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 a direct link between the presence of domesticated honeybee colonies and the infection of flowers, suggesting that honeybees are the source of the viral infections observed in the flowers.