1Heat the oven to 350°F and arrange a rack in the middle. Place cupcake liners in a 12-well muffin pan; alternatively, coat the wells with butter. Set the pan aside.
2Whisk together the flour, sugar, poppy seeds, zests, baking powder, salt, and baking soda in a large bowl to aerate and break up any lumps; set aside.
3Whisk together the egg, yolk, and melted butter in a medium bowl until the eggs are broken up. Add the milk, juices, and vanilla and whisk to combine. Add the wet ingredients to the flour mixture and stir until just evenly combined, about 22 strokes. (Do not overmix; the batter should be thick, but the ingredients should be evenly incorporated.)
4Fill the muffin wells about two-thirds of the way and bake until a toothpick inserted into the center of the muffins comes out clean, about 20 to 25 minutes. Set the pan on a wire rack and let the muffins cool in the pan for 5 minutes before serving.