Alpha Diversity
We used the R package vegan (Oksanen et al., 2022) to compute alpha diversity (observed ASV richness, Shannon diversity index) on the filtered dataset. Observed richness describes the number of observed species and evenness describes the distribution of abundance across the species. The Shannon diversity index is an estimator of species richness and species evenness. We ran generalized linear mixed effects models with a negative binomial error structure for observed ASV richness and a Gaussian distribution for Shannon diversity using the glmmTMB package (Brooks et al., 2017). Location (urban, non-urban), parasite treatment (fumigated, sham-fumigated) and the interaction between location and parasite treatment were considered in all models. Because the microbiota of finches can vary across years (Michel et al., 2018), we also included year (2018, 2019) as a covariate in all models. Nest identification was included as a random effect in all models. We used the Anova function in the car package (Fox & Weisberg, 2018) to determine significance.