Modular evolution and strain-specific partnerships: how Hamiltonella defensa shapes defense and symbiont communities in aphids

Insects frequently carry maternally-transmitted endosymbionts that mediate ecological interactions, including resource acquisition and host defense. All pea aphids ( Acyrthosiphon pisum ), for example, carry the obligate nutritional symbiont Buchnera , while most have one or more of the seven heritable facultative symbionts, which play diverse roles. A common symbiont, Hamiltonella defensa , confers protection against the parasitic wasp Aphidius ervi via a toxin-bearing bacteriophage called APSE, with strain-level variation in protection best predicted by APSE variant. Yet, little is known about Hamiltonella /APSE strain variation in the field, resulting in an incomplete understanding of the full arsenal of symbiont defenses and how these change over space and time. Here, we characterized Hamiltonella /APSE diversity in over 3,000 field-collected aphids from two North American populations across multiple years. We identified bacterial strains representing five Hamiltonella clades, seven APSE variants, and numerous toxin alleles, resulting in at least 38 distinct combinations. We found that APSEs moved laterally among Hamiltonella strains more readily than toxins among phage backbones, together generating modular defensive diversity. Hamiltonella strains exhibited strain-specific coinfection preferences with other symbionts, particularly Fukatsuia , Rickettsia , and Rickettsiella , indicating strain-level structuring of heritable bacterial communities. Geographic and temporal analyses revealed dramatic regional differences and rapid population turnover, with combinations conferring intermediate laboratory protection dominating despite the decline of highly protective strains, suggesting ecological success goes beyond parasitoid resistance alone. This extensive cryptic diversity provides standing genetic variation enabling rapid evolutionary responses to biological control efforts and anthropogenic stressors, including climate change, with implications for pest management and host adaptation.