A: You ate this. Have you brushed your teeth?
B: You ate this. Did you brush your teeth?
Sentence A is in the Simple Past, while B is in the Present Perfect.
Which sentence is more natural?
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To me, the two sentences are equally natural, but express somewhat different ideas. The first, in the present perfect, means "Have you brushed your teeth since you ate it [i.e., at any time between then and now]?". The second, in the simple past, means "Did you brush your teeth after you ate it [i.e., in the past, soon after you ate it]?".