Fig. 2

Experimental and temporal effects on cloacal microbiota alpha diversity and phylogenetic beta diversity. Relationships of population-level variation (mean ± 95% CI whiskers) of (a) dominant OTU richness and (b) Shannon diversity for each experimental treatment and across sampling moments. c PCoA of weighted UniFrac distances among cloacal microbiota samples; ordination of all samples including baseline samples shows differential clustering of experimental treatment (closed circle = high diversity, open triangle = low diversity) and sampling moments (colors), as well as a pattern of transitions (bicolored arrows) that first diverges from and later converges toward the baseline state. Group medians and IQR are shown as large symbols and whiskers. a, b Faded blue closed circles (high diversity) and orange open triangles (low diversity) represent individual measurements connected by a line per individual (faded solid blue = high diversity, faded dashed orange = low diversity). Experimental treatments are taken simultaneously but split along x-axis for visual clarity. Grey area highlights the baseline sampling moment. Asterisks above plots denote pairwise contrasts among sampling moments; P or FDR-corrected q < 0.1 *, 0.01 **, 0.001 ***. Statistics are detailed in Tables 3 and 4