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Neandertal Draft Genome Completed

NEW YORK (GenomeWeb News) – At the American Association for the Advancement of Science annual meeting today in Chicago, Svante Pääbo announced the completion of the draft Neandertal nuclear genome.

Pääbo, director of the Max Planck Institute for Evolutionary Anthropology's Department of Evolutionary Genetics, said the results suggest that Neandertals were not that different from humans from a genomic perspective. Rather, Neandertal nuclear DNA sequence often falls into some of the same patterns of genetic variation observed in modern humans.

In the future, researchers hope to get a better handle on human evolution by comparing human, Neandertal, chimpanzee, and other ape genomes and looking at regions where there are differences, Pääbo explained. By cataloguing the genetic changes that have occurred since Neandertals and looking for sequences under positive selection, he added, researchers plan to leverage the Neandertal genome to get new clues about what makes us human.

"The attraction of getting the Neandertal genome is that it's our closest relative," Pääbo explained.

The team sequenced 3.7 billion base pairs of Neandertal DNA — enough to cover the 3.2 billion base pair genome about 1.2 times — using a combination of Roche 454 and Illumina's sequencing systems.

But because some bases have been covered more than once and others not at all, Pääbo explained, there are still gaps remaining in the Neandertal genome — with the current sequence data representing about 63 percent of the genome.

"We still have a lot of gaps, but we have the first overview of the genome and can now start cataloguing these changes," Pääbo said. "We can begin asking, when there is a difference between the chimp and human genome, what does the Neandertal look like? Like the chimp or like us?"

Compared to previous work, where Pääbo said contamination with human DNA was quite high, the latest sequence data suggests contamination is now less than one or two percent. Based on mitochondrial sequence data, the estimate of contamination is 0.3 percent, whereas estimates based on Y-chromosome data suggest 0.5 percent contamination.

So far the results indicate that there is a roughly eight to 12.8 percent divergence between Neandertals and human reference sequences. Based on estimates calculated from DNA and from population genetic variation, the results suggest Neandertals and humans diverged between 300,000 and 830,000 years ago.

The team has already started comparing specific regions of the Neandertal and human genome. For instance, they found that Neandertals had a version of the lactase gene that would not have allowed them to digest milk after weaning.

When they examined the FOXP2 gene, which is involved in human brain function and contributes to speech and language, the team found that Neandertals have the same two FOXP2 changes found in humans but absent in other apes. That suggests changes in FOXP2 occurred in a shared common ancestor to humans and Neandertals.

In addition, Pääbo said, the researchers have identified a region on chromosome 7 where Neandertal sequence resembles ape sequence but not human sequence, indicating the human genome has undergone a selective sweep in that part of the genome.

Over the next two to three years, Pääbo said the team plans to sequence the Neandertal genome to much deeper coverage — probably 15 to 20-fold. They intend to publish results related to the Neandertal draft genome and its analysis later this year.