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Apparently beehives can spawn when growing trees now.
Oak, birch, or mangrove trees grown from saplings that are within 2 blocks (including diagonally) of a flower on the same y-level have a 5% chance to grow with a bee nest containing 1–3 bees. This holds true in any biome in any dimension, and for any flower including wither roses and flowering azaleas.
I think this already in the game long ago.