(A) Five expression modules identified by Arboretum in the transcriptional response to glucose depletion, when paralogous genes are included in the run. Each row corresponds to a species (tree, left) and each major column to a module (1–5, labels top). Modules labels are color coded by the regulation of the module’s genes following depletion, as noted on top, from bright blue (Module 1) for strong repression to bright red (Module 5) for strong induction. Each module’s height is proportional to the number of genes in that module. The five columns in each module are the expression levels at lag (L), late log (LL), diauxic shift (DS), post-shift (PS), and plateau (P) relative to mid-log phase. Red: induced; blue: repressed; white: no change. (B)–(F) Module assignments of all extant and ancestral species. Each matrix corresponds to the genes in one of the five modules in the LCA (B: Module 1; C: Module 2; D: Module 3; E: Module 4; F: Module 5), and shows the module assignment of these genes in each of the extant and ancestral species from S. cerevisiae (leftmost column) to the LCA (rightmost column). The biological functions listed at the top of each module are general classifiers based on Gene ontology terms enriched in all species in that module (Supplementary file 2). The range of FDR p values and fraction of genes in each module are as follows: Module1: ribosome biogenesis, p<1.07 − 10−52 to 1.56 × 10−112, fraction 32–53%. Module2: cell division, p<3.13 × 10−02 to 4.69 × 10−02, fraction 10.2–32%. Module 3: cell morphogenesis, p<4.48 × 10−02 to 4.56 × 10−02, fraction 22–78.7%. Module 4: mitochondrial, p<2.47 × 10−02 to 3.36 × 10−02, fraction 2.3–36.2%; proteasome, p<2.7 × 10−03 to 5.48 × 10−03, fraction 1.3–13.1%. Module 5: respiration, p<4.2 × 10−02 to 4.43 × 10−02, fraction 34.9–55%. Module assignment in each species is marked by a color code, as in the top of panel a (bright blue: Module 1, light blue: Module 2, white: Module 3, pink: Module 4, red: Module 5). Species are ordered by post-fix ordering (left-child, right-child and parent) of the species tree, as marked on the legend (bottom).