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Allen has a flower fly named after him for his contributions to Dipterology, called Paul Allen's flower fly.
Paul Allen's flower fly (Eristalis alleni) is a flower fly found only in Costa Rican forest in the central highlands.
Another fly found in similar habitats was named after Gates' associate Paul Allen, called Paul Allen's flower fly (Eristalis alleni); according to Chris Thompson, the describer of these species, both names were in "recognition of [their] great contributions to the science of Dipterology".