Extended Data Fig. 1: MA plots of each pairwise comparison that showed DE represented by log2 fold change vs. counts per million (CPM).

Log₂ fold change calculated with limma package in R with a two-sided linear model fit followed by empirical Bayes moderation of the standard errors (using the eBayes function with robust = TRUE parameter), controlling for multiple comparisons with a p-adjusted ≤ 0.05 (using the Benjamini-Hochberg method for false discovery rate,). Dots colored in magenta indicate genes that showed a significant relative increase, and dots colored in blue indicate genes that showed a significant relative decrease in expression between aquaria conditions. Black dots indicate genes that did not show significant DE (each plot represent reads that mapped to 3140 genes). Numbers in the corner of each box represent the total number of genes that were DE with +/− indicating log₂ fold change direction. For details on aquaria conditions, see Fig. 2a and Supplementary Table 1.