Systematic Detection of Polygenic cis-Regulatory Evolution
Figure 1
Illustration of our test for lineage-specific selection.
Four unlinked genes are shown for each of four strains (or subspecies, species, etc). The number of curved blue lines (mRNA molecules) next to each gene represents its transcript level. Red “X”s represent polymorphisms that underlie eQTLs. Comparing strains A versus B, a single trans-eQTL (shown on a fifth chromosome) up-regulates all the genes. Although all four genes show the same direction of expression change, this is not evidence for selection, since the single trans-eQTL could be neutral. Comparing strains A versus C, all four genes have independent cis-eQTLs, but the directions are split between up- and down-regulation; thus there is no evidence for selection here as well. Comparing strains A versus D, again all four genes have independent cis-eQTLs, but now they are all up-regulating. This is consistent with lineage-specific selection for altered expression of this entire gene set (although in practice, more than four genes are needed to achieve statistical significance).