Multiscale structural evolution of proline-rich protein genes shapes primate salivary defenses.

Saliva forms the first biochemical interface with the environment, mediating dietary exposure and oral defense. Proline-rich proteins in saliva protect plant-eating mammals from the harmful effects of consuming tannins. Yet the evolution of the genes encoding these proteins remains poorly resolved. Here, integrating long-read genome assemblies with comparative genomics, phylogenetics, transcriptomics, and dietary data, we investigate the salivary proline-rich protein gene family across 27 primate species to test whether dietary ecology has shaped the evolution of this locus. We find that the proline-rich protein locus is dynamic, shaped by recurrent lineage-specific gene duplications and inversions. Despite pervasive structural variation, proline-rich protein genes consistently rank among the top five most highly expressed transcripts in nonhuman primate parotid glands, indicating constraint on maintaining high expression in saliva. Humans retain abundant proline-rich protein expression, but at reduced levels relative to other primates, potentially reflecting a lineage-specific regulatory shift. We further identify widespread exonic tandem repeats that provide a flexible mechanism for modulating protein composition. Notably, colobine PRH genes independently evolved trinucleotide repeats encoding histidine-rich peptides, coinciding with folivory and suggesting a lineage-specific adaptation. Together, our results position proline-rich proteins as a model for understanding how large-scale structural rearrangements and fine-scale repeat expansions jointly shape the diversity and evolution of proteins in saliva.