Figure captions
Figure 1. Map showing the stock source of the male Chinook salmon used for fertilization of eight pure and hybrid crosses used in this study. Crosses included pure (YIAL) and hybrid (CAP, CHILL, NIT, PUNT, RC, BQ, QUIN) crosses of Chinook salmon. Abbreviations: Robertson Creek “RC”, Big Qualicum River “BQ”, Capilano River “CAP”, Chilliwack River “CHILL”, Nitinat River “NIT”, Puntledge River “PUNT”, Quinsam River “QUIN”.
Figure 2. Alpha diversity using Shannon and Chao1 indices across all hybrid-crosses. Boxplots represent 25th percentile (bottom-end) to 75th percentile (top-end) values. Whiskers represent values 1.5 times above or below interquartile range. Dots represent values >1.5 times and <3 times the interquartile range.
Figure 3. Principal coordinate analysis (PCoA) plot with the principal coordinates (PCs) explaining the highest percent variance. Pairwise Bray-Curtis distances were used to perform PCoA across all gut microbiome samples from the Chinook salmon hybrid-crosses used in the study. Each open circle represents the average PCoA coordinates for a hybrid-cross, and error bars represent 95% confidence intervals (CI). Cross abbreviations are defined in Figure 1.
Figure 4. Unique ASV analysis presenting the largest interaction sizes across hybrid-crosses used in the study, along with family-level taxonomic classifications of those ASVs belonging to those intersections. Amplicon sequence variants table was rarefied to minimum library size prior to analysis. Interactions with size 9 or smaller were removed from plot. Taxonomic classifications are presented for unique ASVs with 10 or more counts across all hybrid-crosses.
Figure 5. LEfSe Biomarkers identification of statistically significant ASVs (FDR P-values of KW sum-rank test) across all hybrid crosses and their associated effect size (LDA scores). The right-hand mini-heatmap represents abundances associated with each ASV across the hybrid-crosses. Filtering was performed to remove ASVs occurring in 5 samples or less, and with 200 reads or less across all remaining samples.
Figure 6. Histograms showing relative frequencies of candidate gut microbiome taxa across all eight Chinook salmon hybrid crosses. Shown are 17 ASVs that showed significant differences in the biomarker LEfSe analysis among the crosses and their associated taxonomic classification. Error bars represent 95% confidence intervals. Letters above error bars represent post-hoc pairwise statistical differences among crosses, based on multiple student T tests of the mean (P < 0.05, adjusted for multiple comparisons with BH). Hybrid cross abbreviations are defined in Figure 1.