3.3.4 Comparisons between tissue type within the same sampling groups
We found that blood and muscle have the lowest number of genes with detected expression in both tissues compared to the other pairwise tissue comparisons (Tables S2 and S4 on Dryad). We observed differences in gene expression among tissue types (blood, muscle, gills) for each of the sampling methods. Of all the genes that are significantly differentially expressed (adjusted p - value <0.05) among tissue types, only 25-32% are more highly expressed in blood compared to gill and muscle (Tables S2 and S4 on Dryad). Conversely, the proportion of significantly differentially expressed genes in gill and muscle was much more even and within ±10 of 50% (Tables S2 and S4 on Dryad).