Preheat oven to 400°F.
Line 12 muffin tins with papers.
To prepare streusel:
Mix brown sugar, whole-wheat flour and cinnamon in a small bowl. Cut in butter with a pastry blender or your fingers until the mixture resembles coarse crumbs.
To prepare muffins:
Whisk whole-wheat flour, all-purpose flour, baking powder, baking soda, salt, cinnamon and nutmeg in a large bowl. Whisk egg and brown sugar in a medium bowl until smooth. Whisk in applesauce, syrup, cider, yogurt and oil.
Make a well in the dry ingredients; add the wet ingredients and stir with a rubber spatula until just combined. Scoop the batter into the prepared muffin cups (they’ll be quite full). Sprinkle with the streusel.
Bake the muffins until the tops are golden brown and spring back when touched lightly, 15 to 25 minutes. Let cool in the pan for 5 minutes. Loosen edges and turn muffins out onto a wire rack to cool slightly before serving.