Figure 1: Genome-wide differences in gene expression between the offspring of first-generation hatchery fish and wild fish reared in an identical environment.

(a) Both first-generation hatchery fish (H) and wild fish (W) were crossed in the hatchery to create offspring with two wild parents (W × W), two hatchery parents (H × H), one hatchery mother and one wild father (H × W), or one wild mother and one hatchery father (W × H). Numbers represent the total number of individuals and families (in parentheses) sequenced in this study. (b) Multidimensional scaling plot illustrating the differences in the gene expression profiles for the offspring of first-generation hatchery fish (H × H; yellow circles) and the offspring of wild fish (W × W; blue circles). A total of 723 genes were differentially expressed between the two groups. (c) To compare the main effect (H × H vs W × W) with background rates of differential expression expected between two groups of families having equal hatchery backgrounds, we compared the number of genes differentially expressed between H × W and W × H fish vs H × H and W × W fish from the 5 matrices in which all cross types were sequenced. There were 426 more differentially expressed genes in the H × H vs W × W comparison than in the H × W vs W × H comparison. To account for siblings we randomly sampled one offspring per family, calculated the number of DE genes, repeated the process 100 times and calculated the mean and 95% confidence intervals (illustrated with error bars; 40 individuals total, 2 siblings per family). This result also suggests that the difference between H × H and W × W fish is a heritable genetic effect rather than simply a maternal effect of the juvenile environment experienced by the mother.