On Thursday May 9th, Svante Pääbo spoke at the Biology of Genomes meeting at Cold Spring Harbor Laboratory. Pääbo’s group, along with 454 Life Sciences, is currently engaged in a project to sequence the Neanderthal genome. The researchers have been able to sequence the complete Neanderthal mtDNA genome with 35-fold coverage. The genome is approximately 16 kilobases long and differs from the CRS at 133 positions. From what I’ve been able to find online, it doesn’t appear that the actual sequencing results have been released to the public. Given current estimates of mtDNA mutation rates, the number of differences between human and Neanderthal mtDNA suggests that the branches diverged approximately 600,000 years ago.
A bit more discussion here:
In late 2006, he was a co-author of a paper reporting that he and his team have sequenced 1 million bases of the Neandertal genome. The paper, “Analysis of one million base pairs of Neanderthal DNA,” was generally well received. But a PLoS Genetics paper titled, “Inconsistencies in Neanderthal Genomic DNA Sequences,” found a lot of problems with results and raised concerns that a lot of the issues are possibly due to modern human DNA contaminants and/or a high rate of sequencing errors. Pääbo has looked into this and in his talk,mentioned that about 10 percent of the DNA library they initially sequenced consisted of modern human DNA. But over the last two years, they have been guarding against contamination by generating DNA libraries in a clean room and by barcoding the Neandertal DNA.