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Answer:
not 100% sure but
Explanation:
might be because each fruit fly has a different eye color because offspring from parents will have different eye color. or it might be from some sort of mutation that happened, that might be why they still have the gene to orange eyes. or red eyed fruit flys(or fly) migrated into a orange eyed populating and had offspring like that, that would also explain why red eyed fruit flys have the orange eyed gene.
again not 100% sure
but I hoped it helped a little