Do interactions between different Selfish Genetic Elements matter?

Abstract Most organisms carry mobile DNA that enhance their own transmission to subsequent generations, generating conflict with the host genome. The selfish transmission invoked by these selfish genetic elements (SGEs) has promoted a variety of countermeasures by the host genome to reduce their impact. Maternally inherited endosymbionts are common in arthropods and frequently manipulate host reproduction, and transposable elements (TEs) are an exceptionally abundant and diverse group of SGEs. Their activity and abundance vary drastically between even closely related species and can generate evolutionary consequences of both lethal and beneficial effects. Yet, despite their plentitude, many questions remain regarding the potential interactions between different SGEs. This is in part a methodological problem as TEs, for example, often reside in highly repetitive genomic regions, making them difficult to detect. Innovations in genomics have driven renewed interest, particularly with long-read sequencing resolving repetitive regions. We can now begin to define and answer important outstanding questions. For instance, it is unclear how different types of SGEs, including TEs, may interact within host genomes. For example, while different SGEs may compete for host resources (such as availability of molecular machinery), they may also cooperate or even behave parasitically toward each other, as in the case of some TEs. Here we take an “ecology of the genome” approach to examine such interactions that, together with choice examples, may help further our understanding of how interactions between different SGE shape genome evolution.