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Abstract Genes within the secretory calcium-binding phosphoprotein locus diversified along with the formation of a calcified skeleton in vertebrates, the emergence of tooth enamel in fish, and the introduction of lactation in mammals, at each stage marking major transitions in life history. The secretory calcium-binding phosphoprotein (SCPP) locus also harbors genes expressed primarily and abundantly in the saliva of humans. Here, we explored the phylogeny and evolution of the saliva-related SCPP genes by harnessing available genomic and transcriptomic resources. We observe extensive diversification of SCPP genes within mammals, driven by gene duplications and losses, with the most pronounced changes occurring in the SCPP genes that are expressed in salivary glands. When comparing rodent and human SCPP genes, we concluded that regulatory shifts and gene turnover events likely facilitated the accelerated gain of salivary gland expression. In primate genomes, we found more recent duplication events that affected genes coding for proteins secreted in saliva. Several saliva-related SCPP genes in the primate lineage show signatures of positive selection, while the other genes in the SCPP locus remain conserved. Our results position saliva-related SCPP genes as highly malleable to evolutionary innovation. Variations shaped by dietary and pathogenic pressures likely influenced the functional properties of saliva proteins, impacting metabolic and immune-related traits in oral health among primates, including humans. 

Mucin proteins provide mechanistic insights into how genes can evolve to gain novel functions. 

Many mammals can digest starch by using an enzyme called amylase, but different species eat different amounts of starchy foods. Amylase is released by the pancreas, and in certain species such as humans, it is also created by the glands that produce saliva, allowing the enzyme to be present in the mouth. There, amylase can start to break down starch, releasing a sweet taste that helps the animal to detect starchy foods. Curiously, humans have multiple copies of the gene that codes for the enzyme, but the exact number varies between people. Previous research has found that populations with more copies also eat more starch; if this correlation also existed in other species, it could help to understand how diets influence and shape genetic information. In addition, it is unclear how amylase came to be present in saliva, as the ancestors of mammals only produced the protein in the pancreas. Pajic et al. analyzed the genomes of a range of mammals and found that the more starch a species had in its diet, the more amylase gene copies it harbored in its genome. In fact, unrelated mammals living in different habitats and eating different types of food have similar numbers of amylase gene copies if they have the same level of starch in their diet. In addition, Pajic et al. discovered that animals such as mice, rats, pigs and dogs, which have lived in close contact with people for thousands of years, quickly adapted to the large amount of starch present in human food. In each of these species, a mechanism called gene duplication independently created new copies of the amylase gene. This could represent the first step towards some of these copies becoming active in the glands that release saliva. In people, having fewer copies of the amylase gene could mean they have a higher risk for diabetes; this number is also tied to the composition of the collection of bacteria that live in the mouth and the gut. Understanding how the copy number of the amylase gene affects biology will help to grasp how it also affects health and wellbeing, in humans and in our four-legged companions.