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 (PRPs) 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 PRP gene family across 27 primate species to test whether dietary ecology has shaped the evolution of this locus. We find that the PRP locus is dynamic, shaped by recurrent lineage-specific gene duplications and inversions. Despite pervasive structural variation, PRP genes consistently rank among the top five most highly expressed transcripts in non-human primate parotid glands, indicating constraint on maintaining high expression in saliva. Humans retain abundant PRP 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 PRPs 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.