Divergence estimates for the differentially expressed and unbiased genes. Pairwise dN (A), dS (B), and dN/dS (C) values were estimated by comparing orthologs between zebrafish and grass carp. Zebrafish lineage-specific dN (D), dS (E), and dN/dS (F) values were estimated using six-species alignments among zebrafish, grass carp, cave fish, medaka, stickleback, and spotted gar. The relative frequency distribution of dN/dS ratios for each category of genes were calculated from zebrafish–grass carp comparison (G) and zebrafish lineage only (H). Outliers were removed from the boxplot. Significant differences are indicated by the asterisks, based on Wilcoxon rank sum test, *P < 0.05, **P < 0.001.
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