To understand why having extra amylase genes is a unique situation, we need to go over how genes work. A gene is really just the instructions for a protein and the protein is the thing that does the work.
Let's use amylase and its gene as an example. The amylase gene has the instructions for making the amylase protein. The amylase protein is what breaks down starch in our diet.
For almost all of the genes we've studied to date, the way to get more protein is to muck with its instructions. You might get a small DNA change that has the gene crank out more amylase. Or a different one that causes a stronger amylase to be made. But the number of copies of a gene stays the same.
This is certainly what happened with our milk example. In that case, a small DNA change causes the lactase gene to stay on longer. There weren't extra lactase genes lying around.
And this has been the case with nearly every other gene studied. But for amylase, we get extra amylase by having extra genes.
Having more than two copies of a gene is called copy number variation or CNV. Scientists didn't used to think that it was very common but as we look deeper into the human genome, we are finding that they thought wrong.
For example, in a recent study scientists found around 1400 of these changes that totaled over 360 million base pairs. That is 12% of our DNA! Obviously CNVs are pretty common. And having these extra genes can have an effect.
We've already talked about the amylase gene. But there is also another gene called CCL3L1 that can come in more than two copies. Scientists have found that folks with extra copies of this gene tend to be more resistant to HIV and so are less likely to end up with AIDS.
As scientists study CNVs more and more, they will undoubtedly find more examples like amylase and CCL3L1. Given how common CNVs are, I suspect we'll be hearing a lot more about CNVs and how they affect our health.
* The increase in the number of amylase genes might have happened earlier in evolution as well. When the researchers compared human DNA to chimpanzee and bonobo DNA, they found that our closest relatives had the usual two copies of the amylase gene. This might mean that the increase in amylase genes happened very soon after the human-chimp split.