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….