I suspect the basic general process of introgression is clear to most of you, though I will get back to it soon. But here are some papers with candidate genes (click "related" for more references):
RRM2P4, dystrophin, xp21.1 and 17q21.31. Also, I should add in the amusing evidence that archaics and moderns had sexual intercourse (amusing, but scientific nonetheless). Finally, a more theoretical paper that just came out.
There are other possibilities, like MC1R, but that could also be frequency dependent selection. More to come soon, I promise....
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Now you have something.
Still the authours seem to remain cautious and consider alternative possibilities (selective pressure, for instance) and I imagine that this paper will cause quite an upheaval and hopefully interesting criticisms and maybe also interesting new studies that may add or substract to the apparent conclussions in it.
Whatever the final conclussions (if any) all that should add to a better understanding of our origins.