Neanderthal Genome Project

In July 2006, the Max Planck Institute for Evolutionary Anthropology and 454 Life Sciences announced that they would be sequencing the Neanderthal genome over the next two years. At three billion base pairs, the Neanderthal genome is roughly the size of the human genome; preliminary sequences reveal very few differences: human and Neanderthal DNA appear to be 99.5 percent identical. Thus some of this pre-modern human lineage lives on in our own genomes. It is thought that a comparison of the Neanderthal genome and Human genome will expand understanding of Neanderthals as well as the evolution of humans and human brains, especially traits such as language and cognition.

Deterioration of the DNA in fossil samples and contamination with modern human DNA complicated the process. The researchers recovered 65,250 base pairs of Neanderthal DNA by extracting all the DNA from the femur bone of a 38,000 year old male Neanderthal specimen from Vindija Cave, Croatia. The researchers were able to differentiate between Neanderthal and modern human DNA because the ancient DNA fragments were only about 50 to 70 base pairs in length, whereas the modern human DNA fragment contaminants were hundreds to thousands of base pairs in length because they had not undergone similar environmental degradation.

Earlier mitochondrial DNA research led by Svante Pääbo in 1997 indicated ancient humans and Neanderthals broke into separate species approximately 500,000 years ago. In the nuclear DNA study led by Edward Rubin in 2006, Neanderthal DNA sequences matched chimpanzee DNA but not modern human DNA at multiple locations, thus enabling the first accurate calculation of when in pre-history Homo sapiens and Homo neanderthalensis were a single genome. This nuclear DNA study indicates the common genetic ancestor lived about 706,000 years ago, and that the ancestors of each separate species were split 330,000 years later. Analysis of nuclear DNA from the Neanderthal femur suggests a low likelihood of interbreeding occurring at any appreciable level prior to the extinction of Homo neanderthalensis, although a definitive conclusion could not be made. Modern humans descended from ancient humans 119,000 years ago.

Importantly, the researchers also demonstrated that Neanderthal genomic sequences can be recovered using a metagenomic library-based approach. All of the DNA in the sample are "immortalized" into metagenomic libraries. A DNA fragment is selected, then propagated in microbes. The Neanderthal DNA can either be sequenced, or specific sequences can be studied.

A group led by Svante Pääbo is now attempting to directly sequence the Neanderthal nuclear DNA genome. Since direct sequencing is random, one must wait for specific sequences for genes that might be different between modern humans and Neanderthals to show in the process. Direct sequencing destroys the original sample, so in principle the metagenomic library approach will forever retain a clone of the Neanderthal DNA for future targeted research.