Wanted: Clean Neandertal DNA

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Science  13 Feb 2009:
Vol. 323, Issue 5916, pp. 868
DOI: 10.1126/science.323.5916.868

Now that one group has finished a rough draft of the genome, other groups are working to remain in the Neandertal sequencing game—but first they need to find well-preserved Neandertal DNA.

It usually pays to have more than one team working on a scientific problem. Take the early work on sequencing Neandertal nuclear DNA, for example. In 2005, Svante Pääbo and his crew at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, gave Neandertal DNA samples to Edward Rubin's group at the U.S. Department of Energy Joint Genome Institute (JGI) in Walnut Creek, California. Together, the two groups helped revitalize the field of ancient DNA by producing more than a million bases of Neandertal nuclear genome sequence (Science, 17 November 2006, p. 1068). Equally important: Differences in their results alerted the field to what later proved to be contaminating DNA in Pääbo's analysis.

Siberian search.

Edward Rubin (right) and Institute of Archaeology and Ethnography Director Anatoly Derevianko are still seeking DNA-rich Neandertals.


But since 2006, when the company 454 Life Sciences, with its faster, cheaper sequencing technology, stepped up to do the entire genome with Pääbo (see main text), the Leipzig group has been pretty much on its own. Rubin and others are hoping, however, to remain in the game—if they can get their hands on enough Neandertal DNA.

Rubin plans to sequence target regions from several different Neandertals to complement Pääbo's approach of massively sequencing one sample. The goal is to determine whether differences noted between Neandertal and Homo sapiens genomes are real or simply reflect variation among individual Neandertals. Alan Cooper of the University of Adelaide in Australia is also working toward scanning DNA from several Neandertals, and Pääbo himself has sequenced a million bases from additional samples.

But Neandertal DNA preserved and excavated under the right conditions is proving elusive. Over the past 2 years, Rubin and his postdoctoral fellows have traveled the world, striking up relationships with paleontologists in hopes of finding relatively uncontaminated, undegraded Neandertal fossils. So far, they have had little luck with 20 Neandertal specimens from Israel, Spain, France, or Siberia. “None of these have had significant fractions of uncontaminated Neandertal DNA,” Rubin laments. “As it turns out, the sequencing of a Neandertal is now much easier than finding a good uncontaminated [sample].”

In the meantime, Rubin's team has been developing methods to extract ever more DNA from each sample. Rubin hopes they will soon get to try these approaches on Neandertals. “We do have some other Neandertal specimens coming in that we are optimistic about,” he says. Ancient DNA expert Eske Willerslev of the University of Copenhagen agrees that it's important to have more than one group producing data. “It's definitely worthwhile to have independent replication of results,” he says.


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