The California Floristic Province (CFP) is a global biodiversity hotspot due to its high endemism rates. Recent phylogeographic studies focusing on invertebrates showed varied geographic patterns of genetic structure in the CFP. The carpenter ant, Camponotus laevigatus (Smith, F., 1858), is primarily found in the CFP and has an obligate mutualistic bacterial endosymbiont (Blochmannia). In this study, we used whole genome sequencing of 29 individuals from 21 colonies to investigate whether Camponotus and its endosymbionts exhibit phylogeographic patterns of codiversification. Using principal components analysis (PCA) and ADMIXTURE to estimate genetic structure, we found that both C. laevigatus and Blochmannia possess three distinct genomic clusters. Furthermore, Isolation by distance (IBD) analyses revealed a strong correlation between geographic distance and genetic diversity in both C. laevigatus and Blochmannia, suggesting limited long term gene flow across the landscape. Finally, we used estimation of effective migration surfaces (EEMS) to estimate patterns of gene flow; EEMS indicated that the Central Valley in California acts as a major barrier to gene flow between the different populations. Overall, our findings showed congruent patterns of phylogeographic structure in C. laevigatus and Blochmannia and demonstrated that geographic distance, the role of the Central Valley as a biogeographic barrier shape the genetic structure of codiversification in this mutualism.
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