Fig. 1.

Overview of the approach. The figure illustrates the rationale, and the search space. (A) Toy example: This sample tree shows four species (s1, s2, s3, s4) partitioned at a select branch b to produce the partition of two species in the left clade (s1, s2 Є S) and two species (s3, s4 Є T) in the right clade. Gene locus g represents the orthologous group of genes across all the four species (g1, g2, g3, g4 Є G) that hypothetically exhibit differential usage of regulating TFs X and Y, where X is used by species in the left clade and Y is used by species in the right clade, and not vice versa. (B) Phylogenetic tree of Ascomycetes: Tree shows relationships between the 23 yeast species surveyed in this analysis. Branches are numbered from 1 to 44. Six branches highlighted in bold and larger font numbering represent the chosen branches across which we partitioned the species to assess lineage-specific cis-regulatory rewiring.