Illustration of approach for finding cis-regulatory selection. Each yeast cell represents a hybrid between two diverged strains. Four genes from a single gene set are shown, with two alleles per gene (red and green). The number of curved lines next to each allele represents that allele's expression level. (A) All four genes are expressed equally from each allele, so there is no allele-specific expression (ASE) or evidence for selection. (B) Each gene has a down-regulating cis-regulatory mutation (blue x), but these act on alleles from each parent with equal frequency, so there is still no evidence for selection. (C) All four genes have ASE in the same direction (down-regulating, red), a pattern indicating lineage-specific selection on cis-regulation (though more than four genes are required to achieve statistical significance).
