Barbarian observes:
Neandertals are significantly different than humans in a number of important details. Their DNA, BTW, is different enough that most scientists now put them in a separate species or subspecies.
"…The Neanderthals are so closely related to us that they fall into our [genetic] variation," Professor Paabo said yesterday. In other words, it would be difficult to distinguish Neanderthal DNA from the DNA of a modern European, Asian or African…â€Â
In comparison to modern DNA 27 differences are seen. The Neanderthal sequence was compared with 2051 human and 59 chimpanzee sequences over 360 base pairs. Twenty five of the 27 variable base pairs coincide with positions that vary in at least one of the human sequences. The sequence was compared with 994 human mtDNA lineages. While these lineages differ among themselves by eight substitutions on average, the range of difference with the Neanderthal sequence is 22-36. The Neanderthal sequence has 28.2 ±1.9 substitutions from the European lineage, 27.1 ±12.2 substitutions from the African lineage, 27.7 ±2.2 substitutions from the Asian lineage, 27.4 ±1.8 substitutions from the American lineage, and 28.3 ±2.7 substitutions from the Australian/Oceanic lineages. This indicates no closer a relationship with Europeans than with the other modern human subsets considered.
The comparison to chimpanzees with modern humans is 55.0 ±3.0, compared to the average between humans and Neanderthals of 25.6 ±2.2. These results indicate a divergence of the human and Neanderthal lineages long before the most recent common mtDNA ancestor of humans. Based on the estimated divergence date of 4-5 million years ago for humans and chimpanzees, the authors estimate the human and Neanderthal divergence at 550,000-690,000 years ago. The age of the common human ancestor, using the same procedure, is about 120,000-150,000 years ago.
These results do not rule out the possibility that Neanderthals contributed other genes to modern humans. However, the results support the hypothesis that modern humans arose in Africa before migrating to Europe and replacing the Neanderthal population with little or no interbreeding.
http://www.jqjacobs.net/anthro/paleo/neanderthal.html
It is possible, of course, for different species to interbreed, and that may have happened from time to time. But Neandertal DNA is well outside the normal variation among anatomically modern humans today.