When it comes to the extremely difficult task of sequencing caveman DNA, the third time may be the charm for David Caramelli. After two controversial attempts, the biological anthropologist at the University of Florence, Italy, and colleagues claim to have successfully sequenced mitochondrial DNA (mtDNA) from the fossils of a Cro-Magnon, a 28,000-year-old European ancestor of living humans. The mtDNA matches that of some modern Europeans but differs from that of Neandertals, shedding light on the fate of these ancient hominids.
Neandertals and modern humans such as the Cro-Magnon people were contemporaries in Europe from about 45,000 to 30,000 years ago, but the Neandertal line ended soon after. One theory, known as the Out of Africa hypothesis, holds that modern humans, whose ancestors had recently migrated from Africa, drove the Neandertals extinct, possibly through warfare, disease, or cognitive advantage. But the competing multiregional hypothesis argues that Neandertals and modern humans interbred and that Neandertals were absorbed into our gene pool. Molecular support for the first theory came in 1997, when geneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced the DNA of a 30,000-year-old Neandertal bone and found little overlap with the DNA of modern humans (ScienceNOW , 10 July 1997). But the passage of time may have erased any Neandertal signature, so researchers have looked to the remains of their contemporaries, such as Cro-Magnons, for answers.
Caramelli and colleagues made their first two stabs at sequencing Cro-Magnon DNA in 2003, extracting it from the bones of a 25,000-year-old boy and 23,000-year-old woman found in the Paglicci Cave in southern Italy. They studied mtDNA because more of it remains in fossils than does nuclear DNA. The team's data revealed that the mtDNA was like that of modern humans and different from that of Neandertals, but critics argued that the samples may have been contaminated with modern human DNA when an undetermined number of people handled the fossils.
In the new study, Caramelli's group isolated mtDNA from a different set of Cro-Magnon remains that had been found in the same cave in 2003. This time, only seven people handled the fossils, and the researchers verified that their DNA did not match that of the purported Cro-Magnon sequence. "In this case, we knew all the people that touched the bones," says team member Guido Barbujani, a population geneticist at the University of Ferrara, Italy. The team also had the work independently replicated, asking a lab in Spain to extract and analyze mtDNA from different splinters of skull and long bones. The upshot is that the Cro-Magnon mtDNA matches that of modern humans and does not contain patterns found in Neandertal mtDNA, the team reports  online today in PLoS ONE. That result argues against the inbreeding hypothesis, says Barbujani.
Despite the team's precautions, other researchers still worry about contamination. The mtDNA sequence the researchers claimed to have obtained from the fossil is quite common in Europe today, making it difficult to rule out the possibility that someone not on the team touched the sample or the lab equipment used in the analysis, says evolutionary geneticist and ancient DNA expert Hendrik Poinar of McMaster University in Hamilton, Canada. "I'm not convinced that you can prove it is Cro-Magnon." It's very hard to eliminate contamination entirely, he says, but perhaps someday it will be possible. "I think that the fact that they keep trying is great."