Neandertal & H. sapiens sapiens interbreeding

Modern Humans, Neanderthals May Have Interbred:

"To me, what happened is that the Neanderthals were [genetically] absorbed into and overwhelmed by modern humans coming into Europe from Africa, and they disappeared through this absorption," Trinkaus said.
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Examining the bones, Trinkaus discovered certain features that he believes are Neanderthal elements incorporated into this early Homo sapien.

Features at the back of the woman's skull and in her lower jaw, especially, "are found in high frequency in Neanderthals" but are absent in bones from older groups of Homo sapiens from Africa, he said.

The paper will be on the PNAS site sometime this week, apparently it is behind an 'embargo wall' right now and already in circulation amongst those with special access. This is a morphology story, it seems that individuals with a mosaic of African and Neandertal traits existed in Europe ~30,000 years ago. What does this tell us? If we didn't have the genetic evidence I think one would have to assume that the highest likelihood is that some interbreeding went on. But didn't we learn last week that humans and Neandertals were separate and distinct lineages, with the latter contributing nothing to the genome of the former?

1) Not all regions of the genome are created equal when it comes to a particular phenotype (e.g., if you looked at Y lineages Mexican Americans should be Spaniards, if you looked at mtDNA lineages they should be Amerindians, and yet they are a mix of both when it comes to the vast majority of their genome, the Y & mtDNA just happen to be convenient for genetic analysis).

2) Selection can operate on specific regions of a genome independently from others. This is why you see "selective sweeps" across lengths of sequence while neutrality seems to be operative elsewhere.

3) There nature of genomic sequences shaped by neutral evolution vs. those subject to selective forces can differ a great deal because of the alternative dynamics at work as a function of time. The former can be far more informative about ancestry than the latter because in the case of the latter not all ancestors are created equal.

4) There are always papers in the pipeline which can modulate your priors. One should credit Trinkaus et. al. because of other pieces of data which will come to light in the near future.