Fig. 3

Study designs for evolutionary questions. A MPRAs can be used to test for changes in regulatory activity across evolutionary time, by assaying orthologous sequences across a phylogeny (pink, blue, and yellow tip lineages) and/or using ancestral sequence reconstruction to assay sequences from extinct taxa (green lineage). B MPRAs can be used for fine mapping of functional alleles identified through sequence-based scans for positive selection. C MPRAs could be used to understand how genetic interactions, namely epistasis and genotype-by-environment interactions, impact regulatory variation. This could be accomplished by assaying a genetically variable MPRA library across trans cellular backgrounds that are either genetically or environmentally diverse