Dr. Paabo has pioneered the extraction and analysis of ancient DNA from fossil bones, overcoming daunting obstacles over the last 13 years in his pursuit of the Neanderthal genome. Perhaps the most serious is that most Neanderthal bones are extensively contaminated with modern human DNA, which is highly similar to Neanderthal DNA. The DNA he has analyzed comes from three small bones from the Vindija cave in Croatia.

“This is a fabulous achievement,” said Ian Tattersall, a paleontologist at the American Museum of Natural History in New York, referring to the draft Neanderthal genome that Dr. Paabo’s team describes in Thursday’s issue of Science.

But he and other archaeologists questioned some of the interpretations put forward by Dr. Paabo and his chief colleagues, Richard E. Green of the Leipzig institute, and David Reich of Harvard Medical School. Geneticists have been making increasingly valuable contributions to human prehistory, but their work depends heavily on complex mathematical statistics that make their arguments hard to follow. And the statistical insights, however informative, do not have the solidity of an archaeological fact.

Image The Neanderthal DNA that Svante Pääbo analyzed came from these three bones. Credit... Max-Planck-Institute EVA

“This is probably not the authors’ last word, and they are obviously groping to explain what they have found,” Dr. Tattersall said.

Richard Klein, a paleontologist at Stanford, said the authors’ theory of an early interbreeding episode did not seem to have taken full account of the archaeological background. “They are basically saying, ‘Here are our data, you have to accept it.’ But the little part I can judge seems to me to be problematic, so I have to worry about the rest,” he said.

In an earlier report on the Neanderthal genome, the reported DNA sequences were found by other geneticists to be extensively contaminated with human DNA. Dr. Paabo’s group has taken extra precautions but it remains to be seen how successful they have been, Dr. Klein said, especially as another group at the Leipzig institute, presumably using the same methods, has obtained results that Dr. Paabo said he could not confirm.