Figure 3. Rearing under natural photic conditions reveals novel changes to gene expression.

A) The number of differentially expressed genes unique to either light/dark conditions or natural conditions is represented in the 4^th and 5^th columns of the table, respectively. These DEGs are inclusive of genes with a higher expression in either cave or surface fish on their respective lighting conditions, represented diagrammatically to the right of the table (Venn diagram). There are a large number of differentially expressed genes that are revealed under natural conditions alone. This large number of DEGs represent a set of genes that have not been previously explored B) Test sets of genes were selected based on their expression at a 4-fold threshold. DEGs unique to natural conditions were assessed. Under light/dark conditions, 345 genes have a higher expression in C^DD compared to S^LD and 399 have a lower expression in C^DD compared to S^LD. The proportion of GO terms in these test sets was compared to the proportion of GO terms found in the whole transcriptome as a reference. The observed occurrence of each term is taken over the expected occurrence of each term based on is proportion in the reference. Each white bar to the right of a term represents an “Enrichment Score” (observed/expected). This indicates that dark-rearing may potentially play a role in the development and function of the circulatory, olfactory, and metabolic systems in A. mexicanus cavefish.