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Preheat oven to 375°F. Line 12 (1/2-cup) muffin cups with paper liners and lightly coat with cooking spray. (Alternatively, coat muffin tin with cooking spray and omit liners.)
Pulse oats in a food processor until ground to the texture of breadcrumbs. Transfer to a mixing bowl and whisk in flour, sugar, baking powder, baking soda, cinnamon, salt, allspice and nutmeg. Stir in squash, cranberries and pecans (if using).
Whisk eggs, yogurt, oil and syrup in another mixing bowl. Stir in apple. Add the squash mixture and fold until evenly moistened. Divide the batter among the muffin cups, filling them almost to the top.
Bake until the muffins are golden brown and the tops spring back when lightly touched, 20 to 25 minutes. Let cool in the pan for 10 minutes, then transfer to a wire rack to cool for at least 5 minutes before serving.