ISMB meeting: Svante Pääbo

This week, the 18^th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) meets in Boston, and Broad-minded bloggers are covering some of the talks. Jill Mesirov, the Broad Institute's director of computational biology and bioinformatics, is one of the co-chairs of the conference and Broad Institute core member David Altshuler will be one of the conference's keynote speakers.

This morning I went to hear a keynote address by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Broad researchers recently collaborated with Pääbo and others from the Max-Planck Institute to analyze the newly available Neanderthal genome. In a Science paper published in May, they revealed new genetic evidence suggesting that Neanderthals and humans may have interbred tens of thousands of years ago.

At this morning’s talk, Pääbo outlined some of the “technical issues” that have thwarted efforts to sequence the Neanderthal genome. In order to retrieve ancient DNA, scientists have to extract it from Neanderthal bones, and in the process, risk contaminating the sample. In addition, the DNA is often degraded or there aren’t enough copies to be able to glean meaningful data. In the new paper, the researchers were able to sequence nuclear DNA from Neanderthal samples, which Pääbo said was made by possible by advances in sequencing technology and better extraction techniques.

Another necessity for sequencing the Neanderthal genome is having a reliable bone from which to extract DNA. Pääbo and his team began with bone fragments from the Vindija Cave in Croatia. From these specimens, Pääbo and his colleagues were able to extract DNA that they could compare to the human genome. In addition to finding evidence of interbreeding (which you can read all about in the Broad news story “A new understanding of the evolutionary path of modern humans") they were able to trace amino acid differences among chimps, Neanderthals, and modern humans.

Looking toward future studies, Pääbo described the importance of “functional analyses of candidate genes” – instead of just generating a list of genes, examining what role each of these genes may play. He gave the example of FOXP2 – a gene that has been implicated in language. (We recently added a story on FOXP2 to our CRX exhibit in the DNAtrium. The story includes illustrations and a video. If you’re interested in learning more, please visit the DNAtrium.)

The human version of FOXP2 is unique among animals – even chimps don’t posses the same version (there are two amino acid differences between the human and chimp genes). Some scientists hypothesize that FOXP2 might be partially responsible for speech – a unique human ability. Pääbo explained that his team found that Neanderthals share the human version of FOXP2.

To find out if FOXP2 might really be involved in speech, scientists have created a mouse model, tweaking the mouse FOXP2 gene to resemble the human version. These mice had altered vocalization – their squeaks were different from those of ordinary mice – and their neurons had more projections. Scientists have also found human families that suffer from a heritable speech problem who have a mutated version of the FOXP2 gene that’s passed down from generation to generation.

Pääbo hopes that researchers can analyze other interesting genes from the human and Neanderthal genomes in a similar way to find out what these genes may be doing. This could give us insights into what makes us distinctly human.