Within‐Host Environmental Heterogeneity Is Associated With Phenotypic but Not Genomic Diversity in <i>Wolbachia</i> Endosymbionts

Hosts represent complex environments where different tissues may act as distinct ecological niches, imposing different constraints that may shape parasite ecology and evolution. Such within-host heterogeneity can generate phenotypic diversity with consequences for virulence and transmission. Our aim was to determine whether the constraints associated with infecting different host tissues lead to the coexistence of multiple parasite sub-populations with distinct phenotypes. We tested this hypothesis using the widespread bacterial endosymbiont Wolbachia. We injected bacteria isolated from three tissues of the common pill-bug into uninfected individuals and tracked temporal changes in Wolbachia load in the recipient host tissues, as well as the virulence associated with each bacterial source. Our results show that colonisation success depends on the tissue of origin of the injected Wolbachia. Genome resequencing did not detect any genetic variation associated with variation in bacterial replication rate, which thus likely results from phenotypic plasticity. Indeed, no recurrent tissue-specific variants were detected, and our conservative filtering pipeline retained only one substitution and one gene conversion event. These findings highlight the genomic stability of Wolbachia across host environments while demonstrating that within-host diversification can occur without genetic divergence. More broadly, they underscore how microenvironmental variation within hosts can shape parasite ecology.