Abstract
The Hawaiian Drosophila radiation exemplifies rapid adaptation and species diversification. Many factors have been attributed to these phenomena, including allopatry, sexual selection, and ecological specialization. In recent years, the microbiome has come to the forefront as an important driver of adaptation that is capable of facilitating host survivorship, enhancing resilience to local environmental challenges, and enabling the use of different dietary resources. To determine the factors that contribute to microbiome community variation in natural populations, we conducted a survey of bacterial and fungal communities from over 500 wild flies collected from across six islands of the Hawaiian archipelago. These samples represent a breadth of host plant specializations, habitats, lifestyles and endemicity. Our findings reveal that microbiome variation is largely driven by abiotic factors including elevation, temperature, rainfall, and evapotranspiration, but is not strongly constrained by phylogenetic relatedness. Identical species inhabiting three separate locations exhibited different microbiomes. By contrast, distantly related species inhabiting the same site had more similar microbiomes. The microbiomes of endemic species also differ from recently introduced invasive Drosophila in terms of diversity, composition, and predicted function. Given the myriad roles of the microbiome in nutrition, reproduction, and mate choice, these results provide a foundation for determining the roles of the microbiome in the ecological divergence of Hawaiian Drosophila .