Hypothesis explaining the mismatches in foamy virus (FV)-host evolutionary history. FV phylogeny (blue) was superimposed upon host phylogeny (black) and is scaled to host divergence times. The scale bar is in units of millions of years. Solid circles represent FV-host co-speciation events. Open-circles represent possible host switching events of which the inferred switching directions are indicated by arrows. A hypothetical scenario of host switching (as indicated by an orange ‘?’) within the New World monkey FV clade is shown in an orange box. An alternative scenario is shown in Additional file 5: Figure S4. For PSFVaye and RhiFV, we speculate that, in the very early history of mammalian evolution, eutherians came to the Madagascar-India landmass with their FVs (red circles) upon which they established stable populations (A). The landmass was then split into the Madagascar and India landmasses resulting in the FV population splitting into two separate groups ~80-90 Ma (B); one FV variant remained on Madagascar and the other was transported to Laurasia via the Indian landmass continental drift (C). The former gave rise to the PSFVaye progenitor while the latter gave rise to RhiFV. Directions of infected FV host population movements are indicated by yellow arrows. However, it is unknown which ancestral species introduced FV to the lemur and bat lineages and when the transmissions occurred (as indicated by a black ‘?’). Additional sequence data from other mammals, especially bats and lemurs, are required to further resolve these aspects of FV evolutionary history.