Possibility of CO2 and/or humidity being a factor is often mentioned.Derek Mitchell has another research article that addresses hive configuration and its impacts on humidity. Apparently, it also covers the implications of higher humidity on varroa reproduction.
From the abstract:
"It is highly likely that honeybees, in temperate climates and in their natural home, with much smaller thermal conductance and entrance, can achieve higher humidities more easily and more frequently than in man-made hives. As a consequence, it is possible that Varroa destructor, a parasite implicated in the spread of pathogenic viruses and colony collapse, which loses fecundity at absolute humidities of 4.3 kPa (approx. 30 gm−3) and above, is impacted by the more frequent occurrence of higher humidities in these low conductance, small entrance nests."
For sure, bees in the trees have much better control of both as well as higher presence of both (vs. the commercial hives, since we are so crazy about "ventilation").
One reason I really want to trial a Warre-formatted hive, but built similar to this: