(A) Phylogenetic tree of the species investigated, inferred from protein sequences of 73 highly conserved genes (Lohse et al., 2013) with the scale representing the number of substitutions per site. The likely position of the NDT80 gene duplication is indicated with a green circle. Ndt80 protein tree shown in Figure 2—figure supplement 1. (B–D) Ndt80 targets identified by Criteria 2 (Figure 1C). (B) The proportion of Ndt80 targets in K. lactis, P. pastoris, and S. stipitis that are shared with the Ndt80 targets in S. cerevisiae, C. albicans, or both. The proportion of targets shared, using all four different criteria for identifying targets (Figure 1C) shown in Figure 2—figure supplement 2. (C) List of genes bound by Ndt80 in all five species tested with functional annotations (color-coded) from S. cerevisiae, as described in the text (SGD, [Cherry et al., 2012]). (D) Histogram of all Ndt80 targets in the five species tested (S. cerevisiae, K. lactis, P. pastoris, S. stipitis, and C. albicans) according to the number of species in which that gene is a target. All target genes (black) and those with 1:1 orthologs across all five species (dashed) are shown. For (B–D), the union of Ndt80A and Ndt80B bound genes were used for S. stipitis and C. albicans. The cis-regulatory site bound by Ndt80 in each species shown in Figure 2—figure supplement 4.