We calculated species richness (Hill’s q = 0), effective species richness (Hill’s q = 1), and inverse Simpson’s [Hills q = 2].

For alpha diversity, we calculated species richness (Hill’s q = 0), effective species richness (Hill’s q = 1), and inverse Simpson’s (Hills q = 2; Jost, 2006). Due to the different number of replicates following sequencing, we did not perform tests of statistical significance. Prior to calculating beta diversity and conducting comparisons of community composition, we accounted for zeros in the dataset (cmultRepl {zCompositions}; Palarea-Albaladejo and Martín-Fernández, 2015), then transformed the data (cdt.acomp{compositions}; Van den Boogaart and Tolosana-Delgado, 2008). For beta diversity and generating PCA plots, we calculated Aitchison distance using the Euclidean distance matrix (Ladin et al., 2021; Gloor et al., 2016; Aitchison, 1983).

Create a table with the alpha diversity measures for each replicate. Note that in 2022 this analysis included rare species.