From Scientific American:
Up to 4 percent of the DNA of people today who live outside Africa came from Neandertals, the result of interbreeding between Neandertals and early modern humans. That conclusion comes from scientists led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who pieced together the first draft of the Neandertal genome—which represents about 60 percent of the entire genome—using DNA obtained from three Neandertal bones that come from Vindija cave in Croatia and are more than 38,000 years old.
The evidence that Neandertals contributed DNA to modern humans came as a shock to the investigators, who published their findings in the May 7 Science. “First I thought it was some kind of statistical fluke,” Pääbo remarked during a press teleconference on May 5. The finding contrasts sharply with his previous work. In 1997 he and his colleagues sequenced the first Neandertal mitochondrial DNA. Mitochondria are the cell’s energy-generating organelles, and they have their own DNA, which is distinct from the much longer DNA sequence that resides in the cell’s nucleus. Their analysis revealed that Neandertals had not made any contributions to modern mitochondrial DNA. Yet because mitochondrial DNA represents only a tiny fraction of an individual’s genetic makeup, the possibility remained that Neandertal nuclear DNA might tell a different story. Still, additional genetic analyses have typically led researchers to conclude that Homo sapiens arose in Africa and replaced the archaic humans it encountered as it spread out from its birthplace without mingling with them—the Out of Africa replacement scenario, as it is known.
More here.