In a small saucepan, combine berries, honey, and lemon zest. Bring to a boil. Reduce to a simmer and cook until thickened, 7 to 8 minutes. Transfer to a bowl; set aside.
Preheat oven to 200 degrees. Have a baking sheet ready to keep cooked pancakes warm. Whisk together flours, wheat germ, baking powder, baking soda, and salt. In a second bowl, whisk together yogurt, butter, and egg. Add dry ingredients and pecans to wet ingredients; whisk until just moistened (be sure not to overmix; a few small lumps are fine).
Heat a large nonstick skillet or cast iron griddle over medium. Lightly butter the skillet. For each pancake, spoon 1/4 cup batter into skillet, using the back of a spoon to spread batter to about 4 inches in diameter.
Cook until surface of pancakes have some bubbles and a few have burst, 1 to 3 minutes. Flip with a thin spatula, and cook until browned on the underside, 1 to 3 minutes more. Transfer to the baking sheet and keep warm in the oven. Continue with more butter and remaining batter. Serve warm, topped with berry compote.