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I believe they are trying to do this exact thing with certain mosquito populations.
Will that fuck with the food chain?
There are thousands upon thousands of species of mosquito, only a few hundred bite humans.
This would only be targeted at the dozen or so that carry major disease like malaria, west Nile, dengue fever, Zika, etc.
Aedes aegypti is at the top of the list.
From what I've read I get the impression that eliminating biting mosquitoes wouldn't have much impact - there are lots of types of mosquitoes and supposedly few are of the biting kind, and at the same time the ones that pollinate or are food for other animals are usually not a significant source of food or pollination, and the ones that do pollinate don't pollinate anything important to us according to a random article I read. So basically for it to matter you would need to be eliminating a kind that bites and makes up a majority of the pollination or food for something else which seems unlikely.