Diet and the evolution of human amylase gene copy number variation

Abstract

Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number-variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.

Figure 1

AMY1 copy number variation and salivary amylase protein expression. (a,b) From the same European-American individuals we estimated diploid AMY1 gene copy number with qPCR (a) and amylase protein levels in saliva by western blot (b). Error bars indicate s.d. (c) Relationship between AMY1 diploid copy number and salivary amylase protein level (n = 50 European-Americans). A considerable amount of variation in AMY1 protein level is not explained by copy number (R² = 0.351), which may reflect other genetic influences on AMY1 expression such as regulatory region single nucleotide polymorphisms (SNPs) or non-genetic factors that may include individual hydration status, stress level, and short-term dietary habits.

Figure 2

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.

Figure 3

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 10 copies and the other with four copies. (b) Biaka individual GM10472 was estimated by qPCR to have 6 (6.11 ± 0.17) diploid AMY1 gene copies, consistent with fiber FISH results. (c) The chimpanzee reference individual (Clint; S006006) was confirmed to have two diploid AMY1 gene copies.

Figure 4

Japanese-Yakut copy number differentiation at AMY1 versus other genome-wide loci. (a) Frequency distributions of WGTP aCGH relative intensity log₂ ratios from AMY1-mapped clone Chr1tp-6D2 for Japanese and Yakut individuals. (b) Relationship between Japanese and Yakut mean log₂ ratios for all autosomal WGTP clones that were copy number variable in both populations. AMY1-mapped clones Chr1tp-6D2 and Chr1tp-30C7 are depicted as solid red and blue circles, respectively.