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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.<\/jats:p>","DOI":"10.1093\/molbev\/msag224","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T12:09:44Z","timestamp":1788178184000},"source":"Crossref","is-referenced-by-count":0,"title":["Multiscale structural evolution of proline-rich protein genes shapes primate salivary defenses"],"prefix":"10.1093","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9977-7500","authenticated-orcid":false,"given":"William D","family":"Aguado","sequence":"first","affiliation":[{"name":"Department of Anthropology, Rutgers, The State University of New Jersey , New Brunswick, NJ 08901 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6998-6926","authenticated-orcid":false,"given":"Charikleia","family":"Karageorgiou","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University at Buffalo, The State University of New York , Buffalo, NY 14260 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-7392-5310","authenticated-orcid":false,"given":"Sarah","family":"Kassem","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University at Buffalo, The State University of New York , Buffalo, NY 14260 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3451-204X","authenticated-orcid":false,"given":"Raquel Hern\u00e1ndez","family":"Rojas","sequence":"additional","affiliation":[{"name":"KSTR Wildlife Rescue , Quepos, 60601 ,","place":["Costa Rica"]},{"name":"Department of Anthropology and Archaeology, University of Calgary , Calgary, AB T2N 1N4 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4441-7521","authenticated-orcid":false,"given":"Carrie C","family":"Veilleux","sequence":"additional","affiliation":[{"name":"Department of Anatomy, Midwestern University , Glendale, AZ 85304 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0612-2514","authenticated-orcid":false,"given":"Amanda D","family":"Melin","sequence":"additional","affiliation":[{"name":"Department of Anthropology and Archaeology, University of Calgary , Calgary, AB T2N 1N4 ,","place":["Canada"]},{"name":"Department of Medical Genetics, University of Calgary , Calgary, AB T2N 4N1 ,","place":["Canada"]},{"name":"Alberta Children's Hospital Research Institute, University of Calgary , Calgary, AB T2N 4N1 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6304-5423","authenticated-orcid":false,"given":"Erin R","family":"Vogel","sequence":"additional","affiliation":[{"name":"Department of Anthropology, Rutgers, The State University of New Jersey , New Brunswick, NJ 08901 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3888-4908","authenticated-orcid":false,"given":"Stefan","family":"Ruhl","sequence":"additional","affiliation":[{"name":"Department of Oral Biology, University at Buffalo, The State University of New York , Buffalo, NY 14214 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4371-679X","authenticated-orcid":false,"given":"Omer","family":"Gokcumen","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University at Buffalo, The State University of New York , Buffalo, NY 14260 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6791-294X","authenticated-orcid":false,"given":"Petar","family":"Pajic","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Yale University , New Haven, CT 06511 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"2026100510072572000_msag224-B1","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2026100510072572000_msag224-B2","doi-asserted-by":"publisher","first-page":"5101","DOI":"10.1111\/j.1742-4658.2005.04945.x","article-title":"Protein database searches using compositionally adjusted substitution 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