DESeq2 analysis
We used DESeq2 modeling to measure the gene expression responses to codominance in each genus. Codominance was coded as a quantitative trait: log10(C:D ratio) multiplied by -1 when it was >0. This measure reaches its maximum (zero) when symbionts are equally represented and diminishes when their relative proportions become unequal. For Cladocopium, out of a total of 15,332 genes assayed, 1,930 were upregulated (false discovery rate, FDR = 0.1) and 89 were downregulated (FDR = 0.1, Fig. S1A). For Durusdinium , out of a total of 15,000 genes, 2,629 were upregulated (FDR = 0.1) and 2,868 were downregulated (FDR = 0.1, Fig. S1B). For the coral host, out of a total of 19,580 genes, 138 were upregulated (FDR = 0.1) and 83 were downregulated (FDR = 0.1, Fig. S1C).
We also evaluated gene expression response to heat treatment, and codominance:heat interaction (i.e., additional response to heat treatment under codominance), for all three partners. Response to heat was virtually absent in both symbiont genera: for Cladocopium,out of a total of 15,332 genes, 0 were upregulated and 1 was downregulated (FDR = 0.1, Fig. S2A), and for Durusdinium , out of a total of 15,000 genes, 1 was upregulated (FDR = 0.1) and 2 were downregulated (FDR = 0.1, Fig. S2B). The coral host, however, did show a pronounced response to heat treatment: out of a total of 19,580 genes, 1,399 were upregulated (FDR = 0.1) and 610 were downregulated (FDR = 0.1, Fig. S2C).