Fig. 4: Alpha and beta diversity in the gut microbiome of non-parasitized (NP) and parasitized (P) populations.

A, B Alpha diversity metrics between non-parasitized Galtaból (n = 24) and Þristikla (n = 25) populations. C, D Alpha diversity metrics between non-parasitized (n = 24) and parasitized (n = 13) Galtaból individuals. Alpha diversity metrics were estimated at the genus-level using a Hill number framework for richness (A, C) and Shannon index (B, D). Violin plots with all samples as colored points show the distribution of the data, while the quartiles (0.25, 0.5, and 0.75) of the metric in each group are shown as black lines. Metrics were compared between populations using a Wilcox test and the resulting p values are shown above the brackets. PCoA of gut microbiome composition of non-parasitized (NP) Galtaból and Þristikla populations (E) and non-parasitized and parasitized Galtaból individuals (F). Shape (“Treatment”) indicates whether the fish were in the non-exposed (circles) or the predator-exposed treatment (triangles). Taxa abundances were summed to the genus-level and normalized using the centered-log ratio transformation. Variations due to extraction batch effects were regressed out (see Supplementary Fig. 3 for before-correction PCoAs). Euclidean distances were then calculated and PERMANOVAs performed. Population in (E) explained 4.2% of the variation in microbiome composition (F = 1.93, p = 0.003), while parasite status in (F) explained 7.2% of the variation (F = 2.42, p = 0.001). In both analyses, sequencing depth explained 5.0–6.4% of the variation in microbiome composition (p < 0.002) Full PERMANOVA results, including PERMANOVAs before batch correction, are reported in Supplementary Table 3.