Hybrid incompatibility caused by an epiallele

Significance Deleterious mutations in different copies of a duplicated gene pair have the potential to cause hybrid incompatibility between diverging subpopulations, contributing to reproductive isolation and speciation. This study demonstrates a case of epigenetic gene silencing rather than pseudogene creation by mutation, contributing to a lethal gene combination on hybridization of two ecotypes of Arabidopsis thaliana . Our findings provide direct evidence that naturally occurring epigenetic variation can contribute to incompatible hybrid genotypes, reducing gene flow between subtypes of the same species.