNA that is passed on through the mother and carried in the egg's cytoplasm, was much more closely related to western Neanderthal samples than had previously been found.

The model works even better on very old DNA, because it's more degraded and thus easier to distinguish from modern samples, Skoglund said.

At the same time, scientists are making tremendous strides extracting truly primeval DNA from fossils, such as the 400,000-year-old fossils  of mysterious, archaic humans found in Sima de los Huesos in Spain.

So if DNA could be extracted from the fossils, the technique could be used on bones of Homo erectus or of "the Hobbit," Homo floresiensis, neither of which have ever been sequenced, Skoglund said.

With small tweaks, the same method could be used for non-human DNA, from ancient plant or animal materials, for example, Skoglund said.

New opportunities

Many of the most important fossils are contaminated. "People have handled these bones while not wearing gloves for centuries," Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz, who was not involved in the study, wrote in an email.

So the new method "takes us one step closer to being able to use even the most contaminated bones to ask questions about evolution," Shapiro said.

The technique faces some limitations, however. For instance, some microbial DNA doesn't degrade very much, so the new method could make faulty estimates when studying ancient microbes, said Ludovic Orlando, a researcher at the University of Copenhagen in Denmark, who was not involved in the study.

"The present method might end up trashing real data in such cases," Orlando told LiveScience.

And the technique could be pricy because, depending on contamination levels, the method requires huge amounts of DNA sequences, Carles Lalueza-Fox, a paleogenomics researcher at Pompeu Fabra University in Spain, who was not involved in the study, wrote in an email. "Thus I would only recommend it for really special samples," he said.

Editor's Note: This story was updated to reflect that the 400,000-year-old archaic human remains recently analyzed were not of Denisovans.

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Tia Ghose
Managing Editor

Tia is the managing editor and was previously a senior writer for Live Science. Her work has appeared in Scientific American, and other outlets. She holds a master's degree in bioengineering from the University of Washington, a graduate certificate in science writing from UC Santa Cruz and a bachelor's degree in mechanical engineering from the University of Texas at Austin. Tia was part of a team at the Milwaukee Journal Sentinel that published the Empty Cradles series on preterm births, which won multiple awards, including the 2012 Casey Medal for Meritorious Journalism.