New Method Allows Researchers To Sort Out DNA Contamination
April Flowers for redOrbit.com – Your Universe Online
Special precautions are usually a part of retrieving ancient DNA to prevent DNA from researchers or the environment from mixing with that of the fossil. Many ancient fossils, however, have been lying forgotten in museum collections for decades that have become contaminated with present-day human DNA before even entering the laboratory.
A solution for this problem, published in Proceedings of the National Academy of Sciences (PNAS), has been found by Uppsala University researchers who created a statistical model for how degradation can be detected in DNA sequences. This model has been shown to be able to isolate DNA from ancient bones, even when the ancient DNA is vastly outnumbered by present-day DNA contamination. This doesn’t take place in the laboratory, but rather in the computer.
“Many extremely interesting DNA data sets from ancient humans never see the light of day because of contamination. The idea behind this method was to change that”, says Pontus Skoglund, a PhD student in evolutionary genetics at Uppsala University.
Skoglund worked with Mattias Jakobsson, professor at the Department of Evolutionary biology at Uppsala University, and Johannes Krause and Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig to apply the method on a real-world fossil. Krause and Pääbo had previously sequenced mitochondrial DNA from a Neanderthal bone from Okladnikov cave in the Altai Mountains in Siberia, but found that there was also modern human DNA in the bone. The team applied the new technique, which removed the modern human DNA. This allowed the researchers to sequence the complete mitochondrial genome of the Okladnikov individual, showing it was closely related to other Neanderthals in Europe.
The model still has one rather large challenge to overcome—it is unable to separate ancient DNA from modern on fossils younger than one thousand years old. This will limit the method’s usefulness in the study of recent historical individuals.
“There are many really interesting ancient human remains that we can rescue from severe contamination with this method. And the method is not limited to Neanderthals, even remains of anatomically modern humans that are contaminated by modern-day humans can be rescued,” says Jakobsson.