We have conducted an in-depth investigation into the underlying drivers of trade-offs in fungal pathogens by examining the relationship between Starship mobile elements, virulence-survival trade-offs, and constraints on pathogen adaptation. We first developed a new, freely-available bioinformatic tool for identifying Starship elements. We then applied that tool to various fungal pathogen species to understand how Starships may be associated with selective, environmental and genetic constraints on pathogen evolution. Using population genetic analyses and meta-analyses of gene expression data, we found that Starships are under strong negative selection and that the expression of their genes changes between survival and infection conditions. We then phenotyped a fungal plant pathogen for virulence and survival related growth under changing temperature conditions, and found that Starship activity is associated with a complex, environmental-dependent trade-off between virulence and survival. Finally, we determined that many adaptive metabolic genes are carried by Starships, suggesting that they may not only constrain pathogen adaptation but also facilitate it. Together, our results have greatly increased our fundamental knowledge of why certain diseases take place while others do not. I shared our findings through a total of twelve invited seminars at international conferences and universities, thus disseminating our research to diverse communities of scientists.