Accounting for cis- regulatory constraint prioritizes genes likely to affect species-specific traits

Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis- regulatory changes underlying adaptation. However, it remains difficult to identify genes most likely to explain species-specific traits. Here, we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that show constrained cis- regulation within species yet show divergence between species. Applying this strategy to data from human-chimpanzee hybrid cortical organoids, we identify signatures of lineage-specific selection on genes related to saccharide metabolism, neurodegeneration, and primary cilia. We also highlight cis- regulatory divergence in CUX1 and EDNRB that may shape the trajectory of human brain development.