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The evolutionary association of mobile genetic elements with host-beneficial genes is known to be hindered by the stability of chromosomal loci and competition with mobile genetic elements lacking accessory genes. Using a mathematical model that incorporates these constraints, we identify two key mechanisms that help overcome them, resulting in the evolutionary linkage of accessory genes, like virulence genes, to prophages. First, we show that migration across bacterial populations favors the association of genes with prophages when the gene is beneficial in certain environments (e.g. virulence genes in the gut) that also trigger higher rates of prophage induction. Second, we show that within-population spatial dynamics also promotes the association of weakly selected genes and phages. Here, virion dispersal allows phage-encoded genes to spread into patches of bacteria lacking the gene, giving them a selective advantage over immobile chromosomal genes. We argue that these mechanisms are less applicable for plasmids and other mobile genetic elements, highlighting a potentially unique role for phages in shaping bacterial adaptation. By demonstrating how phage lifecycle dynamics and spatial heterogeneity drive mobile genetic element\u2013gene associations, our work provides new insights into the evolution of phage-encoded virulence.<\/jats:p>","DOI":"10.1093\/gbe\/evag181","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T11:49:27Z","timestamp":1784116167000},"source":"Crossref","is-referenced-by-count":0,"title":["Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-9554-958X","authenticated-orcid":false,"given":"Sultan Ahmed","family":"Nazir","sequence":"first","affiliation":[{"name":"Theoretical Biology, Utrecht University , Utrecht ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6330-6934","authenticated-orcid":false,"given":"Bram","family":"van 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