Fig. 3.

Interspecific variation in expression. (A) Neighbor-joining tree built from the number of pairwise differentially expressed genes compared with (B) the unrooted genetic tree from Fig. 1A. The scale bar in A is for the number of differentially expressed genes and the scale bar in B is the expected number of substitutions per site. (C) Heatmap depicting scaled expression values of genes separated into two groups by significant contrasts (SI Appendix, SI Materials and Methods). The numbers correspond to the branch of the tree on which the changes are assumed to have occurred. (D) Product/substrate redox ratio of NAD(P)-linked reactions, calculated as described by refs. 74 and 75. Black and gray indicate redox value of isocitrate dehydrogenase and malate dehydrogenase reactions, respectively. 2OG: 2-oxoglutarate. (E and F) Number of differentially expressed genes showing evidence of accelerated expression divergence (two-rate Brownian motion fit better than one-rate Brownian motion and OU) at ΔAIC > 4 or ΔAIC > 10, respectively. (G and H) Proportion of differentially expressed genes unique to each lineage (as determined by pairwise contrasts) showing evidence of accelerated expression divergence at ΔAIC > 4 or ΔAIC > 10, respectively. RvG indicates genes that show contrasting rates of evolution in the red and green fruited lineages.