irs. To ensure that errors caused by damaged DNA were not incorporated into the sequence and that modern human DNA did not contaminate the samples, the researchers ran multiple extractions and amplifications. They also sent a sample to Penn State's Anthropological Genetics Laboratory where Stone, then a Ph.D. candidate at Penn State, ran a parallel extraction and amplification of the DNA.To begin amplification, the researchers used two human primers -- small pieces of DNA that match the beginning of the sequence to be amplified."The first two human primers we chose worked," says Stoneking. "It turns out this was a lucky choice."To check that the amplified DNA was really Neandertal, the researchers prepared primers based on their extracted sample and ran them on numerous human DNA samples."The Neandertal primers did not amplify any human DNA," says Stoneking. "Most human primers would probably not work on Neandertal DNA."The researchers compared the Neandertal sequence with 2,051 human sequences and 59 common chimpanzee sequences. They found that the differences in Neandertal DNA occurred at sites where differences usually occur in both humans and chimps."The changes reflect the evolutionary pattern typical of mitochondrial DNA sequences of living humans and chimpanzees, not that of random damage or degradation," says Stoneking.When the researchers looked at the Neandertal sequence with respect to 994 human mitochondrial DNA lineages including Africans, Europeans, Asians, Native Americans, Australians and Pacific Islanders, they found the number of base pair differences between the Neandertal sequence and these groups was 27 or 28 for all groups."While Neandertals inhabited the same geographic region as contemporary Europeans, the observed differences between the Neandertal sequence and modern Europeans do not indicate a closer relationship to modern Europeans than to other contemporary human populations," says Stoneking. The researchers...
