Amylase Gene Copy Number Analysis and Salivary Expression Across Mammals

Objectives: Diet has been a significant adaptive force shaping human and nonhuman primate variation. One of the best-described examples is the copy number expansion of the amylase gene (AMY) in concordance with the increase of starch consumption in the human lineage. While the evolution of AMY is well described in the human lineage, a comprehensive analysis of evolutionary dynamics shaping the AMY locus across mammals is missing. Here we address the following questions: (i) Can the link between diet and amylase evolution, suggested in the human lineage, be generalized to other mammals? (ii) What are the evolutionary forces that shape amylase copy numbers in mammals? (iii) What are the genetic mechanisms in different nonhuman mammals leading to expression of amylase in salivary glands?
Methods: Amylase gene copy number analysis was performed by digital droplet PCR analysis. Amylase enzymatic activity in saliva was measured using a starch lysis agar plate assay and a high-sensitivity colorimetric in-solution assay.
Results: Our results reveal a staggering diversity of AMY gene copy numbers across extant mammals that consume starch. Our data demonstrate that AMY copy number amplifications evolved independently in multiple mammalian lineages. We could show that broad-range diets which include starch correlated with increased AMY copy number across mammals including several lineages of nonhuman primates. We also provide correlative evidence that amylase expression in saliva evolved independently in different mammalian lineages and was facilitated through gene copy number duplication. Simulation-based analysis suggested that the observed copy number variation among mammals cannot be explained by neutral evolution alone.
Conclusions: We argue that lineage-specific, convergent adaptive forces have shaped copy number variation of the amylase gene among starch-consuming mammalian species. The presence of amylase enzymatic activity in saliva may determine food preference and even niche partitioning among omnivorous starch-consuming mammals in coevolution with the oral microbiome.