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.