Today, February 12, 2009 represents the 200th birthday of Charles Darwin. It is also the 150th year since the publication of his groundbreaking book On the Origin of Species. Earlier in the week I attended the “RB Church Lecture in Biotechnology” presented by Dr Luc Montagnier, 2008 Nobel Prize winner in Physiology or Medicine for his life’s work in HIV and Aids. Both Mike and I have blogged his presentation. Today, Darwin’s birthday, there was a major scientific announcement made simultaneously from Leipzig and Chicago and streamed live over the web. I was lucky enough to tune in. The topic was the Neanderthal Genome. This has been a great week for cutting edge genomics.

The speaker, Svante Paabo told us that this important research was the sequencing of the last diverging species of DNA from our own human genome. We branched from both the previously studied chimpanzee and orang-utan at least 5 to 7 million years ago. The Neanderthal branch is as recent as 300,000 years. Further studies will allow for the cataloguing of significant changes that made us humans what we are, and what similarities we have with our closest relative. This project took at least 2.5 years to complete the study of 200 extracts from 70 fossils and 16 sites. The fossils ranged in age from 38,000 years to 43,000 years.

In order to carry out this research great care was taken to ensure that the DNA was not contaminated by humans, bacteria or fungi from the site. Special techniques were developed to collect the bone fragments in as sterile a way as possible, then to extract the DNA from bone chips. The fragments of DNA were immediately labelled on their ends to ensure they could be followed through the amplification process. Ultimately, 3.7 billion base pairs were sequence representing approximately 1.24 of the genome. At least two systems were used to ensure the purity of the samples. Neanderthal mitochondrial DNA has already been well studied and the samples were also known to be female. Thus any contamination from human mitochondrial DNA or from Y-chromosome DNA could be detected as error.

From the preliminary results released today, the genomic evidence is for a divergence approximately 830,000 years ago. The researchers looked with great interest at the lactose gene which is found on chromosome 2. Most Europeans have the gene which allows them to consume milk as adults. (I looked at this in some detail in a previous blog). The study of Neanderthal DNA showed no such capacity to drink milk. However, the FOXP2 gene which is associated with speech is found in the Neanderthal. This does not specifically mean that they could speak. It does not even confirm that this gene was expressed. It does however show that there is the possiblility that they spoke. Based on the mitochondrial DNA variation, it would appear the populations of Neanderthals were either very small, or that there was a genetic bottleneck in the spreading populations.

To be clear, there has been no evidence found that there was any interbreeding that left genes with current modern humans. Paabo was very clear though that “no evidence found” is a completely different statement than saying there is “no evidence”. Also, Paabo indicated that we now have the tools to study the reverse of the question and to look to see if modern humans left any DNA in the Neanderthal genome. Another item of interest was that copy number variation could not be determined at this stage. This will require the sequencing of many more samples. Based on a question from the audience, Paabo specified that genomics cannot speculate on behaviour or on how we humans interacted with Neanderthals. He leaves that to the archaeologist to study. Paabo also was adamant that based on our current know science cloning a new Neanderthal is not possible. He however did not rule out what kind of advancements may be made in the future.

Paabo summed up his presentation by reemphasizing the need to make sure that there was no contamination of the samples and he looks forward to the type of analysis that will come in the future after this genome is published.