Amylase and human evolution

I made a mistake that was quickly corrected by a correspondent. Yesterday, in writing about copy number variants in human genes, I used the example of the amylase gene on chromosome 1, which exists in variable numbers of copies in human populations, and my offhand remark was that the effect is "nothing that we can detect", but that maybe people with extra copies would be "especially good at breaking down french fries". Well, it turns out that we can detect this, that there was even a very cool study of this enzyme published last year, and that the ability to break down complex starches rapidly may have been a significant factor in human evolution.

So of course I have to tell you all about this now.

Amylase is a digestive enzyme that specifically helps break down complex sugars, like starch, into simpler sugars that can be processed by other enzymes or absorbed by the intestine. You are secreting this enzyme all the time into your saliva, so that as soon as you pop something made of starchy carbohydrates, it's coated with these enzymes that get to work breaking it down. As it's swallowed and enters the stomach and intestine, these enzymes are still busy rendering the starches down into something more manageable for your gut to handle. This is an important function: if you chew starchy foods made from rice, corn, or potatoes, saturating them with the enzyme, blood glucose levels afterwards are measurably higher than if you just swallow the food whole.

As I said yesterday, the amylase gene has another interesting attribute — it seems to be in a hotspot for duplication, and different people have different numbers of copies of the gene. If you just had one copy of the gene per chromosome, your cells would each have a grand total of two copies…but instead, we more typically have 5 to 7, with some people having only 2, and others having 15 or more.

There are a number of ways to count how many copies of the gene there are, but one of the more visually appealing ways is to use fiber FISH (fluorescent in situ hybridization). In this technique, intact DNA is extracted from cells and stretched out, then a probe for the amylase gene that is tagged with a fluorescent label is allowed to bind to the strand, and every place with an amylase gene lights up red. As you can see below, then you can directly count the genes: in this case, the individual at the top has 14 copies of the gene on two chromosomes, the one in the middle has six copies, and the very interesting fellow named Clint at the bottom has only two copies. Clint happens to be a chimpanzee.

High-resolution fiber FISH validation of AMY1 copy number estimates. Red (~10 kb) and green (~8 kb) probes encompass the entire AMY1 gene and a retrotransposon directly upstream of (and unique to) AMY1, respectively. (a) Japanese individual GM18972 was estimated by qPCR to have 14 (13.73 ± 0.93) diploid AMY1 gene copies, consistent with fiber FISH results showing one allele with ten copies and the other with four copies. (b) Biaka individual GM10472 was estimated by qPCR to have six (6.11 ± 0.17) diploid AMY1 gene copies, consistent with fiber FISH results. (c) The reference chimpanzee (Clint; S006006) was confirmed to have two diploid AMY1 gene copies.

Chimpanzees don't exhibit much copy number variation in the amylase gene, but humans do…how interesting. Could this variation be a reflection of something specific in human evolution? Why, yes.

This work by Perry and others went on to look for patterns in different human populations with different dietary historys, and discovered that there is a correlation: cultures with diets heavy in starch, agricultural populations such as Americans, Europeans, and Japanese, or hunter-gathers who live on many roots and tubers, have a higher average copy number than cultures that depend more on hunting and fishing.

Look at the distributions! Populations with little starch in their diets also have a relatively low copy number of 5.44 amylase genes per individual; we french fry eaters have a higher number of 6.72 amylase genes per individual. The difference is small, and the distributions also overlap significantly (note that some with high starch diets only have 2 copies, and some living on low starch diets have 13 copies), but the difference is measurable and significant. It implies that there may have been some selection for greater copy numbers in cultures with diets high in starchy plants.

Diet and AMY1 copy number variation. (a) Comparison of qPCR-estimated AMY1 diploid copy number frequency distributions for populations with traditional diets that incorporate many starch-rich foods (high-starch) and populations with traditional diets that include little or no starch (low- starch). (b) Cumulative distribution plot of diploid AMY1 copy number for each of the seven populations in the study.

We can't entirely rule out drift as a possible cause of the difference; while we can see differences in the enzyme levels in saliva, low levels of the enzyme haven't been shown to be directly deleterious to anyone. It is again implied: oral digestion of starches may be an important pathway for taking in energy during episodes of diarrhea, so it could be critical when individuals are experiencing disease-related stress.

It is very suggestive. The fact that it represents a distinct difference between other apes, such as chimpanzees, and ourselves also suggests that it may have had significant evolutionary consequences. Maybe we aren't primarily the biggest-brained apes; we are the Apes Who Eat Roots As Well As Bananas. A core nutritional difference could have played a more significant factor in our early evolution than small differences in brain size, and may have been an enabler of brain expansion.

Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet. 39(10):1256-60.