Erick Trinkaus has a new article in PNAS, European early modern humans and the fate of the Neandertals:
A consideration of the morphological aspects of the earliest modern humans in Europe (more than ~33,000 B.P.) and the subsequent Gravettian human remains indicates that they possess an anatomical pattern congruent with the autapomorphic (derived) morphology of the earliest (Middle Paleolithic) African modern humans. However, they exhibit a variable suite of features that are either distinctive Neandertal traits and/or plesiomorphic (ancestral) aspects that had been lost among the African Middle Paleolithic modern humans…The ubiquitous and variable presence of these morphological features in the European earlier modern human samples can only be parsimoniously explained as a product of modest levels of assimilation of Neandertals into early modern human populations as the latter dispersed across Europe. This interpretation is in agreement with current analyses of recent and past human molecular data.
The key word is “modest.” Last fall when I was talking about Neandertal introgression I wanted emphasize that the level of interbreeding could be minimal, but if the selective value of the alleles which cross the deme-barrier was high then those alleles should naturally spread. In contrast, those alleles who did not have great selective value would be purified from the gene pool. Finally, alleles which were neutral would could impart information about the extent of interbreeding because their character would be determined by the ancestral proportions.
Out of Africa, total replacement, was elegant in its simplicity. But if the genetic data continues to suggest that the evolutionary dynamics were a bit more complicated than that (i.e., different forces shaping different regions of the genome) then we need to look to the bones & stones people who have been studying morphological variation to flesh out a fuller picture.