A poor evolutionary nutrition narraive posits that because we didn't have X food in the paleolithic, we are maladapted to it. I think Mat Lalonde covered issues with this nicely at AHS and in the latest Paleo Solution podcast.
John Hawks, a biological anthropologist at the University of Wisconsin-Madison, notes that many HLA genes pre-date humans' split from Neanderthals and Denisovans, and that the differences may have arisen by chance as the groups evolved.
Hawks, too, has been digging into the archaic genomes, and his team has already discovered that Neanderthals and Denisovans lack certain forms of genes that may help modern humans to fend off epidemic diseases, such as measles. This is hardly surprising: the low population density of hunter-gatherers meant that epidemics were unlikely, so they probably would not have benefited from these immune genes.
But Hawks's team is now using the find to test whether the defensive genes are linked to autoimmune diseases. In September, Hawks and his colleague Aaron Sams are scheduled to present data at a meeting of the European Society for the Study of Human Evolution in Leipzig, Germany, showing that the Denisovans lacked nearly all of the gene variants linked to coeliac disease, a gut autoimmune disorder present in modern humans. Hawks suspects that the variants may actually be in the same genes that are linked to epidemic resistance — if they are, further study could reveal how recently such autoimmune diseases arose in humans.
Haha, it would be funny if an adaptation to civilization (diseases worsened by high population density), would also turn out to be a maladaptation as civilization progressed.