2. The desert iguanids likely do not reside in habitats with greater food abundance than, say, reptiles in a rainforest. So for them, that doesn’t work. And that still leaves the crocodilian question.

2) Do the select reptiles that you mention live in habitats with better access to food than their lower-temp counterparts? As mentioned in the article, higher body temps (and therefore higher metabolism) will need more fuel to keep running. Perhaps the species with higher body temps have better access to food resources, thus easing evolutionary pressure to keep their temps low. Easier food sources would explain why this trade-off wasn’t available to all species, but it’s just a guess.

I read here (I think) that we humans are a complex evolved virus.

[Moderator's note: That prior comment was stuck in the spam filter because it had too many links, but I rescued it.]

Several things strike me as not a fit for this hypothesis. Examples: Women in the luteal phase have higher body temps than in the proliferative phase but are more susceptible to fungal overgrowth in the luteal phase. Some reptiles run very hot–e.g., some iguanids–and ancient reptiles may have done so, as well, possibly even as endotherms. If this tradeoff was a good one, why did it not persist? Another question that comes to mind concerns crocodilians, with their very slow metabolisms and relatively lower temps. They don’t seem to be particularly susceptible to fungal overgrowths. And then there is the bacteria/fungi question and the microbiota balance between the two. Finally, children run very hot comparatively speaking…yet can have greater susceptibility to fungal overgrowth. So…while this is an interesting possibility for exploration, there are a number of counter examples that come quickly to mind.