Keeping clean.
DNA from Neandertal skeletons is easily contaminated by modern humans.

Philippe Plailly/Photo Researchers Inc.

Bones of Contention, and Dirty Too?

Last year, two pilot projects grabbed the headlines by deciphering nuclear DNA from 38,000-year-old bones of a Neandertal. The studies fanned the flames of the ongoing debate about whether Neandertals and modern humans interbred. Now a reanalysis of this deciphered DNA has found evidence of contamination by modern human genetic material in one project, challenging the original results.

Limitations of sequencing technologies kept archaic human DNA largely out of reach until 2006. But recent advances enabled a team led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, to sequence 1 million nuclear bases, and another led by Edward Rubin, head of the Department of Energy Joint Genome Institute in Walnut Creek, California, to sequence 65,000 bases using a different approach. (ScienceNOW, 15 November 2006). Rubin's analyses put the date at which Neandertals and modern humans diverged at 700,000 years, with no indication of interbreeding. Pääbo's approach resulted in a date that was 200,000 years more recent and showed hints of interbreeding.

Curious about the discrepancy, Jeff Wall and Sung Kim of the University of California, San Francisco, reanalyzed the data. By using the same technique with both sets, Wall and Kim expected to get just one answer because the two groups used the same DNA sample. Instead, the Pääbo data put the European-Neandertal split at 35,000 years, whereas the Rubin date was 325,000 years, a date more in line with the fossil evidence, they report online today in PloS Genetics. When Wall and Kim took a close look at the actual fragments of DNA sequenced, they found that the sequences of the larger fragments were very much like a modern human's, whereas smaller fragments were quite different. Ancient DNA tends to be in smaller fragments because DNA decays over time, so Wall and Kim suspect that the larger fragments represent contamination.

"I think they are pretty much bang-on," says Andrew Clark, a population geneticist at Cornell University. "I think [the work] is a wake-up call about just how careful you have to be."

Pääbo admits that he can't exclude the possibility of contamination. He, nonetheless, emphasizes that tests of the DNA before and after sequencing was done revealed no evidence of modern human DNA. His group is now sequencing the entire Neandertal genome and in the 21 August issue of the Proceedings of the National Academy of Sciences describes the steps taken over the past year to lessen the odds of contamination.

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