(A) Detecting selection from patterns of ASE in hybrids. The example above shows ASE levels (indicated by the wavy lines) for four genes belonging to a particular functional category. Black “X”s indicate down-regulating cis-regulatory differences between the parental alleles. For a given group of functionally related genes evolving neutrally, no bias is expected with respect to the directionality of ASE in hybrids (No selection). However, biased directionality, as in the case in which all down-regulating mutations occurred along the S. cerevisiae lineage (Selection), indicates a history of lineage-specific selection acting on cis-regulation. (B) Reinforcing lineage-specific bias on orthologs involved in divalent cation and heavy metal resistance. (Green triangles) Orthologs within this functional category with reinforcing directionality of bias at both regulatory levels. Significantly more (17) orthologs are reinforcing along the S. cerevisiae lineage as compared with that of S. paradoxus (five). All orthologs are indicated as gray circles. (C) S. cerevisiae strain S288c is more resistant to heavy metals than S. paradoxus strain CBS432. Shown are the log2-transformed relative growth rates (S. cerevisiae/S. paradoxus) for the four heavy metals at two concentrations (L, low; H, high) measured by Warringer et al. (2011). S. cerevisiae outperforms S. paradoxus under all conditions, although in the presence of nickel, the difference is negligible.
