Neanderthal genomes sequenced using new technique that is faster, cheaper and less wasteful

A new sequencing technique that is cheaper and less wasteful has been used to decode and analyse the mitochondrial genomes of five Neanderthal individuals.

The researchers say their technique overcomes difficulties in analysing degraded ancient DNA and offers a useful aid to understanding the genetic variation and evolution of Neanderthals and other ancient specimens.

Last year, a team led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, produced the first complete mitochondrial DNA Neanderthal genome using ’brute force’ shotgun sequencing. However, this technique wastes much time, money and precious ancient DNA as it blindly sequences everything in a sample, even though about 99 per cent of DNA extracted from such ancient fossils actually belongs to bacteria and fungi that have invaded the bone. 

Now, Pääbo and colleagues have created a quicker, less expensive, and less wasteful method to reconstruct the genomes of ancient specimens. ’The samples we used in this new project were even more poorly preserved than that original sample [analysed last year], meaning that the shotgun method would have cost hundreds of millions of pounds,’ says graduate student Adrian Briggs who helped pioneer the new technique. ’Hence the need for our new targeted retrieval method - primer extension capture (PEC).’ 

’We have managed to immortalise a precious DNA source, for example a Neanderthal DNA extract, by making many thousands of copies of every original DNA molecule in that source,’ says Briggs. In doing so, ancient DNA sequences can be stored in a ’library’ and used again and again. The technique uses 5’- biotinylated oligonucleotide primers and a DNA polymerase that isolate Neanderthal mitochondrial DNA sequences from the plethora of contaminant DNA. Sequences of interest are then directly extracted from this amplified library of degraded DNA before the sequencing step. ’This saves on experimental time and costs by several thousand fold,’ Briggs adds.

Eske Willerslev, an expert on ancient DNA at the University of Copenhagen, Denmark, thinks this is an important technological breakthrough. ’The capture approach makes it possible to retrieve very short pieces of DNA that is difficult if not impossible using regular [polymerase chain reaction] approaches,’ he comments. ’This means that the chances of retrieving endogenous rather than contaminant DNA increases significantly.’ 

Using the technique, the team was able to generate high quality complete mitochondrial genome sequences of five Neanderthal individuals that lived roughly between 38,000 and 70,000 years ago. 

By comparing the Neanderthal mitochondrial DNA sequences to each other and to modern humans, the team discovered that Neanderthals have approximately one third of the genetic diversity of humans living today. This reduced diversity has led the researchers to suggest that Neanderthals probably had low population sizes over time. Willerslev thinks this is an important first step in trying to address the changes in genetic diversity and effective population sizes of Neanderthals through time. He does warn, however, that more specimens are needed before firmer conclusions can be drawn.