Studying the genetic basis of ecological interactions with intergenomic epistasis

In a community, the phenotype or fitness of genotypes of a focal species can depend on the genotypes of other species. Such between‐species genetic interactions are increasingly referred to as intergenomic epistasis, analogous to the classical definition of (intragenomic) epistasis in genetics. Here, we propose the first mathematical definition of intergenomic epistasis, which formalises the minimal conditions for the existence of inter‐species genetic interactions. By discussing empirical studies of interacting species from the literature, we argue that intergenomic epistasis is a useful umbrella concept that engulfs multiple co‐evolutionary relationships of interacting species, such as genotype‐specific or gene‐for‐gene interactions. Consequently, intergenomic epistasis can be asserted in a study system when 1) the specific ecological interactions are unknown, 2) the genetic basis of between‐species interactions is unidentified, or 3) the underlying genetic architecture is complex and involves genetic interactions within and between genomes. Moreover, the term itself highlights the importance of genetic factors in the study of ecological interactions, thus encouraging links between research in genetics and ecology. Finally, we argue how models incorporating intergenomic epistasis may facilitate the study of co‐evolution.