The two pieces of evidence from the text that best support the inference that honeybees—not bumblebees—are responsible for infecting the studied flowers are:
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All the infected flowers researchers picked and tested were close to apiaries.
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All of the honeybees researchers collected were infected with both viruses.
These statements indicate that the presence of viruses was associated with the proximity to the commercial honeybee hives, suggesting that honeybees are the likely source of the infection observed in the flowers.