The story of lactase persistence (“lactose tolerance”) evolving is one of the best gene-culture coevolution stories we had. Arguably it was the canonical example. The story was simple, multiple times humans took up dairy-culture, and multiple times humans changed so that they could digest lactose, milk sugar, into adulthood. This is about 30% of the caloric intake of raw milk (the rest being fat and protein). For some people their gut flora reacts negatively to the sugar bath if it’s not digested, leading to discomfort in addition to wasted calories.

In the 2000’s several mutations were discovered around LCT, the gene responsible for producing lactase, which breaks down lactose. One mutation was found across Europe and Central Asia. Another among the Arabs. And Another in East Africa. The “mutational target” was big. The mutation in the European and Central Asian variant breaks a regulatory element that represses the expression of LCT in adults. There are lots of ways to break something. Lactase persistence isn’t really a gain of function, it’s just never shutting off the function, which itself is a feature, not a bug.

The haplotype around LCT is long and indicative of a really strong sweep in Europeans. It was in some ways a positive control for tests of selection.

The problem is that there are now major problems with this narrative. In short, dairy-culture predates the increase in frequency for lactase persistence alleles by thousands of years. The ancient DNA transects in Europe are so good that it seems pretty clear that the frequency was way lower during the Iron Age, and didn’t reach “modern” levels until the historical period.

The same is now known to be true in Africa: Humans were drinking milk before they could digest it.

This doesn’t mean that these mutations have nothing to do with milk. But there needs to be a rethink of the selection story. Perhaps there was a genetic modifier that spread recently which isn’t a big mutational target, and that’s why the lactose digestion alleles rose in the last 3,000 years? I don’t know. No one really does.