Quaternary climatic changes and biogeographic barriers drove codiversification in the obligate mutualism between Camponotus laevigatus and its endosymbiont Blochmaniella

Codiversification often arises when hosts and their endosymbionts share a linked evolutionary history, exhibit vertical transmission, or share ecological and biogeographic processes. Most studies on the codiversification of carpenter ants (genus Camponotus ) have focused on the co-phylogeny of hosts and endosymbionts across multiple species; however, no studies have examined the intraspecific population-level phylogeographic patterns of codiversification within Camponotus . California has been a geographic focus for phylogeographic studies due to its high endemism and complex geographic structure, and Camponotus laevigatus is a carpenter ant primarily found there. Here, we used whole-genome sequencing from C. laevigatus and its endosymbiont, Blochmaniella to investigate phylogeographic patterns of host-endosymbiont codiversification and estimated kinship of ants sampled near one another. We identified three phylogeographic clusters and isolation-by-distance analyses indicated a positive relationship between genetic and geographic distance in C . laevigatus and Blochmaniella . Using estimates of effective migration surfaces, we found that the Central Valley in California acts as a significant barrier to gene flow among populations. Our phylogenetic analyses revealed the congruent phylogenies of C . laevigatus and Blochmaniella , supporting codiversification. We also estimated kinship among individuals from the same and nearby sampling sites; kinship results indicated full-sister relationships among individuals from the same sampling site, except for three pairwise comparisons, and foragers from nearby sampling sites displayed some shared kinship. Lastly, our demographic analysis revealed a Pleistocene divergence, highlighting the role of Quaternary climatic cycles in shaping the population structure of C . laevigatus .