Do all fungi have ancestors with endophytic lifestyles?

Fungi are an essential component of any ecosystem and have diverse ecological roles, ranging from endophytes to epiphytes and pathogens to saprobes. The current estimate of fungal endophytes is around 1 million species, however, we estimate that there is likely over 3 million species and only about 150,000 fungal species have been named and classified to date. Endophytes inhabit internal plant tissues without causing apparent harm to the hosts. Endophytes occur in almost every plant from the coldest climates to the tropics. They are thought to provide several benefits to host plants and improve the hosts’ ability to tolerate several abiotic and biotic stresses. Endophytes produce secondary metabolites with biotechnological, industrial and pharmaceutical application. Some endophytes appear to be host-specific, while some are associated with a wide range of hosts. We discuss the importance of endophytes. The ability to switch lifestyles from endophytes to pathogens or saprobes is discussed. Interactions between endophytes and hosts based on fossil data is also highlighted. Factors that influence the specificity in endophytes are discussed. We argue that the endophytic lifestyle is a common strategy in most fungi and that all fungi have endophytic ancestors. We critically evaluate the influence of co-evolution based on fossil data. We hypothesise the influence of specificity on the estimated number of endophytes and overall species numbers, and present examples of metabolites that they produce. We argue that studying endophytes for novel compounds has limitations as the genera recovered are limited. However, if saprobes were chosen instead, this would result in a much higher species diversity and undoubtedly chemical diversity.