FIGURE 5: Differential expression across species plus environment reveals signatures of genetic assimilation and further supports a role for the cell cycle. (A) We constructed an additive model to identify genes that were differentially expressed between species and environment (S+E), which identified 128 DEGs. With the exception of a single MZ individual, species clustered together. Clustering by environment was observed in MZ but not TRC. Assuming that plasticity represents the ancestral condition, this analysis also provides evidence for genetic assimilation, whereby pelagic MZ exhibited relatively high gene expression compared to benthic MZ, which generally resemble TRC in terms of cpm counts. Pink dots on the cladogram to the left of the heatmap denote gene clusters that exemplify this pattern. We note that 3 MZ exhibited especially robust expression levels. (B) Enriched GO terms associated with genes in the S+E model. Colors are representative of the -log10(p-value). Gray bars indicate no significance. The nature of the additive model precludes us from having an up- vs down-regulated analysis of genes, because it takes into account both species and environment at the same time. These GO terms are similar to previous analyses in returning processes involved in cell cycle regulation.