Just read a really complicated article that went way over my head in Discover Magazine, but thought I'd share it as there are some interesting theories presented.
Here's an excerpt:
So what happened? The authors posit that the 503F allele was selectively favored at some point in the past, and flanking it were the Crohn’s disease risk elevating variants of IRF1 and IL5. All things equal it is best not to have a risk for this disease, but all things are not equal. If there was a strong enough selective pressure on the target, 503F, then the downsides of the fact that it came as a “total package” with some deleterious alleles would be irrelevant. Over a long enough evolutionary time the deleterious alleles would be purified through negative selection because recombination does break apart associations, but there’s a lot of reality which consists of being between beginnings and ends.
Basically, the idea is that agriculture put a selective pressure on the genome that brought along genes that increased risk of Crohn's disease. To put that in more plain words, the rapid change in environment caused by the rise of agriculture (e.g. living off of certain grains), put pressure on the natural selection of genes. Certain gene variants (mutations) were favored in the new environment and so flourished. Unfortunately, those positive gene variants (which helped humans deal with the benefits of agriculture) brought with them negative gene variants (which increased risk of disease).
Interesting theory. The writer that's critiquing the article doesn't completely agree with the conclusion, but definitely some interesting analysis.